Chapter 1 Exploring Life

Chapter Notes

Overview: Biology’s Most Exciting Era

 Biology is the scientific study of life.

 You are starting your study of biology during its most exciting era.
 The largest and best-equipped community of scientists in history is beginning to solve
problems that once seemed unsolvable.
 Biology is an ongoing inquiry about the nature of life.
 Biologists are moving closer to understanding:
 How a single cell develops into an adult animal or plant.
 How plants convert solar energy into the chemical energy of food.
 How the human mind works.
 How living things interact in biological communities.
 How the diversity of life evolved from the first microbes.
 Research breakthroughs in genetics and cell biology are transforming medicine and
agriculture.
 Neuroscience and evolutionary biology are reshaping psychology and sociology.
 Molecular biology is providing new tools for anthropology and criminology.
 New models in ecology are helping society to evaluate environmental issues, such as
the causes and biological consequences of global warming.
 Unifying themes pervade all of biology.

Concept 1.1 Biologists explore life from the microscopic to the global scale
 Life’s basic characteristic is a high degree of order.
 Each level of biological organization has emergent properties.
 Biological organization is based on a hierarchy of structural levels, each building on the
levels below.
 At the lowest level are atoms that are ordered into complex biological molecules.
 Biological molecules are organized into structures called organelles, the components of
cells.
 Cells are the fundamental unit of structure and function of living things.
 Some organisms consist of a single cell; others are multicellular aggregates of specialized
cells.
 Whether multicellular or unicellular, all organisms must accomplish the same functions:
uptake and processing of nutrients, excretion of wastes, response to environmental
stimuli, and reproduction.
 Multicellular organisms exhibit three major structural levels above the cell: similar
cells are grouped into tissues, several tissues coordinate to form organs, and several
organs form an organ system.
Biology Chapter Notes
 For example, to coordinate locomotory movements, sensory information travels from
sense organs to the brain, where nervous tissues composed of billions of interconnected
neurons—supported by connective tissue—coordinate signals that travel via other neurons
to the individual muscle cells.
 Organisms belong to populations, localized groups of organisms belonging to the same
species.
 Populations of several species in the same area comprise a biological community.
 Populations interact with their physical environment to form an ecosystem.
 The biosphere consists of all the environments on Earth that are inhabited by life.
Organisms interact continuously with their environment.
 Each organism interacts with its environment, which includes other organisms as well as
nonliving factors.
 Both organism and environment are affected by the interactions between them.
 The dynamics of any ecosystem include two major processes: the cycling of nutrients and
the flow of energy from sunlight to producers to consumers.
 In most ecosystems, producers are plants and other photosynthetic organisms that
convert light energy to chemical energy.
 Consumers are organisms that feed on producers and other consumers.
 All the activities of life require organisms to perform work, and work requires a source of
energy.
 The exchange of energy between an organism and its environment often involves the
transformation of energy from one form to another.
 In all energy transformations, some energy is lost to the surroundings as heat.
 In contrast to chemical nutrients, which recycle within an ecosystem, energy flows
through an ecosystem, usually entering as light and exiting as heat.
Cells are an organism’s basic unit of structure and function.
 The cell is the lowest level of structure that is capable of performing all the activities of
life.
 For example, the ability of cells to divide is the basis of all reproduction and the basis
of growth and repair of multicellular organisms.
 Understanding how cells work is a major research focus of modern biology.
 At some point, all cells contain deoxyribonucleic acid, or DNA, the heritable material that
directs the cell’s activities.
 DNA is the substance of genes, the units of inheritance that transmit information from
parents to offspring.
 Each of us began life as a single cell stocked with DNA inherited from our parents.
 DNA in human cells is organized into chromosomes.
 Each chromosome has one very long DNA molecule, with hundreds or thousands of
genes arranged along its length.
 The DNA of chromosomes replicates as a cell prepares to divide.
 Each of the two cellular offspring inherits a complete set of genes.
 In each cell, the genes along the length of DNA molecules encode the information for
building the cell’s other molecules.
 DNA thus directs the development and maintenance of the entire organism.
Biology Chapter Notes
 Most genes program the cell’s production of proteins.
 Each DNA molecule is made up of two long chains arranged in a double helix.
 Each link of a chain is one of four nucleotides, encoding the cell’s information in
chemical letters.
 The sequence of nucleotides along each gene codes for a specific protein with a unique
shape and function.
 Almost all cellular activities involve the action of one or more proteins.
 DNA provides the heritable blueprints, but proteins are the tools that actually build and
maintain the cell.
 All forms of life employ essentially the same genetic code.
 Because the genetic code is universal, it is possible to engineer cells to produce
proteins normally found only in some other organism.
 The library of genetic instructions that an organism inherits is called its genome.
 The chromosomes of each human cell contain about 3 billion nucleotides, including
genes coding for more than 70,000 kinds of proteins, each with a specific function.
 Every cell is enclosed by a membrane that regulates the passage of material between a cell
and its surroundings.
 Every cell uses DNA as its genetic material.
 There are two basic types of cells: prokaryotic cells and eukaryotic cells.
 The cells of the microorganisms called bacteria and archaea are prokaryotic.
 All other forms of life have more complex eukaryotic cells.
 Eukaryotic cells are subdivided by internal membranes into various organelles.
 In most eukaryotic cells, the largest organelle is the nucleus, which contains the cell’s
DNA as chromosomes.
 The other organelles are located in the cytoplasm, the entire region between the
nucleus and outer membrane of the cell.
 Prokaryotic cells are much simpler and smaller than eukaryotic cells.
 In a prokaryotic cell, DNA is not separated from the cytoplasm in a nucleus.
 There are no membrane-enclosed organelles in the cytoplasm.
 All cells, regardless of size, shape, or structural complexity, are highly ordered structures
that carry out complicated processes necessary for life.

Concept 1.2 Biological systems are much more than the sum of their parts
 “The whole is greater than the sum of its parts.”
 The combination of components can form a more complex organization called a system.
 Examples of biological systems are cells, organisms, and ecosystems.
 Consider the levels of life.
 With each step upward in the hierarchy of biological order, novel properties emerge
that are not present at lower levels.
 These emergent properties result from the arrangements and interactions between
components as complexity increases.
 A cell is much more than a bag of molecules.
Biology Chapter Notes
  Our thoughts and memories are emergent properties of a complex network of neurons.
 This theme of emergent properties accents the importance of structural arrangement.
 The emergent properties of life are not supernatural or unique to life but simply reflect a
hierarchy of structural organization.
 The emergent properties of life are particularly challenging because of the unparalleled
complexity of living systems.
 The complex organization of life presents a dilemma to scientists seeking to understand
biological processes.
 We cannot fully explain a higher level of organization by breaking it down into its
component parts.
 At the same time, it is futile to try to analyze something as complex as an organism or
cell without taking it apart.
 Reductionism, reducing complex systems to simpler components, is a powerful strategy in
biology.
 The Human Genome Project—the sequencing of the genome of humans and many
other species—is heralded as one of the greatest scientific achievements ever.
 Research is now moving on to investigate the function of genes and the coordination of
the activity of gene products.
 Biologists are beginning to complement reductionism with new strategies for
understanding the emergent properties of life—how all of the parts of biological systems
are functionally integrated.
 The ultimate goal of systems biology is to model the dynamic behavior of whole
biological systems.
 Accurate models allow biologists to predict how a change in one or more variables will
impact other components and the whole system.
 Scientists investigating ecosystems pioneered this approach in the 1960s with elaborate
models diagramming the interactions of species and nonliving components in ecosystems.
 Systems biology is now becoming increasingly important in cellular and molecular
biology, driven in part by the deluge of data from the sequencing of genomes and our
increased understanding of protein functions.
 In 2003, a large research team published a network of protein interactions within a cell
of a fruit fly.
 Three key research developments have led to the increased importance of systems
biology.
1. High-throughput technology. Systems biology depends on methods that can
analyze biological materials very quickly and produce enormous amounts of data.
An example is the automatic DNA-sequencing machines used by the Human
Genome Project.
2. Bioinformatics. The huge databases from high-throughput methods require
computing power, software, and mathematical models to process and integrate
information.
3. Interdisciplinary research teams. Systems biology teams may include engineers,
medical scientists, physicists, chemists, mathematicians, and computer scientists as
well as biologists.
Regulatory mechanisms ensure a dynamic balance in living systems.

Biology Chapter Notes

 Chemical processes within cells are accelerated, or catalyzed, by specialized protein
molecules, called enzymes.
 Each type of enzyme catalyzes a specific chemical reaction.
 In many cases, reactions are linked into chemical pathways, each step with its own
enzyme.
 How does a cell coordinate its various chemical pathways?
 Many biological processes are self-regulating: the output or product of a process
regulates that very process.
 In negative feedback, or feedback inhibition, accumulation of an end product of a
process slows or stops that process.
 Though less common, some biological processes are regulated by positive feedback, in
which an end product speeds up its own production.
 Feedback is common to life at all levels, from the molecular level to the biosphere.
 Such regulation is an example of the integration that makes living systems much greater
than the sum of their parts.

Concept 1.3 Biologists explore life across its great diversity of species
 Biology can be viewed as having two dimensions: a “vertical” dimension covering the
size scale from atoms to the biosphere and a “horizontal” dimension that stretches across
the diversity of life.
 The latter includes not only present-day organisms, but also those that have existed
throughout life’s history.
Living things show diversity and unity.
 Life is enormously diverse.
 Biologists have identified and named about 1.8 million species.
 This diversity includes 5,200 known species of prokaryotes, 100,000 fungi, 290,000
plants, 50,000 vertebrates, and 1,000,000 insects.
 Thousands of newly identified species are added each year.
 Estimates of the total species count range from 10 million to more than 200 million.
 In the face of this complexity, humans are inclined to categorize diverse items into a
smaller number of groups.
 Taxonomy is the branch of biology that names and classifies species into a hierarchical
order.
 Until the past decade, biologists divided the diversity of life into five kingdoms.
 New methods, including comparisons of DNA among organisms, have led to a
reassessment of the number and boundaries of the kingdoms.
 Various classification schemes now include six, eight, or even dozens of kingdoms.
 Coming from this debate has been the recognition that there are three even higher levels
of classifications, the domains.
 The three domains are Bacteria, Archaea, and Eukarya.
 The first two domains, domain Bacteria and domain Archaea, consist of prokaryotes.
 All the eukaryotes are now grouped into various kingdoms of the domain Eukarya.
Biology Chapter Notes
  The recent taxonomic trend has been to split the single-celled eukaryotes and their
close relatives into several kingdoms.
 Domain Eukarya also includes the three kingdoms of multicellular eukaryotes: the
kingdoms Plantae, Fungi, and Animalia.
 These kingdoms are distinguished partly by their modes of nutrition.
 Most plants produce their own sugars and food by photosynthesis.
 Most fungi are decomposers that absorb nutrients by breaking down dead organisms
and organic wastes.
 Animals obtain food by ingesting other organisms.
 Underlying the diversity of life is a striking unity, especially at the lower levels of
organization.
 The universal genetic language of DNA unites prokaryotes and eukaryotes.
 Among eukaryotes, unity is evident in many details of cell structure.
 Above the cellular level, organisms are variously adapted to their ways of life.
 How do we account for life’s dual nature of unity and diversity?
 The process of evolution explains both the similarities and differences among living
things.

Concept 1.4 Evolution accounts for life’s unity and diversity

 The history of life is a saga of a changing Earth billions of years old, inhabited by a
changing cast of living forms.
 Charles Darwin brought evolution into focus in 1859 when he presented two main
concepts in one of the most important and controversial books ever written, On the Origin
of Species by Natural Selection.
 Darwin’s first point was that contemporary species arose from a succession of ancestors
through “descent with modification.”
 This term captured the duality of life’s unity and diversity: unity in the kinship among
species that descended from common ancestors and diversity in the modifications that
evolved as species branched from their common ancestors.
 Darwin’s second point was his mechanism for descent with modification: natural
selection.
 Darwin inferred natural selection by connecting two observations:
 Observation 1: Individual variation. Individuals in a population of any species vary in
many heritable traits.
 Observation 2: Overpopulation and competition. Any population can potentially
produce far more offspring than the environment can support. This creates a struggle
for existence among variant members of a population.
 Inference: Unequal reproductive success. Darwin inferred that those individuals with
traits best suited to the local environment would leave more healthy, fertile offspring.
 Inference: Evolutionary adaptation. Unequal reproductive success can lead to
adaptation of a population to its environment. Over generations, heritable traits that
enhance survival and reproductive success will tend to increase in frequency among a
population’s individuals. The population evolves.
 Natural selection, by its cumulative effects over vast spans of time, can produce new
species from ancestral species.
Biology Chapter Notes
  For example, a population fragmented into several isolated populations in different
environments may gradually diversify into many species as each population adapts
over many generations to different environmental problems.
 Fourteen species of finches found on the Galápagos Islands diversified after an ancestral
finch species reached the archipelago from the South American mainland.
 Each species is adapted to exploit different food sources on different islands.
 Biologists’ diagrams of evolutionary relationships generally take a treelike form.
 Just as individuals have a family tree, each species is one twig of a branching tree of life.
 Similar species like the Galápagos finches share a recent common ancestor.
 Finches share a more distant ancestor with all other birds.
 The common ancestor of all vertebrates is even more ancient.
 Trace life back far enough, and there is a shared ancestor of all living things.
 All of life is connected through its long evolutionary history.

Concept 1.5 Biologists use various forms of inquiry to explore life

 The word science is derived from a Latin verb meaning “to know.”
 At the heart of science is inquiry, people asking questions about nature and focusing on
specific questions that can be answered.
 The process of science blends two types of exploration: discovery science and hypothesis-
based science.
 Discovery science is mostly about discovering nature.
 Hypothesis-based science is mostly about explaining nature.
 Most scientific inquiry combines the two approaches.
 Discovery science describes natural structures and processes as accurately as possible
through careful observation and analysis of data.
 Discovery science built our understanding of cell structure and is expanding our
databases of genomes of diverse species.
 Observation is the use of the senses to gather information, which is recorded as data.
 Data can be qualitative or quantitative.
 Quantitative data are numerical measurements.
 Qualitative data may be in the form of recorded descriptions.
 Jane Goodall has spent decades recording her observations of chimpanzee behavior
during field research in Gambia.
 She has also collected volumes of quantitative data over that time.
 Discovery science can lead to important conclusions based on inductive reasoning.
 Through induction, we derive generalizations based on a large number of specific
observations.
 In science, inquiry frequently involves the proposing and testing of hypotheses.
 A hypothesis is a tentative answer to a well-framed question.
 It is usually an educated postulate, based on past experience and the available data of
discovery science.

Biology Chapter Notes

 A scientific hypothesis makes predictions that can be tested by recording additional
observations or by designing experiments.
 A type of logic called deduction is built into hypothesis-based science.
 In deductive reasoning, reasoning flows from the general to the specific.
 From general premises, we extrapolate to a specific result that we should expect if the
premises are true.
 In hypothesis-based science, deduction usually takes the form of predictions about what
we should expect if a particular hypothesis is correct.
 We test the hypothesis by performing the experiment to see whether or not the results
are as predicted.
 Deductive logic takes the form of “If . . . then” logic.
 Scientific hypotheses must be testable.
 There must be some way to check the validity of the idea.
 Scientific hypotheses must be falsifiable.
 There must be some observation or experiment that could reveal if a hypothesis is
actually not true.
 The ideal in hypothesis-based science is to frame two or more alternative hypotheses and
design experiments to falsify them.
 No amount of experimental testing can prove a hypothesis.
 A hypothesis gains support by surviving various tests that could falsify it, while testing
falsifies alternative hypotheses.
 Facts, in the form of verifiable observations and repeatable experimental results, are the
prerequisites of science.
We can explore the scientific method.
 There is an idealized process of inquiry called the scientific method.
 Very few scientific inquiries adhere rigidly to the sequence of steps prescribed by the
textbook scientific method.
 Discovery science has contributed a great deal to our understanding of nature without
most of the steps of the so-called scientific method.
 We will consider a case study of scientific research.
 This case begins with a set of observations and generalizations from discovery science.
 Many poisonous animals have warning coloration that signals danger to potential
predators.
 Imposter species mimic poisonous species, although they are harmless.
 An example is the bee fly, a nonstinging insect that mimics a honeybee.
 What is the function of such mimicry? What advantage does it give the mimic?
 In 1862, Henry Bates proposed that mimics benefit when predators mistake them for
harmful species.
 This deception may lower the mimic’s risk of predation.
 In 2001, David and Karin Pfennig and William Harcombe of the University of North
Carolina designed a set of field experiments to test Bates’s mimicry hypothesis.
 In North and South Carolina, a poisonous snake called the eastern coral snake has warning
red, yellow, and black coloration.
Biology Chapter Notes
 Predators avoid these snakes. It is unlikely that predators learn to avoid coral snakes, as a
strike is usually lethal.
 Natural selection may have favored an instinctive recognition and avoidance of the
warning coloration of the coral snake.
 The nonpoisonous scarlet king snake mimics the ringed coloration of the coral snake.
 Both king snakes and coral snake live in the Carolinas, but the king snake’s range also
extends into areas without coral snakes.
 The distribution of these two species allowed the Pfennigs and Harcombe to test a key
prediction of the mimicry hypothesis.
 Mimicry should protect the king snake from predators, but only in regions where coral
snakes live.
 Predators in non–coral snake areas should attack king snakes more frequently than
predators that live in areas where coral snakes are present.
 To test the mimicry hypothesis, Harcombe made hundreds of artificial snakes.
 The experimental group had the red, black, and yellow ring pattern of king snakes.
 The control group had plain, brown coloring.
 Equal numbers of both types were placed at field sites, including areas where coral snakes
are absent.
 After four weeks, the scientists retrieved the fake snakes and counted bite or claw marks.
 Foxes, coyotes, raccoons, and black bears attacked snake models.
 The data fit the predictions of the mimicry hypothesis.
 The ringed snakes were attacked by predators less frequently than the brown snakes
only within the geographic range of the coral snakes.
 The snake mimicry experiment provides an example of how scientists design experiments
to test the effect of one variable by canceling out the effects of unwanted variables.
 The design is called a controlled experiment.
 An experimental group (artificial king snakes) is compared with a control group
(artificial brown snakes).
 The experimental and control groups differ only in the one factor the experiment is
designed to test—the effect of the snake’s coloration on the behavior of predators.
 The brown artificial snakes allowed the scientists to rule out such variables as predator
density and temperature as possible determinants of number of predator attacks.
 Scientists do not control the experimental environment by keeping all variables constant.
 Researchers usually “control” unwanted variables, not by eliminating them but by
canceling their effects using control groups.
Let’s look at the nature of science.
 There are limitations to the kinds of questions that science can address.
 These limits are set by science’s requirements that hypotheses are testable and falsifiable
and that observations and experimental results be repeatable.
 The limitations of science are set by its naturalism.
 Science seeks natural causes for natural phenomena.
 Science cannot support or falsify supernatural explanations, which are outside the
bounds of science.
 Everyday use of the term theory implies an untested speculation.
Biology Chapter Notes
 The term theory has a very different meaning in science.
 A scientific theory is much broader in scope than a hypothesis.
 This is a hypothesis: “Mimicking poisonous snakes is an adaptation that protects
nonpoisonous snakes from predators.”
 This is a theory: “Evolutionary adaptations evolve by natural selection.”
 A theory is general enough to generate many new, specific hypotheses that can be tested.
 Compared to any one hypothesis, a theory is generally supported by a much more massive
body of evidence.
 The theories that become widely adopted in science (such as the theory of adaptation by
natural selection) explain many observations and are supported by a great deal of
evidence.
 In spite of the body of evidence supporting a widely accepted theory, scientists may have
to modify or reject theories when new evidence is found.
 As an example, the five-kingdom theory of biological diversity eroded as new
molecular methods made it possible to test some of the hypotheses about the
relationships between living organisms.
 Scientists may construct models in the form of diagrams, graphs, computer programs, or
mathematical equations.
 Models may range from lifelike representations to symbolic schematics.
 Science is an intensely social activity.
 Most scientists work in teams, which often include graduate and undergraduate
students.
 Both cooperation and competition characterize scientific culture.
 Scientists attempt to confirm each other’s observations and may repeat experiments.
 They share information through publications, seminars, meetings, and personal
communication.
 Scientists may be very competitive when converging on the same research question.
 Science as a whole is embedded in the culture of its times.
 For example, recent increases in the proportion of women in biology have had an
impact on the research being performed.
 For instance, there has been a switch in focus in studies of the mating behavior of animals
from competition among males for access to females to the role that females play in
choosing mates.
 Recent research has revealed that females prefer bright coloration that “advertises” a
male’s vigorous health, a behavior that enhances a female’s probability of having
healthy offspring.
 Some philosophers of science argue that scientists are so influenced by cultural and
political values that science is no more objective than other ways of “knowing nature.”
 At the other extreme are those who view scientific theories as though they were natural
laws.
 The reality of science is somewhere in between.
 The cultural milieu affects scientific fashion, but need for repeatability in observation and
hypothesis testing distinguishes science from other fields.
 If there is “truth” in science, it is based on a preponderance of the available evidence.

Biology Chapter Notes

 Science and technology are functions of society.
 Although science and technology may employ similar inquiry patterns, their basic goals
differ.
 The goal of science is to understand natural phenomena.
 Technology applies scientific knowledge for some specific purpose.
 Technology results from scientific discoveries applied to the development of goods and
services.
 Scientists put new technology to work in their research.
 Science and technology are interdependent.
 The discovery of the structure of DNA by Watson and Crick sparked an explosion of
scientific activity.
 These discoveries made it possible to manipulate DNA, enabling genetic technologists
to transplant foreign genes into microorganisms and mass-produce valuable products.
 DNA technology and biotechnology have revolutionized the pharmaceutical industry.
 They have had an important impact on agriculture and the legal profession.
 The direction that technology takes depends less on science than it does on the needs of
humans and the values of society.
 Debates about technology center more on “should we do it” than “can we do it.”
 With advances in technology come difficult choices, informed as much by politics,
economics, and cultural values as by science.
 Scientists should educate politicians, bureaucrats, corporate leaders, and voters about how
science works and about the potential benefits and hazards of specific technologies.

Concept 1.6 A set of themes connects the concepts of biology

 In some ways, biology is the most demanding of all sciences, partly because living
systems are so complex and partly because biology is a multidisciplinary science that
requires knowledge of chemistry, physics, and mathematics.
 Biology is also the science most connected to the humanities and social sciences.

Biology Chapter Notes

 Chapter 2 The Chemical Context of Life
Chapter Notes

Overview: Chemical Foundations of Biology

 Living organisms and the world they live in are subject to the basic laws of physics and
chemistry.
 Biology is a multidisciplinary science, drawing on insights from other sciences.
 Life can be organized into a hierarchy of structural levels.
 At each successive level, additional emergent properties appear.

Concept 2.1 Matter consists of chemical elements in pure form and in combinations
called compounds
 Organisms are composed of matter.
 Matter is anything that takes up space and has mass.
 Matter is made up of elements.
 An element is a substance that cannot be broken down into other substances by chemical
reactions.
 There are 92 naturally occurring elements.
 Each element has a unique symbol, usually the first one or two letters of the name.
Some of the symbols are derived from Latin or German names.
 A compound is a substance consisting of two or more elements in a fixed ratio.
 Table salt (sodium chloride or NaCl) is a compound with equal numbers of atoms of
the elements chlorine and sodium.
 While pure sodium is a metal and chlorine is a gas, they combine to form an edible
compound. This change in characteristics when elements combine to form a compound
is an example of an emergent property.
25 chemical elements are essential to life.
 About 25 of the 92 natural elements are known to be essential for life.
 Four elements—carbon (C), oxygen (O), hydrogen (H), and nitrogen (N)—make up
96% of living matter.
 Most of the remaining 4% of an organism’s weight consists of phosphorus (P), sulfur
(S), calcium (Ca), and potassium (K).
 Trace elements are required by an organism but only in minute quantities.
 Some trace elements, like iron (Fe), are required by all organisms.
 Other trace elements are required by only some species.
 For example, a daily intake of 0.15 milligrams of iodine is required for normal
activity of the human thyroid gland.

Concept 2.2 An element’s properties depend on the structure of its atoms

 Each element consists of unique atoms.
Biology Chapter Notes
 An atom is the smallest unit of matter that still retains the properties of an element.
 Atoms are composed of even smaller parts, called subatomic particles.
 Two of these, neutrons and protons, are packed together to form a dense core, the
atomic nucleus, at the center of an atom.
 Electrons can be visualized as forming a cloud of negative charge around the nucleus.
 Each electron has one unit of negative charge.
 Each proton has one unit of positive charge.
 Neutrons are electrically neutral.
 The attractions between the positive charges in the nucleus and the negative charges of the
electrons keep the electrons in the vicinity of the nucleus.
 A neutron and a proton are almost identical in mass, about 1.7 × 10 −24 gram per particle.
 For convenience, a smaller unit of measure, the dalton, is used to measure the mass of
subatomic particles, atoms, or molecules.
 The mass of a neutron or a proton is close to 1 dalton.
 The mass of an electron is about 1/2000 that of a neutron or proton.
 Therefore, we typically ignore the contribution of electrons when determining the total
mass of an atom.
 All atoms of a particular element have the same number of protons in their nuclei.
 This number of protons is the element’s unique atomic number.
 The atomic number is written as a subscript before the symbol for the element. For
example, 2He means that an atom of helium has 2 protons in its nucleus.
 Unless otherwise indicated, atoms have equal numbers of protons and electrons and,
therefore, no net charge.
 Therefore, the atomic number tells us the number of protons and the number of
electrons that are found in a neutral atom of a specific element.
 The mass number is the sum of the number of protons and neutrons in the nucleus of an
atom.
 Therefore, we can determine the number of neutrons in an atom by subtracting the
number of protons (the atomic number) from the mass number.
 The
4
mass number is written as a superscript before an element’s symbol (for example,
He).
 The atomic weight of an atom, a measure of its mass, can be approximated by the mass
number.
 For example, 4He has a mass number of 4 and an estimated atomic weight of 4 daltons.
More precisely, its atomic weight is 4.003 daltons.
 While all atoms of a given element have the same number of protons, they may differ in
the number of neutrons.
 Two atoms of the same element that differ in the number of neutrons are called isotopes.
 In nature, an element occurs as a mixture of isotopes.
 For example, 99% of carbon atoms have 6 neutrons (12C).
 Most of the remaining 1% of carbon 14
atoms have 7 neutrons ( 13C) while the rarest
carbon isotope, with 8 neutrons, is C.
 Most isotopes are stable; they do not tend to lose particles.
 Both 12C and 13C are stable isotopes.
Biology Chapter Notes
 The nuclei of some isotopes are unstable and decay spontaneously, emitting particles and
energy.
 14C is one of these unstable isotopes, or radioactive isotopes.
 When 14C decays, one of its neutrons is converted to a proton and an electron.
 This converts 14C to 14N, transforming the atom to a different element.
 Radioactive isotopes have many applications in biological research.
 Radioactive decay rates can be used to date fossils.
 Radioactive isotopes can be used to trace atoms through metabolic processes.
 Radioactive isotopes are also used to diagnose medical disorders.
 For example, a known quantity of a substance labeled with a radioactive isotope can be
injected into the blood, and its rate of excretion in the urine can be measured.
 Also, radioactive tracers can be used with imaging instruments to monitor chemical
processes in the body.
 While useful in research and medicine, the energy emitted in radioactive decay is
hazardous to life.
 This energy can destroy molecules within living cells.
 The severity of damage depends on the type and amount of radiation that the organism
absorbs.
Electron configuration influences the chemical behavior of an atom.
 Simplified models of the atom greatly distort the atom’s relative dimensions.
 To gain an accurate perspective of the relative proportions of an atom, if the nucleus was
the size of a golf ball, the electrons would be moving about 1 kilometer from the nucleus.
 Atoms are mostly empty space.
 When two elements interact during a chemical reaction, it is actually their electrons that
are involved.
 The nuclei do not come close enough to interact.
 The electrons of an atom vary in the amount of energy they possess.
 Energy is the ability to do work.
 Potential energy is the energy that matter stores because of its position or location.
 Water stored behind a dam has potential energy that can be used to do work turning
electric generators.
 Because potential energy has been expended, the water stores less energy at the bottom
of the dam than it did in the reservoir.
 Electrons have potential energy because of their position relative to the nucleus.
 The negatively charged electrons are attracted to the positively charged nucleus.
 The farther electrons are from the nucleus, the more potential energy they have.
 Changes in an electron’s potential energy can only occur in steps of a fixed amount,
moving the electron to a fixed location relative to the nucleus.
 An electron cannot exist between these fixed locations.
 The different states of potential energy that the electrons of an atom can have are called
energy levels or electron shells.
 The first shell, closest to the nucleus, has the lowest potential energy.
 Electrons in outer shells have more potential energy.
Biology Chapter Notes
  Electrons can change their position only if they absorb or release a quantity of energy
that matches the difference in potential energy between the two levels.
 The chemical behavior of an atom is determined by its electron configuration—the
distribution of electrons in its electron shells.
 The first 18 elements, including those most important in biological processes, can be
arranged in 8 columns and 3 rows.
 Elements in the same row fill the same shells with electrons.
 Moving from left to right, each element adds one electron (and proton) from the
element before.
 The first electron shell can hold only 2 electrons.
 The two electrons of helium fill the first shell.
 Atoms with more than two electrons must place the extra electrons in higher shells.
 For example, lithium, with three electrons, has two in the first shell and one in the
second shell.
 The second shell can hold up to 8 electrons.
 Neon, with 10 total electrons, has two in the first shell and eight in the second, filling
both shells.
 The chemical behavior of an atom depends mostly on the number of electrons in its
outermost shell, the valence shell.
 Electrons in the valence shell are known as valence electrons.
 Lithium has one valence electron; neon has eight.
 Atoms with the same number of valence electrons have similar chemical behaviors.
 An atom with a completed valence shell, like neon, is nonreactive.
 All other atoms are chemically reactive because they have incomplete valence shells.
 The paths of electrons are often portrayed as concentric paths, like planets orbiting the
sun.
 In reality, an electron occupies a more complex three-dimensional space, an orbital.
 The orbital represents the space in which the electron is found 90% of the time.
 Each orbital can hold a maximum of two electrons.
 The first shell has room for a single spherical 1s orbital for its pair of electrons.
 The second shell can pack pairs of electrons into a spherical 2s orbital and three
dumbbell-shaped 2p orbitals.
 The reactivity of atoms arises from the presence of unpaired electrons in one or more
orbitals of their valence shells.
 Electrons occupy separate orbitals within the valence shell until forced to share
orbitals.
 The four valence electrons of carbon each occupy separate orbitals, but the five
valence electrons of nitrogen are distributed into three unshared orbitals and one
shared orbital.
 When atoms interact to complete their valence shells, it is the unpaired electrons that are
involved.

Biology Chapter Notes

Concept 2.3 The formation and function of molecules depend on chemical bonding
between atoms
 Atoms with incomplete valence shells can interact with each other by sharing or
transferring valence electrons.
 These interactions typically result in the atoms remaining close together, held by
attractions called chemical bonds.
 The strongest chemical bonds are covalent bonds and ionic bonds.
 A covalent bond is formed by the sharing of a pair of valence electrons by two atoms.
 If two atoms come close enough that their unshared orbitals overlap, they will share
their newly paired electrons. Each atom can count both electrons toward its goal of
filling the valence shell.
 For example, if two hydrogen atoms come close enough that their 1s orbitals overlap,
then they can share a pair of electrons, with each atom contributing one.
 Two or more atoms held together by covalent bonds constitute a molecule.
 We can abbreviate the structure of the molecule by substituting a line for each pair of
shared electrons, drawing the structural formula.
 H—H is the structural formula for the covalent bond between two hydrogen atoms.
 The molecular formula indicates the number and types of atoms present in a single
molecule.
 H2 is the molecular formula for hydrogen gas.
 Oxygen needs to add 2 electrons to the 6 already present to complete its valence shell.
 Two oxygen atoms can form a molecule by sharing two pairs of valence electrons.
 These atoms have formed a double covalent bond.
 Every atom has a characteristic total number of covalent bonds that it can form, equal to
the number of unpaired electrons in the outermost shell. This bonding capacity is called
the atom’s valence.
 The valence of hydrogen is 1.
 Oxygen is 2.
 Nitrogen is 3.
 Carbon is 4.
 Phosphorus should have a valence of 3, based on its three unpaired electrons, but in
biological molecules it generally has a valence of 5, forming three single covalent
bonds and one double bond.
 Covalent bonds can form between atoms of the same element or atoms of different
elements.
 While both types are molecules, the latter are also compounds.
 Water, H2O, is a compound in which two hydrogen atoms form single covalent bonds
with an oxygen atom.
 This satisfies the valences of both elements.
 Methane, CH4, satisfies the valences of both C and H.
 The attraction of an atom for the shared electrons of a covalent bond is called its
electronegativity.
 Strongly electronegative atoms attempt to pull the shared electrons toward themselves.
 If electrons in a covalent bond are shared equally, then this is a nonpolar covalent bond.
 A covalent bond between two atoms of the same element is always nonpolar.
Biology Chapter Notes
  A covalent bond between atoms that have similar electronegativities is also nonpolar.
 Because carbon and hydrogen do not differ greatly in electronegativities, the bonds
of CH4 are nonpolar.
 When two atoms that differ in electronegativity bond, they do not share the electron pair
equally and form a polar covalent bond.
 The bonds between oxygen and hydrogen in water are polar covalent because oxygen
has a much higher electronegativity than does hydrogen.
 Compounds with a polar covalent bond have regions of partial negative charge near the
strongly electronegative atom and regions of partial positive charge near the weakly
electronegative atom.
 An ionic bond can form if two atoms are so unequal in their attraction for valence
electrons that one atom strips an electron completely from the other.
 For example, sodium, with one valence electron in its third shell, transfers this electron
to chlorine, with 7 valence electrons in its third shell.
 Now, sodium has a full valence shell (the second) and chlorine has a full valence shell
(the third).
 After the transfer, both atoms are no longer neutral, but have charges and are called ions.
 Sodium has one more proton than electrons and has a net positive charge.
 Atoms with positive charges are cations.
 Chlorine has one more electron than protons and has a net negative charge.
 Atoms with negative charges are anions.
 Because of differences in charge, cations and anions are attracted to each other to form an
ionic bond.
 Atoms in an ionic bond need not have acquired their charges by transferring electrons
with each other.
 Compounds formed by ionic bonds are ionic compounds, or salts. An example is NaCl,
or table salt.
 The formula for an ionic compound indicates the ratio of elements in a+ crystal −of that
salt. NaCl is not a molecule, but a salt crystal with equal numbers of Na and Cl ions.
 Ionic compounds can have ratios of elements different from 1:1.
 For example, the ionic compound magnesium chloride (MgCl 2) has 2 chloride atoms
per magnesium atom.
 Magnesium needs to lose 2 electrons to drop to a full outer shell; each chlorine
atom needs to gain 1.
 Entire molecules that have full electrical charges are also called ions.
 In the salt ammonium chloride (NH4Cl), the anion is Cl− and the cation is NH4+.
 The strength of ionic bonds depends on environmental conditions, such as moisture.
 Water can dissolve salts by reducing the attraction between the salt’s anions and cations.
Weak chemical bonds play important roles in the chemistry of life.
 Within a cell, weak, brief bonds between molecules are important to a variety of
processes.
 For example, signal molecules from one neuron use weak bonds to bind briefly to
receptor molecules on the surface of a receiving neuron.
 This triggers a response by the recipient.
Biology Chapter Notes
 Weak interactions include ionic bonds (weak in water), hydrogen bonds, and van der
Waals interactions.
 Hydrogen bonds form when a hydrogen atom already covalently bonded to a strongly
electronegative atom is attracted to another strongly electronegative atom.
 These strongly electronegative atoms are typically nitrogen or oxygen.
 These bonds form because a polar covalent bond leaves the hydrogen atom with a
partial positive charge and the other atom with a partial negative charge.
 The partially positive–charged hydrogen atom is attracted to regions of full or partial
negative charge on molecules, atoms, or even regions of the same large molecule.
 For example, ammonia molecules and water molecules interact with weak hydrogen
bonds.
 In the ammonia molecule, the hydrogen atoms have partial positive charges, and the
more electronegative nitrogen atom has a partial negative charge.
 In the water molecule, the hydrogen atoms also have partial positive charges, and the
oxygen atom has a partial negative charge.
 Areas with opposite charges are attracted.
 Even molecules with nonpolar covalent bonds can have temporary regions of partial
negative and positive charge.
 Because electrons are constantly in motion, there can be periods when they accumulate
by chance in one area of a molecule.
 This creates ever-changing regions of partial negative and positive charge within a
molecule.
 Molecules or atoms in close proximity can be attracted by these fleeting charge
differences, creating van der Waals interactions.
 While individual bonds (ionic, hydrogen, van der Waals) are weak and temporary,
collectively they are strong and play important biological roles.
A molecule’s biological function is related to its shape.
 The three-dimensional shape of a molecule is an important determinant of its function in a
cell.
 A molecule with two atoms is always linear.
 However, a molecule with more than two atoms has a more complex shape.
 The shape of a molecule is determined by the positions of the electron orbitals that are
shared by the atoms involved in the bond.
 When covalent bonds form, the orbitals in the valence shell of each atom rearrange.
 For atoms with electrons in both s and p orbitals, the formation of a covalent bonds leads
to hybridization of the orbitals to four new orbitals in a tetrahedral shape.
 In a water molecule, two of oxygen’s four hybrid orbitals are shared with hydrogen atoms.
The water molecule is shaped like a V, with its two covalent bonds spread apart at an
angle of 104.5°.
 In a methane molecule (CH4), the carbon atom shares all four of its hybrid orbitals with H
atoms. The carbon nucleus is at the center of the tetrahedron, with hydrogen nuclei at the
four corners.
 Large organic molecules contain many carbon atoms. In these molecules, the tetrahedral
shape of carbon bonded to four other atoms is often a repeating motif.

Biology Chapter Notes

 Biological molecules recognize and interact with one another with a specificity based on
molecular shape.
 For example, signal molecules from a transmitting cell have specific shapes that bind to
complementary receptor molecules on the surface of the receiving cell.
 The temporary attachment of the receptor and signal molecule stimulates activity in the
receptor cell.
 Molecules with similar shapes can have similar biological effects.
 For example, morphine, heroin, and other opiate drugs are similar enough in shape that
they can bind to the same receptors as natural signal molecules called endorphins.
 Binding of endorphins to receptors on brain cells produces euphoria and relieves pain.
Opiates mimic these natural endorphin effects.

Concept 2.4 Chemical reactions make and break chemical bonds

 In chemical reactions, chemical bonds are broken and reformed, leading to new
arrangements of atoms.
 The starting molecules in the process are called reactants, and the final molecules are
called products.
 In a chemical reaction, all of the atoms in the reactants must be present in the products.
 The reactions must be “balanced”.
 Matter is conserved in a chemical reaction.
 Chemical reactions rearrange matter; they do not create or destroy matter.
 For example, we can recombine the covalent bonds of H2 and O2 to form the new bonds of
H2O.
 In this reaction, two molecules of H2 combine with one molecule of O2 to form two
molecules of H2O.
 Photosynthesis is an important chemical reaction.
 Humans and other animals ultimately depend on photosynthesis for food and oxygen.
 Green plants combine carbon dioxide (CO2) from the air and water (H2O) from the soil
to create sugar molecules and release molecular oxygen (O2) as a by-product.
 This chemical reaction is powered by sunlight.
 The overall process of photosynthesis is 6CO2 + 6H2O --> C6H12O6 + 6O2.
 This process occurs in a sequence of individual chemical reactions that rearrange the
atoms of the reactants to form the products.
 Some chemical reactions go to completion; that is, all the reactants are converted to
products.
 Most chemical reactions are reversible, with the products in the forward reaction
becoming the reactants for the reverse reaction.
 For example in this reaction: 3H2 + N2 <=> 2NH3 hydrogen and nitrogen molecules
combine to form ammonia, but ammonia can decompose to hydrogen and nitrogen
molecules.
 Initially, when reactant concentrations are high, they frequently collide to create
products.
 As products accumulate, they collide to reform reactants.

Biology Chapter Notes

 Eventually, the rate of formation of products is the same as the rate of breakdown of
products (formation of reactants), and the system is at chemical equilibrium.
 At equilibrium, products and reactants are continually being formed, but there is no net
change in the concentrations of reactants and products.
 At equilibrium, the concentrations of reactants and products are typically not equal, but
their concentrations have stabilized at a particular ratio.

Biology Chapter Notes

 Chapter 3 Water and the Fitness of the Environment
Chapter Notes

Overview: The Molecule That Supports All of Life

 Because water is the substance that makes life possible on Earth, astronomers hope to find
evidence of water on newly discovered planets orbiting distant stars.
 Life on Earth began in water and evolved there for 3 billion years before colonizing the
land.
 Even terrestrial organisms are tied to water.
 Most cells are surrounded by water.
 Cells are about 70–95% water.
 Water is a reactant in many of the chemical reactions of life.
 Water is the only common substance that exists in the natural world in all three physical
states of matter: solid ice, liquid water, and water vapor.

Concept 3.1 The polarity of water molecules results in hydrogen bonding

 In a water molecule, two hydrogen atoms form single polar covalent bonds with an
oxygen atom.
 Because oxygen is more electronegative than hydrogen, the region around the oxygen
atom has a partial negative charge.
 The regions near the two hydrogen atoms have a partial positive charge.
 A water molecule is a polar molecule in which opposite ends of the molecule have
opposite charges.
 Water has a variety of unusual properties because of the attraction between polar water
molecules.
 The slightly negative regions of one water molecule are attracted to the slightly
positive regions of nearby water molecules, forming hydrogen bonds.
 Each water molecule can form hydrogen bonds with up to four neighbors.

Concept 3.2 Four emergent properties of water contribute to Earth’s fitness for life
Organisms depend on the cohesion of water molecules.
 The hydrogen bonds joining water molecules are weak, about 1/20 as strong as covalent
bonds.
 They form, break, and reform with great frequency. Each hydrogen bond lasts only a few
trillionths of a second.
 At any instant, a substantial percentage of all water molecules are bonded to their
neighbors, creating a high level of structure.
 Collectively, hydrogen bonds hold water together, a phenomenon called cohesion.
 Cohesion among water molecules plays a key role in the transport of water and dissolved
nutrients against gravity in plants.
Biology Chapter Notes
  Water molecules move from the roots to the leaves of a plant through water-
conducting vessels.
 As water molecules evaporate from a leaf, other water molecules from vessels in the
leaf replace them.
 Hydrogen bonds cause water molecules leaving the vessels to tug on molecules farther
down.
 This upward pull is transmitted down to the roots.
 Adhesion, clinging of one substance to another, contributes too, as water adheres to
the wall of the vessels.
 Surface tension, a measure of the force necessary to stretch or break the surface of a
liquid, is related to cohesion.
 Water has a greater surface tension than most other liquids because hydrogen bonds
among surface water molecules resist stretching or breaking the surface.
 Water behaves as if covered by an invisible film.
 Some animals can stand, walk, or run on water without breaking the surface.
Water moderates temperatures on Earth.
 Water stabilizes air temperatures by absorbing heat from warmer air and releasing heat to
cooler air.
 Water can absorb or release relatively large amounts of heat with only a slight change in
its own temperature.
 Atoms and molecules have kinetic energy, the energy of motion, because they are always
moving.
 The faster a molecule moves, the more kinetic energy it has.
 Heat is a measure of the total quantity of kinetic energy due to molecular motion in a
body of matter.
 Temperature measures the intensity of heat in a body of matter due to the average
kinetic energy of molecules.
 As the average speed of molecules increases, a thermometer will record an increase in
temperature.
 Heat and temperature are related, but not identical.
 When two objects of different temperatures come together, heat passes from the warmer
object to the cooler object until the two are the same temperature.
 Molecules in the cooler object speed up at the expense of kinetic energy of the warmer
object.
 Ice cubes cool a glass of pop by absorbing heat from the pop as the ice melts.
 In most biological settings, temperature is measured on the Celsius scale (°C).
 At sea level, water freezes at 0°C and boils at 100°C.
 Human body temperature is typically 37°C.
 While there are several ways to measure heat energy, one convenient unit is the calorie
(cal).
 One calorie is the amount of heat energy necessary to raise the temperature of one g of
water by 1°C.
 A calorie is released when 1 g of water cools by 1°C.
 In many biological processes, the kilocalorie (kcal) is more convenient.
Biology Chapter Notes
  A kilocalorie is the amount of heat energy necessary to raise the temperature of 1000 g
of water by 1°C.
 Another common energy unit, the joule (J), is equivalent to 0.239 cal.
 Water stabilizes temperature because it has a high specific heat.
 The specific heat of a substance is the amount of heat that must be absorbed or lost for 1
g of that substance to change its temperature by 1°C.
 By definition, the specific heat of water is 1 cal per gram per degree Celsius or 1
cal/g/°C.
 Water has a high specific heat compared to other substances.
 For example, ethyl alcohol has a specific heat of 0.6 cal/g/°C.
 The specific heat of iron is 1/10 that of water.
 Water resists changes in temperature because of its high specific heat.
 In other words, water absorbs or releases a relatively large quantity of heat for each
degree of temperature change.
 Water’s high specific heat is due to hydrogen bonding.
 Heat must be absorbed to break hydrogen bonds, and heat is released when hydrogen
bonds form.
 Investment of one calorie of heat causes relatively little change to the temperature of
water because much of the energy is used to disrupt hydrogen bonds, not speed up the
movement of water molecules.
 Water’s high specific heat has effects that range from the level of the whole Earth to the
level of individual organisms.
 A large body of water can absorb a large amount of heat from the sun in daytime
during the summer and yet warm only a few degrees.
 At night and during the winter, the warm water will warm cooler air.
 Therefore, ocean temperatures and coastal land areas have more stable temperatures
than inland areas.
 Living things are made primarily of water. Consequently, they resist changes in
temperature better than they would if composed of a liquid with a lower specific heat.
 The transformation of a molecule from a liquid to a gas is called vaporization or
evaporation.
 This occurs when the molecule moves fast enough to overcome the attraction of other
molecules in the liquid.
 Even in a low-temperature liquid (with low average kinetic energy), some molecules
are moving fast enough to evaporate.
 Heating a liquid increases the average kinetic energy and increases the rate of
evaporation.
 Heat of vaporization is the quantity of heat that a liquid must absorb for 1 g of it to be
converted from liquid to gas.
 Water has a relatively high heat of vaporization, requiring about 580 cal of heat to
evaporate 1 g of water at room temperature.
 This is double the heat required to vaporize the same quantity of alcohol or ammonia.
 This is because hydrogen bonds must be broken before a water molecule can evaporate
from the liquid.
 Water’s high heat of vaporization moderates climate.

Biology Chapter Notes

  Much of the sun’s heat absorbed by tropical oceans is used for evaporation of surface
water.
 As moist tropical air moves to the poles, water vapor condenses to form rain, releasing
heat.
 As a liquid evaporates, the surface of the liquid that remains behind cools, a phenomenon
called evaporative cooling.
 This occurs because the most energetic molecules are the most likely to evaporate,
leaving the lower–kinetic energy molecules behind.
 Evaporative cooling moderates temperature in lakes and ponds.
 Evaporation of sweat in mammals or evaporation of water from the leaves of plants
prevents terrestrial organisms from overheating.
 Evaporation of water from the leaves of plants or the skin of humans removes excess
heat.
Oceans and lakes don’t freeze solid because ice floats.
 Water is unusual because it is less dense as a solid than as a cold liquid.
 Most materials contract as they solidify, but water expands.
 At temperatures above 4°C, water behaves like other liquids, expanding as it warms
and contracting as it cools.
 Water begins to freeze when its molecules are no longer moving vigorously enough to
break their hydrogen bonds.
 When water reaches 0°C, water becomes locked into a crystalline lattice, with each water
molecule bonded to a maximum of four partners.
 As ice starts to melt, some of the hydrogen bonds break, and water molecules can slip
closer together than they can while in the ice state.
 Ice is about 10% less dense than water at 4°C.
 Therefore, ice floats on the cool water below.
 This oddity has important consequences for life.
 If ice sank, eventually all ponds, lakes, and even the ocean would freeze solid.
 During the summer, only the upper few centimeters of the ocean would thaw.
 Instead, the surface layer of ice insulates liquid water below, preventing it from
freezing and allowing life to exist under the frozen surface.
Water is the solvent of life.
 A liquid that is a completely homogeneous mixture of two or more substances is called a
solution.
 A sugar cube in a glass of water will eventually dissolve to form a uniform solution of
sugar and water.
 The dissolving agent is the solvent, and the substance that is dissolved is the solute.
 In our example, water is the solvent and sugar is the solute.
 In an aqueous solution, water is the solvent.
 Water is not a universal solvent, but it is very versatile because of the polarity of water
molecules.
 Water is an effective solvent because it readily forms hydrogen bonds with charged
and polar covalent molecules.

Biology Chapter Notes

  For example, when a crystal of salt (NaCl) is placed in water, the Na + cations interact
with the partial negative charges of the oxygen regions of water molecules.
−
 The Cl anions interact with the partial positive charges of the hydrogen regions of
water molecules.
 Each dissolved ion is surrounded by a sphere of water molecules, a hydration shell.
 Eventually, water dissolves all the ions, resulting in a solution with two solutes: sodium
and chloride ions.
 Polar molecules are also soluble in water because they form hydrogen bonds with water.
 Even large molecules, like proteins, can dissolve in water if they have ionic and polar
regions.
 Any substance that has an affinity for water is hydrophilic (water-loving).
 These substances are dominated by ionic or polar bonds.
 Some hydrophilic substances do not dissolve because their molecules are too large.
 For example, cotton is hydrophilic because cellulose, its major constituent, has
numerous polar covalent bonds. However, its giant cellulose molecules are too large to
dissolve in water.
 Water molecules form hydrogen bonds with the cellulose fibers of cotton, allowing
you to dry yourself with your cotton towel as the water is pulled into the towel.
 Substances that have no affinity for water are hydrophobic (water-fearing).
 These substances are nonionic and have nonpolar covalent bonds.
 Because there are no consistent regions with partial or full charges, water molecules
cannot form hydrogen bonds with hydrophobic molecules.
 Oils such as vegetable oil are hydrophobic because the dominant bonds, carbon-carbon
and carbon-hydrogen, share electrons equally.
 Hydrophobic molecules are major ingredients of cell membranes.
 Biological chemistry is “wet” chemistry with most reactions involving solutes dissolved
in water.
 Chemical reactions depend on collisions of molecules and therefore on the concentrations
of solutes in aqueous solution.
 We measure the number of molecules in units called moles.
 The actual number of molecules in a mole is called Avogadro’s number, 6.02 × 10 23.
 A mole is equal to the molecular weight of a substance but scaled up from daltons to
grams.
 To illustrate, how could we measure out a mole of table sugar—sucrose (C12H22O11)?
 A carbon atom weighs 12 daltons, hydrogen 1 dalton, and oxygen 16 daltons.
 One molecule of sucrose would weigh 342 daltons, the sum of weights of all the atoms
in sucrose, or the molecular weight of sucrose.
 To get one mole of sucrose, we would weigh out 342 g.
 The advantage of using moles as a measurement is that a mole of one substance has the
same number of molecules as a mole of any other substance.
 If substance A has a molecular weight of 10 daltons and substance B has a molecular
weight of 100 daltons, then we know that 10 g of substance A has the same number of
molecules as 100 g of substance B.

Biology Chapter Notes

  A mole of sucrose contains 6.02 × 10 23 molecules23 and weighs 342 g, while a mole of
ethyl alcohol (C2H6O) also contains 6.02 × 10 molecules but weighs only 46 g
because the molecules are smaller.
 Measuring in moles allows scientists to combine substances in fixed ratios of
molecules.
 In “wet” chemistry, we are typically combining solutions or measuring the quantities of
materials in aqueous solutions.
 The concentration of a material in solution is called its molarity.
 A one molar solution has one mole of a substance dissolved in one liter of solvent,
typically water.
 To make a 1 molar (1M) solution of sucrose, we would slowly add water to 342 g of
sucrose until the total volume was 1 liter and all the sugar was dissolved.

Concept 3.3 Dissociation of water molecules leads to acidic and basic conditions that
affect living organisms
 Occasionally, a hydrogen atom participating in a hydrogen bond between two water
molecules shifts from one molecule to the other.
 The hydrogen atom leaves its electron behind and is transferred as a single proton—a
hydrogen ion (H+).
−
 The water molecule that lost the proton is now a hydroxide ion (OH ).
+
 The water molecule with the extra proton is now a hydronium ion (H3O ).
 A simplified way to view this process is to say that a water molecule dissociates into a
hydrogen ion and a hydroxide ion:
+ −
 H2O <=> H + OH
 This reaction is reversible.
 At equilibrium, the concentration of water molecules greatly exceeds that of H+ and OH−.
 In pure water, only one water molecule in every 554 million is dissociated.
+ − −7 °
 At equilibrium, the concentration of H or OH is 10 M (at 25 C).
 Although the dissociation of water is reversible and statistically rare, it is very important
in the chemistry of life.
 Because hydrogen and hydroxide ions are very reactive, changes in their concentrations
can drastically affect the chemistry of a cell.
 Adding certain solutes, called acids and bases, disrupts the equilibrium and modifies the
concentrations of hydrogen and hydroxide ions.
 The pH scale is used to describe how acidic or basic a solution is.
Organisms are sensitive to changes in pH.
 An acid is a substance that increases the hydrogen ion concentration in a solution.
 When hydrochloric acid is added to water, hydrogen ions dissociate from chloride
ions: HCl -> H+ + Cl−
 Addition of an acid makes a solution more acidic.
 Any substance that reduces the hydrogen ion concentration in a solution is a base.
 Some bases reduce the H+ concentration directly by accepting hydrogen ions.
Biology Chapter Notes
  Ammonia (NH3) acts as a base when the nitrogen’s unshared electron pair attracts a
hydrogen ion from the solution, creating an ammonium ion (NH4+).
+ +
 NH3 + H <=> NH4
 Other bases reduce H+ indirectly by dissociating to OH−, which then combines with H+ to
form water.
−
 NaOH -> Na + OH
+
OH− + H+ -> H2O
 Solutions with more OH− than H+ are basic solutions.
 Solutions with more H+ than OH− are acidic solutions.
 Solutions in which concentrations of OH− and H+ are equal are neutral solutions.
 Some acids and bases (HCl and NaOH) are strong acids or bases.
 These molecules dissociate completely in water.
 Other acids and bases (NH3) are weak acids or bases.
 For these molecules, the binding and release of hydrogen ions are reversible.
 At equilibrium, there will be a fixed ratio of products to reactants.
 Carbonic acid (H2CO3) is a weak acid:
 H2CO3 <=> HCO3− + H+
 At equilibrium, 1% of the H2CO3 molecules will be dissociated.
 In any solution, the product of the H+ and OH− concentrations is constant at 10−14.
 Brackets ([H+] and [OH−]) indicate the molar concentration of the enclosed substance.
+ − −14
 [H ] [OH ] = 10
+ −7 − −7
 In a neutral solution, [H ] = 10 M and [OH ] = 10 M
 Adding acid to− a solution shifts the balance between H+ and OH− toward H+ and leads to a
decline in OH .
+ −5 − −9
 If [H ] = 10 M, then [OH ] = 10 M
 Hydroxide concentrations decline because some of the additional acid combines with
hydroxide to form water.
 Adding a base does the opposite, increasing OH − concentration and lowering H+
concentration.
 The H+ and OH− concentrations of solutions can vary by a factor of 100 trillion or more.
 To express this variation more conveniently, the H+ and OH− concentrations are typically
expressed via the pH scale.
 The pH scale, ranging from 1 to 14, compresses the range of concentrations by
employing logarithms.
+ + −pH
 pH = − log [H ] or [H ] = 10
 In a neutral solution, [H+] = 10−7 M, and the pH = 7.
 Values for pH decline as [H+] increase.
 While the pH scale is based on [H+], values for [OH−] can be easily calculated from the
product relationship.
 The pH of a neutral solution is 7.
 Acidic solutions have pH values less than 7, and basic solutions have pH values greater
than 7.
 Most biological fluids have pH values in the range of 6 to 8.
Biology Chapter Notes
  However, the human stomach has strongly acidic digestive juice with a pH of about 2.
 Each pH unit represents a tenfold difference in H+ and OH− concentrations.
+ −
 A small change in pH actually indicates a substantial change in H and OH
concentrations.
 The chemical processes in the cell can be disrupted by changes to the H + and OH−
concentrations away from their normal values, usually near pH 7.
 To maintain cellular pH values at a constant level, biological fluids have buffers.
 Buffers resist changes to the pH of a solution when H+ or OH− is added to the solution.
 Buffers accept hydrogen ions from the solution when they are in excess and donate
hydrogen ions when they have been depleted.
 Buffers typically consist of a weak acid and its corresponding base.
 One important buffer in human blood and other biological solutions is carbonic acid,
which dissociates to yield a bicarbonate ion and a hydrogen ion.
 The chemical equilibrium between carbonic acid and bicarbonate acts as a pH
regulator. +The equilibrium shifts left or right as other metabolic processes add or
remove H from the solution.
Acid precipitation threatens the fitness of the environment.
 Acid precipitation is a serious assault on water quality in some industrialized areas.
 Uncontaminated rain has a slightly acidic pH of 5.6.
 The acid is a product of the formation of carbonic acid from carbon dioxide and water.
 Acid precipitation occurs when rain, snow, or fog has a pH that is more acidic than 5.6.
 Acid precipitation is caused primarily by sulfur oxides and nitrogen oxides in the
atmosphere.
 These molecules react with water to form strong acids that fall to the surface with rain
or snow.
 The major source of these oxides is the burning of fossil fuels (coal, oil, and gas) in
factories and automobiles.
 The presence of tall smokestacks allows this pollution to spread from its site of origin to
contaminate relatively pristine areas thousands of kilometers away.
 In 2001, rain in the Adirondack Mountains of upstate New York had an average pH of
4.3.
 The effects of acids in lakes and streams are more pronounced in the spring during
snowmelt.
 As the surface snows melt and drain down through the snowfield, the meltwater
accumulates acid and brings it into lakes and streams all at once.
 The pH of early meltwater may be as low as 3.
 Acid precipitation has a great impact on the eggs and the early developmental stages of
aquatic organisms that are abundant in the spring.
 Thus, strong acidity can alter the structure of molecules and impact ecological
communities.
 Direct impacts of acid precipitation on forests and terrestrial life are more controversial.
 However, acid precipitation can impact soils by affecting the solubility of soil minerals.
 Acid precipitation can wash away key soil buffers and plant nutrients such as calcium
and magnesium ions.
Biology Chapter Notes
  It can also increase the concentrations of compounds such as aluminum to toxic levels.
 This has done major damage to forests in Europe and substantial damage of forests in
North America.
 Progress has been made in reducing acid precipitation.

Biology Chapter Notes

 Chapter 4 Carbon and the Molecular Diversity of Life
Chapter Notes
Overview: Carbon – The Backbone of Biological Molecules
· Although cells are 70–95% water, the rest consists mostly of carbon-based compounds.
· Carbon is unparalleled in its ability to form large, complex, and diverse molecules.
· Carbon accounts for the diversity of biological molecules and has made possible the great diversity of
living things.
· Proteins, DNA, carbohydrates, and other molecules that distinguish living matter from inorganic material
are all composed of carbon atoms bonded to each other and to atoms of other elements.
· These other elements commonly include hydrogen (H), oxygen (O), nitrogen (N), sulfur (S), and
phosphorus (P).

Concept 4.1 Organic chemistry is the study of carbon compounds

· The study of carbon compounds, organic chemistry, deals with any compound with carbon (organic
compounds).
· Organic compounds can range from simple molecules, such as CO2 or CH4, to complex molecules such
as proteins, which may weigh more than 100,000 daltons.
· The overall percentages of the major elements of life (C, H, O, N, S, and P) are quite uniform from one
organism to another.
· However, because of carbon’s versatility, these few elements can be combined to build an inexhaustible
variety of organic molecules.
· Variations in organic molecules can distinguish even between individuals of a single species.
· The science of organic chemistry began in attempts to purify and improve the yield of products obtained
from other organisms.
· Initially, chemists learned to synthesize simple compounds in the laboratory, but had no success with
more complex compounds.
· The Swedish chemist Jons Jacob Berzelius was the first to make a distinction between organic
compounds that seemed to arise only in living organisms and inorganic compounds that were found in the
nonliving world.
· This led early organic chemists to propose vitalism, the belief that physical and chemical laws did not
apply to living things.
· Support for vitalism began to wane as organic chemists learned to synthesize complex organic
compounds in the laboratory.
Biology Chapter Notes
· In the early 1800s, the German chemist Friedrich Wöhler and his students were able to synthesize urea
from totally inorganic materials.
· In 1953, Stanley Miller at the University of Chicago set up a laboratory simulation of chemical
conditions on the primitive Earth and demonstrated the spontaneous synthesis of organic compounds.
· Such spontaneous synthesis of organic compounds may have been an early stage in the origin of life.
· Organic chemists finally rejected vitalism and embraced mechanism, accepting that the same physical
and chemical laws govern all natural phenomena including the processes of life.
· Organic chemistry was redefined as the study of carbon compounds regardless of their origin.
· Organisms do produce the majority of organic compounds.
· The laws of chemistry apply to inorganic and organic compounds alike.

Concept 4.2 Carbon atoms can form diverse molecules by bonding to four other atoms
· With a total of 6 electrons, a carbon atom has 2 in the first electron shell and 4 in the second shell.
· Carbon has little tendency to form ionic bonds by losing or gaining 4 electrons to complete its valence
shell.
· Instead, carbon usually completes its valence shell by sharing electrons with other atoms in four covalent
bonds.
· This tetravalence by carbon makes large, complex molecules possible.
· When carbon forms covalent bonds with four other atoms, they are arranged at the corners of an
imaginary tetrahedron with bond angles of 109.5°.
· In molecules with multiple carbons, every carbon bonded to four other atoms has a tetrahedral shape.
· However, when two carbon atoms are joined by a double bond, all bonds around those carbons are in the
same plane and have a flat, three-dimensional structure.
· The three-dimensional shape of an organic molecule determines its function.
· The electron configuration of carbon makes it capable of forming covalent bonds with many different
elements.
· The valences of carbon and its partners can be viewed as the building code that governs the architecture
of organic molecules.
· In carbon dioxide, one carbon atom forms two double bonds with two different oxygen atoms.
· In the structural formula, O=C=O, each line represents a pair of shared electrons. This arrangement
completes the valence shells of all atoms in the molecule.
· While CO2 can be classified as either organic or inorganic, its importance to the living world is clear.
Biology Chapter Notes
· CO2 is the source of carbon for all organic molecules found in organisms. It is usually fixed into organic
molecules by the process of photosynthesis.
· Urea, CO(NH2)2, is another simple organic molecule in which each atom forms covalent bonds to
complete its valence shell.
Variation in carbon skeletons contributes to the diversity of organic molecules.
· Carbon chains form the skeletons of most organic molecules.
· The skeletons vary in length and may be straight, branched, or arranged in closed rings.
· The carbon skeletons may include double bonds.
· Atoms of other elements can be bonded to the atoms of the carbon skeleton.
· Hydrocarbons are organic molecules that consist of only carbon and hydrogen atoms.
· Hydrocarbons are the major component of petroleum, a fossil fuel that consists of the partially
decomposed remains of organisms that lived millions of years ago.
· Fats are biological molecules that have long hydrocarbon tails attached to a nonhydrocarbon component.
· Petroleum and fat are hydrophobic compounds that cannot dissolve in water because of their many
nonpolar carbon-to-hydrogen bonds.
· Isomers are compounds that have the same molecular formula but different structures and, therefore,
different chemical properties.
· For example, butane and isobutane have the same molecular formula, C4H10, but butane has a straight
skeleton and isobutane has a branched skeleton.
· The two butanes are structural isomers, molecules that have the same molecular formula but differ in
the covalent arrangement of atoms.
· Geometric isomers are compounds with the same covalent partnerships that differ in the spatial
arrangement of atoms around a carbon–carbon double bond.
· The double bond does not allow atoms to rotate freely around the bond axis.
· The biochemistry of vision involves a light-induced change in the structure of rhodopsin in the retina
from one geometric isomer to another.
· Enantiomers are molecules that are mirror images of each other.
· Enantiomers are possible when four different atoms or groups of atoms are bonded to a carbon.
· In this case, the four groups can be arranged in space in two different ways that are mirror images.
· They are like left-handed and right-handed versions of the molecule.
· Usually one is biologically active, while the other is inactive.

Biology Chapter Notes

· Even subtle structural differences in two enantiomers have important functional significance because of
emergent properties from specific arrangements of atoms.
· One enantiomer of the drug thalidomide reduced morning sickness, the desired effect, but the other
isomer caused severe birth defects.
· The L-dopa isomer is an effective treatment of Parkinson’s disease, but the D-dopa isomer is inactive.

Concept 4.3 Functional groups are the parts of molecules involved in chemical reactions
· The components of organic molecules that are most commonly involved in chemical reactions are known
as functional groups.
· If we consider hydrocarbons to be the simplest organic molecules, we can view functional groups as
attachments that replace one or more of the hydrogen atoms bonded to the carbon skeleton of the
hydrocarbon.
· Each functional group behaves consistently from one organic molecule to another.
· The number and arrangement of functional groups help give each molecule its unique properties.
· As an example, the basic structure of testosterone (a male sex hormone) and estradiol (a female sex
hormone) is the same.
· Both are steroids with four fused carbon rings, but they differ in the functional groups attached to the
rings.
· These functional groups interact with different targets in the body.
· There are six functional groups that are most important to the chemistry of life: hydroxyl, carbonyl,
carboxyl, amino, sulfhydryl, and phosphate groups.
· All are hydrophilic and increase the solubility of organic compounds in water.
· In a hydroxyl group (—OH), a hydrogen atom forms a polar covalent bond with an oxygen atom, which
forms a polar covalent bond to the carbon skeleton.
· Because of these polar covalent bonds, hydroxyl groups increase the solubility of organic molecules.
· Organic compounds with hydroxyl groups are alcohols, and their names typically end in -ol.
· A carbonyl group (>CO) consists of an oxygen atom joined to the carbon skeleton by a double bond.
· If the carbonyl group is on the end of the skeleton, the compound is an aldehyde.
· If the carbonyl group is within the carbon skeleton, then the compound is a ketone.
· Isomers with aldehydes versus ketones have different properties.
· A carboxyl group (—COOH) consists of a carbon atom with a double bond to an oxygen atom and a
single bond to the oxygen of a hydroxyl group.
Biology Chapter Notes
· Compounds with carboxyl groups are carboxylic acids.
· A carboxyl group acts as an acid because the combined electronegativities of the two adjacent oxygen
atoms increase the dissociation of hydrogen as an ion (H+).
· An amino group (—NH2) consists of a nitrogen atom bonded to two hydrogen atoms and the carbon
skeleton.
· Organic compounds with amino groups are amines.
· The amino group acts as a base because the amino group can pick up a hydrogen ion (H+) from the
solution.
· Amino acids, the building blocks of proteins, have amino and carboxyl groups.
· A sulfhydryl group (—SH) consists of a sulfur atom bonded to a hydrogen atom and to the backbone.
· This group resembles a hydroxyl group in shape.
· Organic molecules with sulfhydryl groups are thiols.
· Two sulfhydryl groups can interact to help stabilize the structure of proteins.
· A phosphate group (—OPO32−) consists of a phosphorus atom bound to four oxygen atoms (three with
single bonds and one with a double bond).
· A phosphate group connects to the carbon backbone via one of its oxygen atoms.
· Phosphate groups are anions with two negative charges, as two protons have dissociated from the
oxygen atoms.
· One function of phosphate groups is to transfer energy between organic molecules.
· Adenosine triphosphate, or ATP, is the primary energy-transferring molecule in living cells.
These are the chemical elements of life.
· Living matter consists mainly of carbon, oxygen, hydrogen, and nitrogen, with smaller amounts of sulfur
and phosphorus.
· These elements are linked by strong covalent bonds.
· Carbon, with its four covalent bonds, is the basic building block in molecular architecture.
· The great diversity of organic molecules with their special properties emerges from the unique
arrangement of the carbon skeleton and the functional groups attached to the skeleton.

Biology Chapter Notes

 Chapter 5 The Structure and Function of
Macromolecules
Chapter Notes

Overview: The Molecules of Life

 Within cells, small organic molecules are joined together to form larger molecules.
 These large macromolecules may consist of thousands of covalently bonded atoms and
weigh more than 100,000 daltons.
 The four major classes of macromolecules are carbohydrates, lipids, proteins, and nucleic
acids.

Concept 5.1 Most macromolecules are polymers, built from monomers

 Three of the four classes of macromolecules—carbohydrates, proteins, and nucleic
acids—form chainlike molecules called polymers.
 A polymer is a long molecule consisting of many similar or identical building blocks
linked by covalent bonds.
 The repeated units are small molecules called monomers.
 Some of the molecules that serve as monomers have other functions of their own.
 The chemical mechanisms that cells use to make and break polymers are similar for all
classes of macromolecules.
 Monomers are connected by covalent bonds that form through the loss of a water
molecule. This reaction is called a condensation reaction or dehydration reaction.
 When a bond forms between two monomers, each monomer contributes part of the
water molecule that is lost. One monomer provides a hydroxyl group (—OH), while
the other provides a hydrogen (—H).
 Cells invest energy to carry out dehydration reactions.
 The process is aided by enzymes.
 The covalent bonds connecting monomers in a polymer are disassembled by hydrolysis, a
reaction that is effectively the reverse of dehydration.
 In hydrolysis, bonds are broken by the addition of water molecules. A hydrogen atom
attaches to one monomer, and a hydroxyl group attaches to the adjacent monomer.
 Our food is taken in as organic polymers that are too large for our cells to absorb.
Within the digestive tract, various enzymes direct hydrolysis of specific polymers. The
resulting monomers are absorbed by the cells lining the gut and transported to the
bloodstream for distribution to body cells.
 The body cells then use dehydration reaction to assemble the monomers into new
polymers that carry out functions specific to the particular cell type.
An immense variety of polymers can be built from a small set of monomers.
 Each cell has thousands of different kinds of macromolecules.
 These molecules vary among cells of the same individual. They vary more among
unrelated individuals of a species, and even more between species.
Biology Chapter Notes
 This diversity comes from various combinations of the 40–50 common monomers and
some others that occur rarely.
 These monomers can be connected in a great many combinations, just as the 26 letters
in the alphabet can be used to create a great diversity of words.

Concept 5.2 Carbohydrates serve as fuel and building material

 Carbohydrates include sugars and their polymers.
 The simplest carbohydrates are monosaccharides, or simple sugars.
 Disaccharides, or double sugars, consist of two monosaccharides joined by a condensation
reaction.
 Polysaccharides are polymers of many monosaccharides.
Sugars, the smallest carbohydrates, serve as fuel and a source of carbon.
 Monosaccharides generally have molecular formulas that are some multiple of the unit
CH2O.
 For example, glucose has the formula C6H12O6.
 Monosaccharides have a carbonyl group (>C=O) and multiple hydroxyl groups (—OH).
 Depending on the location of the carbonyl group, the sugar is an aldose or a ketose.
 Most names for sugars end in -ose.
 Glucose, an aldose, and fructose, a ketose, are structural isomers.
 Monosaccharides are also classified by the number of carbons in the carbon skeleton.
 Glucose and other six-carbon sugars are hexoses.
 Five-carbon backbones are pentoses; three-carbon sugars are trioses.
 Monosaccharides may also exist as enantiomers.
 For example, glucose and galactose, both six-carbon aldoses, differ in the spatial
arrangement of their parts around asymmetrical carbons.
 Monosaccharides, particularly glucose, are a major fuel for cellular work.
 They also function as the raw material for the synthesis of other monomers, such as amino
acids and fatty acids.
 While often drawn as a linear skeleton, monosaccharides in aqueous solutions form rings.
 Two monosaccharides can join with a glycosidic linkage to form a disaccharide via
dehydration.
 Maltose, malt sugar, is formed by joining two glucose molecules.
 Sucrose, table sugar, is formed by joining glucose and fructose. Sucrose is the major
transport form of sugars in plants.
 Lactose, milk sugar, is formed by joining glucose and galactose.
Polysaccharides, the polymers of sugars, have storage and structural roles.
 Polysaccharides are polymers of hundreds to thousands of monosaccharides joined by
glycosidic linkages.
 Some polysaccharides serve for storage and are hydrolyzed as sugars are needed.
 Other polysaccharides serve as building materials for the cell or the whole organism.

Biology Chapter Notes

 Starch is a storage polysaccharide composed entirely of glucose monomers.
 Most of these monomers are joined by 1–4 linkages (number 1 carbon to number 4
carbon) between the glucose molecules.
 The simplest form of starch, amylose, is unbranched and forms a helix.
 Branched forms such as amylopectin are more complex.
 Plants store surplus glucose as starch granules within plastids, including chloroplasts, and
withdraw it as needed for energy or carbon.
 Animals that feed on plants, especially parts rich in starch, have digestive enzymes that
can hydrolyze starch to glucose.
 Animals store glucose in a polysaccharide called glycogen.
 Glycogen is highly branched like amylopectin.
 Humans and other vertebrates store a day’s supply of glycogen in the liver and
muscles.
 Cellulose is a major component of the tough wall of plant cells.
 Plants produce almost one hundred billion tons of cellulose per year. It is the most
abundant organic compound on Earth.
 Like starch, cellulose is a polymer of glucose. However, the glycosidic linkages in these
two polymers differ.
 The difference is based on the fact that there are actually two slightly different ring
structures for glucose.
 These two ring forms differ in whether the hydroxyl group attached to the number 1
carbon is fixed above (beta glucose) or below (alpha glucose) the plane of the ring.
 Starch is a polysaccharide of alpha glucose monomers.
 Cellulose is a polysaccharide of beta glucose monomers, making every other glucose
monomer upside down with respect to its neighbors.
 The differing glycosidic links in starch and cellulose give the two molecules distinct
three-dimensional shapes.
 While polymers built with alpha glucose form helical structures, polymers built with
beta glucose form straight structures.
 The straight structures built with beta glucose allow H atoms on one strand to form
hydrogen bonds with OH groups on other strands.
 In plant cell walls, parallel cellulose molecules held together in this way are grouped
into units called microfibrils, which form strong building materials for plants (and for
humans, as lumber).
 The enzymes that digest starch by hydrolyzing its alpha linkages cannot hydrolyze the
beta linkages in cellulose.
 Cellulose in human food passes through the digestive tract and is eliminated in feces as
“insoluble fiber.”
 As it travels through the digestive tract, cellulose abrades the intestinal walls and
stimulates the secretion of mucus, aiding in the passage of food.
 Some microbes can digest cellulose to its glucose monomers through the use of cellulase
enzymes.
 Many eukaryotic herbivores, from cows to termites, have symbiotic relationships with
cellulolytic microbes, providing the microbe and the host animal access to a rich source of
energy.
 Some fungi can also digest cellulose.
Biology Chapter Notes
 Another important structural polysaccharide is chitin, used in the exoskeletons of
arthropods (including insects, spiders, and crustaceans).
 Chitin is similar to cellulose, except that it contains a nitrogen-containing appendage
on each glucose monomer.
 Pure chitin is leathery but can be hardened by the addition of calcium carbonate.
 Chitin also provides structural support for the cell walls of many fungi.

Concept 5.3 Lipids are a diverse group of hydrophobic molecules

 Unlike other macromolecules, lipids do not form polymers.
 The unifying feature of lipids is that they all have little or no affinity for water.
 This is because they consist mostly of hydrocarbons, which form nonpolar covalent
bonds.
 Lipids are highly diverse in form and function.
Fats store large amounts of energy.
 Although fats are not strictly polymers, they are large molecules assembled from smaller
molecules by dehydration reactions.
 A fat is constructed from two kinds of smaller molecules: glycerol and fatty acids.
 Glycerol is a three-carbon alcohol with a hydroxyl group attached to each carbon.
 A fatty acid consists of a carboxyl group attached to a long carbon skeleton, often 16
to 18 carbons long.
 The many nonpolar C—H bonds in the long hydrocarbon skeleton make fats
hydrophobic.
 Fats separate from water because the water molecules hydrogen bond to one another
and exclude the fats.
 In a fat, three fatty acids are joined to glycerol by an ester linkage, creating a
triacylglycerol, or triglyceride.
 The three fatty acids in a fat can be the same or different.
 Fatty acids may vary in length (number of carbons) and in the number and locations of
double bonds.
 If the fatty acid has no carbon-carbon double bonds, then the molecule is a saturated
fatty acid, saturated with hydrogens at every possible position.
 If the fatty acid has one or more carbon-carbon double bonds formed by the removal of
hydrogen atoms from the carbon skeleton, then the molecule is an unsaturated fatty
acid.
 A saturated fatty acid is a straight chain, but an unsaturated fatty acid has a kink wherever
there is a double bond.
 Fats made from saturated fatty acids are saturated fats.
 Most animal fats are saturated.
 Saturated fats are solid at room temperature.
 Fats made from unsaturated fatty acids are unsaturated fats.
 Plant and fish fats are liquid at room temperature and are known as oils.

Biology Chapter Notes

  The kinks caused by the double bonds prevent the molecules from packing tightly
enough to solidify at room temperature.
 The phrase “hydrogenated vegetable oils” on food labels means that unsaturated fats
have been synthetically converted to saturated fats by the addition of hydrogen.
 Peanut butter and margarine are hydrogenated to prevent lipids from separating out
as oil.
 A diet rich in saturated fats may contribute to cardiovascular disease (atherosclerosis)
through plaque deposits.
 The process of hydrogenating vegetable oils produces saturated fats and also
unsaturated fats with trans double bonds. These trans fat molecules contribute more
than saturated fats to atherosclerosis.
 The major function of fats is energy storage.
 A gram of fat stores more than twice as much energy as a gram of a polysaccharide
such as starch.
 Because plants are immobile, they can function with bulky energy storage in the form
of starch. Plants use oils when dispersal and compact storage is important, as in seeds.
 Animals must carry their energy stores with them and benefit from having a more
compact fuel reservoir of fat.
 Humans and other mammals store fats as long-term energy reserves in adipose cells
that swell and shrink as fat is deposited or withdrawn from storage.
 Adipose tissue also functions to cushion vital organs, such as the kidneys.
 A layer of fat can also function as insulation.
 This subcutaneous layer is especially thick in whales, seals, and most other marine
mammals.
Phospholipids are major components of cell membranes.
 Phospholipids have two fatty acids attached to glycerol and a phosphate group at the
third position.
 The phosphate group carries a negative charge.
 Additional smaller groups may be attached to the phosphate group to form a variety of
phospholipids.
 The interaction of phospholipids with water is complex.
 The fatty acid tails are hydrophobic, but the phosphate group and its attachments form
a hydrophilic head.
 When phospholipids are added to water, they self-assemble into assemblages with the
hydrophobic tails pointing toward the interior.
 This type of structure is called a micelle.
 Phospholipids are arranged as a bilayer at the surface of a cell.
 Again, the hydrophilic heads are on the outside of the bilayer, in contact with the
aqueous solution, and the hydrophobic tails point toward the interior of the bilayer.
 The phospholipid bilayer forms a barrier between the cell and the external
environment.
 Phospholipids are the major component of all cell membranes.
Steroids include cholesterol and certain hormones.
 Steroids are lipids with a carbon skeleton consisting of four fused rings.
 Different steroids are created by varying functional groups attached to the rings.
Biology Chapter Notes
 Cholesterol, an important steroid, is a component in animal cell membranes.
 Cholesterol is also the precursor from which all other steroids are synthesized.
 Many of these other steroids are hormones, including the vertebrate sex hormones.
 While cholesterol is an essential molecule in animals, high levels of cholesterol in the
blood may contribute to cardiovascular disease.
 Both saturated fats and trans fats exert their negative impact on health by affecting
cholesterol levels.

Concept 5.4 Proteins have many structures, resulting in a wide range of functions
 Proteins account for more than 50% of the dry mass of most cells. They are instrumental
in almost everything that an organism does.
 Protein functions include structural support, storage, transport, cellular signaling,
movement, and defense against foreign substances.
 Most important, protein enzymes function as catalysts in cells, regulating metabolism
by selectively accelerating chemical reactions without being consumed.
 Humans have tens of thousands of different proteins, each with a specific structure and
function.
 Proteins are the most structurally complex molecules known.
 Each type of protein has a complex three-dimensional shape or conformation.
 All protein polymers are constructed from the same set of 20 amino acid monomers.
 Polymers of proteins are called polypeptides.
 A protein consists of one or more polypeptides folded and coiled into a specific
conformation.
Amino acids are the monomers from which proteins are constructed.
 Amino acids are organic molecules with both carboxyl and amino groups.
 At the center of an amino acid is an asymmetric carbon atom called the alpha carbon.
 Four components are attached to the alpha carbon: a hydrogen atom, a carboxyl group, an
amino group, and a variable R group (or side chain).
 Different R groups characterize the 20 different amino acids.
 R groups may be as simple as a hydrogen atom (as in the amino acid glycine), or it may
be a carbon skeleton with various functional groups attached (as in glutamine).
 The physical and chemical properties of the R group determine the unique characteristics
of a particular amino acid.
 One group of amino acids has hydrophobic R groups.
 Another group of amino acids has polar R groups that are hydrophilic.
 A third group of amino acids includes those with functional groups that are charged
(ionized) at cellular pH.
 Some acidic R groups are negative in charge due to the presence of a carboxyl
group.
 Basic R groups have amino groups that are positive in charge.
 Note that all amino acids have carboxyl and amino groups. The terms acidic and
basic in this context refer only to these groups in the R groups.
Biology Chapter Notes
 Amino acids are joined together when a dehydration reaction removes a hydroxyl group
from the carboxyl end of one amino acid and a hydrogen from the amino group of
another.
 The resulting covalent bond is called a peptide bond.
 Repeating the process over and over creates a polypeptide chain.
 At one end is an amino acid with a free amino group (the N-terminus) and at the other
is an amino acid with a free carboxyl group (the C-terminus).
 Polypeptides range in size from a few monomers to thousands.
 Each polypeptide has a unique linear sequence of amino acids.
The amino acid sequence of a polypeptide can be determined.
 Frederick Sanger and his colleagues at Cambridge University determined the amino acid
sequence of insulin in the 1950s.
 Sanger used protein-digesting enzymes and other catalysts to hydrolyze the insulin at
specific places.
 The fragments were then separated by a technique called chromatography.
 Hydrolysis by another agent broke the polypeptide at different sites, yielding a second
group of fragments.
 Sanger used chemical methods to determine the sequence of amino acids in the small
fragments.
 He then searched for overlapping regions among the pieces obtained by hydrolyzing
with the different agents.
 After years of effort, Sanger was able to reconstruct the complete primary structure of
insulin.
 Most of the steps in sequencing a polypeptide have since been automated.
Protein conformation determines protein function.
 A functional protein consists of one or more polypeptides that have been twisted, folded,
and coiled into a unique shape.
 It is the order of amino acids that determines what the three-dimensional conformation of
the protein will be.
 A protein’s specific conformation determines its function.
 When a cell synthesizes a polypeptide, the chain generally folds spontaneously to assume
the functional conformation for that protein.
 The folding is reinforced by a variety of bonds between parts of the chain, which in turn
depend on the sequence of amino acids.
 Many proteins are globular, while others are fibrous in shape.
 In almost every case, the function of a protein depends on its ability to recognize and bind
to some other molecule.
 For example, an antibody binds to a particular foreign substance.
 An enzyme recognizes and binds to a specific substrate, facilitating a chemical
reaction.
 Natural signal molecules called endorphins bind to specific receptor proteins on the
surface of brain cells in humans, producing euphoria and relieving pain.
 Morphine, heroin, and other opiate drugs mimic endorphins because they are
similar in shape and can bind to the brain’s endorphin receptors.
Biology Chapter Notes
 The function of a protein is an emergent property resulting from its specific molecular
order.
 Three levels of structure—primary, secondary, and tertiary structures—organize the
folding within a single polypeptide.
 Quaternary structure arises when two or more polypeptides join to form a protein.
 The primary structure of a protein is its unique sequence of amino acids.
 Lysozyme, an enzyme that attacks bacteria, consists of 129 amino acids.
 The precise primary structure of a protein is determined by inherited genetic
information.
 Even a slight change in primary structure can affect a protein’s conformation and ability
to function.
 The substitution of one amino acid (valine) for the normal one (glutamic acid) at a
particular position in the primary structure of hemoglobin, the protein that carries
oxygen in red blood cells, can cause sickle-cell disease, an inherited blood disorder.
 The abnormal hemoglobins crystallize, deforming the red blood cells into a sickle
shape and clogging capillaries.
 Most proteins have segments of their polypeptide chains repeatedly coiled or folded.
 These coils and folds are referred to as secondary structure and result from hydrogen
bonds between the repeating constituents of the polypeptide backbone.
 The weakly positive hydrogen atom attached to the nitrogen atom has an affinity for
the oxygen atom of a nearby peptide bond.
 Each hydrogen bond is weak, but the sum of many hydrogen bonds stabilizes the
structure of part of the protein.
 Typical secondary structures are coils (an alpha helix) or folds (beta pleated sheets).
 The structural properties of silk are due to beta pleated sheets.
 The presence of so many hydrogen bonds makes each silk fiber stronger than a steel
strand of the same weight.
 Tertiary structure is determined by interactions among various R groups.
 These interactions include hydrogen bonds between polar and/or charged areas, ionic
bonds between charged R groups, and hydrophobic interactions and van der Waals
interactions among hydrophobic R groups.
 While these three interactions are relatively weak, strong covalent bonds called
disulfide bridges that form between the sulfhydryl groups (SH) of two cysteine
monomers act to rivet parts of the protein together.
 Quaternary structure results from the aggregation of two or more polypeptide subunits.
 Collagen is a fibrous protein of three polypeptides that are supercoiled like a rope.
 This provides structural strength for collagen’s role in connective tissue.
 Hemoglobin is a globular protein with quaternary structure.
 It consists of four polypeptide subunits: two alpha and two beta chains.
 Both types of subunits consist primarily of alpha-helical secondary structure.
 Each subunit has a nonpeptide heme component with an iron atom that binds oxygen.
 What are the key factors determining protein conformation?
 A polypeptide chain of a given amino acid sequence can spontaneously arrange itself into
a 3D shape determined and maintained by the interactions responsible for secondary and
tertiary structure.
Biology Chapter Notes
  The folding occurs as the protein is being synthesized within the cell.
 However, protein conformation also depends on the physical and chemical conditions of
the protein’s environment.
 Alterations in pH, salt concentration, temperature, or other factors can unravel or
denature a protein.
 These forces disrupt the hydrogen bonds, ionic bonds, and disulfide bridges that
maintain the protein’s shape.
 Most proteins become denatured if the are transferred to an organic solvent. The
polypeptide chain refolds so that its hydrophobic regions face outward, toward the
solvent.
 Denaturation can also be caused by heat, which disrupts the weak interactions that
stabilize conformation.
 This explains why extremely high fevers can be fatal. Proteins in the blood become
denatured by the high body temperatures.
 Some proteins can return to their functional shape after denaturation, but others cannot,
especially in the crowded environment of the cell.
 Biochemists now know the amino acid sequences of more than 875,000 proteins and the
3D shapes of about 7,000.
 Nevertheless, it is still difficult to predict the conformation of a protein from its
primary structure alone.
 Most proteins appear to undergo several intermediate stages before reaching their
“mature” configuration.
 The folding of many proteins is assisted by chaperonins or chaperone proteins.
 Chaperonins do not specify the final structure of a polypeptide but rather work to
segregate and protect the polypeptide while it folds spontaneously.
 At present, scientists use X-ray crystallography to determine protein conformation.
 This technique requires the formation of a crystal of the protein being studied.
 The pattern of diffraction of an X-ray by the atoms of the crystal can be used to determine
the location of the atoms and to build a computer model of its structure.
 Nuclear magnetic resonance (NMR) spectroscopy has recently been applied to this
problem.
 This method does not require protein crystallization.

Concept 5.5 Nucleic acids store and transmit hereditary information

 The amino acid sequence of a polypeptide is programmed by a unit of inheritance known
as a gene.
 A gene consists of DNA, a polymer known as a nucleic acid.
There are two types of nucleic acids: RNA and DNA.
 There are two types of nucleic acids: ribonucleic acid (RNA) and deoxyribonucleic acid
(DNA).
 These are the molecules that allow living organisms to reproduce their complex
components from generation to generation.
 DNA provides directions for its own replication.
Biology Chapter Notes
 DNA also directs RNA synthesis and, through RNA, controls protein synthesis.
 Organisms inherit DNA from their parents.
 Each DNA molecule is very long, consisting of hundreds to thousands of genes.
 Before a cell reproduces itself by dividing, its DNA is copied. The copies are then
passed to the next generation of cells.
 While DNA encodes the information that programs all the cell’s activities, it is not
directly involved in the day-to-day operations of the cell.
 Proteins are responsible for implementing the instructions contained in DNA.
 Each gene along a DNA molecule directs the synthesis of a specific type of messenger
RNA molecule (mRNA).
 The mRNA molecule interacts with the cell’s protein-synthesizing machinery to direct the
ordering of amino acids in a polypeptide.
 The flow of genetic information is from DNA -> RNA -> protein.
 Protein synthesis occurs on cellular structures called ribosomes.
 In eukaryotes, DNA is located in the nucleus, but most ribosomes are in the cytoplasm.
mRNA functions as an intermediary, moving information and directions from the nucleus
to the cytoplasm.
 Prokaryotes lack nuclei but still use RNA as an intermediary to carry a message from
DNA to the ribosomes.
A nucleic acid strand is a polymer of nucleotides.
 Nucleic acids are polymers made of nucleotide monomers.
 Each nucleotide consists of three parts: a nitrogenous base, a pentose sugar, and a
phosphate group.
 The nitrogen bases are rings of carbon and nitrogen that come in two types: purines and
pyrimidines.
 Pyrimidines have a single six-membered ring.
 There are three different pyrimidines: cytosine (C), thymine (T), and uracil (U).
 Purines have a six-membered ring joined to a five-membered ring.
 The two purines are adenine (A) and guanine (G).
 The pentose joined to the nitrogen base is ribose in nucleotides of RNA and deoxyribose
in DNA.
 The only difference between the sugars is the lack of an oxygen atom on carbon two in
deoxyribose.
 Because the atoms in both the nitrogenous base and the sugar are numbered, the sugar
atoms have a prime after the number to distinguish them.
 Thus, the second carbon in the sugar ring is the 2’ (2 prime) carbon and the carbon that
sticks up from the ring is the 5’ carbon.
 The combination of a pentose and a nitrogenous base is a nucleoside.
 The addition of a phosphate group creates a nucleoside monophosphate or nucleotide.
 Polynucleotides are synthesized when adjacent nucleotides are joined by covalent bonds
called phosphodiester linkages that form between the —OH group on the 3’ of one
nucleotide and the phosphate on the 5’ carbon of the next.
 This creates a repeating backbone of sugar-phosphate units, with appendages
consisting of the nitrogenous bases.
Biology Chapter Notes
 The two free ends of the polymer are distinct.
 One end has a phosphate attached to a 5’ carbon; this is the 5’ end.
 The other end has a hydroxyl group on a 3’ carbon; this is the 3’ end.
 The sequence of bases along a DNA or mRNA polymer is unique for each gene.
 Because genes are normally hundreds to thousands of nucleotides long, the number of
possible base combinations is virtually limitless.
 The linear order of bases in a gene specifies the order of amino acids—the primary
structure—of a protein, which in turn determines three-dimensional conformation and
function.
Inheritance is based on replication of the DNA double helix.
 An RNA molecule is a single polynucleotide chain.
 DNA molecules have two polynucleotide strands that spiral around an imaginary axis to
form a double helix.
 The double helix was first proposed as the structure of DNA in 1953 by James Watson
and Francis Crick.
 The sugar-phosphate backbones of the two polynucleotides are on the outside of the helix.
 The two backbones run in opposite 5’ -> 3’ directions from each other, an arrangement
referred to as antiparallel.
 Pairs of nitrogenous bases, one from each strand, connect the polynucleotide chains with
hydrogen bonds.
 Most DNA molecules have thousands to millions of base pairs.
 Because of their shapes, only some bases are compatible with each other.
 Adenine (A) always pairs with thymine (T) and guanine (G) with cytosine (C).
 With these base-pairing rules, if we know the sequence of bases on one strand, we know
the sequence on the opposite strand.
 The two strands are complementary.
 Prior to cell division, each of the strands serves as a template to order nucleotides into a
new complementary strand.
 This results in two identical copies of the original double-stranded DNA molecule,
which are then distributed to the daughter cells.
 This mechanism ensures that a full set of genetic information is transmitted whenever a
cell reproduces.
We can use DNA and proteins as tape measures of evolution.
 Genes (DNA) and their products (proteins) document the hereditary background of an
organism.
 Because DNA molecules are passed from parents to offspring, siblings have greater
similarity in their DNA and protein than do unrelated individuals of the same species.
 This argument can be extended to develop a “molecular genealogy” to relationships
between species.
 Two species that appear to be closely related based on fossil and molecular evidence
should also be more similar in DNA and protein sequences than are more distantly related
species.
 In fact, that is so.
Biology Chapter Notes
  For example, if we compare the sequence of 146 amino acids in a hemoglobin
polypeptide, we find that humans and gorillas differ in just 1 amino acid.
 Humans and gibbons differ in 2 amino acids.
 Humans and rhesus monkeys differ in 8 amino acids.
 More distantly related species have more differences.
 Humans and mice differ in 27 amino acids.
 Humans and frogs differ in 67 amino acids.
 Molecular biology can be used to assess evolutionary kinship.


Biology Chapter Notes

 Chapter 6 A Tour of the Cell
Chapter Notes

Overview: The Importance of Cells

 All organisms are made of cells.

 Many organisms are single-celled.
 Even in multicellular organisms, the cell is the basic unit of structure and function.
 The cell is the simplest collection of matter that can live.
 All cells are related by their descent from earlier cells.

Concept 6.1 To study cells, biologists use microscopes and the tools of biochemistry
 The discovery and early study of cells progressed with the invention of microscopes in
1590 and their improvement in the 17th century.
 In a light microscope (LM), visible light passes through the specimen and then through
glass lenses.
 The lenses refract light such that the image is magnified into the eye or onto a video
screen.
 Microscopes vary in magnification and resolving power.
 Magnification is the ratio of an object’s image to its real size.
 Resolving power is a measure of image clarity.
 It is the minimum distance two points can be separated and still be distinguished as
two separate points.
 Resolution is limited by the shortest wavelength of the radiation used for imaging.
 The minimum resolution of a light microscope is about 200 nanometers (nm), the size of a
small bacterium.
 Light microscopes can magnify effectively to about 1,000 times the size of the actual
specimen.
 At higher magnifications, the image blurs.
 Techniques developed in the 20th century have enhanced contrast and enabled particular
cell components to be stained or labeled so they stand out.
 While a light microscope can resolve individual cells, it cannot resolve much of the
internal anatomy, especially the organelles.
 To resolve smaller structures, we use an electron microscope (EM), which focuses a
beam of electrons through the specimen or onto its surface.
 Because resolution is inversely related to wavelength used, electron microscopes
(whose electron beams have shorter wavelengths than visible light) have finer
resolution.
 Theoretically, the resolution of a modern EM could reach 0.002 nanometer (nm), but
the practical limit is closer to about 2 nm.
 Transmission electron microscopes (TEMs) are used mainly to study the internal
ultrastructure of cells.
Biology Chapter Notes
  A TEM aims an electron beam through a thin section of the specimen.
 The image is focused and magnified by electromagnets.
 To enhance contrast, the thin sections are stained with atoms of heavy metals.
 Scanning electron microscopes (SEMs) are useful for studying surface structures.
 The sample surface is covered with a thin film of gold.
 The beam excites electrons on the surface of the sample.
 These secondary electrons are collected and focused on a screen.
 The result is an image of the topography of the specimen.
 The SEM has great depth of field, resulting in an image that seems three-dimensional.
 Electron microscopes reveal organelles that are impossible to resolve with the light
microscope.
 However, electron microscopes can only be used on dead cells.
 Light microscopes do not have as high a resolution, but they can be used to study live
cells.
 Microscopes are major tools in cytology, the study of cell structures.
 Cytology combined with biochemistry, the study of molecules and chemical processes in
metabolism, to produce modern cell biology.
Cell biologists can isolate organelles to study their functions.
 The goal of cell fractionation is to separate the major organelles of the cells so their
individual functions can be studied.
 This process is driven by an ultracentrifuge, a machine that can spin at up to 130,000
revolutions per minute and apply forces of more than 1 million times gravity (1,000,000
g).
 Fractionation begins with homogenization, gently disrupting the cell.
 The homogenate is spun in a centrifuge to separate heavier pieces into the pellet while
lighter particles remain in the supernatant.
 As the process is repeated at higher speeds and for longer durations, smaller and
smaller organelles can be collected in subsequent pellets.
 Cell fractionation prepares isolates of specific cell components.
 This enables the functions of these organelles to be determined, especially by the
reactions or processes catalyzed by their proteins.
 For example, one cellular fraction was enriched in enzymes that function in cellular
respiration.
 Electron microscopy revealed that this fraction is rich in mitochondria.
 This evidence helped cell biologists determine that mitochondria are the site of cellular
respiration.
 Cytology and biochemistry complement each other in correlating cellular structure and
function.

Concept 6.2 Eukaryotic cells have internal membranes that compartmentalize their
functions
Prokaryotic and eukaryotic cells differ in size and complexity.
Biology Chapter Notes
 All cells are surrounded by a plasma membrane.
 The semifluid substance within the membrane is the cytosol, containing the organelles.
 All cells contain chromosomes that have genes in the form of DNA.
 All cells also have ribosomes, tiny organelles that make proteins using the instructions
contained in genes.
 A major difference between prokaryotic and eukaryotic cells is the location of
chromosomes.
 In a eukaryotic cell, chromosomes are contained in a membrane-enclosed organelle, the
nucleus.
 In a prokaryotic cell, the DNA is concentrated in the nucleoid without a membrane
separating it from the rest of the cell.
 In eukaryote cells, the chromosomes are contained within a membranous nuclear
envelope.
 The region between the nucleus and the plasma membrane is the cytoplasm.
 All the material within the plasma membrane of a prokaryotic cell is cytoplasm.
 Within the cytoplasm of a eukaryotic cell are a variety of membrane-bound organelles of
specialized form and function.
 These membrane-bound organelles are absent in prokaryotes.
 Eukaryotic cells are generally much bigger than prokaryotic cells.
 The logistics of carrying out metabolism set limits on cell size.
 At the lower limit, the smallest bacteria, mycoplasmas, are between 0.1 to 1.0 micron.
 Most bacteria are 1–10 microns in diameter.
 Eukaryotic cells are typically 10–100 microns in diameter.
 Metabolic requirements also set an upper limit to the size of a single cell.
 As a cell increases in size, its volume increases faster than its surface area.
 Smaller objects have a greater ratio of surface area to volume.
 The plasma membrane functions as a selective barrier that allows the passage of oxygen,
nutrients, and wastes for the whole volume of the cell.
 The volume of cytoplasm determines the need for this exchange.
 Rates of chemical exchange across the plasma membrane may be inadequate to maintain a
cell with a very large cytoplasm.
 The need for a surface sufficiently large to accommodate the volume explains the
microscopic size of most cells.
 Larger organisms do not generally have larger cells than smaller organisms—simply
more cells.
 Cells that exchange a lot of material with their surroundings, such as intestinal cells, may
have long, thin projections from the cell surface called microvilli. Microvilli increase
surface area without significantly increasing cell volume.
Internal membranes compartmentalize the functions of a eukaryotic cell.
 A eukaryotic cell has extensive and elaborate internal membranes, which partition the cell
into compartments.

Biology Chapter Notes

 These membranes also participate directly in metabolism, as many enzymes are built into
membranes.
 The compartments created by membranes provide different local environments that
facilitate specific metabolic functions, allowing several incompatible processes to go on
simultaneously in a cell.
 The general structure of a biological membrane is a double layer of phospholipids.
 Other lipids and diverse proteins are embedded in the lipid bilayer or attached to its
surface.
 Each type of membrane has a unique combination of lipids and proteins for its specific
functions.
 For example, enzymes embedded in the membranes of mitochondria function in
cellular respiration.

Concept 6.3 The eukaryotic cell’s genetic instructions are housed in the nucleus and
carried out by the ribosomes
 The nucleus contains most of the genes in a eukaryotic cell.
 Additional genes are located in mitochondria and chloroplasts.
 The nucleus averages about 5 microns in diameter.
 The nucleus is separated from the cytoplasm by a double membrane called the nuclear
envelope.
 The two membranes of the nuclear envelope are separated by 20–40 nm.
 The envelope is perforated by pores that are about 100 nm in diameter.
 At the lip of each pore, the inner and outer membranes of the nuclear envelope are
fused to form a continuous membrane.
 A protein structure called a pore complex lines each pore, regulating the passage of
certain large macromolecules and particles.
 The nuclear side of the envelope is lined by the nuclear lamina, a network of protein
filaments that maintains the shape of the nucleus.
 There is evidence that a framework of fibers called the nuclear matrix extends through
the nuclear interior.
 Within the nucleus, the DNA and associated proteins are organized into discrete units
called chromosomes, structures that carry the genetic information.
 Each chromosome is made up of fibrous material called chromatin, a complex of proteins
and DNA.
 Stained chromatin appears through light microscopes and electron microscopes as a
diffuse mass.
 As the cell prepares to divide, the chromatin fibers coil up and condense, becoming thick
enough to be recognized as the familiar chromosomes.
 Each eukaryotic species has a characteristic number of chromosomes.
 A typical human cell has 46 chromosomes.
 A human sex cell (egg or sperm) has only 23 chromosomes.
 In the nucleus is a region of densely stained fibers and granules adjoining chromatin, the
nucleolus.
Biology Chapter Notes
  In the nucleolus, ribosomal RNA (rRNA) is synthesized and assembled with proteins
from the cytoplasm to form ribosomal subunits.
 The subunits pass through the nuclear pores to the cytoplasm, where they combine to
form ribosomes.
 The nucleus directs protein synthesis by synthesizing messenger RNA (mRNA).
 The mRNA travels to the cytoplasm through the nuclear pores and combines with
ribosomes to translate its genetic message into the primary structure of a specific
polypeptide.
Ribosomes build a cell’s proteins.
 Ribosomes, containing rRNA and protein, are the organelles that carry out protein
synthesis.
 Cell types that synthesize large quantities of proteins (e.g., pancreas cells) have large
numbers of ribosomes and prominent nucleoli.
 Some ribosomes, free ribosomes, are suspended in the cytosol and synthesize proteins that
function within the cytosol.
 Other ribosomes, bound ribosomes, are attached to the outside of the endoplasmic
reticulum or nuclear envelope.
 These synthesize proteins that are either included in membranes or exported from the
cell.
 Ribosomes can shift between roles depending on the polypeptides they are synthesizing.

Concept 6.4 The endomembrane system regulates protein traffic and performs
metabolic functions in the cell
 Many of the internal membranes in a eukaryotic cell are part of the endomembrane
system.
 These membranes are either directly continuous or connected via transfer of vesicles, sacs
of membrane.
 In spite of these connections, these membranes are diverse in function and structure.
 The thickness, molecular composition and types of chemical reactions carried out by
proteins in a given membrane may be modified several times during a membrane’s
life.
 The endomembrane system includes the nuclear envelope, endoplasmic reticulum, Golgi
apparatus, lysosomes, vacuoles, and the plasma membrane.
The endoplasmic reticulum manufactures membranes and performs many other
biosynthetic functions.
 The endoplasmic reticulum (ER) accounts for half the membranes in a eukaryotic cell.
 The ER includes membranous tubules and internal, fluid-filled spaces called cisternae.
 The ER membrane is continuous with the nuclear envelope, and the cisternal space of the
ER is continuous with the space between the two membranes of the nuclear envelope.
 There are two connected regions of ER that differ in structure and function.
 Smooth ER looks smooth because it lacks ribosomes.
 Rough ER looks rough because ribosomes (bound ribosomes) are attached to the
outside, including the outside of the nuclear envelope.
Biology Chapter Notes
 The smooth ER is rich in enzymes and plays a role in a variety of metabolic processes.
 Enzymes of smooth ER synthesize lipids, including oils, phospholipids, and steroids.
 These include the sex hormones of vertebrates and adrenal steroids.
 In the smooth ER of the liver, enzymes help detoxify poisons and drugs such as
alcohol and barbiturates.
 Frequent use of these drugs leads to the proliferation of smooth ER in liver cells,
increasing the rate of detoxification.
 This increases tolerance to the target and other drugs, so higher doses are required
to achieve the same effect.
 Smooth ER stores calcium ions.
 Muscle cells have a specialized smooth ER that pumps calcium ions from the
cytosol and stores them in its cisternal space.
 When a nerve impulse stimulates a muscle cell, calcium ions rush from the ER into
the cytosol, triggering contraction.
 Enzymes then pump the calcium back, readying the cell for the next stimulation.
 Rough ER is especially abundant in cells that secrete proteins.
 As a polypeptide is synthesized on a ribosome attached to rough ER, it is threaded into
the cisternal space through a pore formed by a protein complex in the ER membrane.
 As it enters the cisternal space, the new protein folds into its native conformation.
 Most secretory polypeptides are glycoproteins, proteins to which a carbohydrate is
attached.
 Secretory proteins are packaged in transport vesicles that carry them to their next
stage.
 Rough ER is also a membrane factory.
 Membrane-bound proteins are synthesized directly into the membrane.
 Enzymes in the rough ER also synthesize phospholipids from precursors in the cytosol.
 As the ER membrane expands, membrane can be transferred as transport vesicles to
other components of the endomembrane system.
The Golgi apparatus is the shipping and receiving center for cell products.
 Many transport vesicles from the ER travel to the Golgi apparatus for modification of
their contents.
 The Golgi is a center of manufacturing, warehousing, sorting, and shipping.
 The Golgi apparatus is especially extensive in cells specialized for secretion.
 The Golgi apparatus consists of flattened membranous sacs—cisternae—looking like a
stack of pita bread.
 The membrane of each cisterna separates its internal space from the cytosol.
 One side of the Golgi, the cis side, is located near the ER. The cis face receives
material by fusing with transport vesicles from the ER.
 The other side, the trans side, buds off vesicles that travel to other sites.
 During their transit from the cis to the trans side, products from the ER are usually
modified.
 The Golgi can also manufacture its own macromolecules, including pectin and other
noncellulose polysaccharides.
 The Golgi apparatus is a very dynamic structure.
Biology Chapter Notes
  According to the cisternal maturation model, the cisternae of the Golgi progress from
the cis to the trans face, carrying and modifying their protein cargo as they move.
 Finally, the Golgi sorts and packages materials into transport vesicles.
 Molecular identification tags are added to products to aid in sorting.
 Products are tagged with identifiers such as phosphate groups. These act like ZIP
codes on mailing labels to identify the product’s final destination.
Lysosomes are digestive compartments.
 A lysosome is a membrane-bound sac of hydrolytic enzymes that an animal cell uses to
digest macromolecules.
 Lysosomal enzymes can hydrolyze proteins, fats, polysaccharides, and nucleic acids.
 These enzymes work best at pH 5.
 Proteins in the lysosomal membrane pump hydrogen ions from the cytosol into the
lumen of the lysosomes.
 Rupture of one or a few lysosomes has little impact on a cell because the lysosomal
enzymes are not very active at the neutral pH of the cytosol.
 However, massive rupture of many lysosomes can destroy a cell by autodigestion.
 Lysosomal enzymes and membrane are synthesized by rough ER and then transferred to
the Golgi apparatus for further modification.
 Proteins on the inner surface of the lysosomal membrane are spared by digestion by their
three-dimensional conformations, which protect vulnerable bonds from hydrolysis.
 Lysosomes carry out intracellular digestion in a variety of circumstances.
 Amoebas eat by engulfing smaller organisms by phagocytosis.
 The food vacuole formed by phagocytosis fuses with a lysosome, whose enzymes
digest the food.
 As the polymers are digested, monomers pass to the cytosol to become nutrients for the
cell.
 Lysosomes can play a role in recycling of the cell’s organelles and macromolecules.
 This recycling, or autophagy, renews the cell.
 During autophagy, a damaged organelle or region of cytosol becomes surrounded by
membrane.
 A lysosome fuses with the resulting vesicle, digesting the macromolecules and
returning the organic monomers to the cytosol for reuse.
 The lysosomes play a critical role in the programmed destruction of cells in multicellular
organisms.
 This process plays an important role in development.
 The hands of human embryos are webbed until lysosomes digest the cells in the tissue
between the fingers.
 This important process is called programmed cell death, or apoptosis.
Vacuoles have diverse functions in cell maintenance.
 Vesicles and vacuoles (larger versions) are membrane-bound sacs with varied functions.
 Food vacuoles are formed by phagocytosis and fuse with lysosomes.
 Contractile vacuoles, found in freshwater protists, pump excess water out of the cell
to maintain the appropriate concentration of salts.
 A large central vacuole is found in many mature plant cells.
Biology Chapter Notes
  The membrane surrounding the central vacuole, the tonoplast, is selective in its
transport of solutes into the central vacuole.
 The functions of the central vacuole include stockpiling proteins or inorganic ions,
disposing of metabolic byproducts, holding pigments, and storing defensive
compounds that defend the plant against herbivores.
 Because of the large vacuole, the cytosol occupies only a thin layer between the
plasma membrane and the tonoplast. The presence of a large vacuole increases
surface area to volume ratio for the cell.

Concept 6.5 Mitochondria and chloroplasts change energy from one form to another
 Mitochondria and chloroplasts are the organelles that convert energy to forms that cells
can use for work.
 Mitochondria are the sites of cellular respiration, generating ATP from the catabolism of
sugars, fats, and other fuels in the presence of oxygen.
 Chloroplasts, found in plants and algae, are the sites of photosynthesis.
 They convert solar energy to chemical energy and synthesize new organic compounds
such as sugars from CO2 and H2O.
 Mitochondria and chloroplasts are not part of the endomembrane system.
 In contrast to organelles of the endomembrane system, each mitochondrion or
chloroplast has two membranes separating the innermost space from the cytosol.
 Their membrane proteins are not made by the ER, but rather by free ribosomes in the
cytosol and by ribosomes within the organelles themselves.
 Both organelles have small quantities of DNA that direct the synthesis of the polypeptides
produced by these internal ribosomes.
 Mitochondria and chloroplasts grow and reproduce as semiautonomous organelles.
 Almost all eukaryotic cells have mitochondria.
 There may be one very large mitochondrion or hundreds to thousands of individual
mitochondria.
 The number of mitochondria is correlated with aerobic metabolic activity.
 A typical mitochondrion is 1–10 microns long.
 Mitochondria are quite dynamic: moving, changing shape, and dividing.
 Mitochondria have a smooth outer membrane and a convoluted inner membrane with
infoldings called cristae.
 The inner membrane divides the mitochondrion into two internal compartments.
 The first is the intermembrane space, a narrow region between the inner and outer
membranes.
 The inner membrane encloses the mitochondrial matrix, a fluid-filled space with
DNA, ribosomes, and enzymes.
 Some of the metabolic steps of cellular respiration are catalyzed by enzymes in the
matrix.
 The cristae present a large surface area for the enzymes that synthesize ATP.
 The chloroplast is one of several members of a generalized class of plant structures called
plastids.
 Amyloplasts are colorless plastids that store starch in roots and tubers.
 Chromoplasts store pigments for fruits and flowers.
Biology Chapter Notes
  Chloroplasts contain the green pigment chlorophyll as well as enzymes and other
molecules that function in the photosynthetic production of sugar.
 Chloroplasts measure about 2 microns × 5 microns and are found in leaves and other
green organs of plants and algae.
 The contents of the chloroplast are separated from the cytosol by an envelope consisting
of two membranes separated by a narrow intermembrane space.
 Inside the innermost membrane is a fluid-filled space, the stroma, in which float
membranous sacs, the thylakoids.
 The stroma contains DNA, ribosomes, and enzymes.
 The thylakoids are flattened sacs that play a critical role in converting light to chemical
energy. In some regions, thylakoids are stacked like poker chips into grana.
 The membranes of the chloroplast divide the chloroplast into three compartments: the
intermembrane space, the stroma, and the thylakoid space.
 Like mitochondria, chloroplasts are dynamic structures.
 Their shape is plastic, and they can reproduce themselves by pinching in two.
 Mitochondria and chloroplasts are mobile and move around the cell along tracks of the
cytoskeleton.
Peroxisomes generate and degrade H2O2 in performing various metabolic functions.
 Peroxisomes contain enzymes that transfer hydrogen from various substrates to oxygen.
 An intermediate product of this process is hydrogen peroxide (H2O2), a poison.
 The peroxisome contains an enzyme that converts H2O2 to water.
 Some peroxisomes break fatty acids down to smaller molecules that are transported to
mitochondria as fuel for cellular respiration.
 Peroxisomes in the liver detoxify alcohol and other harmful compounds.
 Specialized peroxisomes, glyoxysomes, convert the fatty acids in seeds to sugars,
which the seedling can use as a source of energy and carbon until it is capable of
photosynthesis.
 Peroxisomes are bound by a single membrane.
 They form not from the endomembrane system, but by incorporation of proteins and
lipids from the cytosol.
 They split in two when they reach a certain size.

Concept 6.6 The cytoskeleton is a network of fibers that organizes structures and
activities in the cell
 The cytoskeleton is a network of fibers extending throughout the cytoplasm.
 The cytoskeleton organizes the structures and activities of the cell.
The cytoskeleton provides support, motility, and regulation.
 The cytoskeleton provides mechanical support and maintains cell shape.
 The cytoskeleton provides anchorage for many organelles and cytosolic enzymes.
 The cytoskeleton is dynamic and can be dismantled in one part and reassembled in
another to change the shape of the cell.

Biology Chapter Notes

 The cytoskeleton also plays a major role in cell motility, including changes in cell location
and limited movements of parts of the cell.
 The cytoskeleton interacts with motor proteins to produce motility.
 Cytoskeleton elements and motor proteins work together with plasma membrane
molecules to move the whole cell along fibers outside the cell.
 Motor proteins bring about movements of cilia and flagella by gripping cytoskeletal
components such as microtubules and moving them past each other.
 The same mechanism causes muscle cells to contract.
 Inside the cell, vesicles can travel along “monorails” provided by the cytoskeleton.
 The cytoskeleton manipulates the plasma membrane to form food vacuoles during
phagocytosis.
 Cytoplasmic streaming in plant cells is caused by the cytoskeleton.
 Recently, evidence suggests that the cytoskeleton may play a role in the regulation of
biochemical activities in the cell.
 There are three main types of fibers making up the cytoskeleton: microtubules,
microfilaments, and intermediate filaments.
 Microtubules, the thickest fibers, are hollow rods about 25 microns in diameter and 200
nm to 25 microns in length.
 Microtubule fibers are constructed of the globular protein tubulin.
 Each tubulin molecule is a dimer consisting of two subunits.
 A microtubule changes in length by adding or removing tubulin dimers.
 Microtubules shape and support the cell and serve as tracks to guide motor proteins
carrying organelles to their destination.
 Microtubules are also responsible for the separation of chromosomes during cell division.
 In many cells, microtubules grow out from a centrosome near the nucleus.
 These microtubules resist compression to the cell.
 In animal cells, the centrosome has a pair of centrioles, each with nine triplets of
microtubules arranged in a ring.
 Before a cell divides, the centrioles replicate.
 A specialized arrangement of microtubules is responsible for the beating of cilia and
flagella.
 Many unicellular eukaryotic organisms are propelled through water by cilia and
flagella.
 Cilia or flagella can extend from cells within a tissue layer, beating to move fluid over
the surface of the tissue.
 For example, cilia lining the windpipe sweep mucus carrying trapped debris out of
the lungs.
 Cilia usually occur in large numbers on the cell surface.
 They are about 0.25 microns in diameter and 2–20 microns long.
 There are usually just one or a few flagella per cell.
 Flagella are the same width as cilia, but 10–200 microns long.
 Cilia and flagella differ in their beating patterns.
 A flagellum has an undulatory movement that generates force in the same direction as
the flagellum’s axis.
Biology Chapter Notes
  Cilia move more like oars with alternating power and recovery strokes that generate
force perpendicular to the cilium’s axis.
 In spite of their differences, both cilia and flagella have the same ultrastructure.
 Both have a core of microtubules sheathed by the plasma membrane.
 Nine doublets of microtubules are arranged in a ring around a pair at the center. This
“9 + 2” pattern is found in nearly all eukaryotic cilia and flagella.
 Flexible “wheels” of proteins connect outer doublets to each other and to the two
central microtubules.
 The outer doublets are also connected by motor proteins.
 The cilium or flagellum is anchored in the cell by a basal body, whose structure is
identical to a centriole.
 The bending of cilia and flagella is driven by the arms of a motor protein, dynein.
 Addition and removal of a phosphate group causes conformation changes in dynein.
 Dynein arms alternately grab, move, and release the outer microtubules.
 Protein cross-links limit sliding. As a result, the forces exerted by the dynein arms
cause the doublets to curve, bending the cilium or flagellum.
 Microfilaments are solid rods about 7 nm in diameter.
 Each microfilament is built as a twisted double chain of actin subunits.
 Microfilaments can form structural networks due to their ability to branch.
 The structural role of microfilaments in the cytoskeleton is to bear tension, resisting
pulling forces within the cell.
 They form a three-dimensional network just inside the plasma membrane to help support
the cell’s shape, giving the cell cortex the semisolid consistency of a gel.
 Microfilaments are important in cell motility, especially as part of the contractile
apparatus of muscle cells.
 In muscle cells, thousands of actin filaments are arranged parallel to one another.
 Thicker filaments composed of myosin interdigitate with the thinner actin fibers.
 Myosin molecules act as motor proteins, walking along the actin filaments to shorten
the cell.
 In other cells, actin-myosin aggregates are less organized but still cause localized
contraction.
 A contracting belt of microfilaments divides the cytoplasm of animal cells during cell
division.
 Localized contraction brought about by actin and myosin also drives amoeboid
movement.
 Pseudopodia, cellular extensions, extend and contract through the reversible
assembly and contraction of actin subunits into microfilaments.
 Microfilaments assemble into networks that convert sol to gel.
 According to a widely accepted model, filaments near the cell’s trailing edge
interact with myosin, causing contraction.
 The contraction forces the interior fluid into the pseudopodium, where the actin
network has been weakened.
 The pseudopodium extends until the actin reassembles into a network.

 In plant cells, actin-myosin interactions and sol-gel transformations drive cytoplasmic

streaming.
Biology Chapter Notes
  This creates a circular flow of cytoplasm in the cell, speeding the distribution of
materials within the cell.
 Intermediate filaments range in diameter from 8–12 nanometers, larger than
microfilaments but smaller than microtubules.
 Intermediate filaments are a diverse class of cytoskeletal units, built from a family of
proteins called keratins.
 Intermediate filaments are specialized for bearing tension.
 Intermediate filaments are more permanent fixtures of the cytoskeleton than are the other
two classes.
 They reinforce cell shape and fix organelle location.

Concept 6.7 Extracellular components and connections between cells help coordinate
cellular activities
Plant cells are encased by cell walls.
 The cell wall, found in prokaryotes, fungi, and some protists, has multiple functions.
 In plants, the cell wall protects the cell, maintains its shape, and prevents excessive uptake
of water.
 It also supports the plant against the force of gravity.
 The thickness and chemical composition of cell walls differs from species to species and
among cell types within a plant.
 The basic design consists of microfibrils of cellulose embedded in a matrix of proteins
and other polysaccharides. This is the basic design of steel-reinforced concrete or
fiberglass.
 A mature cell wall consists of a primary cell wall, a middle lamella with sticky
polysaccharides that holds cells together, and layers of secondary cell wall.
 Plant cell walls are perforated by channels between adjacent cells called plasmodesmata.
The extracellular matrix (ECM) of animal cells functions in support, adhesion,
movement, and regulation.
 Though lacking cell walls, animal cells do have an elaborate extracellular matrix
(ECM).
 The primary constituents of the extracellular matrix are glycoproteins, especially collagen
fibers, embedded in a network of glycoprotein proteoglycans.
 In many cells, fibronectins in the ECM connect to integrins, intrinsic membrane proteins
that span the membrane and bind on their cytoplasmic side to proteins attached to
microfilaments of the cytoskeleton.
 The interconnections from the ECM to the cytoskeleton via the fibronectin-integrin
link permit the integration of changes inside and outside the cell.
 The ECM can regulate cell behavior.
 Embryonic cells migrate along specific pathways by matching the orientation of their
microfilaments to the “grain” of fibers in the extracellular matrix.
 The extracellular matrix can influence the activity of genes in the nucleus via a
combination of chemical and mechanical signaling pathways.
Biology Chapter Notes
  This may coordinate the behavior of all the cells within a tissue.
Intercellular junctions help integrate cells into higher levels of structure and function.
 Neighboring cells in tissues, organs, or organ systems often adhere, interact, and
communicate through direct physical contact.
 Plant cells are perforated with plasmodesmata, channels allowing cytosol to pass
between cells.
 Water and small solutes can pass freely from cell to cell.
 In certain circumstances, proteins and RNA can be exchanged.
 Animals have 3 main types of intercellular links: tight junctions, desmosomes, and gap
junctions.
 In tight junctions, membranes of adjacent cells are fused, forming continuous belts
around cells.
 This prevents leakage of extracellular fluid.
 Desmosomes (or anchoring junctions) fasten cells together into strong sheets, much like
rivets.
 Intermediate filaments of keratin reinforce desmosomes.
 Gap junctions (or communicating junctions) provide cytoplasmic channels between
adjacent cells.
 Special membrane proteins surround these pores.
 Ions, sugars, amino acids, and other small molecules can pass.
 In embryos, gap junctions facilitate chemical communication during development.
A cell is a living unit greater than the sum of its parts.
 While the cell has many structures with specific functions, all these structures must work
together.
 For example, macrophages use actin filaments to move and extend pseudopodia to
capture their bacterial prey.
 Food vacuoles are digested by lysosomes, a product of the endomembrane system of
ER and Golgi.
 The enzymes of the lysosomes and proteins of the cytoskeleton are synthesized on the
ribosomes.
 The information for the proteins comes from genetic messages sent by DNA in the
nucleus.
 All of these processes require energy in the form of ATP, most of which is supplied by the
mitochondria.
 A cell is a living unit greater than the sum of its parts.

Biology Chapter Notes

 Chapter 7 Membrane Structure and Function
Chapter Notes

Overview: Life at the Edge

 The plasma membrane separates the living cell from its nonliving surroundings.
 This thin barrier, 8 nm thick, controls traffic into and out of the cell.
 Like all biological membranes, the plasma membrane is selectively permeable, allowing
some substances to cross more easily than others.

Concept 7.1 Cellular membranes are fluid mosaics of lipids and proteins
 The main macromolecules in membranes are lipids and proteins, but carbohydrates are
also important.
 The most abundant lipids are phospholipids.
 Phospholipids and most other membrane constituents are amphipathic molecules.
 Amphipathic molecules have both hydrophobic regions and hydrophilic regions.
 The arrangement of phospholipids and proteins in biological membranes is described by
the fluid mosaic model.
Membrane models have evolved to fit new data.
 Models of membranes were developed long before membranes were first seen with
electron microscopes in the 1950s.
 In 1915, membranes isolated from red blood cells were chemically analyzed and found
to be composed of lipids and proteins.
 In 1925, E. Gorter and F. Grendel reasoned that cell membranes must be a
phospholipid bilayer two molecules thick.
 The molecules in the bilayer are arranged such that the hydrophobic fatty acid tails are
sheltered from water while the hydrophilic phosphate groups interact with water.
 Actual membranes adhere more strongly to water than do artificial membranes
composed only of phospholipids.
 One suggestion was that proteins on the surface of the membrane increased adhesion.
 In 1935, H. Davson and J. Danielli proposed a sandwich model in which the
phospholipid bilayer lies between two layers of globular proteins.
 Early images from electron microscopes seemed to support the Davson-Danielli
model, and until the 1960s, it was widely accepted as the structure of the plasma
membrane and internal membranes.
 Further investigation revealed two problems.
 First, not all membranes were alike. Membranes differ in thickness, appearance
when stained, and percentage of proteins.
 Membranes with different functions differ in chemical composition and
structure.
 Second, measurements showed that membrane proteins are not very soluble in
water.
Biology Chapter Notes
  Membrane proteins are amphipathic, with hydrophobic and hydrophilic regions.
 If membrane proteins were at the membrane surface, their hydrophobic regions
would be in contact with water.
 In 1972, S. J. Singer and G. Nicolson presented a revised model that proposed that the
membrane proteins are dispersed and individually inserted into the phospholipid bilayer.
 In this fluid mosaic model, the hydrophilic regions of proteins and phospholipids are in
maximum contact with water, and the hydrophobic regions are in a nonaqueous
environment within the membrane.
 A specialized preparation technique, freeze-fracture, splits a membrane along the middle
of the phospholipid bilayer.
 When a freeze-fracture preparation is viewed with an electron microscope, protein
particles are interspersed in a smooth matrix, supporting the fluid mosaic model.
Membranes are fluid.
 Membrane molecules are held in place by relatively weak hydrophobic interactions.
 Most of the lipids and some proteins drift laterally in the plane of the membrane, but
rarely flip-flop from one phospholipid layer to the other.
 The lateral movements of phospholipids are rapid, about 2 microns per second. A
phospholipid can travel the length of a typical bacterial cell in 1 second.
 Many larger membrane proteins drift within the phospholipid bilayer, although they move
more slowly than the phospholipids.
 Some proteins move in a very directed manner, perhaps guided or driven by motor
proteins attached to the cytoskeleton.
 Other proteins never move and are anchored to the cytoskeleton.
 Membrane fluidity is influenced by temperature. As temperatures cool, membranes switch
from a fluid state to a solid state as the phospholipids pack more closely.
 Membrane fluidity is also influenced by its components. Membranes rich in unsaturated
fatty acids are more fluid that those dominated by saturated fatty acids because the kinks
in the unsaturated fatty acid tails at the locations of the double bonds prevent tight
packing.
 The steroid cholesterol is wedged between phospholipid molecules in the plasma
membrane of animal cells.
 At warm temperatures (such as 37°C), cholesterol restrains the movement of
phospholipids and reduces fluidity.
 At cool temperatures, it maintains fluidity by preventing tight packing.
 Thus, cholesterol acts as a “temperature buffer” for the membrane, resisting changes in
membrane fluidity as temperature changes.
 To work properly with active enzymes and appropriate permeability, membranes must be
about as fluid as salad oil.
 Cells can alter the lipid composition of membranes to compensate for changes in fluidity
caused by changing temperatures.
 For example, cold-adapted organisms such as winter wheat increase the percentage of
unsaturated phospholipids in their membranes in the autumn.
 This prevents membranes from solidifying during winter.
Membranes are mosaics of structure and function.
Biology Chapter Notes
 A membrane is a collage of different proteins embedded in the fluid matrix of the lipid
bilayer.
 Proteins determine most of the membrane’s specific functions.
 The plasma membrane and the membranes of the various organelles each have unique
collections of proteins.
 There are two major populations of membrane proteins.
 Peripheral proteins are not embedded in the lipid bilayer at all.
 Instead, they are loosely bound to the surface of the protein, often connected to
integral proteins.
 Integral proteins penetrate the hydrophobic core of the lipid bilayer, often completely
spanning the membrane (as transmembrane proteins).
 The hydrophobic regions embedded in the membrane’s core consist of stretches of
nonpolar amino acids, often coiled into alpha helices.
 Where integral proteins are in contact with the aqueous environment, they have
hydrophilic regions of amino acids.
 On the cytoplasmic side of the membrane, some membrane proteins connect to the
cytoskeleton.
 On the exterior side of the membrane, some membrane proteins attach to the fibers of
the extracellular matrix.
 The proteins of the plasma membrane have six major functions:
4. Transport of specific solutes into or out of cells.
5. Enzymatic activity, sometimes catalyzing one of a number of steps of a metabolic
pathway.
6. Signal transduction, relaying hormonal messages to the cell.
7. Cell-cell recognition, allowing other proteins to attach two adjacent cells together.
8. Intercellular joining of adjacent cells with gap or tight junctions.
9. Attachment to the cytoskeleton and extracellular matrix, maintaining cell shape
and stabilizing the location of certain membrane proteins.
Membrane carbohydrates are important for cell-cell recognition.
 The plasma membrane plays the key role in cell-cell recognition.
 Cell-cell recognition, the ability of a cell to distinguish one type of neighboring cell
from another, is crucial to the functioning of an organism.
 This attribute is important in the sorting and organization of cells into tissues and
organs during development.
 It is also the basis for rejection of foreign cells by the immune system.
 Cells recognize other cells by binding to surface molecules, often carbohydrates, on
the plasma membrane.
 Membrane carbohydrates are usually branched oligosaccharides with fewer than 15 sugar
units.
 They may be covalently bonded to lipids, forming glycolipids, or more commonly to
proteins, forming glycoproteins.
 The oligosaccharides on the external side of the plasma membrane vary from species to
species, from individual to individual, and even from cell type to cell type within the same
individual.
 This variation distinguishes each cell type.
Biology Chapter Notes
  The four human blood groups (A, B, AB, and O) differ in the external carbohydrates
on red blood cells.
Membranes have distinctive inside and outside faces.
 Membranes have distinct inside and outside faces. The two layers may differ in lipid
composition. Each protein in the membrane has a directional orientation in the membrane.
 The asymmetrical orientation of proteins, lipids and associated carbohydrates begins
during the synthesis of membrane in the ER and Golgi apparatus.
 Membrane lipids and proteins are synthesized in the endoplasmic reticulum.
Carbohydrates are added to proteins in the ER, and the resulting glycoproteins are further
modified in the Golgi apparatus. Glycolipids are also produced in the Golgi apparatus.
 When a vesicle fuses with the plasma membrane, the outside layer of the vesicle becomes
continuous with the inside layer of the plasma membrane. In that way, molecules that
originate on the inside face of the ER end up on the outside face of the plasma membrane.

Concept 7.2 Membrane structure results in selective permeability

 A steady traffic of small molecules and ions moves across the plasma membrane in both
directions.
 For example, sugars, amino acids, and other nutrients enter a muscle cell, and
metabolic waste products leave.
 The cell absorbs oxygen and expels carbon dioxide.
 It also regulates concentrations of inorganic ions, such as Na +, K+, Ca2+, and Cl−, by
shuttling them across the membrane.
 However, substances do not move across the barrier indiscriminately; membranes are
selectively permeable.
 The plasma membrane allows the cell to take up many varieties of small molecules and
ions and exclude others. Substances that move through the membrane do so at different
rates.
 Movement of a molecule through a membrane depends on the interaction of the molecule
with the hydrophobic core of the membrane.
 Hydrophobic molecules, such as hydrocarbons, CO 2, and O2, can dissolve in the lipid
bilayer and cross easily.
 The hydrophobic core of the membrane impedes the direct passage of ions and polar
molecules, which cross the membrane with difficulty.
 This includes small molecules, such as water, and larger molecules, such as glucose
and other sugars.
 An ion, whether a charged atom or molecule, and its surrounding shell of water also
has difficulty penetrating the hydrophobic core.
 Proteins assist and regulate the transport of ions and polar molecules.
 Specific ions and polar molecules can cross the lipid bilayer by passing through transport
proteins that span the membrane.
 Some transport proteins, called channel proteins, have a hydrophilic channel that
certain molecules or ions can use as a tunnel through the membrane.
 For example, the passage of water through the membrane can be greatly facilitated by
channel proteins known as aquaporins.

Biology Chapter Notes

  Other transport proteins, called carrier proteins, bind to molecules and change shape
to shuttle them across the membrane.
 Each transport protein is specific as to the substances that it will translocate.
 For example, the glucose transport protein in the liver will carry glucose into the cell
but will not transport fructose, its structural isomer.

Concept 7.3 Passive transport is diffusion of a substance across a membrane with no

energy investment
 Diffusion is the tendency of molecules of any substance to spread out in the available
space.
 Diffusion is driven by the intrinsic kinetic energy (thermal motion or heat) of
molecules.
 Movements of individual molecules are random.
 However, movement of a population of molecules may be directional.
 Imagine a permeable membrane separating a solution with dye molecules from pure
water. If the membrane has microscopic pores that are large enough, dye molecules will
cross the barrier randomly.
 The net movement of dye molecules across the membrane will continue until both sides
have equal concentrations of the dye.
 At this dynamic equilibrium, as many molecules cross one way as cross in the other
direction.
 In the absence of other forces, a substance will diffuse from where it is more concentrated
to where it is less concentrated, down its concentration gradient.
 No work must be done to move substances down the concentration gradient.
 Diffusion is a spontaneous process that decreases free energy and increases entropy by
creating a randomized mixture.
 Each substance diffuses down its own concentration gradient, independent of the
concentration gradients of other substances.
 The diffusion of a substance across a biological membrane is passive transport because it
requires no energy from the cell to make it happen.
 The concentration gradient itself represents potential energy and drives diffusion.
 Because membranes are selectively permeable, the interactions of the molecules with the
membrane play a role in the diffusion rate.
 Diffusion of molecules of limited permeability through the lipid bilayer may be assisted
by transport proteins.
Osmosis is the passive transport of water.
 Differences in the relative concentration of dissolved materials in two solutions can lead
to the movement of ions from one to the other.
 The solution with the higher concentration of solutes is hypertonic relative to the other
solution.
 The solution with the lower concentration of solutes is hypotonic relative to the other
solution.
 These are comparative terms.
Biology Chapter Notes
  Tap water is hypertonic compared to distilled water but hypotonic compared to
seawater.
 Solutions with equal solute concentrations are isotonic.
 Imagine that two sugar solutions differing in concentration are separated by a membrane
that will allow water through, but not sugar.
 The hypertonic solution has a lower water concentration than the hypotonic solution.
 More of the water molecules in the hypertonic solution are bound up in hydration
shells around the sugar molecules, leaving fewer unbound water molecules.
 Unbound water molecules will move from the hypotonic solution, where they are
abundant, to the hypertonic solution, where they are rarer. Net movement of water
continues until the solutions are isotonic.
 The diffusion of water across a selectively permeable membrane is called osmosis.
 The direction of osmosis is determined only by a difference in total solute concentration.
 The kinds of solutes in the solutions do not matter.
 This makes sense because the total solute concentration is an indicator of the
abundance of bound water molecules (and, therefore, of free water molecules).
 When two solutions are isotonic, water molecules move at equal rates from one to the
other, with no net osmosis.
 The movement of water by osmosis is crucial to living organisms.
Cell survival depends on balancing water uptake and loss.
 An animal cell (or other cell without a cell wall) immersed in an isotonic environment experiences no net
movement of water across its plasma membrane.
 Water molecules move across the membrane but at the same rate in both directions.
 The volume of the cell is stable.
 The same cell in a hypertonic environment will lose water, shrivel, and probably die.
 A cell in a hypotonic solution will gain water, swell, and burst.
 For organisms living in an isotonic environment (for example, many marine
invertebrates), osmosis is not a problem.
 The cells of most land animals are bathed in extracellular fluid that is isotonic to the
cells.
 Organisms without rigid walls have osmotic problems in either a hypertonic or hypotonic
environment and must have adaptations for osmoregulation, the control of water balance,
to maintain their internal environment.
 For example, Paramecium, a protist, is hypertonic to the pond water in which it lives.
 In spite of a cell membrane that is less permeable to water than other cells, water still
continually enters the Paramecium cell.
 To solve this problem, Paramecium cells have a specialized organelle, the contractile
vacuole, which functions as a bilge pump to force water out of the cell.
 The cells of plants, prokaryotes, fungi, and some protists have walls that contribute to the
cell’s water balance.
 A plant cell in a hypotonic solution will swell until the elastic cell wall opposes further
uptake.
 At this point the cell is turgid (very firm), a healthy state for most plant cells.

Biology Chapter Notes

 Turgid cells contribute to the mechanical support of the plant.
 If a plant cell and its surroundings are isotonic, there is no movement of water into the
cell. The cell becomes flaccid (limp), and the plant may wilt.
 The cell wall provides no advantages when a plant cell is immersed in a hypertonic
solution. As the plant cell loses water, its volume shrinks. Eventually, the plasma
membrane pulls away from the wall. This plasmolysis is usually lethal.
Specific proteins facilitate passive transport of water and selected solutes.
 Many polar molecules and ions that are normally impeded by the lipid bilayer of the
membrane diffuse passively with the help of transport proteins that span the membrane.
 The passive movement of molecules down their concentration gradient via transport
proteins is called facilitated diffusion.
 Two types of transport proteins facilitate the movement of molecules or ions across
membranes: channel proteins and carrier proteins.
 Some channel proteins simply provide hydrophilic corridors for the passage of specific
molecules or ions.
 For example, water channel proteins, aquaporins, greatly facilitate the diffusion of
water.
 Many ion channels function as gated channels. These channels open or close depending
on the presence or absence of a chemical or physical stimulus.
 If chemical, the stimulus is a substance other than the one to be transported.
 For example, stimulation of a receiving neuron by specific neurotransmitters opens
gated channels to allow sodium ions into the cell.
 When the neurotransmitters are not present, the channels are closed.
 Some transport proteins do not provide channels but appear to actually translocate the
solute-binding site and solute across the membrane as the transport protein changes shape.
 These shape changes may be triggered by the binding and release of the transported
molecule.
 In certain inherited diseases, specific transport systems may be defective or absent.
 Cystinuria is a human disease characterized by the absence of a protein that transports
cysteine and other amino acids across the membranes of kidney cells.
 An individual with cystinuria develops painful kidney stones as amino acids
accumulate and crystallize in the kidneys.

Concept 7.4 Active transport uses energy to move solutes against their gradients
 Some transport proteins can move solutes across membranes against their concentration
gradient, from the side where they are less concentrated to the side where they are more
concentrated.
 This active transport requires the cell to expend metabolic energy.
 Active transport enables a cell to maintain its internal concentrations of small molecules
that would otherwise diffuse across the membrane.
 Active transport is performed by specific proteins embedded in the membranes.
 ATP supplies the energy for most active transport.

Biology Chapter Notes

  ATP can power active transport by transferring a phosphate group from ATP (forming
ADP) to the transport protein.
 This may induce a conformational change in the transport protein, translocating the
solute across the membrane.
 The sodium-potassium +
pump actively maintains the gradient of sodium ions (Na +) and
potassium ions (K ) across the plasma membrane of animal cells.
 Typically,+ K+ concentration is low outside an animal cell and high inside the cell,
while Na concentration is high outside an animal cell and low inside the cell.
 The sodium-potassium pump maintains these concentration gradients, using the energy
of one ATP to pump three Na+ out and two K+ in.
Some ion pumps generate voltage across membranes.
 All cells maintain a voltage across their plasma membranes.
 Voltage is electrical potential energy due to the separation of opposite charges.
 The cytoplasm of a cell is negative in charge compared to the extracellular fluid
because of an unequal distribution of cations and anions on opposite sides of the
membrane.
 The voltage across a membrane is called a membrane potential, and ranges from −50
to −200 millivolts (mV). The inside of the cell is negative compared to the outside.
 The membrane potential acts like a battery.
 The membrane potential favors the passive transport of cations into the cell and anions out
of the cell.
 Two combined forces, collectively called the electrochemical gradient, drive the
diffusion of ions across a membrane.
 One is a chemical force based on an ion’s concentration gradient.
 The other is an electrical force based on the effect of the membrane potential on the
ion’s movement.
 An ion does not simply diffuse down its concentration gradient but diffuses down its
electrochemical gradient.
 For example, there is a higher concentration of Na + outside a resting nerve cell than
inside.
 When the neuron is stimulated, a gated channel opens and Na++ diffuse into the cell
down their electrochemical gradient. The diffusion of Na is driven by their
concentration gradient and by the attraction of cations to the negative side of the
membrane.
 Special transport proteins, electrogenic pumps, generate the voltage gradient across a
membrane.
 The sodium-potassium pump+in animals +
restores the electrochemical gradient not only
by the active transport of Na and K , setting up a concentration gradient, but because
it pumps two K+ inside for every three Na+ that it moves out, setting up a voltage
across the membrane.
 The sodium-potassium pump is the major electrogenic pump of animal cells.
 In plants, bacteria, and fungi, a proton pump is the major electrogenic pump, actively
transporting H+ out of the cell.
 Proton pumps in the cristae of mitochondria and the thylakoids of chloroplasts concentrate
H+ behind membranes.

Biology Chapter Notes

 These electrogenic pumps store energy that can be accessed for cellular work.
In cotransport, a membrane protein couples the transport of two solutes.
 A single ATP-powered pump that transports one solute can indirectly drive the active
transport of several other solutes in a mechanism called cotransport.
 As the solute that has been actively transported diffuses back passively through a transport
protein, its movement can be coupled with the active transport of another substance
against its concentration gradient.
 Plants commonly use the gradient of hydrogen ions generated by proton pumps to drive
the active transport of amino acids, sugars, and other nutrients into the cell.
 One specific transport protein couples the diffusion of protons out of the cell and the
transport of sucrose into the cell. Plants use the mechanism of sucrose-proton cotransport
to load sucrose into specialized cells in the veins of leaves for distribution to
nonphotosynthetic organs such as roots.

Concept 7.5 Bulk transport across the plasma membrane occurs by exocytosis and
endocytosis
 Small molecules and water enter or leave the cell through the lipid bilayer or by transport
proteins.
 Large molecules, such as polysaccharides and proteins, cross the membrane via vesicles.
 During exocytosis, a transport vesicle budded from the Golgi apparatus is moved by the
cytoskeleton to the plasma membrane.
 When the two membranes come in contact, the bilayers fuse and spill the contents to the
outside.
 Many secretory cells use exocytosis to export their products.
 During endocytosis, a cell brings in macromolecules and particulate matter by forming
new vesicles from the plasma membrane.
 Endocytosis is a reversal of exocytosis, although different proteins are involved in the two
processes.
 A small area of the plasma membrane sinks inward to form a pocket.
 As the pocket deepens, it pinches in to form a vesicle containing the material that had
been outside the cell.
 There are three types of endocytosis: phagocytosis (“cellular eating”), pinocytosis
(“cellular drinking”), and receptor-mediated endocytosis.
 In phagocytosis, the cell engulfs a particle by extending pseudopodia around it and
packaging it in a large vacuole.
 The contents of the vacuole are digested when the vacuole fuses with a lysosome.
 In pinocytosis, a cell creates a vesicle around a droplet of extracellular fluid. All included
solutes are taken into the cell in this nonspecific process.
 Receptor-mediated endocytosis allows greater specificity, transporting only certain
substances.
 This process is triggered when extracellular substances, or ligands, bind to special
receptors on the membrane surface. The receptor proteins are clustered in regions of the

Biology Chapter Notes

 membrane called coated pits, which are lined on their cytoplasmic side by a layer of coat
proteins.
 Binding of ligands to receptors triggers the formation of a vesicle by the coated pit,
bringing the bound substances into the cell.
 Receptor-mediated endocytosis enables a cell to acquire bulk quantities of specific
materials that may be in low concentrations in the environment.
 Human cells use this process to take in cholesterol for use in the synthesis of
membranes and as a precursor for the synthesis of steroids.
 Cholesterol travels in the blood in low-density lipoproteins (LDL), complexes of
protein and lipid.
 These lipoproteins act as ligands to bind to LDL receptors and enter the cell by
endocytosis.
 In an inherited disease called familial hypercholesterolemia, the LDL receptors are
defective, leading to an accumulation of LDL and cholesterol in the blood.
 This contributes to early atherosclerosis.

Biology Chapter Notes

 Chapter 8 An Introduction to Metabolism
Chapter Notes

Overview: The Energy of Life

Concept 8.1 An organism’s metabolism transforms matter and energy, subject to the
laws of thermodynamics
 The totality of an organism’s chemical reactions is called metabolism.
 Metabolism is an emergent property of life that arises from interactions between
molecules within the orderly environment of the cell.
The chemistry of life is organized into metabolic pathways.
 Metabolic pathways begin with a specific molecule, which is then altered in a series of
defined steps to form a specific product.
 A specific enzyme catalyzes each step of the pathway.
 Catabolic pathways release energy by breaking down complex molecules to simpler
compounds.
 A major pathway of catabolism is cellular respiration, in which the sugar glucose is
broken down in the presence of oxygen to carbon dioxide and water.
 Anabolic pathways consume energy to build complicated molecules from simpler
compounds. They are also called biosynthetic pathways.
 The synthesis of protein from amino acids is an example of anabolism.
 The energy released by catabolic pathways can be stored and then used to drive anabolic
pathways.
 Energy is fundamental to all metabolic processes, and therefore an understanding of
energy is key to understanding how the living cell works.
 Bioenergetics is the study of how organisms manage their energy resources.
Organisms transform energy.
 Energy is the capacity to do work.
 Energy exists in various forms, and cells transform energy from one type into another.
 Kinetic energy is the energy associated with the relative motion of objects.
 Objects in motion can perform work by imparting motion to other matter.
 Photons of light can be captured and their energy harnessed to power photosynthesis in
green plants.
 Heat or thermal energy is kinetic energy associated with the random movement of
atoms or molecules.
 Potential energy is the energy that matter possesses because of its location or structure.
 Chemical energy is a form of potential energy stored in molecules because of the
arrangement of their atoms.
 Energy can be converted from one form to another.
 For example, as a boy climbs stairs to a diving platform, he is releasing chemical
energy stored in his cells from the food he ate for lunch.
Biology Chapter Notes
  The kinetic energy of his muscle movement is converted into potential energy as he
climbs higher.
 As he dives, the potential energy is converted back to kinetic energy.
 Kinetic energy is transferred to the water as he enters it.
 Some energy is converted to heat due to friction.
The energy transformations of life are subject to two laws of thermodynamics.
 Thermodynamics is the study of energy transformations.
 In this field, the term system refers to the matter under study and the surroundings include
everything outside the system.
 A closed system, approximated by liquid in a thermos, is isolated from its surroundings.
 In an open system, energy and matter can be transferred between the system and its
surroundings.
 Organisms are open systems.
 They absorb energy—light or chemical energy in the form of organic molecules—and
release heat and metabolic waste products such as urea or CO2 to their surroundings.
 The first law of thermodynamics states that energy can be transferred and transformed,
but it cannot be created or destroyed.
 The first law is also known as the principle of conservation of energy.
 Plants do not produce energy; they transform light energy to chemical energy.
 During every transfer or transformation of energy, some energy is converted to heat,
which is the energy associated with the random movement of atoms and molecules.
 A system can use heat to do work only when there is a temperature difference that results
in heat flowing from a warmer location to a cooler one.
 If temperature is uniform, as in a living cell, heat can only be used to warm the
organism.
 Energy transfers and transformations make the universe more disordered due to this loss
of usable energy.
 Entropy is a quantity used as a measure of disorder or randomness.
 The more random a collection of matter, the greater its entropy.
 The second law of thermodynamics states that every energy transfer or transformation
increases the entropy of the universe.
 While order can increase locally, there is an unstoppable trend toward randomization
of the universe.
 Much of the increased entropy of the universe takes the form of increasing heat, which
is the energy of random molecular motion.
 In most energy transformations, ordered forms of energy are converted at least partly to
heat.
 Automobiles convert only 25% of the energy in gasoline into motion; the rest is lost as
heat.
 Living cells unavoidably convert organized forms of energy to heat.
 For a process to occur on its own, without outside help in the form of energy input, it must
increase the entropy of the universe.
 The word spontaneous describes a process that can occur without an input of energy.
 Spontaneous processes need not occur quickly.
Biology Chapter Notes
  Some spontaneous processes are instantaneous, such as an explosion. Some are very
slow, such as the rusting of an old car.
 Another way to state the second law of thermodynamics is for a process to occur
spontaneously, it must increase the entropy of the universe.
 Living systems create ordered structures from less ordered starting materials.
 For example, amino acids are ordered into polypeptide chains.
 The structure of a multicellular body is organized and complex.
 However, an organism also takes in organized forms of matter and energy from its
surroundings and replaces them with less ordered forms.
 For example, an animal consumes organic molecules as food and catabolizes them to
low-energy carbon dioxide and water.
 Over evolutionary time, complex organisms have evolved from simpler ones.
 This increase in organization does not violate the second law of thermodynamics.
 The entropy of a particular system, such as an organism, may decrease as long as the
total entropy of the universe—the system plus its surroundings—increases.
 Organisms are islands of low entropy in an increasingly random universe.
 The evolution of biological order is perfectly consistent with the laws of
thermodynamics.

Concept 8.2 The free-energy change of a reaction tells us whether the reaction occurs
spontaneously
 How can we determine which reactions occur spontaneously and which ones require an
input of energy?
 The concept of free energy provides a useful function for measuring spontaneity of a
system.
 Free energy is the portion of a system’s energy that is able to perform work when
temperature and pressure is uniform throughout the system, as in a living cell.
 The free energy (G) in a system is related to the total enthalpy (in biological systems,
equivalent to energy) (H) and the entropy (S) by this relationship:
 G = H − TS, where T is temperature in Kelvin units.
 Increases in temperature amplify the entropy term.
 Not all the energy in a system is available for work because the entropy component
must be subtracted from the enthalpy component.
 What remains is the free energy that is available for work.
 Free energy can be thought of as a measure of the stability of a system.
 Systems that are high in free energy—compressed springs, separated charges, organic
polymers—are unstable and tend to move toward a more stable state, one with less free
energy.
 Systems that tend to change spontaneously are those that have high enthalpy, low
entropy, or both.
 In any spontaneous process, the free energy of a system decreases.
 We can represent this change in free energy from the start of a process until its finish by:
 G = Gfinal state − Gstarting state
 Or G = H − TS
Biology Chapter Notes
 For a process to be spontaneous, the system must either give up enthalpy (decrease in H),
give up order (increase in S), or both.
 G must be negative for a process to be spontaneous.
 Every spontaneous process is characterized by a decrease in the free energy of the
system.
 Processes that have a positive or zero G are never spontaneous.
 The greater the decrease in free energy, the more work a spontaneous process can
perform.
 Nature runs “downhill.”
 A system at equilibrium is at maximum stability.
 In a chemical reaction at equilibrium, the rates of forward and backward reactions are
equal, and there is no change in the concentration of products or reactants.
 At equilibrium G = 0, and the system can do no work.
 A process is spontaneous and can perform work only when it is moving toward
equilibrium.
 Movements away from equilibrium are nonspontaneous and require the addition of
energy from an outside energy source (the surroundings).
 Chemical reactions can be classified as either exergonic or endergonic based on free
energy.
 An exergonic reaction proceeds with a net release of free energy; G is negative.
 The magnitude of G for an exergonic reaction is the maximum amount of work the
reaction can perform.
 The greater the decrease in free energy, the greater the amount of work that can be done.
 For the overall reaction of cellular respiration: C6H12O6 + 6O2 -> 6CO2 + 6H2O
 G = −686 kcal/mol
 For each mole (180 g) of glucose broken down by respiration, 686 kcal of energy are
made available to do work in the cell.
 The products have 686 kcal less free energy than the reactants.
 An endergonic reaction is one that absorbs free energy from its surroundings.
 Endergonic reactions store energy in molecules; G is positive.
 Endergonic reactions are nonspontaneous, and the magnitude of G is the quantity of
energy required to drive the reaction.
 If cellular respiration releases 686 kcal, then photosynthesis, the reverse reaction, must
require an equivalent investment of energy.
 For the conversion of carbon dioxide and water to sugar, G = +686 kcal/mol.
 Photosynthesis is strongly endergonic, powered by the absorption of light energy.
 Reactions in a closed system eventually reach equilibrium and can do no work.
 A cell that has reached metabolic equilibrium has a G = 0 and is dead!
 Metabolic disequilibrium is one of the defining features of life.
 Cells maintain disequilibrium because they are open systems. The constant flow of
materials into and out of the cell keeps metabolic pathways from ever reaching
equilibrium.
 A cell continues to do work throughout its life.

Biology Chapter Notes

 A catabolic process in a cell releases free energy in a series of reactions, not in a single
step.
 Some reversible reactions of respiration are constantly “pulled” in one direction, as the
product of one reaction does not accumulate but becomes the reactant in the next step.
 Sunlight provides a daily source of free energy for photosynthetic organisms.
 Nonphotosynthetic organisms depend on a transfer of free energy from photosynthetic
organisms in the form of organic molecules.

Concept 8.3 ATP powers cellular work by coupling exergonic reactions to endergonic
reactions
 A cell does three main kinds of work:
10.Mechanical work, such as the beating of cilia, contraction of muscle cells, and
movement of chromosomes during cellular reproduction.
11.Transport work, the pumping of substances across membranes against the direction of
spontaneous movement.
12.Chemical work, driving endergonic reactions such as the synthesis of polymers from
monomers.
 Cells manage their energy resources to do this work by energy coupling, the use of an
exergonic process to drive an endergonic one.
 In most cases, the immediate source of energy to power cellular work is ATP.
 ATP (adenosine triphosphate) is a type of nucleotide consisting of the nitrogenous base
adenine, the sugar ribose, and a chain of three phosphate groups.
 The bonds between phosphate groups can be broken by hydrolysis.
 Hydrolysis of the end phosphate group forms adenosine diphosphate.
 ATP -> ADP + Pi
 This reaction releases 7.3 kcal of energy per mole of ATP under standard
conditions (1 M of each reactant and product, 25°C, pH 7).
 In the cell, G for hydrolysis of ATP is about −13 kcal/mol.
 While the phosphate bonds of ATP are sometimes referred to as high-energy phosphate
bonds, these are actually fairly weak covalent bonds.
 However, they are unstable, and their hydrolysis yields energy because the products
are more stable.
 The release of energy during the hydrolysis of ATP comes from the chemical change to a
state of lower free energy, not from the phosphate bonds themselves.
 Why does the hydrolysis of ATP yield so much energy?
 Each of the three phosphate groups has a negative charge.
 These three like charges are crowded together, and their mutual repulsion contributes
to the instability of this region of the ATP molecule.
 In the cell, the energy from the hydrolysis of ATP is directly coupled to endergonic
processes by the transfer of the phosphate group to another molecule.
 This recipient molecule is now phosphorylated.
 This molecule is now more reactive (less stable) than the original unphosphorylated
molecules.

Biology Chapter Notes

 Mechanical, transport, and chemical work in the cell are nearly always powered by the
hydrolysis of ATP.
 In each case, a phosphate group is transferred from ATP to another molecule and the
phosphorylated molecule undergoes a change that performs work.
 ATP is a renewable resource that can be regenerated by the addition of a phosphate group
to ADP.
 The energy to phosphorylate ADP comes from catabolic reactions in the cell.
 A working muscle cell recycles its entire pool of ATP once each minute.
 More than 10 million ATP molecules are consumed and regenerated per second per
cell.
 Regeneration of ATP is an endergonic process, requiring an investment of energy.
 G = 7.3 kcal/mol.
 Catabolic (exergonic) pathways, especially cellular respiration, provide the energy for the
exergonic regeneration of ATP.
 The chemical potential energy temporarily stored in ATP drives most cellular work.

Concept 8.4 Enzymes speed up metabolic reactions by lowering energy barriers

 Spontaneous chemical reactions may occur so slowly as to be imperceptible.
 The hydrolysis of table sugar (sucrose) to glucose and fructose is exergonic.
 G = −7 kcal/mol
 Despite this, your sugar sits in its bowl with no observable hydrolysis.
 If we add a small amount of the enzyme catalyst sucrase to a solution of sugar, all the
sucrose will be hydrolyzed within seconds.
 A catalyst is a chemical agent that speeds up the rate of a reaction without being
consumed by the reaction.
 An enzyme is a catalytic protein.
 Enzymes regulate metabolic pathways.
 Every chemical reaction involves bond breaking and bond forming.
 To hydrolyze sucrose, the bond between glucose and fructose must be broken and new
bonds must form with hydrogen and hydroxyl ions from water.
 To reach a state where bonds can break and reform, reactant molecules must absorb
energy from their surroundings. When the new bonds of the product molecules form,
energy is released as heat as the molecules assume stable shapes with lower energy.
 The initial investment of energy for starting a reaction is the free energy of activation or
activation energy (EA).
 Activation energy is the amount of energy necessary to push the reactants over an energy
barrier so that the reaction can proceed.
 At the summit, the molecules are in an unstable condition, the transition state.
 Activation energy may be supplied in the form of heat that the reactant molecules
absorb from the surroundings.
 The bonds of the reactants break only when the molecules have absorbed enough
energy to become unstable and, therefore, more reactive.
 The absorption of thermal energy increases the speed of the reactant molecules, so they
collide more often and more forcefully.
Biology Chapter Notes
  Thermal agitation of the atoms in the molecules makes bonds more likely to break.
 As the molecules settle into new, stable bonding arrangements, energy is released to
the surroundings.
 In exergonic reactions, the activation energy is released back to the surroundings, and
additional energy is released with the formation of new bonds.
 For some processes, EA is not high, and the thermal energy provided by room temperature
is sufficient for many reactants to reach the transition state.
 In many cases, EA is high enough that the transition state is rarely reached and that the
reaction hardly proceeds at all. In these cases, the reaction will only occur at a noticeable
rate if the reactants are heated.
 A spark plug provides the energy to energize a gasoline-oxygen mixture and cause
combustion.
 Without that activation energy, the hydrocarbons of gasoline are too stable to react
with oxygen.
 Proteins, DNA, and other complex organic molecules are rich in free energy. Their
hydrolysis is spontaneous, with the release of large amounts of energy.
 However, there is not enough energy at the temperatures typical of the cell for the vast
majority of organic molecules to make it over the hump of activation energy.
 How are the barriers for selected reactions surmounted to allow cells to carry out the
processes of life?
 Heat would speed up reactions, but it would also denature proteins and kill cells.
 Enzymes speed reactions by lowering EA.
 The transition state can then be reached even at moderate temperatures.
 Enzymes do not change G.
 They hasten reactions that would occur eventually.
 Because enzymes are so selective, they determine which chemical processes will occur
at any time.
Enzymes are substrate specific.
 The reactant that an enzyme acts on is the substrate.
 The enzyme binds to a substrate, or substrates, forming an enzyme-substrate complex.
 While the enzyme and substrate are bound, the catalytic action of the enzyme converts the
substrate to the product or products.
 The reaction catalyzed by each enzyme is very specific.
 What accounts for this molecular recognition?
 The specificity of an enzyme results from its three-dimensional shape.
 Only a portion of the enzyme binds to the substrate.
 The active site of an enzyme is typically a pocket or groove on the surface of the
protein into which the substrate fits.
 The active site is usually formed by only a few amino acids.
 The specificity of an enzyme is due to the fit between the active site and the substrate.
 As the substrate enters the active site, interactions between the substrate and the amino
acids of the protein causes the enzyme to change shape slightly, leading to a tighter
induced fit that brings chemical groups in position to catalyze the reaction.

Biology Chapter Notes

 The active site is an enzyme’s catalytic center.
 In most cases, substrates are held in the active site by weak interactions, such as hydrogen
bonds and ionic bonds.
 R groups of a few amino acids on the active site catalyze the conversion of substrate to
product.
 The product then leaves the active site.
 A single enzyme molecule can catalyze thousands of reactions a second.
 Enzymes are unaffected by the reaction and are reusable.
 Most metabolic enzymes can catalyze a reaction in both the forward and reverse
directions.
 The actual direction depends on the relative concentrations of products and reactants.
 Enzymes catalyze reactions in the direction of equilibrium.
 Enzymes use a variety of mechanisms to lower activation energy and speed up a reaction.
 In reactions involving more than one reactant, the active site brings substrates together
in the correct orientation for the reaction to proceed.
 As the active site binds the substrate, it may put stress on bonds that must be broken,
making it easier for the reactants to reach the transition state.
 R groups at the active site may create a microenvironment that is conducive to a
specific reaction.
 An active site may be a pocket of low pH, facilitating H+ transfer to the substrate as
a key step in catalyzing the reaction.
 Enzymes may briefly bind covalently to substrates.
 Subsequent steps of the reaction restore the R groups within the active site to their
original state.
 The rate that a specific number of enzymes convert substrates to products depends in part
on substrate concentrations.
 At low substrate concentrations, an increase in substrate concentration speeds binding
to available active sites.
 However, there is a limit to how fast a reaction can occur.
 At high substrate concentrations, the active sites on all enzymes are engaged.
 The enzyme is saturated.
 The rate of the reaction is determined by the speed at which the active site can
convert substrate to product.
 The only way to increase productivity at this point is to add more enzyme molecules.
A cell’s physical and chemical environment affects enzyme activity.
 The activity of an enzyme is affected by general environmental conditions, such as
temperature and pH.
 Each enzyme works best at certain optimal conditions, which favor the most active
conformation for the enzyme molecule.
 Temperature has a major impact on reaction rate.
 As temperature increases, collisions between substrates and active sites occur more
frequently as molecules move more rapidly.
 As temperature increases further, thermal agitation begins to disrupt the weak bonds
that stabilize the protein’s active conformation, and the protein denatures.
Biology Chapter Notes
  Each enzyme has an optimal temperature.
 Most human enzymes have optimal temperatures of about 35–40°C.
 Bacteria that live in hot springs contain enzymes with optimal temperatures of 70°C
or above.
 Each enzyme also has an optimal pH.
 Maintenance of the active conformation of the enzyme requires a particular pH.
 This falls between pH 6 and 8 for most enzymes.
 However, digestive enzymes in the stomach are designed to work best at pH 2, while
those in the intestine have an optimum of pH 8.
 Many enzymes require nonprotein helpers, called cofactors, for catalytic activity.
 Cofactors bind permanently or reversibly to the enzyme.
 Some inorganic cofactors include zinc, iron, and copper.
 Organic cofactors are called coenzymes.
 Many vitamins are coenzymes.
 Binding by inhibitors prevents enzymes from catalyzing reactions.
 If inhibitors attach to the enzyme by covalent bonds, inhibition may be irreversible.
 If inhibitors bind by weak bonds, inhibition may be reversible.
 Some reversible inhibitors resemble the substrate and compete for binding to the active
site.
 These molecules are called competitive inhibitors.
 Competitive inhibition can be overcome by increasing the concentration of the
substrate.
 Noncompetitive inhibitors impede enzymatic reactions by binding to another part of the
molecule.
 Binding by the inhibitor causes the enzyme to change shape, rendering the active site
less effective at catalyzing the reaction.
 Toxins and poisons are often irreversible enzyme inhibitors.
 Sarin is the nerve gas that was released by terrorists in the Tokyo subway in 1995.
 Sarin binds covalently to the R group on the amino acid serine.
 Serine is found in the active site of acetylcholinesterase, an important nervous system
enzyme.

Concept 8.5 Regulation of enzyme activity helps control metabolism

Metabolic control often depends on allosteric regulation.
 In many cases, the molecules that naturally regulate enzyme activity behave like
reversible noncompetitive inhibitors.
 Regulatory molecules often bind weakly to an allosteric site, a specific receptor on the
enzyme away from the active site.
 Binding by these molecules can either inhibit or stimulate enzyme activity.
 Most allosterically regulated enzymes are constructed of two or more polypeptide chains.
 Each subunit has its own active site.
 Allosteric sites are often located where subunits join.
Biology Chapter Notes
 The binding of an activator stabilizes the conformation that has functional active sites,
while the binding of an inhibitor stabilizes the inactive form of the enzyme.
 As the chemical conditions in the cell shift, the pattern of allosteric regulation may shift as
well.
 By binding to key enzymes, reactants and products of ATP hydrolysis may play a major
role in balancing the flow of traffic between anabolic and catabolic pathways.
 For example, ATP binds to several catabolic enzymes allosterically, inhibiting their
activity by lowering their affinity for substrate.
 ADP functions as an activator of the same enzymes.
 ATP and ADP also affect key enzymes in anabolic pathways.
 In this way, allosteric enzymes control the rates of key reactions in metabolic
pathways.
 In enzymes with multiple catalytic subunits, binding by a substrate to one active site
stabilizes favorable conformational changes at all other subunits, a process called
cooperativity.
 This mechanism amplifies the response of enzymes to substrates, priming the enzyme
to accept additional substrates.
 A common method of metabolic control is feedback inhibition in which an early step in a
metabolic pathway is switched off by the pathway’s final product.
 The product acts as an inhibitor of an enzyme in the pathway.
 Feedback inhibition prevents a cell from wasting chemical resources by synthesizing more
product than is needed.
The localization of enzymes within a cell helps order metabolism.
 Structures within the cell help bring order to metabolic pathways.
 A team of enzymes for several steps of a metabolic pathway may be assembled as a
multienzyme complex.
 The product from the first reaction can then pass quickly to the next enzyme until the final
product is released.
 Some enzymes and enzyme complexes have fixed locations within the cells as structural
components of particular membranes.
 Others are confined within membrane-enclosed eukaryotic organelles.
 Metabolism, the intersecting set of chemical pathways characteristic of life, is a
choreographed interplay of thousands of different kinds of cellular molecules.

Biology Chapter Notes

Chapter 9 Cellular Respiration: Harvesting Chemical
Energy
Chapter Notes

Overview: Life Is Work

 To perform their many tasks, living cells require energy from outside sources.
 Energy enters most ecosystems as sunlight and leaves as heat.
 Photosynthesis generates oxygen and organic molecules that the mitochondria of
eukaryotes use as fuel for cellular respiration.
 Cells harvest the chemical energy stored in organic molecules and use it to regenerate
ATP, the molecule that drives most cellular work.
 Respiration has three key pathways: glycolysis, the citric acid cycle, and oxidative
phosphorylation.

Concept 9.1 Catabolic pathways yield energy by oxidizing organic fuels

 The arrangement of atoms of organic molecules represents potential energy.
 Enzymes catalyze the systematic degradation of organic molecules that are rich in energy
to simpler waste products with less energy.
 Some of the released energy is used to do work; the rest is dissipated as heat.
 Catabolic metabolic pathways release the energy stored in complex organic molecules.
 One type of catabolic process, fermentation, leads to the partial degradation of sugars in
the absence of oxygen.
 A more efficient and widespread catabolic process, cellular respiration, consumes
oxygen as a reactant to complete the breakdown of a variety of organic molecules.
 In eukaryotic cells, mitochondria are the site of most of the processes of cellular
respiration.
 Cellular respiration is similar in broad principle to the combustion of gasoline in an
automobile engine after oxygen is mixed with hydrocarbon fuel.
 Food is the fuel for respiration. The exhaust is carbon dioxide and water.
 The overall process is:
 organic compounds + O2  CO2 + H2O + energy (ATP + heat).
 Carbohydrates, fats, and proteins can all be used as the fuel, but it is most useful to
consider glucose.
 C6H12O6 + 6O2  6CO2 + 6H2O + Energy (ATP + heat)
 The catabolism of glucose is exergonic with a  G of −686 kcal per mole of glucose.
 Some of this energy is used to produce ATP, which can perform cellular work.
Redox reactions release energy when electrons move closer to electronegative atoms.

Biology Chapter Notes

 Catabolic pathways transfer the electrons stored in food molecules, releasing energy that
is used to synthesize ATP.
 Reactions that result in the transfer of one or more electrons from one reactant to another
are oxidation-reduction reactions, or redox reactions.
 The loss of electrons is called oxidation.
 The addition of electrons is called reduction.
 The formation of table salt from sodium and chloride is a redox reaction.
 Na + Cl  Na+ + Cl−
 Here sodium is oxidized and chlorine is reduced (its charge drops from 0 to −1).
 More generally: Xe− + Y  X + Ye−
 X, the electron donor, is the reducing agent and reduces Y.
 Y, the electron recipient, is the oxidizing agent and oxidizes X.
 Redox reactions require both a donor and acceptor.
 Redox reactions also occur when the transfer of electrons is not complete but involves a
change in the degree of electron sharing in covalent bonds.
 In the combustion of methane to form water and carbon dioxide, the nonpolar covalent
bonds of methane (C—H) and oxygen (O=O) are converted to polar covalent bonds
(C=O and O—H).
 When methane reacts with oxygen to form carbon dioxide, electrons end up farther
away from the carbon atom and closer to their new covalent partners, the oxygen
atoms, which are very electronegative.
 In effect, the carbon atom has partially “lost” its shared electrons. Thus, methane has
been oxidized.
 The two atoms of the oxygen molecule share their electrons equally. When oxygen reacts
with the hydrogen from methane to form water, the electrons of the covalent bonds are
drawn closer to the oxygen.
 In effect, each oxygen atom has partially “gained” electrons, and so the oxygen
molecule has been reduced.
 Oxygen is very electronegative, and is one of the most potent of all oxidizing agents.
 Energy must be added to pull an electron away from an atom.
 The more electronegative the atom, the more energy is required to take an electron away
from it.
 An electron loses potential energy when it shifts from a less electronegative atom toward
a more electronegative one.
 A redox reaction that relocates electrons closer to oxygen, such as the burning of methane,
releases chemical energy that can do work.
The “fall” of electrons during respiration is stepwise, via NAD+ and an electron transport
chain.
 Cellular respiration does not oxidize glucose in a single step that transfers all the
hydrogen in the fuel to oxygen at one time.
 Rather, glucose and other fuels are broken down in a series of steps, each catalyzed by a
specific enzyme.
 At key steps, electrons are stripped from the glucose.
 In many oxidation reactions, the electron is transferred with a proton, as a hydrogen
atom.
Biology Chapter Notes
 The hydrogen atoms +are not transferred directly to oxygen but are passed first to a
coenzyme called NAD (nicotinamide adenine dinucleotide).
 How does NAD+ trap electrons from glucose?
 Dehydrogenase enzymes strip two hydrogen atoms from the fuel (e.g., glucose),
oxidizing it.

The enzyme passes two electrons and one proton to NAD+.

The other proton is released as H+ to the surrounding solution.
 By receiving two electrons and only one proton, NAD + has its charge neutralized when it
is reduced to NADH.
 NAD+ functions as the oxidizing agent in many of the redox steps during the
catabolism of glucose.
 The electrons carried by NADH have lost very little of their potential energy in this
process.
 Each NADH molecule formed during respiration represents stored energy. This energy is
tapped to synthesize ATP as electrons “fall” from NADH to oxygen.
 How are electrons extracted from food and stored by NADH finally transferred to
oxygen?
 Unlike the explosive release of heat energy that occurs when H 2 and O2 are combined
(with a spark for activation energy), cellular respiration uses an electron transport
chain to break the fall of electrons to O2 into several steps.
 The electron transport chain consists of several molecules (primarily proteins) built into
the inner membrane of a mitochondrion.
 Electrons released from food are shuttled by NADH to the “top” higher-energy end of the
chain.
 At the “bottom” lower-energy end, oxygen captures the electrons along with H + to form
water.
 Electron transfer from NADH to oxygen is an exergonic reaction with a free energy
change of −53 kcal/mol.
 Electrons are passed to increasingly electronegative molecules in the chain until they
reduce oxygen, the most electronegative receptor.
 In summary, during cellular respiration, most electrons travel the following “downhill”
route: food  NADH  electron transport chain  oxygen.
These are the stages of cellular respiration: a preview.
 Respiration occurs in three metabolic stages: glycolysis, the citric acid cycle, and the
electron transport chain and oxidative phosphorylation.
 Glycolysis occurs in the cytoplasm.
 It begins catabolism by breaking glucose into two molecules of pyruvate.
 The citric acid cycle occurs in the mitochondrial matrix.
 It completes the breakdown of glucose by oxidizing a derivative of pyruvate to carbon
dioxide.
 Several steps in glycolysis and the citric acid cycle are redox reactions in which
dehydrogenase enzymes transfer electrons from substrates to NAD+, forming NADH.
 NADH passes these electrons to the electron transport chain.

Biology Chapter Notes

 In the electron transport chain, the electrons move from molecule to molecule until they
combine with molecular oxygen and hydrogen ions to form water.
 As they are passed along the chain, the energy carried by these electrons is transformed in
the mitochondrion into a form that can be used to synthesize ATP via oxidative
phosphorylation.
 The inner membrane of the mitochondrion is the site of electron transport and
chemiosmosis, processes that together constitute oxidative phosphorylation.
 Oxidative phosphorylation produces almost 90% of the ATP generated by respiration.
 Some ATP is also formed directly during glycolysis and the citric acid cycle by
substrate-level phosphorylation.
 Here an enzyme transfers a phosphate group from an organic substrate to ADP,
forming ATP.
 For each molecule of glucose degraded to carbon dioxide and water by respiration, the
cell makes up to 38 ATP, each with 7.3 kcal/mol of free energy.
 Respiration uses the small steps in the respiratory pathway to break the large
denomination of energy contained in glucose into the small change of ATP.
 The quantity of energy in ATP is more appropriate for the level of work required in the
cell.

Concept 9.2 Glycolysis harvests chemical energy by oxidizing glucose to pyruvate

 During glycolysis, glucose, a six carbon-sugar, is split into two three-carbon sugars.
 These smaller sugars are oxidized and rearranged to form two molecules of pyruvate, the
ionized form of pyruvic acid.
 Each of the ten steps in glycolysis is catalyzed by a specific enzyme.
 These steps can be divided into two phases: an energy investment phase and an energy
payoff phase.
 In the energy investment phase, the cell invests ATP to provide activation energy by
phosphorylating glucose.
 This requires 2 ATP per glucose.
 In the+ energy payoff phase, ATP is produced by substrate-level phosphorylation and
NAD is reduced to NADH by electrons released by the oxidation of glucose.
 The net yield from glycolysis is 2 ATP and 2 NADH per glucose.
 No CO2 is produced during glycolysis.
 Glycolysis can occur whether O2 is present or not.

Concept 9.3 The citric acid cycle completes the energy-yielding oxidation of organic
molecules
 More than three-quarters of the original energy in glucose is still present in the two
molecules of pyruvate.
 If oxygen is present, pyruvate enters the mitochondrion where enzymes of the citric acid
cycle complete the oxidation of the organic fuel to carbon dioxide.

Biology Chapter Notes

 After pyruvate enters the mitochondrion via active transport, it is converted to a
compound called acetyl coenzyme A or acetyl CoA.
 This step is accomplished by a multienzyme complex that catalyzes three reactions:
o A carboxyl group is removed as CO2.
o The remaining two-carbon fragment is oxidized to form acetate. An enzyme transfers
the pair of electrons to NAD+ to form NADH.
o Acetate combines with coenzyme A to form the very reactive molecule acetyl CoA.
 Acetyl CoA is now ready to feed its acetyl group into the citric acid cycle for further
oxidation.
 The citric acid cycle is also called the Krebs cycle in honor of Hans Krebs, who was
largely responsible for elucidating its pathways in the 1930s.
 The citric acid cycle oxidizes organic fuel derived from pyruvate.
 The citric acid cycle has eight steps, each catalyzed by a specific enzyme.
 The acetyl group of acetyl CoA joins the cycle by combining with the compound
oxaloacetate, forming citrate.
 The next seven steps decompose the citrate back to oxaloacetate. It is the regeneration
of oxaloacetate that makes this process a cycle.
 Three CO2 molecules are released, including the one released during the conversion of
pyruvate to acetyl CoA.
 The cycle generates one ATP per turn by substrate-level phosphorylation.
 A GTP molecule is formed by substrate-level phosphorylation.
 The GTP is then used to synthesize an ATP, the only ATP generated directly by the
citric acid cycle.
 Most of the chemical energy is transferred to NAD+ and FAD during the redox reactions.
 The reduced coenzymes NADH and FADH2 then transfer high-energy electrons to the
electron transport chain.
 Each cycle produces one ATP by substrate-level phosphorylation, three NADH, and one
FADH2 per acetyl CoA.

Concept 9.4 During oxidative phosphorylation, chemiosmosis couples electron transport

to ATP synthesis
The inner mitochondrial membrane couples electron transport to ATP synthesis.
 Only 4 of 38 ATP ultimately produced by respiration of glucose are produced by
substrate-level phosphorylation.
 Two are produced during glycolysis, and 2 are produced during the citric acid cycle.
 NADH and FADH2 account for the vast majority of the energy extracted from the food.
 These reduced coenzymes link glycolysis and the citric acid cycle to oxidative
phosphorylation, which uses energy released by the electron transport chain to power
ATP synthesis.
 The electron transport chain is a collection of molecules embedded in the cristae, the
folded inner membrane of the mitochondrion.
 The folding of the cristae increases its surface area, providing space for thousands of
copies of the chain in each mitochondrion.

Biology Chapter Notes

  Most components of the chain are proteins bound to prosthetic groups, nonprotein
components essential for catalysis.
 Electrons drop in free energy as they pass down the electron transport chain.
 During electron transport along the chain, electron carriers alternate between reduced and
oxidized states as they accept and donate electrons.
 Each component of the chain becomes reduced when it accepts electrons from its
“uphill” neighbor, which is less electronegative.
 It then returns to its oxidized form as it passes electrons to its more electronegative
“downhill” neighbor.
 Electrons carried by NADH are transferred to the first molecule in the electron transport
chain, a flavoprotein.
 The electrons continue along the chain that includes several cytochrome proteins and one
lipid carrier.
 The prosthetic group of each cytochrome is a heme group with an iron atom that
accepts and donates electrons.
 The last cytochrome of the chain, cyt a3, passes its electrons to oxygen, which is very
electronegative.
 Each oxygen atom also picks up a pair of hydrogen ions from the aqueous solution to
form water.
 For every two electron carriers (four electrons), one O2 molecule is reduced to two
molecules of water.
 The electrons carried by FADH2 have lower free energy and are added at a lower energy
level than those carried by NADH.
 The electron transport chain provides about one-third less energy for ATP synthesis
when the electron donor is FADH2 rather than NADH.
 The electron transport chain generates no ATP directly.
 Its function is to break the large free energy drop from food to oxygen into a series of
smaller steps that release energy in manageable amounts.
 How does the mitochondrion couple electron transport and energy release to ATP
synthesis?
 The answer is a mechanism called chemiosmosis.
 A protein complex, ATP synthase, in the cristae actually makes ATP from ADP and Pi.
 ATP uses the energy of an existing proton gradient to power ATP synthesis.
 The proton gradient develops between the intermembrane space and the matrix.
 The proton gradient is produced by the movement of electrons along the electron transport
chain.
 The chain is an energy converter that uses the exergonic flow of electrons to pump H +
from the matrix into the intermembrane space.
 The protons pass back to the matrix through a channel in ATP synthase, using the
exergonic flow of H+ to drive the phosphorylation of ADP.
 Thus, the energy stored in a H+ gradient across a membrane couples the redox reactions of
the electron transport chain to ATP synthesis.
 From studying the structure of ATP synthase, scientists have learned how the flow of H+
through this large enzyme powers ATP generation.
Biology Chapter Notes
 ATP synthase is a multisubunit complex with four main parts, each made up of multiple
polypeptides:
o A rotor in the inner mitochondrial membrane.
o A knob that protrudes into the mitochondrial matrix.
o An internal rod extending from the rotor into the knob.
o A stator, anchored next to the rotor, which holds the knob stationary.
 Protons flow down a narrow space between the stator and rotor, causing the rotor and its
attached rod to rotate.
 The spinning rod causes conformational changes in the stationary knob, activating
three catalytic sites in the knob where ADP and inorganic phosphate combine to make
ATP.
 How does the inner mitochondrial membrane generate and maintain the H + gradient that
drives ATP synthesis in the ATP synthase protein complex?
 Creating the H+ gradient is the function of the electron transport chain.
 The ETC is an energy converter that uses the exergonic flow of electrons to pump H +
across the membrane from the mitochondrial matrix to the intermembrane space.
 The H+ has a tendency to diffuse down its gradient.
 The ATP synthase molecules are the only place that H+ can diffuse back to the matrix.
 The exergonic flow of H+ is used by the enzyme to generate ATP.
 This coupling of the redox reactions of the electron transport chain to ATP synthesis is
called chemiosmosis.
 How does the electron transport chain pump protons?
 Certain members of the electron transport chain accept and release H + along with
electrons.
 At certain steps along the chain, electron transfers cause H+ to be taken up and released
into the surrounding solution.
 The electron carriers are spatially arranged in the membrane in such a way that protons
are accepted from the mitochondrial matrix and deposited in the intermembrane space.
 The H+ gradient that results is the proton-motive force.
 The gradient has the capacity to do work.
 Chemiosmosis is an energy-coupling mechanism that uses energy stored in the form of an
H+ gradient across a membrane to drive cellular work.
 In mitochondria, the energy for proton gradient formation comes from exergonic redox
reactions, and ATP synthesis is the work performed.
 Chemiosmosis in chloroplasts also+ generates ATP, but light drives the electron flow down
an electron transport chain and H gradient formation.
 Prokaryotes generate H+ gradients across their plasma membrane.
 They can use this proton-motive force not only to generate ATP, but also to pump
nutrients and waste products across the membrane and to rotate their flagella.
Here is an accounting of ATP production by cellular respiration.
 During cellular respiration, most energy flows from glucose  NADH  electron
transport chain  proton-motive force  ATP.
 Let’s consider the products generated when cellular respiration oxidizes a molecule of
glucose to six CO2 molecules.
Biology Chapter Notes
 Four ATP molecules are produced by substrate-level phosphorylation during glycolysis
and the citric acid cycle.
 Many more ATP molecules are generated by oxidative phosphorylation.
 Each NADH from the citric acid cycle and the conversion of pyruvate contributes enough
energy to the proton-motive force to generate a maximum of 3 ATP.
 The NADH from glycolysis may also yield 3 ATP.
 Each FADH2 from the citric acid cycle can be used to generate about 2 ATP.
 Why is our accounting so inexact?
 There are three reasons that we cannot state an exact number of ATP molecules generated
by one molecule of glucose.
o Phosphorylation and the redox reactions are not directly coupled to each other, so the
ratio of number of NADH to number of ATP is not a whole number.
 One NADH results in 10 H+ being transported across the inner mitochondrial
membrane.
 Between 3 and 4 H+ must reenter the mitochondrial matrix via ATP synthase to
generate 1 ATP.
 Therefore, 1 NADH generates enough proton-motive force for synthesis of 2.5 to 3.3
ATP.
 We round off and say that 1 NADH generates 3 ATP.
o The ATP yield varies slightly depending on the type of shuttle used to transport
electrons from the cytosol into the mitochondrion.
 The mitochondrial inner membrane is impermeable to NADH, so the two electrons of
the NADH produced in glycolysis must be conveyed into the mitochondrion by one of
several electron shuttle systems.
 In some shuttle systems, the electrons are passed to NAD +, which generates 3 ATP. In
others, the electrons are passed to FAD, which generates only 2 ATP.
o The proton-motive force generated by the redox reactions of respiration may drive
other kinds of work, such as mitochondrial uptake of pyruvate from the cytosol.
 If all the proton-motive force generated by the electron transport chain were used to
drive ATP synthesis, one glucose molecule could generate a maximum of 34 ATP by
oxidative phosphorylation plus 4 ATP (net) from substrate-level phosphorylation to
give a total yield of 36–38 ATP (depending on the efficiency of the shuttle).
 How efficient is respiration in generating ATP?
 Complete oxidation of glucose releases 686 kcal/mol.
 Phosphorylation of ADP to form ATP requires at least 7.3 kcal/mol.
 Efficiency of respiration is 7.3 kcal/mol times 38 ATP/glucose divided by 686
kcal/mol glucose, which equals 0.4 or 40%.
 Approximately 60% of the energy from glucose is lost as heat.
 Some of that heat is used to maintain our high body temperature (37°C).
 Cellular respiration is remarkably efficient in energy conversion.

Concept 9.5 Fermentation enables some cells to produce ATP without the use of oxygen
 Without electronegative oxygen to pull electrons down the transport chain, oxidative
phosphorylation ceases.

Biology Chapter Notes

 However, fermentation provides a mechanism by which some cells can oxidize organic
fuel and generate ATP without the use of oxygen.
 In glycolysis, glucose is oxidized to two pyruvate molecules with NAD + as the
oxidizing agent.
 Glycolysis is exergonic and produces 2 ATP (net).
 If oxygen is present, additional ATP can be generated when NADH delivers its
electrons to the electron transport chain.
 Glycolysis generates 2 ATP whether oxygen is present (aerobic) or not (anaerobic).
 Anaerobic catabolism of sugars can occur by fermentation.
 Fermentation can generate ATP from glucose by substrate-level phosphorylation as long
as there is a supply of NAD+ to accept electrons.
 If the NAD+ pool is exhausted, glycolysis shuts down.
 Under aerobic conditions, NADH transfers its electrons to the electron transfer chain,
recycling NAD+.
 Under anaerobic conditions, various fermentation pathways generate ATP by glycolysis
and recycle NAD+ by transferring electrons from NADH to pyruvate or derivatives of
pyruvate.
 In alcohol fermentation, pyruvate is converted to ethanol in two steps.
 First, pyruvate is converted to a two-carbon compound, acetaldehyde, by the removal
of CO2.
 Second, acetaldehyde is reduced by NADH to ethanol.
 Alcohol fermentation by yeast is used in brewing and winemaking.
 During lactic acid fermentation, pyruvate is reduced directly by NADH to form lactate
(the ionized form of lactic acid) without release of CO2.
 Lactic acid fermentation by some fungi and bacteria is used to make cheese and
yogurt.
 Human muscle cells switch from aerobic respiration to lactic acid fermentation to
generate ATP when O2 is scarce.
 The waste product, lactate, may cause muscle fatigue, but ultimately it is converted
back to pyruvate in the liver.
 Fermentation and cellular respiration are anaerobic and aerobic alternatives, respectively,
for producing ATP from sugars.
 Both use glycolysis to oxidize sugars to pyruvate with a net production of 2 ATP by
substrate-level phosphorylation.
 Both use NAD+ as an oxidizing agent to accept electrons from food during glycolysis.
 The two processes differ in their mechanism for oxidizing NADH to NAD+.
 In fermentation,+ the electrons of NADH are passed to an organic molecule to
regenerate NAD .
 In respiration, the electrons of NADH are ultimately passed to O 2, generating ATP by
oxidative phosphorylation.
 More ATP is generated from the oxidation of pyruvate in the citric acid cycle.
 Without oxygen, the energy still stored in pyruvate is unavailable to the cell.
 Under aerobic respiration, a molecule of glucose yields 38 ATP, but the same molecule
of glucose yields only 2 ATP under anaerobic respiration.

Biology Chapter Notes

 Yeast and many bacteria are facultative anaerobes that can survive using either
fermentation or respiration.
 At a cellular level, human muscle cells can behave as facultative anaerobes.
 For facultative anaerobes, pyruvate is a fork in the metabolic road that leads to two
alternative routes.
 Under aerobic conditions, pyruvate is converted to acetyl CoA and oxidation continues
in the citric acid cycle.
 Under anaerobic conditions, pyruvate serves as an electron acceptor to recycle NAD+.
 The oldest bacterial fossils are more than 3.5 billion years old, appearing long before
appreciable quantities of O2 accumulated in the atmosphere.
 Therefore, the first prokaryotes may have generated ATP exclusively from glycolysis.
 The fact that glycolysis is a ubiquitous metabolic pathway and occurs in the cytosol
without membrane-enclosed organelles suggests that glycolysis evolved early in the
history of life.

Concept 9.6 Glycolysis and the citric acid cycle connect to many other metabolic
pathways
 Glycolysis can accept a wide range of carbohydrates for catabolism.
 Polysaccharides like starch or glycogen can be hydrolyzed to glucose monomers that
enter glycolysis.
 Other hexose sugars, such as galactose and fructose, can also be modified to undergo
glycolysis.
 The other two major fuels, proteins and fats, can also enter the respiratory pathways used
by carbohydrates.
 Proteins must first be digested to individual amino acids.
 Amino acids that will be catabolized must have their amino groups removed via
deamination.
 The nitrogenous waste is excreted as ammonia, urea, or another waste product.
 The carbon skeletons are modified by enzymes and enter as intermediaries into glycolysis
or the citric acid cycle, depending on their structure.
 Catabolism can also harvest energy stored in fats.
 Fats must be digested to glycerol and fatty acids.
 Glycerol can be converted to glyceraldehyde phosphate, an intermediate of glycolysis.
 The rich energy of fatty acids is accessed as fatty acids are split into two-carbon
fragments via beta oxidation.
 These molecules enter the citric acid cycle as acetyl CoA.
 A gram of fat oxides by respiration generates twice as much ATP as a gram of
carbohydrate.
 The metabolic pathways of respiration also play a role in anabolic pathways of the cell.
 Intermediaries in glycolysis and the citric acid cycle can be diverted to anabolic pathways.
 For example, a human cell can synthesize about half the 20 different amino acids by
modifying compounds from the citric acid cycle.
 Glucose can be synthesized from pyruvate; fatty acids can be synthesized from acetyl
CoA.
Biology Chapter Notes
 Glycolysis and the citric acid cycle function as metabolic interchanges that enable cells to
convert one kind of molecule to another as needed.
 For example, excess carbohydrates and proteins can be converted to fats through
intermediaries of glycolysis and the citric acid cycle.
 Metabolism is remarkably versatile and adaptable.
Feedback mechanisms control cellular respiration.
 Basic principles of supply and demand regulate the metabolic economy.
 If a cell has an excess of a certain amino acid, it typically uses feedback inhibition to
prevent the diversion of intermediary molecules from the citric acid cycle to the
synthesis pathway of that amino acid.
 The rate of catabolism is also regulated, typically by the level of ATP in the cell.
 If ATP levels drop, catabolism speeds up to produce more ATP.
 Control of catabolism is based mainly on regulating the activity of enzymes at strategic
points in the catabolic pathway.
 One strategic point occurs in the third step of glycolysis, catalyzed by
phosphofructokinase.
 Allosteric regulation of phosphofructokinase sets the pace of respiration.
 This enzyme catalyzes the earliest step that irreversibly commits the substrate to
glycolysis.
 Phosphofructokinase is an allosteric enzyme with receptor sites for specific inhibitors
and activators.
 It is inhibited by ATP and stimulated by AMP (derived from ADP).
 When ATP levels are high, inhibition of this enzyme slows glycolysis.
 As ATP levels drop and ADP and AMP levels rise, the enzyme becomes active
again and glycolysis speeds up.
 Citrate, the first product of the citric acid cycle, is also an inhibitor of
phosphofructokinase.
 This synchronizes the rate of glycolysis and the citric acid cycle.
 If intermediaries from the citric acid cycle are diverted to other uses (e.g., amino acid
synthesis), glycolysis speeds up to replace these molecules.
 Metabolic balance is augmented by the control of other enzymes at other key locations in
glycolysis and the citric acid cycle.
 Cells are thrifty, expedient, and responsive in their metabolism.

Biology Chapter Notes

 Chapter 10 Photosynthesis
Chapter Notes

Overview: The Process That Feeds the Biosphere

 Life on Earth is solar powered.

 The chloroplasts of plants use a process called photosynthesis to capture light energy from
the sun and convert it to chemical energy stored in sugars and other organic molecules.
Plants and other autotrophs are the producers of the biosphere.
 Photosynthesis nourishes almost all the living world directly or indirectly.
 All organisms use organic compounds for energy and for carbon skeletons.
 Organisms obtain organic compounds by one of two major modes: autotrophic
nutrition or heterotrophic nutrition.
 Autotrophs produce their organic molecules from CO2 and other inorganic raw materials
obtained from the environment.
 Autotrophs are the ultimate sources of organic compounds for all heterotrophic
organisms.
 Autotrophs are the producers of the biosphere.
 Autotrophs can be separated by the source of energy that drives their metabolism.
 Photoautotrophs use light as a source of energy to synthesize organic compounds.
 Photosynthesis occurs in plants, algae, some other protists, and some prokaryotes.
 Chemoautotrophs harvest energy from oxidizing inorganic substances, such as sulfur
and ammonia.
 Chemoautotrophy is unique to prokaryotes.
 Heterotrophs live on organic compounds produced by other organisms.
 These organisms are the consumers of the biosphere.
 The most obvious type of heterotrophs feeds on other organisms.
 Animals feed this way.
 Other heterotrophs decompose and feed on dead organisms or on organic litter, like
feces and fallen leaves.
 Most fungi and many prokaryotes get their nourishment this way.
 Almost all heterotrophs are completely dependent on photoautotrophs for food and for
oxygen, a by-product of photosynthesis.

Concept 10.1 Photosynthesis converts light energy to the chemical energy of food
 All green parts of a plant have chloroplasts.
 However, the leaves are the major site of photosynthesis for most plants.
 There are about half a million chloroplasts per square millimeter of leaf surface.
 The color of a leaf comes from chlorophyll, the green pigment in the chloroplasts.
 Chlorophyll plays an important role in the absorption of light energy during
photosynthesis.
Biology Chapter Notes
 Chloroplasts are found mainly in mesophyll cells forming the tissues in the interior of the
leaf.
 O2 exits and CO2 enters the leaf through microscopic pores called stomata in the leaf.
 Veins deliver water from the roots and carry off sugar from mesophyll cells to
nonphotosynthetic areas of the plant.
 A typical mesophyll cell has 30–40 chloroplasts, each about 2–4 microns by 4–7 microns
long.
 Each chloroplast has two membranes around a central aqueous space, the stroma.
 In the stroma is an elaborate system of interconnected membranous sacs, the thylakoids.
 The interior of the thylakoids forms another compartment, the thylakoid space.
 Thylakoids may be stacked into columns called grana.
 Chlorophyll is located in the thylakoids.
 Photosynthetic prokaryotes lack chloroplasts.
 Their photosynthetic membranes arise from infolded regions of the plasma
membranes, folded in a manner similar to the thylakoid membranes of chloroplasts.
Evidence that chloroplasts split water molecules enabled researchers to track atoms
through photosynthesis.
 Powered by light, the green parts of plants produce organic compounds and O 2 from CO2
and H2O.
 The equation describing the process of photosynthesis is:
 6CO2 + 12H2O + light energy  C6H12O6 + 6O2+ 6H2O
 C6H12O6 is glucose.
 Water appears on both sides of the equation because 12 molecules of water are consumed,
and 6 molecules are newly formed during photosynthesis.
 We can simplify the equation by showing only the net consumption of water:
 6CO2 + 6H2O + light energy  C6H12O6 + 6O2
 The overall chemical change during photosynthesis is the reverse of cellular respiration.
 In its simplest possible form: CO2 + H2O + light energy  [CH2O] + O2
 [CH2O] represents the general formula for a sugar.
 One of the first clues to the mechanism of photosynthesis came from the discovery that
the O2 given off by plants comes from H2O, not CO2.
 Before the 1930s, the prevailing hypothesis was that photosynthesis split carbon
dioxide and then added water to the carbon:
 Step 1: CO2  C + O2
 Step 2: C + H2O  CH2O
 C. B. van Niel challenged this hypothesis.
 In the bacteria that he was studying, hydrogen sulfide (H 2S), not water, is used in
photosynthesis.
 These bacteria produce yellow globules of sulfur as a waste, rather than oxygen.
 Van Niel proposed this chemical equation for photosynthesis in sulfur bacteria:
 CO2 + 2H2S  [CH2O] + H2O + 2S
 He generalized this idea and applied it to plants, proposing this reaction for their
photosynthesis:
Biology Chapter Notes
  CO2 + 2H2O  [CH2O] + H2O + O2
 Thus, van Niel hypothesized that plants split water as a source of electrons from hydrogen
atoms, releasing oxygen as a byproduct.
 Other scientists confirmed van Niel’s hypothesis twenty years later.
 They used 18O, a heavy isotope, as a tracer.
 They could label either C18O2 or H218O.
 They found that the 18O label only appeared in the oxygen produced in photosynthesis
when water was the source of the tracer.
 Hydrogen extracted from water is incorporated into sugar, and oxygen is released to the
atmosphere (where it can be used in respiration).
 Photosynthesis is a redox reaction.
 It reverses the direction of electron flow in respiration.
 Water is split and electrons transferred with H+ from water to CO2, reducing it to sugar.
 Because the electrons increase in potential energy as they move from water to sugar,
the process requires energy.
 The energy boost is provided by light.
Here is a preview of the two stages of photosynthesis.
 Photosynthesis is two processes, each with multiple stages.
 The light reactions (photo) convert solar energy to chemical energy.
 The Calvin cycle (synthesis) uses energy from the light reactions to incorporate CO2 from
the atmosphere into sugar.
 In the light reactions, light energy absorbed by chlorophyll in +the thylakoids drives the
transfer of electrons and hydrogen from water to NADP (nicotinamide adenine
dinucleotide phosphate), forming NADPH.
 NADPH, an electron acceptor, provides reducing power via energized electrons to the
Calvin cycle.
 Water is split in the process, and O2 is released as a by-product.
 The light reaction also generates ATP using chemiosmosis, in a process called
photophosphorylation.
 Thus light energy is initially converted to chemical energy in the form of two compounds:
NADPH and ATP.
 The Calvin cycle is named for Melvin Calvin who, with his colleagues, worked out many
of its steps in the 1940s.
 The cycle begins with the incorporation of CO2 into organic molecules, a process known
as carbon fixation.
 The fixed carbon is reduced with electrons provided by NADPH.
 ATP from the light reactions also powers parts of the Calvin cycle.
 Thus, it is the Calvin cycle that makes sugar, but only with the help of ATP and NADPH
from the light reactions.
 The metabolic steps of the Calvin cycle are sometimes referred to as the light-independent
reactions, because none of the steps requires light directly.
 Nevertheless, the Calvin cycle in most plants occurs during daylight, because that is when
the light reactions can provide the NADPH and ATP the Calvin cycle requires.
Biology Chapter Notes
 While the light reactions occur at the thylakoids, the Calvin cycle occurs in the stroma.

Concept 10.2 The light reactions convert solar energy to the chemical energy of ATP
and NADPH
 The thylakoids convert light energy into the chemical energy of ATP and NADPH.
 Light is a form of electromagnetic radiation.
 Like other forms of electromagnetic energy, light travels in rhythmic waves.
 The distance between crests of electromagnetic waves is called the wavelength.
 Wavelengths of electromagnetic radiation range from less than a nanometer (gamma
rays) to more than a kilometer (radio waves).
 The entire range of electromagnetic radiation is the electromagnetic spectrum.
 The most important segment for life is a narrow band between 380 to 750 nm, the band of
visible light.
 While light travels as a wave, many of its properties are those of a discrete particle, the
photon.
 Photons are not tangible objects, but they do have fixed quantities of energy.
 The amount of energy packaged in a photon is inversely related to its wavelength.
 Photons with shorter wavelengths pack more energy.
 While the sun radiates a full electromagnetic spectrum, the atmosphere selectively screens
out most wavelengths, permitting only visible light to pass in significant quantities.
 Visible light is the radiation that drives photosynthesis.
 When light meets matter, it may be reflected, transmitted, or absorbed.
 Different pigments absorb photons of different wavelengths, and the wavelengths that
are absorbed disappear.
 A leaf looks green because chlorophyll, the dominant pigment, absorbs red and blue
light, while transmitting and reflecting green light.
 A spectrophotometer measures the ability of a pigment to absorb various wavelengths of
light.
 It beams narrow wavelengths of light through a solution containing the pigment and
measures the fraction of light transmitted at each wavelength.
 An absorption spectrum plots a pigment’s light absorption versus wavelength.
 The light reaction can perform work with those wavelengths of light that are absorbed.
 There are several pigments in the thylakoid that differ in their absorption spectra.
 Chlorophyll a, the dominant pigment, absorbs best in the red and violet-blue
wavelengths and least in the green.
 Other pigments with different structures have different absorption spectra.
 Collectively, these photosynthetic pigments determine an overall action spectrum for
photosynthesis.
 An action spectrum measures changes in some measure of photosynthetic activity (for
example, O2 release) as the wavelength is varied.
 The action spectrum of photosynthesis was first demonstrated in 1883 in an elegant
experiment performed by Thomas Engelmann.

Biology Chapter Notes

  In this experiment, different segments of a filamentous alga were exposed to different
wavelengths of light.
 Areas receiving wavelengths favorable to photosynthesis produced excess O2.
 Engelmann used the abundance of aerobic bacteria that clustered along the alga at
different segments as a measure of O2 production.
 The action spectrum of photosynthesis does not match exactly the absorption spectrum of
any one photosynthetic pigment, including chlorophyll a.
 Only chlorophyll a participates directly in the light reaction, but accessory photosynthetic
pigments absorb light and transfer energy to chlorophyll a.
 Chlorophyll b, with a slightly different structure than chlorophyll a, has a slightly
different absorption spectrum and funnels the energy from these wavelengths to
chlorophyll a.
 Carotenoids can funnel the energy from other wavelengths to chlorophyll a and also
participate in photoprotection against excessive light.
 These compounds absorb and dissipate excessive light energy that would otherwise
damage chlorophyll.
 They also interact with oxygen to form reactive oxidative molecules that could damage
the cell.
 When a molecule absorbs a photon, one of that molecule’s electrons is elevated to an
orbital with more potential energy.
 The electron moves from its ground state to an excited state.
 The only photons that a molecule can absorb are those whose energy matches exactly
the energy difference between the ground state and excited state of this electron.
 Because this energy difference varies among atoms and molecules, a particular
compound absorbs only photons corresponding to specific wavelengths.
 Thus, each pigment has a unique absorption spectrum.
 Excited electrons are unstable.
 Generally, they drop to their ground state in a billionth of a second, releasing heat energy.
 Some pigments, including chlorophyll, can also release a photon of light in a process
called fluorescence.
 If a solution of chlorophyll isolated from chloroplasts is illuminated, it will fluoresce
and give off heat.
 Chlorophyll excited by absorption of light energy produces very different results in an
intact chloroplast than it does in isolation.
 In the thylakoid membrane, chlorophyll is organized along with proteins and smaller
organic molecules into photosystems.
 A photosystem is composed of a reaction center surrounded by a light-harvesting
complex.
 Each light-harvesting complex consists of pigment molecules (which may include
chlorophyll a, chlorophyll b, and carotenoid molecules) bound to particular proteins.
 Together, these light-harvesting complexes act like light-gathering “antenna complexes”
for the reaction center.
 When any antenna molecule absorbs a photon, it is transmitted from molecule to molecule
until it reaches a particular chlorophyll a molecule, the reaction center.

Biology Chapter Notes

 At the reaction center is a primary electron acceptor, which accepts an excited electron
from the reaction center chlorophyll a.
 The solar-powered transfer of an electron from a special chlorophyll a molecule to the
primary electron acceptor is the first step of the light reactions.
 Each photosystem—reaction-center chlorophyll and primary electron acceptor surrounded
by an antenna complex—functions in the chloroplast as a light-harvesting unit.
 There are two types of photosystems in the thylakoid membrane.
 Photosystem I (PS I) has a reaction center chlorophyll a that has an absorption peak at
700 nm.
 Photosystem II (PS II) has a reaction center chlorophyll a that has an absorption peak
at 680 nm.
 The differences between these reaction centers (and their absorption spectra) lie not in
the chlorophyll molecules, but in the proteins associated with each reaction center.
 These two photosystems work together to use light energy to generate ATP and
NADPH.
 During the light reactions, there are two possible routes for electron flow: cyclic and
noncyclic.
 Noncyclic electron flow, the predominant route, produces both ATP and NADPH.
o Photosystem II absorbs a photon of light. One of the electrons of P680 is excited to a
higher energy state.
o This electron is captured by the primary electron acceptor, leaving the reaction center
oxidized.
o An enzyme extracts electrons from water and supplies them to the oxidized reaction
center. This reaction splits water into two hydrogen ions and an oxygen atom that
combines with another oxygen atom to form O2.
o Photoexcited electrons pass along an electron transport chain before ending up at an
oxidized photosystem I reaction center.
o As these electrons “fall” to a lower energy level, their energy is harnessed to produce
ATP.
o Meanwhile, light energy has excited an electron of PS I’s P700 reaction center. The
photoexcited electron was captured by PS I’s primary electron acceptor, creating an
electron “hole” in P700. This hole is filled by an electron that reaches the bottom of the
electron transport chain from PS II.
o Photoexcited electrons are passed from PS I’s primary electron acceptor down a
second electron transport chain through the protein ferredoxin (Fd).
o The enzyme NADP+ reductase +
transfers electrons from Fd to NADP+. Two electrons
are required for NADP ’s reduction to NADPH. NADPH will carry the reducing
power of these high-energy electrons to the Calvin cycle.
 The light reactions use the solar power of photons absorbed by both photosystem I and
photosystem II to provide chemical energy in the form of ATP and reducing power in the
form of the electrons carried by NADPH.
 Under certain conditions, photoexcited electrons from photosystem I, but not photosystem
II, can take an alternative pathway, cyclic electron flow.
 Excited electrons cycle from their reaction center to a primary acceptor, along an
electron transport chain, and return to the oxidized P700 chlorophyll.
 As electrons flow along the electron transport chain, they generate ATP by cyclic
photophosphorylation.
 There is no production of NADPH and no release of oxygen.
Biology Chapter Notes
 What is the function of cyclic electron flow?
 Noncyclic electron flow produces ATP and NADPH in roughly equal quantities.
 However, the Calvin cycle consumes more ATP than NADPH.
 Cyclic electron flow allows the chloroplast to generate enough surplus ATP to satisfy the
higher demand for ATP in the Calvin cycle.
 Chloroplasts and mitochondria generate ATP by the same mechanism: chemiosmosis.
 In both organelles, an electron transport chain pumps protons across a membrane as
electrons are passed along a series of increasingly electronegative carriers.
 This transforms redox energy to a proton-motive force in the form of an H+ gradient
across the membrane.
 ATP synthase molecules harness the proton-motive force to generate ATP as H+
diffuses back across the membrane.
 Some of the electron carriers, including the cytochromes, are very similar in chloroplasts
and mitochondria.
 The ATP synthase complexes of the two organelles are also very similar.
 There are differences between oxidative phosphorylation in mitochondria and
photophosphorylation in chloroplasts.
 Mitochondria transfer chemical energy from food molecules to ATP; chloroplasts
transform light energy into the chemical energy of ATP.
 The spatial organization of chemiosmosis also differs in the two organelles.
 The inner membrane of the mitochondrion pumps protons from the mitochondrial matrix
out to the intermembrane space. The thylakoid membrane of the chloroplast pumps
protons from the stroma into the thylakoid space inside the thylakoid.
 The thylakoid membrane makes ATP as the hydrogen ions diffuse down their
concentration gradient from the thylakoid space back to the stroma through ATP synthase
complexes, whose catalytic knobs are on the stroma side of the membrane.
 The proton gradient, or pH gradient, across the thylakoid membrane is substantial.
 When chloroplasts are illuminated, the pH in the thylakoid space drops+ to about 5 and
the pH in the stroma increases to about 8, a thousandfold different in H concentration.
 The light-reaction “machinery” produces ATP and NADPH on the stroma side of the
thylakoid.
 Noncyclic electron flow pushes electrons from water, where they have low potential
energy, to NADPH, where they have high potential energy.
 This process also produces ATP and oxygen as a by-product.

Concept 10.3 The Calvin cycle uses ATP and NADPH to convert CO2 to sugar
 The Calvin cycle regenerates its starting material after molecules enter and leave the
cycle.
 The Calvin cycle is anabolic, using energy to build sugar from smaller molecules.
 Carbon enters the cycle as CO2 and leaves as sugar.
 The cycle spends the energy of ATP and the reducing power of electrons carried by
NADPH to make sugar.

Biology Chapter Notes

 The actual sugar product of the Calvin cycle is not glucose, but a three-carbon sugar,
glyceraldehyde-3-phosphate (G3P).
 Each turn of the Calvin cycle fixes one carbon.
 For the net synthesis of one G3P molecule, the cycle must take place three times, fixing
three molecules of CO2.
 To make one glucose molecule requires six cycles and the fixation of six CO 2 molecules.
 The Calvin cycle has three phases.
Phase 1: Carbon fixation
 In the carbon fixation phase, each CO2 molecule is attached to a five-carbon sugar,
ribulose bisphosphate (RuBP).
 This is catalyzed by RuBP carboxylase or rubisco.
 Rubisco is the most abundant protein in chloroplasts and probably the most abundant
protein on Earth.
 The six-carbon intermediate is unstable and splits in half to form two molecules of 3-
phosphoglycerate for each CO2.
Phase 2: Reduction
 During reduction, each 3-phosphoglycerate receives another phosphate group from ATP
to form 1,3-bisphosphoglycerate.
 A pair of electrons from NADPH reduces each 1,3-bisphosphoglycerate to G3P.
 The electrons reduce a carboxyl group to the aldehyde group of G3P, which stores
more potential energy.
 If our goal was the net production of one G3P, we would start with 3CO 2 (3C) and three
RuBP (15C).
 After fixation and reduction, we would have six molecules of G3P (18C).
 One of these six G3P (3C) is a net gain of carbohydrate.
 This molecule can exit the cycle and be used by the plant cell.
Phase 3: Regeneration
 The other five G3P (15C) remain in the cycle to regenerate three RuBP. In a complex
series of reactions, the carbon skeletons of five molecules of G3P are rearranged by the
last steps of the Calvin cycle to regenerate three molecules of RuBP.
 For the net synthesis of one G3P molecule, the Calvin cycle consumes nine ATP and six
NADPH.
 The light reactions regenerate ATP and NADPH.
 The G3P from the Calvin cycle is the starting material for metabolic pathways that
synthesize other organic compounds, including glucose and other carbohydrates.

Concept 10.4 Alternative mechanisms of carbon fixation have evolved in hot, arid
climates
 One of the major problems facing terrestrial plants is dehydration.
 At times, solutions to this problem require tradeoffs with other metabolic processes,
especially photosynthesis.
Biology Chapter Notes
 The stomata are not only the major route for gas exchange (CO 2 in and O2 out), but also
for the evaporative loss of water.
 On hot, dry days, plants close their stomata to conserve water. This causes problems for
photosynthesis.
 In most plants (C3 plants), initial fixation of CO2 occurs via rubisco, forming a three-
carbon compound, 3-phosphoglycerate.
 C3 plants include rice, wheat, and soybeans.
 When their stomata partially close on a hot, dry day, CO 2 levels drop as CO2 is consumed
in the Calvin cycle.
 At the same time, O2 levels rise as the light reaction converts light to chemical energy.
 While rubisco normally accepts CO2, when the O2:CO2 ratio increases (on a hot, dry day
with closed stomata), rubisco can add O2 to RuBP.
 When rubisco adds O2 to RuBP, RuBP splits into a three-carbon piece and a two-carbon
piece in a process called photorespiration.
 The two-carbon fragment is exported from the chloroplast and degraded to CO 2 by
mitochondria and peroxisomes.
 Unlike normal respiration, this process produces no ATP.
 In fact, photorespiration consumes ATP.
 Unlike photosynthesis, photorespiration does not produce organic molecules.
 In fact, photorespiration decreases photosynthetic output by siphoning organic
material from the Calvin cycle.
 A hypothesis for the existence of photorespiration is that it is evolutionary baggage.
 When rubisco first evolved, the atmosphere had far less O 2 and more CO2 than it does
today.
 The inability of the active site of rubisco to exclude O 2 would have made little
difference.
 Today it does make a difference.
 Photorespiration can drain away as much as 50% of the carbon fixed by the Calvin
cycle on a hot, dry day.
 Certain plant species have evolved alternate modes of carbon fixation to minimize
photorespiration.
 C4 plants first fix CO2 in a four-carbon compound.
 Several thousand plants, including sugarcane and corn, use this pathway.
 A unique leaf anatomy is correlated with the mechanism of C4 photosynthesis.
 In C4 plants, there are two distinct types of photosynthetic cells: bundle-sheath cells and
mesophyll cells.
 Bundle-sheath cells are arranged into tightly packed sheaths around the veins of the
leaf.
 Mesophyll cells are more loosely arranged cells located between the bundle sheath and
the leaf surface.
 The Calvin cycle is confined to the chloroplasts of the bundle-sheath cells.
 However, the cycle is preceded by the incorporation of CO2 into organic molecules in the
mesophyll.

Biology Chapter Notes

 The key enzyme, phosphoenolpyruvate carboxylase, adds CO 2 to phosphoenolpyruvate
(PEP) to form oxaloacetate.
 PEP carboxylase has a very high affinity for CO2 and can fix CO2 efficiently when
rubisco cannot (i.e., on hot, dry days when the stomata are closed).
 The mesophyll cells pump these four-carbon compounds into bundle-sheath cells.
 The bundle-sheath cells strip a carbon from the four-carbon compound as CO2, and
return the three-carbon remainder to the mesophyll cells.
 The bundle-sheath cells then use rubisco to start the Calvin cycle with an abundant
supply of CO2.
 In effect, the mesophyll cells pump CO2 into the bundle-sheath cells, keeping CO2 levels
high enough for rubisco to accept CO2 and not O2.
 C4 photosynthesis minimizes photorespiration and enhances sugar production.
 C4 plants thrive in hot regions with intense sunlight.
 A second strategy to minimize photorespiration is found in succulent plants, cacti,
pineapples, and several other plant families.
 These plants are known as CAM plants for crassulacean acid metabolism.
 They open their stomata during the night and close them during the day.
 Temperatures are typically lower at night, and humidity is higher.
 During the night, these plants fix CO2 into a variety of organic acids in mesophyll
cells.
 During the day, the light reactions supply ATP and NADPH to the Calvin cycle, and
CO2 is released from the organic acids.
 Both C4 and CAM plants add CO2 into organic intermediates before it enters the Calvin
cycle.
 In C4 plants, carbon fixation and the Calvin cycle are spatially separated.
 In CAM plants, carbon fixation and the Calvin cycle are temporally separated.
 Both eventually use the Calvin cycle to make sugar from carbon dioxide.
Here is a review of the importance of photosynthesis.
 In photosynthesis, the energy that enters the chloroplasts as sunlight becomes stored as
chemical energy in organic compounds.
 Sugar made in the chloroplasts supplies the entire plant with chemical energy and carbon
skeletons to synthesize all the major organic molecules of cells.
 About 50% of the organic material is consumed as fuel for cellular respiration in plant
mitochondria.
 Carbohydrate in the form of the disaccharide sucrose travels via the veins to
nonphotosynthetic cells.
 There, it provides fuel for respiration and the raw materials for anabolic pathways,
including synthesis of proteins and lipids and formation of the extracellular
polysaccharide cellulose.
 Cellulose, the main ingredient of cell walls, is the most abundant organic molecule
in the plant, and probably on the surface of the planet.
 Plants also store excess sugar by synthesis of starch.
 Starch is stored in chloroplasts and in storage cells in roots, tubers, seeds, and fruits.
 Heterotrophs, including humans, may completely or partially consume plants for fuel and
raw materials.
Biology Chapter Notes
 On a global scale, photosynthesis is the most important process on Earth.
 It is responsible for the presence of oxygen in our atmosphere.
 Each year, photosynthesis synthesizes 160 billion metric tons of carbohydrate.

Biology Chapter Notes

 Chapter 11 Cell Communication
Chapter Notes

Overview: The Cellular Internet

 Cell-to-cell communication is absolutely essential for multicellular organisms.

 Cells must communicate to coordinate their activities.
 Communication between cells is also important for many unicellular organisms.
 Biologists have discovered universal mechanisms of cellular regulation involving the
same small set of cell-signaling mechanisms.
 The ubiquity of these mechanisms provides additional evidence for the evolutionary
relatedness of all life.
 Cells most often communicate by chemical signals, although signals may take other
forms.

Concept 11.1 External signals are converted into responses within the cell
 What messages are passed from cell to cell? How do cells respond to these messages?
 We will first consider communication in microbes, to gain insight into the evolution of
cell signaling.
Cell signaling evolved early in the history of life.
 One topic of cell “conversation” is sex.
 Saccharomyces cerevisiae, the yeast of bread, wine, and beer, identifies potential mates
by chemical signaling.
 There are two sexes, a and , each of which secretes a specific signaling molecule, a
factor and  factor, respectively.
 These factors each bind to receptor proteins on the other mating type.
 Once the mating factors have bound to the receptors, the two cells grow toward each other
and undergo other cellular changes.
 The two cells fuse, or mate, to form an a/ cell containing the genes of both cells.
 The process by which a signal on a cell’s surface is converted into a specific cellular
response is a series of steps called a signal-transduction pathway.
 The molecular details of these pathways are strikingly similar in yeast and animal
cells, even though their last common ancestor lived more than a billion years ago.
 Signaling systems of bacteria and plants also share similarities.
 These similarities suggest that ancestral signaling molecules evolved long ago in
prokaryotes and have since been adopted for new uses by single-celled eukaryotes and
multicellular descendents.
Communicating cells may be close together or far apart.
 Multicellular organisms release signaling molecules that target other cells.
 Cells may communicate by direct contact.
Biology Chapter Notes
  Both animals and plants have cell junctions that connect to the cytoplasm of adjacent
cells.
 Signaling substances dissolved in the cytosol can pass freely between adjacent cells.
 Animal cells can communicate by direct contact between membrane-bound cell
surface molecules.
 Such cell-cell recognition is important to such processes as embryonic development
and the immune response.
 In other cases, messenger molecules are secreted by the signaling cell.
 Some transmitting cells release local regulators that influence cells in the local
vicinity.
 One class of local regulators in animals, growth factors, includes compounds that
stimulate nearby target cells to grow and multiply.
 This is an example of paracrine signaling, which occurs when numerous cells
simultaneously receive and respond to growth factors produced by a single cell in their
vicinity.
 In synaptic signaling, a nerve cell produces a neurotransmitter that diffuses across a
synapse to a single cell that is almost touching the sender.
 The neurotransmitter stimulates the target cell.
 The transmission of a signal through the nervous system can also be considered an
example of long-distance signaling.
 Local signaling in plants is not well understood. Because of their cell walls, plants must
have different mechanisms from animals.
 Plants and animals use hormones for long-distance signaling.
 In animals, specialized endocrine cells release hormones into the circulatory system,
by which they travel to target cells in other parts of the body.
 Plant hormones, called growth regulators, may travel in vessels but more often travel
from cell to cell or move through air by diffusion.
 Hormones and local regulators range widely in size and type.
 The plant hormone ethylene (C2H4), which promotes fruit ripening and regulates
growth, is a hydrocarbon of only six atoms, capable of passing through cell walls.
 Insulin, which regulates blood sugar levels in mammals, is a protein with thousands of
atoms.
 What happens when a cell encounters a signal?
 The signal must be recognized by a specific receptor molecule, and the information it
carries must be changed into another form, or transduced, inside the cell before the
cell can respond.
The three stages of cell signaling are reception, transduction, and response.
 E. W. Sutherland and his colleagues pioneered our understanding of cell signaling.
 Their work investigated how the animal hormone epinephrine stimulates breakdown of
the storage polysaccharide glycogen in liver and skeletal muscle.
 Breakdown of glycogen releases glucose derivatives that can be used for fuel in
glycolysis or released as glucose in the blood for fuel elsewhere.
 Thus one effect of epinephrine, which is released from the adrenal gland during times
of physical or mental stress, is mobilization of fuel reserves.
 Sutherland’s research team discovered that epinephrine activated a cytosolic enzyme,
glycogen phosphorylase.
Biology Chapter Notes
  However, epinephrine did not activate the phosphorylase directly in vitro but could
only act via intact cells.
 Therefore, there must be an intermediate step or steps occurring inside the cell.
 The plasma membrane must be involved in transmitting the epinephrine signal.
 The process involves three stages: reception, transduction, and response.
 In reception, a chemical signal binds to a cellular protein, typically at the cell’s
surface or inside the cell.
 In transduction, binding leads to a change in the receptor that triggers a series of
changes in a series of different molecules along a signal-transduction pathway. The
molecules in the pathway are called relay molecules.
 In response, the transduced signal triggers a specific cellular activity.

Concept 11.2 Reception: A signal molecule binds to a receptor protein, causing it to

change shape
 The cell targeted by a particular chemical signal has a receptor protein on or in the target
cell that recognizes the signal molecule.
 Recognition occurs when the signal binds to a specific site on the receptor that is
complementary in shape to the signal.
 The signal molecule behaves as a ligand, a small molecule that binds with specificity to a
larger molecule.
 Ligand binding causes the receptor protein to undergo a change in shape.
 This may activate the receptor so that it can interact with other molecules.
 For other receptors, this causes aggregation of receptor molecules, leading to further
molecular events inside the cell.
 Most signal receptors are plasma membrane proteins, whose ligands are large water-
soluble molecules that are too large to cross the plasma membrane.
Some receptor proteins are intracellular.
 Some signal receptors are dissolved in the cytosol or nucleus of target cells.
 To reach these receptors, the signals pass through the target cell’s plasma membrane.
 Such chemical messengers are either hydrophobic enough or small enough to cross the
phospholipid interior of the plasma membrane.
 Hydrophobic messengers include the steroid and thyroid hormones of animals.
 Nitric oxide (NO) is a gas whose small size allows it to pass between membrane
phospholipids.
 Testosterone is secreted by the testis and travels through the blood to enter cells
throughout the body.
 The cytosol of target cells contains receptor molecules that bind testosterone,
activating the receptor.
 These activated proteins enter the nucleus and turn on specific genes that control male
sex characteristics.
 How does the activated hormone-receptor complex turn on genes?
 These activated proteins act as transcription factors.

Biology Chapter Notes

 Transcription factors control which genes are turned on—that is, which genes are
transcribed into messenger RNA.
 mRNA molecules leave the nucleus and carry information that directs the synthesis
(translation) of specific proteins at the ribosome.
 Other intracellular receptors (such as thyroid hormone receptors) are found in the nucleus
and bind to the signal molecules there.
Most signal receptors are plasma membrane proteins.
 Most signal molecules are water-soluble and too large to pass through the plasma
membrane.
 They influence cell activities by binding to receptor proteins on the plasma membrane.
 Binding leads to changes in the shape of the receptor or to the aggregation of receptors.
 These cause changes in the intracellular environment.
 There are three major types of membrane receptors: G-protein-linked receptors, receptor
tyrosine kinases, and ion-channel receptors.
 A G-protein-linked receptor consists of a receptor protein associated with a G protein on
the cytoplasmic side.
 Seven alpha helices span the membrane.
 G-protein-linked receptors bind many different signal molecules, including yeast
mating factors, epinephrine and many other hormones, and neurotransmitters.
 The G protein acts as an on/off switch.
 If GDP is bound to the G protein, the G protein is inactive.
 When the appropriate signal molecule binds to the extracellular side of the receptor,
the G protein binds GTP (instead of GDP) and becomes active.
 The activated G protein dissociates from the receptor and diffuses along the
membrane, where it binds to an enzyme, altering its activity.
 The activated enzyme triggers the next step in a pathway leading to a cellular response.
 The G protein can also act as a GTPase enzyme to hydrolyze GTP to GDP.
 This change turns the G protein off.
 Now inactive, the G protein leaves the enzyme, which returns to its original state.
 The whole system can be shut down quickly when the extracellular signal molecule is no
longer present.
 G-protein receptor systems are extremely widespread and diverse in their functions.
 They play important roles during embryonic development.
 Vision and smell in humans depend on these proteins.
 Similarities among G proteins and G-protein-linked receptors of modern organisms
suggest that this signaling system evolved very early.
 Several human diseases involve G-protein systems.
 Bacterial infections causing cholera and botulism interfere with G-protein function.
 The tyrosine-kinase receptor system is especially effective when the cell needs to trigger
several signal transduction pathways and cellular responses at once.
 This system helps the cell regulate and coordinate many aspects of cell growth and
reproduction.

Biology Chapter Notes

 The tyrosine-kinase receptor belongs to a major class of plasma membrane receptors that
have enzymatic activity.
 A kinase is an enzyme that catalyzes the transfer of phosphate groups.
 The cytoplasmic side of these receptors functions as a tyrosine kinase, transferring a
phosphate group from ATP to tyrosine on a substrate protein.
 An individual tyrosine-kinase receptor consists of several parts:
 An extracellular signal-binding site.
 A single alpha helix spanning the membrane.
 An intracellular tail with several tyrosines.
 The signal molecule binds to an individual receptor.
 Ligands bind to two receptors, causing the two receptors to aggregate and form a
dimer.
 This dimerization activates the tyrosine-kinase section of the receptors, each of which
then adds phosphate from ATP to the tyrosine tail of the other polypeptide.
 The fully activated receptor proteins activate a variety of specific relay proteins that bind
to specific phosphorylated tyrosine molecules.
 One tyrosine-kinase receptor dimer may activate ten or more different intracellular
proteins simultaneously.
 These activated relay proteins trigger many different transduction pathways and
responses.
 A ligand-gated ion channel is a type of membrane receptor that can act as a gate when
the receptor changes shape.
 When a signal molecule binds as a ligand to the receptor protein, the gate opens to allow
the flow of specific ions, such as Na+ or Ca2+, through a channel in the receptor.
 Binding by a ligand to the extracellular side changes the protein’s shape and opens the
channel.
 When the ligand dissociates from the receptor protein, the channel closes.
 The change in ion concentration within the cell may directly affect the activity of the cell.
 Ligand-gated ion channels are very important in the nervous system.
 For example, neurotransmitter molecules released at a synapse between two neurons
bind as ligands to ion channels on the receiving cell, causing the channels to open.
 Ions flow in and trigger an electrical signal that propagates down the length of the
receiving cell.
 Some gated ion channels respond to electrical signals, instead of ligands.

Concept 11.3 Transduction: Cascades of molecular interactions relay signals from

receptors to target molecules in the cell
 The transduction stage of signaling is usually a multistep pathway.
 These pathways often greatly amplify the signal.
 If some molecules in a pathway transmit a signal to multiple molecules of the next
component in the series, the result can be large numbers of activated molecules at the
end of the pathway.
 A small number of signal molecules can produce a large cellular response.
Biology Chapter Notes
 Also, multistep pathways provide more opportunities for coordination and regulation than
do simpler systems.
Pathways relay signals from receptors to cellular responses.
 Signal-transduction pathways act like falling dominoes.
 The signal-activated receptor activates another protein, which activates another, and so
on, until the protein that produces the final cellular response is activated.
 The relay molecules that relay a signal from receptor to response are mostly proteins.
 The interaction of proteins is a major theme of cell signaling.
 Protein interaction is a unifying theme of all cellular regulation.
 The original signal molecule is not passed along the pathway and may not even enter the
cell.
 It passes on information.
 At each step, the signal is transduced into a different form, often by a conformational
change in a protein.
 The conformational change is often brought about by phosphorylation.
Protein phosphorylation, a common mode of regulation in cells, is a major mechanism of
signal transduction.
 The phosphorylation of proteins by a specific enzyme (a protein kinase) is a widespread
cellular mechanism for regulating protein activity.
 Most protein kinases act on other substrate proteins, unlike tyrosine kinases that act on
themselves.
 Most phosphorylation occurs at either serine or threonine amino acids of the substrate
protein (unlike tyrosine phosphorylation in tyrosine kinases).
 Many of the relay molecules in a signal-transduction pathway are protein kinases that act
on other protein kinases to create a “phosphorylation cascade.”
 Each protein phosphorylation leads to a conformational change because of the interaction
between the newly added phosphate group and charged or polar amino acids on the
protein.
 Phosphorylation of a protein typically converts it from an inactive form to an active form.
 Rarely, phosphorylation inactivates protein activity.
 A single cell may have hundreds of different protein kinases, each specific for a different
substrate protein.
 Fully 2% of our genes are thought to code for protein kinases.
 Together, they regulate a large proportion of the thousands of cell proteins.
 Abnormal activity of protein kinases can cause abnormal cell growth and may contribute
to the development of cancer.
 The responsibility for turning off a signal-transduction pathway belongs to protein
phosphatases.
 These enzymes rapidly remove phosphate groups from proteins, a process called
dephosphorylation.
 Phosphatases also make the protein kinases available for reuse, enabling the cell to
respond again to a signal.
 At any given moment, the activity of a protein regulated by phosphorylation depends on
the balance of active kinase molecules and active phosphatase molecules.
Biology Chapter Notes
 When the extracellular signal molecule is absent, active phosphatase molecules
predominate, and the signaling pathway and cellular response are shut down.
 The phosphorylation/dephosphorylation system acts as a molecular switch in the cell,
turning activities on and off as required.
Certain signal molecules and ions are key components of signaling pathways (second
messengers).
 Many signaling pathways involve small, water-soluble, nonprotein molecules or ions
called second messengers.
 These molecules rapidly diffuse throughout the cell.
 Second messengers participate in pathways initiated by both G-protein-linked receptors
and tyrosine-kinase receptors.
 Two of the most widely used second messengers are cyclic AMP and Ca2+.
 Once Sutherland knew that epinephrine caused glycogen breakdown without entering the
cell, he looked for a second messenger inside the cell.
 Binding by epinephrine leads to increases in the cytosolic concentration of cyclic AMP,
or cAMP.
 This occurs because the activated receptor activates adenylyl cyclase, which converts
ATP to cAMP.
 The normal cellular concentration of cAMP can be boosted twentyfold within seconds.
 cAMP is short-lived, as phosphodiesterase converts it to AMP.
 Another surge of epinephrine is needed to reboost the cytosolic concentration of
cAMP.
 Caffeine-containing beverages such as coffee provide an artificial way to keep the body
alert.
 Caffeine blocks the conversion of cAMP to AMP, maintaining the system in a state of
activation in the absence of epinephrine.
 Many hormones and other signal molecules trigger the formation of cAMP.
 G-protein-linked receptors, G proteins, and protein kinases are other components of
cAMP pathways.
 cAMP diffuses through the cell and activates a serine/threonine kinase called protein
kinase A.
 The activated kinase phosphorylates various other proteins.
 Regulation of cell metabolism is also provided by G-protein systems that inhibit adenylyl
cyclase.
 These use a different signal molecule to activate a different receptor that activates an
inhibitory G protein.
 Certain microbes cause disease by disrupting G-protein signaling pathways.
 The cholera bacterium, Vibrio cholerae, may be present in water contaminated with
human feces.
 This bacterium colonizes the small intestine and produces a toxin that modifies a G
protein that regulates salt and water secretion.
 The modified G protein is unable to hydrolyze GTP to GDP and remains stuck in its
active form, continuously stimulating adenylyl cyclase to make cAMP.
 The resulting high concentration of cAMP causes the intestinal cells to secrete large
amounts of water and salts into the intestines, leading to profuse diarrhea and death
from loss of water and salts.
Biology Chapter Notes
 Treatments for certain human conditions involve signaling pathways.
 One pathway uses cyclic GMP, or cGMP, as a signaling molecule. Its effects include
the relaxation of smooth muscle cells in artery walls.
 A compound was developed to treat chest pains. This compound inhibits the hydrolysis
of cGMP to GMP, prolonging the signal and increasing blood flow to the heart muscle.
 Under the trade name Viagra, this compound is now widely used as a treatment for
erectile dysfunction. Viagra causes dilation of blood vessels, allowing increased blood
flow to the penis.
 Many signal molecules in animals induce responses in their target cells via signal-
transduction pathways that increase the cytosolic concentration of Ca 2+.
 In animal cells, increases in Ca2+ may cause contraction of muscle cells, secretion of
certain substances, and cell division.
 In plant cells, increases in Ca2+ trigger responses such as the pathway for greening in
response to light.
 Cells use Ca2+ as a second messenger in both G-protein pathways and tyrosine-kinase
pathways.
 The Ca2+ concentration in the cytosol is typically much lower than that outside the cell,
often by a factor of 10,000 or more.
 Various protein pumps transport Ca2+ outside the cell or into the endoplasmic
reticulum or other organelles.
 As a result, the concentration of Ca2+ in the ER is usually much higher than the
concentration in the cytosol.
 Because cytosolic Ca2+ is so low, small 2+ changes in the absolute numbers of ions causes a
relatively large percentage change in Ca concentration.
 Signal-transduction pathways trigger the release of Ca2+ from the cell’s ER.
 The pathways leading to release involve still other second messengers, diacylglycerol
(DAG) and inositol trisphosphate (IP3).
 DAG and IP3 are created when a phospholipase cleaves membrane phospholipid PIP 2.
 The phospholipase may be activated by a G protein or by a tyrosine-kinase receptor.
 IP3 activates a gated-calcium channel, releasing Ca2+ from the ER.
 Calcium ions activate the next protein in a signal-transduction pathway.

Concept 11.4 Response: Cell signaling leads to regulation of cytoplasmic activities or

transcription
 Ultimately, a signal-transduction pathway leads to the regulation of one or more cellular
activities.
 This may be the opening or closing of an ion channel or a change in cell metabolism.
 For example, epinephrine helps regulate cellular energy metabolism by activating
enzymes that catalyze the breakdown of glycogen.
 The stimulation of glycogen breakdown by epinephrine involves a G-protein-linked
receptor, a G protein, adenylyl cyclase, cAMP, and several protein kinases before
glycogen phosphorylase is activated.
 Other signaling pathways do not regulate the activity of enzymes but the synthesis of
enzymes or other proteins.

Biology Chapter Notes

 Activated receptors may act as transcription factors that turn specific genes on or off in
the nucleus.
Elaborate pathways amplify and specify the cell’s response to signals.
 Signaling pathways with multiple steps have two benefits.
o They amplify the response to a signal.
o They contribute to the specificity of the response.
 At each catalytic step in a cascade, the number of activated products is much greater than
in the preceding step.
 In the epinephrine-triggered pathway, binding by a small number of epinephrine
molecules can lead to the release of hundreds of millions of glucose molecules.
 Various types of cells may receive the same signal but produce very different responses.
 For example, epinephrine triggers liver or striated muscle cells to break down
glycogen, but stimulates cardiac muscle cells to contract, leading to a rapid heartbeat.
 The explanation for this specificity is that different kinds of cells have different
collections of proteins.
 The response of a particular cell to a signal depends on its particular collection of
receptor proteins, relay proteins, and proteins needed to carry out the response.
 Two cells that respond differently to the same signal differ in one or more of the
proteins that handle and respond to the signal.
 A signal may trigger a single pathway in one cell but trigger a branched pathway in
another.
 Two pathways may converge to modulate a single response.
 Branching of pathways and interactions between pathways are important for regulating
and coordinating a cell’s response to incoming information.
 Rather than relying on diffusion of large relay molecules such as proteins, many signal
pathways are linked together physically by scaffolding proteins.
 Scaffolding proteins may themselves be relay proteins to which several other relay
proteins attach.
 This hardwiring enhances the speed, accuracy, and efficiency of signal transfer
between cells.
 The importance of relay proteins that serve as branch or intersection points in signaling
pathways is underscored when these proteins are defective or missing.
 The inherited disorder Wiskott-Aldrich syndrome (WAS) is caused by the absence of a
single relay protein.
 Symptoms include abnormal bleeding, eczema, and a predisposition to infections and
leukemia, due largely to the absence of the protein in the cells of the immune system.
 The WAS protein is located just beneath the cell surface, where it interacts with the
microfilaments of the cytoskeleton and with several signaling pathways, including
those that regulate immune cell proliferation.
 When the WAS protein is absent, the cytoskeleton is not properly organized and
signaling pathways are disrupted.
 As important as activating mechanisms are inactivation mechanisms.
 For a cell to remain alert and capable of responding to incoming signals, each
molecular change in its signaling pathways must last only a short time.

Biology Chapter Notes

  If signaling pathway components become locked into one state, whether active or
inactive, the proper function of the cell can be disrupted.
 Binding of signal molecules to receptors must be reversible, allowing the receptors to
return to their inactive state when the signal is released.
 Similarly, activated signals (cAMP and phosphorylated proteins) must be inactivated
by appropriate enzymes to prepare the cell for a fresh signal.

Biology Chapter Notes

 Chapter 12 The Cell Cycle
Chapter Notes

Overview: The Key Roles of Cell Division

 The ability of organisms to reproduce their kind is the one characteristic that best
distinguishes living things from nonliving matter.
 The continuity of life is based on the reproduction of cells, or cell division.
Cell division functions in reproduction, growth, and repair.
 The division of a unicellular organism reproduces an entire organism, increasing the
population.
 Cell division on a larger scale can produce progeny for some multicellular organisms.
 This includes organisms that can grow by cuttings.
 Cell division enables a multicellular organism to develop from a single fertilized egg or
zygote.
 In a multicellular organism, cell division functions to repair and renew cells that die from
normal wear and tear or accidents.
 Cell division is part of the cell cycle, the life of a cell from its origin in the division of a
parent cell until its own division into two.

Concept 12.1 Cell division results in genetically identical daughter cells

 Cell division requires the distribution of identical genetic material—DNA—to two
daughter cells.
 What is remarkable is the fidelity with which DNA is passed along, without dilution, from
one generation to the next.
 A dividing cell duplicates its DNA, allocates the two copies to opposite ends of the cell,
and then splits into two daughter cells.
 A cell’s genetic information, packaged as DNA, is called its genome.
 In prokaryotes, the genome is often a single long DNA molecule.
 In eukaryotes, the genome consists of several DNA molecules.
 A human cell must duplicate about 2 m of DNA and separate the two copies such that
each daughter cell ends up with a complete genome.
 DNA molecules are packaged into chromosomes.
 Every eukaryotic species has a characteristic number of chromosomes in each cell
nucleus.
 Human somatic cells (body cells) have 46 chromosomes, made up of two sets of 23
(one from each parent).
 Human gametes (sperm or eggs) have one set of 23 chromosomes, half the number
in a somatic cell.
 Eukaryotic chromosomes are made of chromatin, a complex of DNA and associated
protein.
Biology Chapter Notes
  Each single chromosome contains one long, linear DNA molecule carrying hundreds
or thousands of genes, the units that specify an organism’s inherited traits.
 The associated proteins maintain the structure of the chromosome and help control gene
activity.
 When a cell is not dividing, each chromosome is in the form of a long, thin chromatin
fiber.
 Before cell division, chromatin condenses, coiling and folding to make a smaller package.
 Each duplicated chromosome consists of two sister chromatids, which contain identical
copies of the chromosome’s DNA.
 The chromatids are initially attached by adhesive proteins along their lengths.
 As the chromosomes condense, the region where the chromatids connect shrinks to a
narrow area, the centromere.
 Later in cell division, the sister chromatids are pulled apart and repackaged into two new
nuclei at opposite ends of the parent cell.
 Once the sister chromatids separate, they are considered individual chromosomes.
 Mitosis, the formation of the two daughter nuclei, is usually followed by division of the
cytoplasm, cytokinesis.
 These processes start with one cell and produce two cells that are genetically identical to
the original parent cell.
 Each of us inherited 23 chromosomes from each parent: one set in an egg and one set
in sperm.
 The fertilized egg, or zygote, underwent cycles of mitosis and cytokinesis to produce a
fully developed multicellular human made up of 200 trillion somatic cells.
 These processes continue every day to replace dead and damaged cells.
 Essentially, these processes produce clones—cells with identical genetic information.
 In contrast, gametes (eggs or sperm) are produced only in gonads (ovaries or testes) by a
variation of cell division called meiosis.
 Meiosis yields four nonidentical daughter cells, each with half the chromosomes of the
parent.
 In humans, meiosis reduces the number of chromosomes from 46 to 23.
 Fertilization fuses two gametes together and doubles the number of chromosomes to
46 again.

Concept 12.2 The mitotic phase alternates with interphase in the cell cycle
 The mitotic (M) phase of the cell cycle alternates with the much longer interphase.
 The M phase includes mitosis and cytokinesis.
 Interphase accounts for 90% of the cell cycle.
 During interphase, the cell grows by producing proteins and cytoplasmic organelles,
copies its chromosomes, and prepares for cell division.
 Interphase has three subphases: the G1 phase (“first gap”), the S phase (“synthesis”), and
the G2 phase (“second gap”).
 During all three subphases, the cell grows by producing proteins and cytoplasmic
organelles such as mitochondria and endoplasmic reticulum.
 However, chromosomes are duplicated only during the S phase.
Biology Chapter Notes
 The daughter cells may then repeat the cycle.
 A typical human cell might divide once every 24 hours.
 Of this time, the M phase would last less than an hour, while the S phase might take
10–12 hours, or half the cycle.
 The rest of the time would be divided between the G1 and G2 phases.
 The G1 phase varies most in length from cell to cell.
 Mitosis is a continuum of changes.
 For convenience, mitosis is usually broken into five subphases: prophase,
prometaphase, metaphase, anaphase, and telophase.
 In late interphase, the chromosomes have been duplicated but are not condensed.
 A nuclear membrane bounds the nucleus, which contains one or more nucleoli.
 The centrosome has replicated to form two centrosomes.
 In animal cells, each centrosome features two centrioles.
 In prophase, the chromosomes are tightly coiled, with sister chromatids joined together.
 The nucleoli disappear.
 The mitotic spindle begins to form.
 It is composed of centrosomes and the microtubules that extend from them.
 The radial arrays of shorter microtubules that extend from the centrosomes are called
asters.
 The centrosomes move away from each other, apparently propelled by lengthening
microtubules.
 During prometaphase, the nuclear envelope fragments, and microtubules from the spindle
interact with the condensed chromosomes.
 Each of the two chromatids of a chromosome has a kinetochore, a specialized protein
structure located at the centromere.
 Kinetochore microtubules from each pole attach to one of two kinetochores.
 Nonkinetochore microtubules interact with those from opposite ends of the spindle.
 The spindle fibers push the sister chromatids until they are all arranged at the metaphase
plate, an imaginary plane equidistant from the poles, defining metaphase.
 At anaphase, the centromeres divide, separating the sister chromatids.
 Each is now pulled toward the pole to which it is attached by spindle fibers.
 By the end, the two poles have equivalent collections of chromosomes.
 At telophase, daughter nuclei begin to form at the two poles.
 Nuclear envelopes arise from the fragments of the parent cell’s nuclear envelope and
other portions of the endomembrane system.
 The chromosomes become less tightly coiled.
 Cytokinesis, division of the cytoplasm, is usually well underway by late telophase.
 In animal cells, cytokinesis involves the formation of a cleavage furrow, which pinches
the cell in two.
 In plant cells, vesicles derived from the Golgi apparatus produce a cell plate at the
middle of the cell.
The mitotic spindle distributes chromosomes to daughter cells: a closer look.

Biology Chapter Notes

 The mitotic spindle, fibers composed of microtubules and associated proteins, is a major
driving force in mitosis.
 As the spindle assembles during prophase, the elements come from partial disassembly of
the cytoskeleton.
 The spindle fibers elongate by incorporating more subunits of the protein tubulin.
 Assembly of the spindle microtubules starts in the centrosome.
 The centrosome (microtubule-organizing center) is a nonmembranous organelle that
organizes the cell’s microtubules.
 In animal cells, the centrosome has a pair of centrioles at the center, but the centrioles
are not essential for cell division.
 During interphase, the single centrosome replicates to form two centrosomes.
 As mitosis starts, the two centrosomes are located near the nucleus.
 As the spindle microtubules grow from them, the centrioles are pushed apart.
 By the end of prometaphase, they are at opposite ends of the cell.
 An aster, a radial array of short microtubules, extends from each centrosome.
 The spindle includes the centrosomes, the spindle microtubules, and the asters.
 Each sister chromatid has a kinetochore of proteins and chromosomal DNA at the
centromere.
 The kinetochores of the joined sister chromatids face in opposite directions.
 During prometaphase, some spindle microtubules (called kinetochore microtubules) attach
to the kinetochores.
 When a chromosome’s kinetochore is “captured” by microtubules, the chromosome
moves toward the pole from which those microtubules come.
 When microtubules attach to the other pole, this movement stops and a tug-of-war ensues.
 Eventually, the chromosome settles midway between the two poles of the cell, on the
metaphase plate.
 Nonkinetochore microtubules from opposite poles overlap and interact with each other.
 By metaphase, the microtubules of the asters have grown and are in contact with the
plasma membrane.
 The spindle is now complete.
 Anaphase commences when the proteins holding the sister chromatids together are
inactivated.
 Once the chromosomes are separate, full-fledged chromosomes, they move toward
opposite poles of the cell.
 How do the kinetochore microtubules function into the poleward movement of
chromosomes?
 One hypothesis is that the chromosomes are “reeled in” by the shortening of microtubules
at the spindle poles.
 Experimental evidence supports the hypothesis that motor proteins on the kinetochore
“walk” the attached chromosome along the microtubule toward the nearest pole.
 Meanwhile, the excess microtubule sections depolymerize at their kinetochore ends.
 What is the function of the nonkinetochore microtubules?

Biology Chapter Notes

 Nonkinetochore microtubules are responsible for lengthening the cell along the axis
defined by the poles.
 These microtubules interdigitate and overlap across the metaphase plate.
 During anaphase, the area of overlap is reduced as motor proteins attached to the
microtubules walk them away from one another, using energy from ATP.
 As microtubules push apart, the microtubules lengthen by the addition of new tubulin
monomers to their overlapping ends, allowing continued overlap.
Cytokinesis divides the cytoplasm: a closer look.
 Cytokinesis, division of the cytoplasm, typically follows mitosis.
 In animal cells, cytokinesis occurs by a process called cleavage.
 The first sign of cleavage is the appearance of a cleavage furrow in the cell surface near
the old metaphase plate.
 On the cytoplasmic side of the cleavage furrow is a contractile ring of actin
microfilaments associated with molecules of the motor protein myosin.
 Contraction of the ring pinches the cell in two.
 Cytokinesis in plants, which have cell walls, involves a completely different mechanism.
 During telophase, vesicles from the Golgi coalesce at the metaphase plate, forming a cell
plate.
 The plate enlarges until its membranes fuse with the plasma membrane at the
perimeter.
 The contents of the vesicles form new cell wall material between the daughter cells.
Mitosis in eukaryotes may have evolved from binary fission in bacteria.
 Prokaryotes reproduce by binary fission, not mitosis.
 Most bacterial genes are located on a single bacterial chromosome that consists of a
circular DNA molecule and associated proteins.
 While bacteria are smaller and simpler than eukaryotic cells, they still have large amounts
of DNA that must be copied and distributed equally to two daughter cells.
 The circular bacterial chromosome is highly folded and coiled in the cell.
 In binary fission, chromosome replication begins at one point in the circular chromosome,
the origin of replication site, producing two origins.
 As the chromosome continues to replicate, one origin moves toward each end of the
cell.
 While the chromosome is replicating, the cell elongates.
 When replication is complete, its plasma membrane grows inward to divide the parent
cell into two daughter cells, each with a complete genome.
 Researchers have developed methods to allow them to observe the movement of bacterial
chromosomes.
 The movement is similar to the poleward movements of the centromere regions of
eukaryotic chromosomes.
 However, bacterial chromosomes lack visible mitotic spindles or even microtubules.
 The mechanism behind the movement of the bacterial chromosome is becoming clearer
but is still not fully understood.
 Several proteins have been identified and play important roles.
Biology Chapter Notes
 How did mitosis evolve?
 There is evidence that mitosis had its origins in bacterial binary fission.
 Some of the proteins involved in binary fission are related to eukaryotic proteins.
 Two of these are related to eukaryotic tubulin and actin proteins.
 As eukaryotes evolved, the ancestral process of binary fission gave rise to mitosis.
 Possible intermediate evolutionary steps are seen in the division of two types of
unicellular algae.
 In dinoflagellates, replicated chromosomes are attached to the nuclear envelope.
 In diatoms, the spindle develops within the nucleus.
 In most eukaryotic cells, the nuclear envelope breaks down and a spindle separates the
chromosomes.

Concept 12.3 The cell cycle is regulated by a molecular control system

 The timing and rates of cell division in different parts of an animal or plant are crucial for
normal growth, development, and maintenance.
 The frequency of cell division varies with cell type.
 Some human cells divide frequently throughout life (skin cells).
 Others have the ability to divide, but keep it in reserve (liver cells).
 Mature nerve and muscle cells do not appear to divide at all after maturity.
 Investigation of the molecular mechanisms regulating these differences provide important
insights into the operation of normal cells, and may also explain cancer cells escape
controls.
Cytoplasmic signals drive the cell cycle.
 The cell cycle appears to be driven by specific chemical signals present in the cytoplasm.
 Some of the initial evidence for this hypothesis came from experiments in which cultured
mammalian cells at different phases of the cell cycle were fused to form a single cell with
two nuclei.
 Fusion of an S phase cell and a G1 phase cell induces the G1 nucleus to start S phase.
 This suggests that chemicals present in the S phase nucleus stimulated the fused
cell.
 Fusion of a cell in mitosis (M phase) with one in interphase (even G 1 phase) induces
the second cell to enter mitosis.
 The sequential events of the cell cycle are directed by a distinct cell cycle control system.
 Cyclically operating molecules trigger and coordinate key events in the cell cycle.
 The control cycle has a built-in clock, but it is also regulated by external adjustments
and internal controls.
 A checkpoint in the cell cycle is a critical control point where stop and go-ahead signals
regulate the cycle.
 The signals are transmitted within the cell by signal transduction pathways.
 Animal cells generally have built-in stop signals that halt the cell cycle at checkpoints
until overridden by go-ahead signals.
 Many signals registered at checkpoints come from cellular surveillance mechanisms.
 These indicate whether key cellular processes have been completed correctly.
Biology Chapter Notes
  Checkpoints also register signals from outside the cell.
 Three major checkpoints are found in the G1, G2, and M phases.
 For many cells, the G1 checkpoint, the “restriction point” in mammalian cells, is the most
important.
 If the cell receives a go-ahead signal at the G1 checkpoint, it usually completes the cell
cycle and divides.
 If it does not receive a go-ahead signal, the cell exits the cycle and switches to a
nondividing state, the G0 phase.
 Most cells in the human body are in this phase.
 Liver cells can be “called back” to the cell cycle by external cues, such as growth
factors released during injury.
 Highly specialized nerve and muscle cells never divide.
 Rhythmic fluctuations in the abundance and activity of cell cycle control molecules pace
the events of the cell cycle.
 These regulatory molecules include protein kinases that activate or deactivate other
proteins by phosphorylating them.
 These kinases are present in constant amounts but require attachment of a second protein,
a cyclin, to become activated.
 Levels of cyclin proteins fluctuate cyclically.
 Because of the requirement for binding of a cyclin, the kinases are called cyclin-
dependent kinases, or Cdks.
 Cyclin levels rise sharply throughout interphase, and then fall abruptly during mitosis.
 Peaks in the activity of one cyclin-Cdk complex, MPF, correspond to peaks in cyclin
concentration.
 MPF (“maturation-promoting factor” or “M-phase-promoting-factor”) triggers the cell’s
passage past the G2 checkpoint to the M phase.
 MPF promotes mitosis by phosphorylating a variety of other protein kinases.
 MPF stimulates fragmentation of the nuclear envelope by phosphorylation of various
proteins of the nuclear lamina.
 It also triggers the breakdown of cyclin, dropping cyclin and MPF levels during
mitosis and inactivating MPF.
 The noncyclin part of MPF, the Cdk, persists in the cell in inactive form until it
associates with new cyclin molecules synthesized during the S and G2 phases of the
next round of the cycle.
 At least three Cdk proteins and several cyclins regulate the key G1 checkpoint.
 Similar mechanisms are also involved in driving the cell cycle past the M phase
checkpoint.
Internal and external cues help regulate the cell cycle.
 While research scientists know that active Cdks function by phosphorylating proteins, the
identity of all these proteins is still under investigation.
 Scientists do not yet know what Cdks actually do in most cases.
 Some steps in the signaling pathways that regulate the cell cycle are clear.
 Some signals originate inside the cell, others outside.

Biology Chapter Notes

 The M phase checkpoint ensures that all the chromosomes are properly attached to the
spindle at the metaphase plate before anaphase.
 This ensures that daughter cells do not end up with missing or extra chromosomes.
 A signal to delay anaphase originates at kinetochores that have not yet attached to spindle
microtubules.
 This keeps the anaphase-promoting complex (APC) in an inactive state.
 When all kinetochores are attached, the APC activates, triggering breakdown of cyclin
and inactivation of proteins holding sister chromatids together.
 A variety of external chemical and physical factors can influence cell division.
 For example, cells fail to divide if an essential nutrient is left out of the culture
medium.
 Particularly important for mammalian cells are growth factors, proteins released by one
group of cells that stimulate other cells to divide.
 For example, platelet-derived growth factors (PDGF), produced by platelet blood
cells, bind to tyrosine-kinase receptors of fibroblasts, a type of connective tissue cell.
 This triggers a signal-transduction pathway that allows cells to pass the G 1 checkpoint
and divide.
 Each cell type probably responds specifically to a certain growth factor or combination of
factors.
 The role of PDGF is easily seen in cell culture.
 Fibroblasts in culture will only divide in the presence of a medium that also contains
PDGF.
 In a living organism, platelets release PDGF in the vicinity of an injury.
 The resulting proliferation of fibroblasts helps heal the wound.
 At least 50 different growth factors can trigger specific cells to divide.
 The effect of an external physical factor on cell division can be seen in density-
dependent inhibition of cell division.
 Cultured cells normally divide until they form a single layer on the inner surface of the
culture container.
 If a gap is created, the cells will grow to fill the gap.
 At high densities, the amount of growth factors and nutrients is insufficient to allow
continued cell growth.
 Most animal cells also exhibit anchorage dependence for cell division.
 To divide, they must be anchored to a substratum, typically the extracellular matrix of
a tissue.
 Control appears to be mediated by pathways involving plasma membrane proteins and
elements of the cytoskeleton linked to them.
 Cancer cells exhibit neither density-dependent inhibition nor anchorage dependence.
Cancer cells have escaped from cell cycle controls.
 Cancer cells divide excessively and invade other tissues because they are free of the
body’s control mechanisms.
 Cancer cells do not stop dividing when growth factors are depleted.
 This is either because a cancer cell manufactures its own growth factors, has an
abnormality in the signaling pathway, or has an abnormal cell cycle control system.
Biology Chapter Notes
 If and when cancer cells stop dividing, they do so at random points, not at the normal
checkpoints in the cell cycle.
 Cancer cells may divide indefinitely if they have a continual supply of nutrients.
 In contrast, nearly all mammalian cells divide 20 to 50 times under culture conditions
before they stop, age, and die.
 Cancer cells may be “immortal.”
 HeLa cells from a tumor removed from a woman (Henrietta Lacks) in 1951 are still
reproducing in culture.
 The abnormal behavior of cancer cells begins when a single cell in a tissue undergoes a
transformation that converts it from a normal cell to a cancer cell.
 Normally, the immune system recognizes and destroys transformed cells.
 However, cells that evade destruction proliferate to form a tumor, a mass of abnormal
cells.
 If the abnormal cells remain at the originating site, the lump is called a benign tumor.
 Most do not cause serious problems and can be fully removed by surgery.
 In a malignant tumor, the cells become invasive enough to impair the functions of one or
more organs.
 In addition to chromosomal and metabolic abnormalities, cancer cells often lose
attachment to nearby cells, are carried by the blood and lymph system to other tissues, and
start more tumors in an event called metastasis.
 Cancer cells are abnormal in many ways.
 They may have an unusual number of chromosomes, their metabolism may be
disabled, and they may cease to function in any constructive way.
 Cancer cells may secrete signal molecules that cause blood vessels to grow toward the
tumor.
 Treatments for metastasizing cancers include high-energy radiation and chemotherapy
with toxic drugs.
 These treatments target actively dividing cells.
 Chemotherapeutic drugs interfere with specific steps in the cell cycle.
 For example, Taxol prevents mitotic depolymerization, preventing cells from
proceeding past metaphase.
 The side effects of chemotherapy are due to the drug’s effects on normal cells.
 Researchers are beginning to understand how a normal cell is transformed into a cancer
cell.
 The causes are diverse, but cellular transformation always involves the alteration of
genes that influence the cell cycle control system.

Biology Chapter Notes

 Chapter 13 Meiosis and Sexual Life Cycles
Chapter Notes

Overview: Hereditary Similarity and Variation

 Living organisms are distinguished by their ability to reproduce their own kind.
 Offspring resemble their parents more than they do less closely related individuals of the
same species.
 The transmission of traits from one generation to the next is called heredity or inheritance.
 However, offspring differ somewhat from parents and siblings, demonstrating variation.
 Farmers have bred plants and animals for desired traits for thousands of years, but the
mechanisms of heredity and variation eluded biologists until the development of genetics
in the 20th century.
 Genetics is the scientific study of heredity and variation.

Concept 13.1 Offspring acquire genes from parents by inheriting chromosomes

 Parents endow their offspring with coded information in the form of genes.
 Your genome is comprised of the tens of thousands of genes that you inherited from
your mother and your father.
 Genes program specific traits that emerge as we develop from fertilized eggs into adults.
 Genes are segments of DNA. Genetic information is transmitted as specific sequences of
the four deoxyribonucleotides in DNA.
 This is analogous to the symbolic information of language in which words and
sentences are translated into mental images.
 Cells translate genetic “sentences” into freckles and other features with no resemblance
to genes.
 Most genes program cells to synthesize specific enzymes and other proteins whose
cumulative action produces an organism’s inherited traits.
 The transmission of hereditary traits has its molecular basis in the precise replication of
DNA.
 This produces copies of genes that can be passed from parents to offspring.
 In plants and animals, sperm and ova (unfertilized eggs) transmit genes from one
generation to the next.
 After fertilization (fusion of a sperm cell and an ovum), genes from both parents are
present in the nucleus of the fertilized egg, or zygote.
 Almost all the DNA in a eukaryotic cell is subdivided into chromosomes in the nucleus.
 Tiny amounts of DNA are also found in mitochondria and chloroplasts.
 Every living species has a characteristic number of chromosomes.
 Humans have 46 chromosomes in almost all of their cells.
 Each chromosome consists of a single DNA molecule associated with various proteins.

Biology Chapter Notes

 Each chromosome has hundreds or thousands of genes, each at a specific location, its
locus.
Like begets like, more or less: a comparison of asexual and sexual reproduction.
 Only organisms that reproduce asexually can produce offspring that are exact copies of
themselves.
 In asexual reproduction, a single individual is the sole parent to donate genes to its
offspring.
 Single-celled eukaryotes can reproduce asexually by mitotic cell division to produce
two genetically identical daughter cells.
 Some multicellular eukaryotes, like Hydra, can reproduce by budding, producing a
mass of cells by mitosis.
 An individual that reproduces asexually gives rise to a clone, a group of genetically
identical individuals.
 Members of a clone may be genetically different as a result of mutation.
 In sexual reproduction, two parents produce offspring that have unique combinations of
genes inherited from the two parents.
 Unlike a clone, offspring produced by sexual reproduction vary genetically from their
siblings and their parents.

Concept 13.2 Fertilization and meiosis alternate in sexual life cycles

 A life cycle is the generation-to-generation sequence of stages in the reproductive history
of an organism.
 It starts at the conception of an organism and continues until the organism produces its
own offspring.
Human cells contain sets of chromosomes.
 In humans, each somatic cell (all cells other than sperm or ovum) has 46 chromosomes.
 Each chromosome can be distinguished by size, position of the centromere, and pattern
of staining with certain dyes.
 Images of the 46 human chromosomes can be arranged in pairs in order of size to produce
a karyotype display.
 The two chromosomes comprising a pair have the same length, centromere position,
and staining pattern.
 These homologous chromosome pairs carry genes that control the same inherited
characters.
 Two distinct sex chromosomes, the X and the Y, are an exception to the general pattern
of homologous chromosomes in human somatic cells.
 The other 22 pairs are called autosomes.
 The pattern of inheritance of the sex chromosomes determines an individual’s sex.
 Human females have a homologous pair of X chromosomes (XX).
 Human males have an X and a Y chromosome (XY).
 Only small parts of the X and Y are homologous.
 Most of the genes carried on the X chromosome do not have counterparts on the tiny
Y.
Biology Chapter Notes
  The Y chromosome also has genes not present on the X.
 The occurrence of homologous pairs of chromosomes is a consequence of sexual
reproduction.
 We inherit one chromosome of each homologous pair from each parent.
 The 46 chromosomes in each somatic cell are two sets of 23, a maternal set (from your
mother) and a paternal set (from your father).
 The number of chromosomes in a single set is represented by n.
 Any cell with two sets of chromosomes is called a diploid cell and has a diploid number
of chromosomes, abbreviated as 2n.
 Sperm cells or ova (gametes) have only one set of chromosomes—22 autosomes and an
X (in an ovum) and 22 autosomes and an X or a Y (in a sperm cell).
 A gamete with a single chromosome set is haploid, abbreviated as n.
 Any sexually reproducing species has a characteristic haploid and diploid number of
chromosomes.
 For humans, the haploid number of chromosomes is 23 (n = 23), and the diploid
number is 46 (2n = 46).
Let’s discuss the role of meiosis in the human life cycle.
 The human life cycle begins when a haploid sperm cell fuses with a haploid ovum.
 These cells fuse (syngamy), resulting in fertilization.
 The fertilized egg (zygote) is diploid because it contains two haploid sets of chromosomes
bearing genes from the maternal and paternal family lines.
 As an organism develops from a zygote to a sexually mature adult, mitosis generates all
the somatic cells of the body.
 Each somatic cell contains a full diploid set of chromosomes.
 Gametes, which develop in the gonads (testes or ovaries), are not produced by mitosis.
 If gametes were produced by mitosis, the fusion of gametes would produce offspring
with four sets of chromosomes after one generation, eight after a second, and so on.
 Instead, gametes undergo the process of meiosis in which the chromosome number is
halved.
 Human sperm or ova have a haploid set of 23 different chromosomes, one from each
homologous pair.
 Fertilization restores the diploid condition by combining two haploid sets of
chromosomes.
Organisms display a variety of sexual life cycles.
 Fertilization and meiosis alternate in all sexual life cycles.
 However, the timing of meiosis and fertilization does vary among species.
 These variations can be grouped into three main types of life cycles.
 In most animals, including humans, gametes are the only haploid cells.
 Gametes do not divide but fuse to form a diploid zygote that divides by mitosis to
produce a multicellular organism.
 Plants and some algae have a second type of life cycle called alternation of generations.
 This life cycle includes two multicellular stages, one haploid and one diploid.
Biology Chapter Notes
  The multicellular diploid stage is called the sporophyte.
 Meiosis in the sporophyte produces haploid spores that develop by mitosis into the
haploid gametophyte stage.
 Gametes produced via mitosis by the gametophyte fuse to form the zygote, which
grows into the sporophyte by mitosis.
 Most fungi and some protists have a third type of life cycle.
 Gametes fuse to form a zygote, which is the only diploid phase.
 The zygote undergoes meiosis to produce haploid cells.
 These haploid cells grow by mitosis to form the haploid multicellular adult organism.
 The haploid adult produces gametes by mitosis.
 Note that either haploid or diploid cells can divide by mitosis, depending on the type of
life cycle. However, only diploid cells can undergo meiosis.
 Although the three types of sexual life cycles differ in the timing of meiosis and
fertilization, they share a fundamental feature: each cycle of chromosome halving and
doubling contributes to genetic variation among offspring.

Concept 13.3 Meiosis reduces the number of chromosome sets from diploid to haploid
 Many steps of meiosis resemble steps in mitosis.
 Both are preceded by the replication of chromosomes.
 However, in meiosis, there are two consecutive cell divisions, meiosis I and meiosis II,
resulting in four daughter cells.
 The first division, meiosis I, separates homologous chromosomes.
 The second, meiosis II, separates sister chromatids.
 The four daughter cells have only half as many chromosomes as the parent cell.
 Meiosis I is preceded by interphase, in which the chromosomes are replicated to form
sister chromatids.
 These are genetically identical and joined at the centromere.
 The single centrosome is replicated, forming two centrosomes.
 Division in meiosis I occurs in four phases: prophase I, metaphase I, anaphase I, and
telophase I.
Prophase I
 Prophase I typically occupies more than 90% of the time required for meiosis.
 During prophase I, the chromosomes begin to condense.
 Homologous chromosomes loosely pair up along their length, precisely aligned gene for
gene.
 In crossing over, DNA molecules in nonsister chromatids break at corresponding
places and then rejoin the other chromatid.
 In synapsis, a protein structure called the synaptonemal complex forms between
homologues, holding them tightly together along their length.
 As the synaptonemal complex disassembles in late prophase, each chromosome pair
becomes visible as a tetrad, or group of four chromatids.
 Each tetrad has one or more chiasmata, sites where the chromatids of homologous
chromosomes have crossed and segments of the chromatids have been traded.
Biology Chapter Notes
  Spindle microtubules form from the centrosomes, which have moved to the poles.
 The breakdown of the nuclear envelope and nucleoli take place.
 Kinetochores of each homologue attach to microtubules from one of the poles.
Metaphase I
 At metaphase I, the tetrads are all arranged at the metaphase plate, with one chromosome
facing each pole.
 Microtubules from one pole are attached to the kinetochore of one chromosome of
each tetrad, while those from the other pole are attached to the other.
Anaphase I
 In anaphase I, the homologous chromosomes separate. One chromosome moves toward
each pole, guided by the spindle apparatus.
 Sister chromatids remain attached at the centromere and move as a single unit toward the
pole.
Telophase I and cytokinesis
 In telophase I, movement of homologous chromosomes continues until there is a haploid
set at each pole.
 Each chromosome consists of two sister chromatids.
 Cytokinesis usually occurs simultaneously, by the same mechanisms as mitosis.
 In animal cells, a cleavage furrow forms. In plant cells, a cell plate forms.
 No chromosome replication occurs between the end of meiosis I and the beginning of
meiosis II, as the chromosomes are already replicated.
Meiosis II
 Meiosis II is very similar to mitosis.
 During prophase II, a spindle apparatus forms and attaches to kinetochores of each
sister chromatid.
 Spindle fibers from one pole attach to the kinetochore of one sister chromatid, and
those of the other pole attach to kinetochore of the other sister chromatid.
 At metaphase II, the sister chromatids are arranged at the metaphase plate.
 Because of crossing over in meiosis I, the two sister chromatids of each chromosome
are no longer genetically identical.
 The kinetochores of sister chromatids attach to microtubules extending from opposite
poles.
 At anaphase II, the centomeres of sister chromatids separate and two newly individual
chromosomes travel toward opposite poles.
 In telophase II, the chromosomes arrive at opposite poles.
 Nuclei form around the chromosomes, which begin expanding, and cytokinesis
separates the cytoplasm.
 At the end of meiosis, there are four haploid daughter cells.
There are key differences between mitosis and meiosis.
 Mitosis and meiosis have several key differences.

Biology Chapter Notes

  The chromosome number is reduced from diploid to haploid in meiosis but is
conserved in mitosis.
 Mitosis produces daughter cells that are genetically identical to the parent and to each
other.
 Meiosis produces cells that are genetically distinct from the parent cell and from each
other.
 Three events, unique to meiosis, occur during the first division cycle.
o During prophase I of meiosis, replicated homologous chromosomes line up and
become physically connected along their lengths by a zipperlike protein complex, the
synaptonemal complex, in a process called synapsis. Genetic rearrangement between
nonsister chromatids called crossing over also occurs. Once the synaptonemal complex
is disassembled, the joined homologous chromosomes are visible as a tetrad. X-shaped
regions called chiasmata are visible as the physical manifestation of crossing over.
Synapsis and crossing over do not occur in mitosis.
o At metaphase I of meiosis, homologous pairs of chromosomes align along the
metaphase plate. In mitosis, individual replicated chromosomes line up along the
metaphase plate.
o At anaphase I of meiosis, it is homologous chromosomes, not sister chromatids, that
separate and are carried to opposite poles of the cell. Sister chromatids of each
replicated chromosome remain attached. In mitosis, sister chromatids separate to
become individual chromosomes.
 Meiosis I is called the reductional division because it halves the number of chromosome
sets per cell—a reduction from the diploid to the haploid state.
 The sister chromatids separate during the second meiosis division, meiosis II.

Concept 13.4 Genetic variation produced in sexual life cycles contributes to evolution
 What is the origin of genetic variation?
 Mutations are the original source of genetic diversity.
 Once different versions of genes arise through mutation, reshuffling during meiosis and
fertilization produce offspring with their own unique set of traits.
Sexual life cycles produce genetic variation among offspring.
 The behavior of chromosomes during meiosis and fertilization is responsible for most of
the variation that arises in each generation.
 Three mechanisms contribute to genetic variation:
o Independent assortment of chromosomes.
o Crossing over.
o Random fertilization.
 Independent assortment of chromosomes contributes to genetic variability due to the
random orientation of homologous pairs of chromosomes at the metaphase plate during
meiosis I.
 There is a fifty-fifty chance that a particular daughter cell of meiosis I will get the
maternal chromosome of a certain homologous pair and a fifty-fifty chance that it will
receive the paternal chromosome.
 Each homologous pair of chromosomes segregates independently of the other
homologous pairs during metaphase I.
Biology Chapter Notes
 Therefore, the first meiotic division results in independent assortment of maternal and
paternal chromosomes into daughter cells.
 The numbern of combinations possible when chromosomes assort independently into
gametes is 2 , where n is the haploid number of the organism.
 If n = 3, there are 23 = 8 possible combinations.
 For humans with n = 23, there are 223, or more than 8 million possible combinations of
chromosomes.
 Crossing over produces recombinant chromosomes, which combine genes inherited
from each parent.
 Crossing over begins very early in prophase I as homologous chromosomes pair up gene
by gene.
 In crossing over, homologous portions of two nonsister chromatids trade places.
 For humans, this occurs an average of one to three times per chromosome pair.
 Recent research suggests that, in some organisms, crossing over may be essential for
synapsis and the proper assortment of chromosomes in meiosis I.
 Crossing over, by combining DNA inherited from two parents into a single chromosome,
is an important source of genetic variation.
 At metaphase II, nonidentical sister chromatids sort independently from one another,
increasing by even more the number of genetic types of daughter cells that are formed by
meiosis.
 The random nature of fertilization adds to the genetic variation arising from meiosis.
 Any sperm can fuse with any egg.
 The ovum is one of more than 8 million possible chromosome combinations.
 The successful sperm is one of more than 8 million possibilities.
 The resulting zygote could contain any one of more than 70 trillion possible
combinations of chromosomes.
 Crossing over adds even more variation to this.
 Each zygote has a unique genetic identity.
 The three sources of genetic variability in a sexually reproducing organism are:
o Independent assortment of homologous chromosomes during meiosis I and of
nonidentical sister chromatids during meiosis II.
o Crossing over between homologous chromosomes during prophase I.
o Random fertilization of an ovum by a sperm.
 All three mechanisms reshuffle the various genes carried by individual members of a
population.
Evolutionary adaptation depends on a population’s genetic variation.
 Darwin recognized the importance of genetic variation in evolution.
 A population evolves through the differential reproductive success of its variant
members.
 Those individuals best suited to the local environment leave the most offspring,
transmitting their genes in the process.
 This natural selection results in adaptation, the accumulation of favorable genetic
variations.

Biology Chapter Notes

 If the environment changes or a population moves to a new environment, new genetic
combinations that work best in the new conditions will produce more offspring, and these
genes will increase.
 The formerly favored genes will decrease.
 Sex and mutation continually generate new genetic variability.
 Although Darwin realized that heritable variation makes evolution possible, he did not
have a theory of inheritance.
 Gregor Mendel, a contemporary of Darwin’s, published a theory of inheritance that
supported Darwin’s theory.
 However, this work was largely unknown until 1900, after Darwin and Mendel had
both been dead for more than 15 years.

Biology Chapter Notes

 Chapter 14 Mendel and the Gene Idea
Chapter Notes

Overview: Drawing from the Deck of Genes

 Every day we observe heritable variations (such as brown, green, or blue eyes) among
individuals in a population.
 These traits are transmitted from parents to offspring.
 One possible explanation for heredity is a “blending” hypothesis.
 This hypothesis proposes that genetic material contributed by each parent mixes in a
manner analogous to the way blue and yellow paints blend to make green.
 With blending inheritance, a freely mating population will eventually give rise to a
uniform population of individuals.
 Everyday observations and the results of breeding experiments tell us that heritable
traits do not blend to become uniform.
 An alternative model, “particulate” inheritance, proposes that parents pass on discrete
heritable units, genes, that retain their separate identities in offspring.
 Genes can be sorted and passed on, generation after generation, in undiluted form.
 Modern genetics began in an abbey garden, where a monk named Gregor Mendel
documented a particulate mechanism of inheritance.

Concept 14.1 Mendel used the scientific approach to identify two laws of inheritance
 Mendel discovered the basic principles of heredity by breeding garden peas in carefully
planned experiments.
 Mendel grew up on a small farm in what is today the Czech Republic.
 In 1843, Mendel entered an Augustinian monastery.
 He studied at the University of Vienna from 1851 to 1853, where he was influenced by a
physicist who encouraged experimentation and the application of mathematics to science
and by a botanist who stimulated Mendel’s interest in the causes of variation in plants.
 These influences came together in Mendel’s experiments.
 After university, Mendel taught at the Brunn Modern School and lived in the local
monastery.
 The monks at this monastery had a long tradition of interest in the breeding of plants,
including peas.
 Around 1857, Mendel began breeding garden peas to study inheritance.
 Pea plants have several advantages for genetic study.
 Pea plants are available in many varieties with distinct heritable features, or
characters, with different variant traits.
 Mendel could strictly control which plants mated with which.
 Each pea plant has male (stamens) and female (carpal) sexual organs.
 In nature, pea plants typically self-fertilize, fertilizing ova with the sperm nuclei from
their own pollen.
Biology Chapter Notes
  However, Mendel could also use pollen from another plant for cross-pollination.
 Mendel tracked only those characters that varied in an “either-or” manner, rather than a
“more-or-less” manner.
 For example, he worked with flowers that were either purple or white.
 He avoided traits, such as seed weight, that varied on a continuum.
 Mendel started his experiments with varieties that were true-breeding.
 When true-breeding plants self-pollinate, all their offspring have the same traits.
 In a typical breeding experiment, Mendel would cross-pollinate (hybridize) two
contrasting, true-breeding pea varieties.
 The true-breeding parents are the P generation, and their hybrid offspring are the F1
generation.
 Mendel would then allow the F1 hybrids to self-pollinate to produce an F2 generation.
 It was mainly Mendel’s quantitative analysis of F 2 plants that revealed two fundamental
principles of heredity: the law of segregation and the law of independent assortment.
By the law of segregation, the two alleles for a character are separated during the
formation of gametes.
 If the blending model was correct, the F1 hybrids from a cross between purple-flowered
and white-flowered pea plants would have pale purple flowers.
 Instead, F1 hybrids all have purple flowers, just as purple as their purple-flowered parents.
 When Mendel allowed the F1 plants to self-fertilize, the F2 generation included both
purple-flowered and white-flowered plants.
 The white trait, absent in the F1, reappeared in the F2.
 Mendel used very large sample sizes and kept accurate records of his results.
 Mendel recorded 705 purple-flowered F2 plants and 224 white-flowered F2 plants.
 This cross produced a traits ratio of three purple to one white in the F2 offspring.
 Mendel reasoned that the heritable factor for white flowers was present in the F 1 plants,
but did not affect flower color.
 Purple flower color is a dominant trait, and white flower color is a recessive trait.
 The reappearance of white-flowered plants in the F2 generation indicated that the heritable
factor for the white trait was not diluted or “blended” by coexisting with the purple-flower
factor in F1 hybrids.
 Mendel found similar 3-to-1 ratios of two traits among F2 offspring when he conducted
crosses for six other characters, each represented by two different traits.
 For example, when Mendel crossed two true-breeding varieties, one producing round
seeds and the other producing wrinkled seeds, all the F1 offspring had round seeds.
 In the F2 plants, 75% of the seeds were round and 25% were wrinkled.
 Mendel developed a hypothesis to explain these results that consisted of four related
ideas. We will explain each idea with the modern understanding of genes and
chromosomes.
o Alternative versions of genes account for variations in inherited characters.
 The gene for flower color in pea plants exists in two versions, one for purple flowers
and one for white flowers.
 These alternate versions are called alleles.
 Each gene resides at a specific locus on a specific chromosome.
Biology Chapter Notes
  The DNA at that locus can vary in its sequence of nucleotides.
 The purple-flower and white-flower alleles are two DNA variations at the flower-color
locus.
o For each character, an organism inherits two alleles, one from each parent.
 A diploid organism inherits one set of chromosomes from each parent.
 Each diploid organism has a pair of homologous chromosomes and, therefore, two
copies of each gene.
 These homologous loci may be identical, as in the true-breeding plants of the P
generation.
 Alternatively, the two alleles may differ.
o If the two alleles at a locus differ, then one, the dominant allele, determines the
organism’s appearance. The other, the recessive allele, has no noticeable effect on the
organism’s appearance.
 In the flower-color example, the F1 plants inherited a purple-flower allele from one
parent and a white-flower allele from the other.
 They had purple flowers because the allele for that trait is dominant.
o 4. Mendel’s law of segregation states that the two alleles for a heritable character
separate and segregate during gamete production and end up in different gametes.
 This segregation of alleles corresponds to the distribution of homologous
chromosomes to different gametes in meiosis.
 If an organism has two identical alleles for a particular character, then that allele is
present as a single copy in all gametes.
 If different alleles are present, then 50% of the gametes will receive one allele and
50% will receive the other.
 Mendel’s law of segregation accounts for the 3:1 ratio that he observed in the F 2
generation.
 The F1 hybrids produce two classes of gametes, half with the purple-flower allele and half
with the white-flower allele.
 During self-pollination, the gametes of these two classes unite randomly.
 This produces four equally likely combinations of sperm and ovum.
 A Punnett square predicts the results of a genetic cross between individuals of known
genotype.
 Let us describe a Punnett square analysis of the flower-color example.
 We will use a capital letter to symbolize the dominant allele and a lowercase letter to
symbolize the recessive allele.
 P is the purple-flower allele, and p is the white-flower allele.
 What will be the physical appearance of the F2 offspring?
 One in four F2 offspring will inherit two white-flower alleles and produce white
flowers.
 Half of the F2 offspring will inherit one white-flower allele and one purple-flower
allele and produce purple flowers.
 One in four F2 offspring will inherit two purple-flower alleles and produce purple
flowers.
 Mendel’s model accounts for the 3:1 ratio in the F2 generation.
 An organism with two identical alleles for a character is homozygous for that character.
Biology Chapter Notes
 Organisms with two different alleles for a character is heterozygous for that character.
 An organism’s traits are called its phenotype.
 Its genetic makeup is called its genotype.
 Two organisms can have the same phenotype but have different genotypes if one is
homozygous dominant and the other is heterozygous.
 For flower color in peas, the only individuals with white flowers are those that are
homozygous recessive (pp) for the flower-color gene.
 However, PP and Pp plants have the same phenotype (purple flowers) but different
genotypes (homozygous dominant and heterozygous).
 How can we tell the genotype of an individual with the dominant phenotype?
 The organism must have one dominant allele, but could be homozygous dominant or
heterozygous.
 The answer is to carry out a testcross.
 The mystery individual is bred with a homozygous recessive individual.
 If any of the offspring display the recessive phenotype, the mystery parent must be
heterozygous.
By the law of independent assortment, each pair of alleles segregates independently into
gametes.
 Mendel’s first experiments followed only a single character, such as flower color.
 All F1 progeny produced in these crosses were monohybrids, heterozygous for one
character.
 A cross between two heterozygotes is a monohybrid cross.
 Mendel identified the second law of inheritance by following two characters at the same
time.
 In one such dihybrid cross, Mendel studied the inheritance of seed color and seed shape.
 The allele for yellow seeds (Y) is dominant to the allele for green seeds (y).
 The allele for round seeds (R) is dominant to the allele for wrinkled seeds (r).
 Mendel crossed true-breeding plants that had yellow, round seeds (YYRR) with true-
breeding plants that has green, wrinkled seeds (yyrr).
 One possibility is that the two characters are transmitted from parents to offspring as a
package.
 The Y and R alleles and y and r alleles stay together.
 If this were the case, the F1 offspring would produce yellow, round seeds.
 The F2 offspring would produce two phenotypes (yellow + round; green + wrinkled) in a
3:1 ratio, just like a monohybrid cross.
 This was not consistent with Mendel’s results.
 An alternative hypothesis is that the two pairs of alleles segregate independently of each
other.
 The presence of a specific allele for one trait in a gamete has no impact on the presence
of a specific allele for the second trait.
 In our example, the F1 offspring would still produce yellow, round seeds.
 However, when the F1s produced gametes, genes would be packaged into gametes with all
possible allelic combinations.
Biology Chapter Notes
  Four classes of gametes (YR, Yr, yR, and yr) would be produced in equal amounts.
 When sperm with four classes of alleles and ova with four classes of alleles combined,
there would be 16 equally probable ways in which the alleles can combine in the F 2
generation.
 These combinations produce four distinct phenotypes in a 9:3:3:1 ratio.
 This was consistent with Mendel’s results.
 Mendel repeated the dihybrid cross experiment for other pairs of characters and always
observed a 9:3:3:1 phenotypic ratio in the F2 generation.
 Each character appeared to be inherited independently.
 If you follow just one character in these crosses, you will observe a 3:1 F 2 ratio, just as if
this were a monohybrid cross.
 The independent assortment of each pair of alleles during gamete formation is now called
Mendel’s law of independent assortment.
 Mendel’s law of independent assortment states that each pair of alleles segregates
independently during gamete formation.
 Strictly speaking, this law applies only to genes located on different, nonhomologous
chromosomes.
 Genes located near each other on the same chromosome tend to be inherited together and
have more complex inheritance patterns than those predicted for the law of independent
assortment.

Concept 14.2 The laws of probability govern Mendelian inheritance

 Mendel’s laws of segregation and independent assortment reflect the same laws of
probability that apply to tossing coins or rolling dice.
 The probability scale ranges from 0 (an event with no chance of occurring) to 1 (an event
that is certain to occur).
 The probability of tossing heads with a normal coin is 1/2.
 The probability of rolling a 3 with a six-sided die is 1/6, and the probability of rolling
any other number is 1 − 1/6 = 5/6.
 When tossing a coin, the outcome of one toss has no impact on the outcome of the next
toss.
 Each toss is an independent event, just like the distribution of alleles into gametes.
 Like a coin toss, each ovum from a heterozygous parent has a 1/2 chance of carrying
the dominant allele and a 1/2 chance of carrying the recessive allele.
 The same odds apply to the sperm.
 We can use the multiplication rule to determine the chance that two or more independent
events will occur together in some specific combination.
 Compute the probability of each independent event.
 Multiply the individual probabilities to obtain the overall probability of these events
occurring together.
 The probability that two coins tossed at the same time will land heads up is 1/2 × 1/2 =
1/4.

Biology Chapter Notes

  Similarly, the probability that a heterozygous pea plant (Pp) will self-fertilize to
produce a white-flowered offspring (pp) is the chance that a sperm with a white allele
will fertilize an ovum with a white allele.
 This probability is 1/2 × 1/2 = 1/4.
 The rule of multiplication also applies to dihybrid crosses.
 For a heterozygous parent (YyRr) the probability of producing a YR gamete is 1/2 × 1/2
= 1/4.
 We can use this to predict the probability of a particular F 2 genotype without
constructing a 16-part Punnett square.
 The probability that an F2 plant from heterozygous parents will have a YYRR genotype
is 1/16 (1/4 chance for a YR ovum and 1/4 chance for a YR sperm).
 The rule of addition also applies to genetic problems.
 Under the rule of addition, the probability of an event that can occur two or more different
ways is the sum of the separate probabilities of those ways.
 For example, there are two ways that F1 gametes can combine to form a heterozygote.
 The dominant allele could come from the sperm and the recessive from the ovum
(probability = 1/4).
 Or the dominant allele could come from the ovum and the recessive from the sperm
(probability = 1/4).
 The probability of obtaining a heterozygote is 1/4 + 1/4 = 1/2.
 We can combine the rules of multiplication and addition to solve complex problems in
Mendelian genetics.
 Let’s determine the probability of an offspring having two recessive phenotypes for at
least two of three traits resulting from a trihybrid cross between pea plants that are
PpYyRr and Ppyyrr.
 There are five possible genotypes that fulfill this condition: ppyyRr, ppYyrr, Ppyyrr,
PPyyrr, and ppyyrr.
 We can use the rule of multiplication to calculate the probability for each of these
genotypes and then use the rule of addition to pool the probabilities for fulfilling the
condition of at least two recessive traits.
 The probability of producing a ppyyRr offspring:
 The probability of producing pp = 1/2 × 1/2 = 1/4.
 The probability of producing yy = 1/2 × 1 = 1/2.
 The probability of producing Rr = 1/2 × 1 = 1/2.
 Therefore, the probability of all three being present (ppyyRr) in one offspring is 1/4 ×
1/2 × 1/2 = 1/16.
 For ppYyrr: 1/4 × 1/2 × 1/2 = 1/16.
 For Ppyyrr: 1/2 × 1/2 × 1/2 = 1/8 or 2/16.
 For PPyyrr: 1/4 × 1/2 × 1/2 = 1/16.
 For ppyyrr: 1/4 × 1/2 × 1/2 = 1/16.
 Therefore, the chance that a given offspring will have at least two recessive traits is 1/16 +
2/16 + 1/16 + 1/16 = 6/16.
Mendel discovered the particulate behavior of genes: a review.

Biology Chapter Notes

 While we cannot predict with certainty the genotype or phenotype of any particular seed
from the F2 generation of a dihybrid cross, we can predict the probability that it will have
a specific genotype or phenotype.
 Mendel’s experiments succeeded because he counted so many offspring, was able to
discern the statistical nature of inheritance, and had a keen sense of the rules of chance.
 Mendel’s laws of independent assortment and segregation explain heritable variation in
terms of alternative forms of genes that are passed along according to simple rules of
probability.
 These laws apply not just to garden peas, but to all diploid organisms that reproduce by
sexual reproduction.
 Mendel’s studies of pea inheritance endure not only in genetics, but as a case study of the
power of scientific reasoning using the hypothetico-deductive approach.

Concept 14.3 Inheritance patterns are often more complex than predicted by simple
Mendelian genetics
 In the 20th century, geneticists have extended Mendelian principles not only to diverse
organisms, but also to patterns of inheritance more complex than Mendel described.
 In fact, Mendel had the good fortune to choose a system that was relatively simple
genetically.
 Each character that Mendel studied is controlled by a single gene.
 Each gene has only two alleles, one of which is completely dominant to the other.
 The heterozygous F1 offspring of Mendel’s crosses always looked like one of the parental
varieties because one allele was dominant to the other.
 The relationship between genotype and phenotype is rarely so simple.
 The inheritance of characters determined by a single gene deviates from simple
Mendelian patterns when alleles are not completely dominant or recessive, when a gene
has more than two alleles, or when a gene produces multiple phenotypes.
 We will consider examples of each of these situations.
 Alleles show different degrees of dominance and recessiveness in relation to each other.
 One extreme is the complete dominance characteristic of Mendel’s crosses.
 At the other extreme from complete dominance is codominance, in which two alleles
affect the phenotype in separate, distinguishable ways.
 For example, the M, N, and MN blood groups of humans are due to the presence of
two specific molecules on the surface of red blood cells.
 People of group M (genotype MM) have one type of molecule on their red blood cells,
people of group N (genotype NN) have the other type, and people of group MN
(genotype MN) have both molecules present.
 The MN phenotype is not intermediate between M and N phenotypes but rather
exhibits both the M and the N phenotype.
 Some alleles show incomplete dominance, in which heterozygotes show a distinct
intermediate phenotype not seen in homozygotes.
 This is not blending inheritance because the traits are separable (particulate), as shown
in further crosses.

Biology Chapter Notes

  Offspring of a cross between heterozygotes show three phenotypes: each parental and
the heterozygote.
 The phenotypic and genotypic ratios are identical: 1:2:1.
 A clear example of incomplete dominance is seen in flower color of snapdragons.
 A cross between a white-flowered plant and a red-flowered plant will produce all pink
F1 offspring.
 Self-pollination of the F1 offspring produces 25% white, 25% red, and 50% pink F2
offspring.
 The relative effects of two alleles range from complete dominance of one allele, through
incomplete dominance of either allele, to codominance of both alleles.
 It is important to recognize that a dominant allele does not somehow subdue a recessive
allele.
 Alleles are simply variations in a gene’s nucleotide sequence.
 When a dominant allele coexists with a recessive allele in a heterozygote, they do not
interact at all.
 To illustrate the relationship between dominance and phenotype, let us consider Mendel’s
character of round versus wrinkled pea seed shape.
 Pea plants with wrinkled seeds have two copies of the recessive allele.
 The seeds are wrinkled due to the accumulation of monosaccharides because of the
lack of a key enzyme that converts them to starch.
 Excess water enters the seed due to the accumulation of monosaccharides.
 The seeds wrinkle when the excess water dries.
 Both homozygous dominants and heterozygotes produce enough enzymes to convert
all the monosaccharides into starch.
 As a result, they do not fill with excess water and form smooth seeds as they dry.
 For any character, dominance/recessiveness relationships depend on the level at which we
examine the phenotype.
 For example, humans with Tay-Sachs disease lack a functioning enzyme to
metabolize certain lipids. These lipids accumulate in the brain, harming brain cells, and
ultimately leading to death.
 Children with two Tay-Sachs alleles (homozygotes) have the disease.
 Both heterozygotes with one working allele and homozygotes with two working alleles
are healthy and normal at the organismal level.
 The activity level of the lipid-metabolizing enzyme is reduced in heterozygotes. At the
biochemical level, the alleles show incomplete dominance.
 Heterozygous individuals produce equal numbers of normal and dysfunctional enzyme
molecules. At the molecular level, the Tay-Sachs and functional alleles are
codominant.
 A dominant allele is not necessarily more common in a population than the recessive
allele.
 For example, one baby in 400 is born with polydactyly, a condition in which
individuals are born with extra fingers or toes.
 Polydactyly is due to a dominant allele.
 However, the recessive allele is far more prevalent than the dominant allele.
 399 individuals out of 400 have five digits per appendage.
 Many genes exist in populations in more than two allelic forms.
Biology Chapter Notes
 The ABO blood groups in humans are determined by three alleles, IA, IB, and i.
 Both the IA and IB alleles are dominant to the i allele.
 The IA and IB alleles are codominant to each other.
 Because each individual carries two alleles, there are six possible genotypes and four
possible blood types.
 Individuals that are IAIA or IAi are type A and have type A carbohydrates on the surface
of their red blood cells.
 Individuals that are IBIB or IBi are type B and have type B carbohydrates on the surface
of their red blood cells.
 Individuals that are IAIB are type AB and have both type A and type B carbohydrates
on the surface of their red blood cells.
 Individuals that are ii are type O and have neither carbohydrate on the surface of their
red blood cells.
 Matching compatible blood groups is critical for blood transfusions because a person
produces antibodies against foreign blood factors.
 If the donor’s blood has an A or B carbohydrate that is foreign to the recipient,
antibodies in the recipient’s blood will bind to the foreign molecules, cause the
donated blood cells to clump together, and can kill the recipient.
 The genes that we have covered so far affect only one phenotypic character.
 However, most genes are pleiotropic, affecting more than one phenotypic character.
 For example, the wide-ranging symptoms of sickle-cell disease are due to a single
gene.
 Considering the intricate molecular and cellular interactions responsible for an organism’s
development, it is not surprising that a gene can affect a number of characteristics.
 In epistasis, a gene at one locus alters the phenotypic expression of a gene at a second
locus.
 For example, in mice and many other mammals, coat color depends on two genes.
 One, the epistatic gene, determines whether pigment will be deposited in hair or not.
 Presence (C) is dominant to absence (c) of pigment.
 The second gene determines whether the pigment to be deposited is black (B) or brown
(b).
 The black allele is dominant to the brown allele.
 An individual that is cc has a white (albino) coat regardless of the genotype of the
second gene.
 A cross between two black mice that are heterozygous (BbCc) will follow the law of
independent assortment.
 However, unlike the 9:3:3:1 offspring ratio of a normal Mendelian experiment, the
offspring ratio is nine black, three brown, and four white.
 All cc mice will be albino, regardless of the alleles they inherit at the B gene.
 Some characters cannot be classified as either-or, as Mendel’s genes were.
 Quantitative characters vary in a population along a continuum.
 These are usually due to polygenic inheritance, the additive effects of two or more genes
on a single phenotypic character.
 For example, skin color in humans is controlled by at least three independent genes.

Biology Chapter Notes

  Imagine that each gene has two alleles, one light and one dark, which demonstrate
incomplete dominance.
 An AABBCC individual is very dark; an aabbcc individual is very light.
 A cross between two AaBbCc individuals (with intermediate skin shade) will produce
offspring covering a wide range of shades.
 Individuals with intermediate skin shades will be most common, but some very light
and very dark individuals could be produced as well.
 The range of phenotypes will form a normal distribution, if the number of offspring is
great enough.
 Phenotype depends on environment and genes.
 A person becomes darker if they tan, despite their inherited skin color.
 A single tree may have leaves that vary in size, shape, and greenness, depending on
exposure to wind and sun.
 For humans, nutrition influences height, exercise alters build, sun-tanning darkens
skin, and experience improves performance on intelligence tests.
 Even identical twins, who are genetically identical, accumulate phenotypic differences
as a result of their unique experiences.
 The relative importance of genes and the environment in influencing human
characteristics is a very old and hotly contested debate.
 The product of a genotype is generally not a rigidly defined phenotype, but a range of
phenotypic possibilities, the norm of reaction, that are determined by the environment.
 In some cases, the norm of reaction has no breadth, and a given genotype specifies a
particular phenotype (for example, blood type).
 In contrast, a person’s red and white blood cell count varies with factors such as
altitude, customary exercise level, and presence of infection.
 Norms of reaction are broadest for polygenic characters.
 For these multifactorial characters, environment contributes to their quantitative
nature.
 A reductionist emphasis on single genes and single phenotypic characters presents an
inadequate perspective on heredity and variation.
 A more comprehensive theory of Mendelian genetics must view organisms as a whole.
 The term phenotype can refer not only to specific characters such as flower color or blood
group, but also to an organism in its entirety, including all aspects of its physical
appearance.
 Genotype can refer not just to a single genetic locus, but also to an organism’s entire
genetic makeup.
 An organism’s phenotype reflects its overall genotype and its unique environmental
history.

Concept 14.4 Many human traits follow Mendelian patterns of inheritance

 While peas are convenient subjects for genetic research, humans are not.
 The generation time is too long, fecundity is too low, and breeding experiments are
unacceptable.
 Yet humans are subject to the same rules governing inheritance as other organisms.
Biology Chapter Notes
 New techniques in molecular biology have led to many breakthrough discoveries in the
study of human genetics.
Pedigree analysis reveals Mendelian patterns in human inheritance.
 Rather than manipulate mating patterns of people, geneticists analyze the results of
matings that have already occurred.
 In a pedigree analysis, information about the presence or absence of a particular
phenotypic trait is collected from as many individuals in a family as possible, across
generations.
 The distribution of these characters is then mapped on the family tree.
 For example, the occurrence of widow’s peak (W) is dominant to a straight hairline
(w).
 Phenotypes of family members and knowledge of dominant/recessive relations
between alleles allow researchers to predict the genotypes of members of this family.
 For example, if an individual in the third generation lacks a widow’s peak, but both her
parents have widow’s peaks, then her parents must be heterozygous for that gene.
 If some siblings in the second generation lack a widow’s peak and one of the
grandparents (first generation) also lacks one, then we know the other grandparent
must be heterozygous, and we can determine the genotype of many other individuals.
 We can use the same family tree to trace the distribution of attached earlobes (f), a
recessive characteristic.
 Individuals with a dominant allele (F) have free earlobes.
 Some individuals may be ambiguous, especially if they have the dominant phenotype and
could be heterozygous or homozygous dominant.
 A pedigree can help us understand the past and predict the future.
 We can use normal Mendelian rules, including multiplication and addition, to predict the
probability of specific phenotypes.
 For example, these rules could be used to predict the probability that a child with
WwFf parents will have a widow’s peak and attached earlobes.
 The chance of having a widow’s peak is 3/4 (1/2 [WW] + 1/4 [Ww]).
 The chance of having attached earlobes is 1/4 [ff].
 This combination has a probability of 3/4 × 1/4 = 3/16.
Many human disorders follow Mendelian patterns of inheritance.
 Thousands of genetic disorders, including disabling or deadly hereditary diseases, are
inherited as simple recessive traits.
 These conditions range from relatively mild (albinism) to life-threatening (cystic
fibrosis).
 The recessive behavior of the alleles causing these conditions occurs because the allele
codes for a malfunctioning protein or for no protein at all.
 Heterozygotes have a normal phenotype because one normal allele produces enough of
the required protein.
 A recessively inherited disorder shows up only in homozygous individuals who inherit a
recessive allele from each parent.
 Individuals who lack the disorder are either homozygous dominant or heterozygotes.

Biology Chapter Notes

 While heterozygotes may lack obvious phenotypic effects, they are carriers who may
transmit a recessive allele to their offspring.
 Most people with recessive disorders are born to carriers with normal phenotypes.
 Two carriers have a 1/4 chance of having a child with the disorder, 1/2 chance of
having a child who is a carrier, and 1/4 chance of having a child without a defective
allele.
 Genetic disorders are not evenly distributed among all groups of humans.
 This results from the different genetic histories of the world’s people during times when
populations were more geographically and genetically isolated.
 Cystic fibrosis strikes one of every 2,500 whites of European descent.
 One in 25 people of European descent is a carrier for this condition.
 The normal allele for this gene codes for a membrane protein that transports Cl −
between cells and extracellular fluid.
 If these channels are defective or absent, there are abnormally high extracellular levels
of chloride.
 This causes the mucus coats of certain cells to become thicker and stickier than
normal.
 This mucus buildup in the pancreas, lungs, digestive tract, and elsewhere causes poor
absorption of nutrients, chronic bronchitis, and bacterial infections.
 Without treatment, affected children die before five, but with treatment, they can live
past their late 20s or even 30s.
 Tay-Sachs disease is another lethal recessive disorder.
 It is caused by a dysfunctional enzyme that fails to break down specific brain lipids.
 The symptoms begin with seizures, blindness, and degeneration of motor and mental
performance a few months after birth.
 Inevitably, the child dies after a few years.
 Among Ashkenazic Jews (those from central Europe), this disease occurs in one of
3,600 births, about 100 times greater than the incidence among non-Jews or
Mediterranean (Sephardic) Jews.
 The most common inherited disease among people of African descent is sickle-cell
disease, which affects one of 400 African-Americans.
 Sickle-cell disease is caused by the substitution of a single amino acid in hemoglobin.
 When oxygen levels in the blood of an affected individual are low, sickle-cell
hemoglobin aggregate into long rods that deform red blood cells into a sickle shape.
 This sickling creates a cascade of symptoms, demonstrating the pleiotropic effects of
this allele, as sickled cells clump and clog capillaries throughout the body.
 Doctors can use regular blood transfusions to prevent brain damage and new drugs to
prevent or treat other problems.
 At the organismal level, the nonsickle allele is incompletely dominant to the sickle-cell
allele.
 Carriers are said to have sickle-cell trait.
 These individuals are usually healthy, although some suffer some symptoms of sickle-
cell disease under blood oxygen stress.
 At the molecular level, the two alleles are codominant as both normal and abnormal
(sickle-cell) hemoglobins are synthesized.
 About one in ten African-Americans has sickle-cell trait.
Biology Chapter Notes
  The high frequency of heterozygotes is unusual for an allele with severe detrimental
effects in homozygotes.
 Individuals with one sickle-cell allele have increased resistance to malaria, a parasite
that spends part of its life cycle in red blood cells.
 In tropical Africa, where malaria is common, the sickle-cell allele is both a boon and a
bane.
 Homozygous normal individuals die of malaria and homozygous recessive
individuals die of sickle-cell disease, while carriers are relatively free of both.
 The relatively high frequency of sickle-cell trait in African-Americans is a vestige of their
African roots.
 Normally it is relatively unlikely that two carriers of the same rare, harmful allele will
meet and mate.
 However, consanguineous matings between close relatives increase the risk.
 Individuals who share a recent common ancestor are more likely to carry the same
recessive alleles.
 Most societies and cultures have laws or taboos forbidding marriages between close
relatives.
 Although most harmful alleles are recessive, a number of human disorders are due to
dominant alleles.
 For example, achondroplasia, a form of dwarfism, has an incidence of one case in 25,000
people.
 Heterozygous individuals have the dwarf phenotype.
 Those who are not achondroplastic dwarfs, 99.99% of the population, are homozygous
recessive for this trait.
 This provides another example of a trait for which the recessive allele is far more
prevalent than the dominant allele.
 Lethal dominant alleles are much less common than lethal recessives.
 If a lethal dominant kills an offspring before it can mature and reproduce, the allele
will not be passed on to future generations.
 In contrast, a lethal recessive allele can be passed on by heterozygous carriers who
have normal phenotypes.
 A lethal dominant allele can escape elimination if it causes death at a relatively advanced
age, after the individual has already passed on the lethal allele to his or her children.
 One example is Huntington’s disease, a degenerative disease of the nervous system.
 The dominant lethal allele has no obvious phenotypic effect until an individual is about
35 to 45 years old.
 The deterioration of the nervous system is irreversible and inevitably fatal.
 Any child born to a parent who has the allele for Huntington’s disease has a 50% chance
of inheriting the disease and the disorder.
 In the United States, this devastating disease afflicts one in 10,000 people.
 Recently, molecular geneticists have used pedigree analysis of affected families to track
the Huntington’s allele to a locus near the tip of chromosome 4.
 This has led to the development of a test that can detect the presence of the
Huntington’s allele in an individual’s genome.

Biology Chapter Notes

 While some diseases are inherited in a simple Mendelian fashion due to alleles at a single
locus, many other disorders have a multifactorial basis.
 These may have a genetic component plus a significant environmental influence.
 Multifactorial disorders include heart disease; diabetes; cancer; alcoholism; and certain
mental illnesses, such as schizophrenia and manic-depressive disorder.
 The genetic component of such disorders is typically polygenic.
 At present, little is understood about the genetic contribution to most multifactorial
diseases.
 The best public health strategy is education about relevant environmental factors and
promotion of healthy behavior.
Technology is providing new tools for genetic testing and counseling.
 A preventive approach to simple Mendelian disorders is sometimes possible.
 The risk that a particular genetic disorder will occur can sometimes be assessed before a
child is conceived or early in pregnancy.
 Many hospitals have genetic counselors to provide information to prospective parents who
are concerned about a family history of a specific disease.
 Consider a hypothetical couple, John and Carol, who are planning to have their first child.
 In both of their families’ histories, a recessive lethal disorder is present. Both John and
Carol had brothers who died of the disease.
 While not one of John, Carol, or their parents have the disease, their parents must have
been carriers (Aa × Aa).
 John and Carol each have a 2/3 chance of being carriers and a 1/3 chance of being
homozygous dominant.
 The probability that their first child will have the disease is 2/3 (chance that John is a
carrier) × 2/3 (chance that Carol is a carrier) × 1/4 (chance that the offspring of two
carriers is homozygous recessive) = 1/9.
 If their first child is born with the disease, we know that John and Carol’s genotype
must be Aa and they are both carriers.
 In that case, the chance that their next child will also have the disease is 1/4.
 Mendel’s laws are simply the rules of probability applied to heredity.
 Because chance has no memory, the genotype of each child is unaffected by the
genotypes of older siblings.
 The chance that John and Carol’s first three children will have the disorder is 1/4 × 1/4
× 1/4 = 1/64. Should that outcome happen, the likelihood that a fourth child will also
have the disorder is still 1/4.
 Because most children with recessive disorders are born to parents with a normal
phenotype, the key to assessing risk is identifying whether prospective parents are carriers
of the recessive trait.
 Recently developed tests for several disorders can distinguish normal phenotypes in
heterozygotes from homozygous dominants.
 These results allow individuals with a family history of a genetic disorder to make
informed decisions about having children.
 However, issues of confidentiality, discrimination, and counseling may arise.
 Tests are also available to determine in utero if a child has a particular disorder.

Biology Chapter Notes

 One technique, amniocentesis, can be used from the 14th to 16th week of pregnancy to
assess whether the fetus has a specific disease.
 Fetal cells extracted from amniotic fluid are cultured and karyotyped to identify some
disorders.
 Other disorders can be identified from chemicals in the amniotic fluids.
 A second technique, chorionic villus sampling (CVS) allows faster karyotyping and can
be performed as early as the eighth to tenth week of pregnancy.
 This technique extracts a sample of fetal tissue from the chorionic villi of the placenta.
 This technique is not suitable for tests requiring amniotic fluid.
 Other techniques, ultrasound and fetoscopy, allow fetal health to be assessed visually in
utero.
 Both fetoscopy and amniocentesis cause complications such as maternal bleeding or
fetal death in about 1% of cases.
 Therefore, these techniques are usually reserved for cases in which the risk of a genetic
disorder or other type of birth defect is relatively great.
 If fetal tests reveal a serious disorder, the parents face the difficult choice of terminating
the pregnancy or preparing to care for a child with a genetic disorder.
 Some genetic traits can be detected at birth by simple tests that are now routinely
performed in hospitals.
 One test can detect the presence of a recessively inherited disorder, phenylketonuria
(PKU).
 This disorder occurs in one in 10,000 to 15,000 births.
 Individuals with this disorder accumulate the amino acid phenylalanine and its
derivative phenylpyruvate in the blood to toxic levels.
 This leads to mental retardation.
 If the disorder is detected, a special diet low in phenylalanine usually promotes normal
development.
 Unfortunately, few other genetic diseases are so treatable.

Biology Chapter Notes

 Chapter 15 The Chromosomal Basis of Inheritance
Chapter Notes

Overview: Locating Genes on Chromosomes

 Today we know that genes—Gregor Mendel’s “hereditary factors”—are located on

chromosomes.
 A century ago, the relationship of genes and chromosomes was not so obvious.
 Many biologists were skeptical about Mendel’s laws of segregation and independent
assortment until evidence mounted that they had a physical basis in the behavior of
chromosomes.

Concept 15.1 Mendelian inheritance has its physical basis in the behavior of
chromosomes
 Around 1900, cytologists and geneticists began to see parallels between the behavior of
chromosomes and the behavior of Mendel’s factors.
 Using improved microscopy techniques, cytologists worked out the process of mitosis
in 1875 and meiosis in the 1890s.
 Chromosomes and genes are both present in pairs in diploid cells.
 Homologous chromosomes separate and alleles segregate during meiosis.
 Fertilization restores the paired condition for both chromosomes and genes.
 Around 1902, Walter Sutton, Theodor Boveri, and others noted these parallels and a
chromosome theory of inheritance began to take form:
 Genes occupy specific loci on chromosomes.
 Chromosomes undergo segregation during meiosis.
 Chromosomes undergo independent assortment during meiosis.
 The behavior of homologous chromosomes during meiosis can account for the
segregation of the alleles at each genetic locus to different gametes.
 The behavior of nonhomologous chromosomes can account for the independent
assortment of alleles for two or more genes located on different chromosomes.
Morgan traced a gene to a specific chromosome.
 In the early 20th century, Thomas Hunt Morgan was the first geneticist to associate a
specific gene with a specific chromosome.
 Like Mendel, Morgan made an insightful choice in his experimental animal. Morgan
worked with Drosophila melanogaster, a fruit fly that eats fungi on fruit.
 Fruit flies are prolific breeders and have a generation time of two weeks.
 Fruit flies have three pairs of autosomes and a pair of sex chromosomes (XX in
females, XY in males).
 Morgan spent a year looking for variant individuals among the flies he was breeding.
 He discovered a single male fly with white eyes instead of the usual red.
 The normal character phenotype is the wild type.

Biology Chapter Notes

 Alternative traits are called mutant phenotypes because they are due to alleles that
originate as mutations in the wild-type allele.
 When Morgan crossed his white-eyed male with a red-eyed female, all the F1 offspring
had red eyes, suggesting that the red allele was dominant to the white allele.
 Crosses between the F1 offspring produced the classic 3:1 phenotypic ratio in the F 2
offspring.
 Surprisingly, the white-eyed trait appeared only in F2 males.
 All the F2 females and half the F2 males had red eyes.
 Morgan concluded that a fly’s eye color was linked to its sex.
 Morgan deduced that the gene with the white-eyed mutation is on the X chromosome,
with no corresponding allele present on the Y chromosome.
 Females (XX) may have two red-eyed alleles and have red eyes or may be
heterozygous and have red eyes.
 Males (XY) have only a single allele. They will be red-eyed if they have a red-eyed
allele or white-eyed if they have a white-eyed allele.

Concept 15.2 Linked genes tend to be inherited together because they are located near
each other on the same chromosome
 Each chromosome has hundreds or thousands of genes.
 Genes located on the same chromosome that tend to be inherited together are called
linked genes.
 Results of crosses with linked genes deviate from those expected according to
independent assortment.
 Morgan observed this linkage and its deviations when he followed the inheritance of
characters for body color and wing size.
 The wild-type body color is gray (b+), and the mutant is black (b).
 The wild-type wing size is normal (vg+), and the mutant has vestigial wings (vg).
 The mutant alleles are recessive to the wild-type alleles.
 Neither gene is on a sex chromosome.
 Morgan crossed F1 heterozygous females (b+bvg+vg) with homozygous recessive males
(bbvgvg).
 According to independent assortment, this should produce 4 phenotypes in a 1:1:1:1 ratio.
 Surprisingly, Morgan observed a large number of wild-type (gray-normal) and double-
mutant (black-vestigial) flies among the offspring.
 These phenotypes are those of the parents.
 Morgan reasoned that body color and wing shape are usually inherited together because
the genes for these characters are on the same chromosome.
 The other two phenotypes (gray-vestigial and black-normal) were fewer than expected
from independent assortment (but totally unexpected from dependent assortment).
 What led to this genetic recombination, the production of offspring with new
combinations of traits?
Independent assortment of chromosomes and crossing over produce genetic
recombinants.
Biology Chapter Notes
 Genetic recombination can result from independent assortment of genes located on
nonhomologous chromosomes or from crossing over of genes located on homologous
chromosomes.
 Mendel’s dihybrid cross experiments produced offspring that had a combination of traits
that did not match either parent in the P generation.
 If the P generation consists of a yellow-round seed parent (YYRR) crossed with a
green-wrinkled seed parent (yyrr), all F1 plants have yellow-round seeds (YyRr).
 A cross between an F1 plant and a homozygous recessive plant (a testcross) produces
four phenotypes.
 Half are the parental types, with phenotypes that match the original P parents, with
either yellow-round seeds or green-wrinkled seeds.
 Half are recombinants, new combinations of parental traits, with yellow-wrinkled or
green-round seeds.
 A 50% frequency of recombination is observed for any two genes located on different
(nonhomologous) chromosomes.
 The physical basis of recombination between unlinked genes is the random orientation of
homologous chromosomes at metaphase I of meiosis, which leads to the independent
assortment of alleles.
 The F1 parent (YyRr) produces gametes with four different combinations of alleles: YR,
Yr, yR, and yr.
 The orientation of the tetrad containing the seed-color gene has no bearing on the
orientation of the tetrad with the seed-shape gene.
 In contrast, linked genes, genes located on the same chromosome, tend to move together
through meiosis and fertilization.
 Under normal Mendelian genetic rules, we would not expect linked genes to recombine
into assortments of alleles not found in the parents.
 If the seed color and seed coat genes were linked, we would expect the F 1 offspring to
produce only two types of gametes, YR and yr, when the tetrads separate.
 One homologous chromosome carries the Y and R alleles on the same chromosome,
and the other homologous chromosome carries the y and r alleles.
 The results of Morgan’s testcross for body color and wing shape did not conform to either
independent assortment or complete linkage.
 Under independent assortment, the testcross should produce a 1:1:1:1 phenotypic ratio.
 If completely linked, we should expect to see a 1:1:0:0 ratio with only parental
phenotypes among offspring.
 Most of the offspring had parental phenotypes, suggesting linkage between the genes.
 However, 17% of the flies were recombinants, suggesting incomplete linkage.
 Morgan proposed that some mechanism must occasionally break the physical connection
between genes on the same chromosome.
 This process, called crossing over, accounts for the recombination of linked genes.
 Crossing over occurs while replicated homologous chromosomes are paired during
prophase of meiosis I.
 One maternal and one paternal chromatid break at corresponding points and then rejoin
with each other.
 The occasional production of recombinant gametes during meiosis accounts for the
occurrence of recombinant phenotypes in Morgan’s testcross.
Biology Chapter Notes
 The percentage of recombinant offspring, the recombination frequency, is related to the
distance between linked genes.
Geneticists can use recombination data to map a chromosome’s genetic loci.
 One of Morgan’s students, Alfred Sturtevant, used crossing over of linked genes to
develop a method for constructing a genetic map, an ordered list of the genetic loci along
a particular chromosome.
 Sturtevant hypothesized that the frequency of recombinant offspring reflected the distance
between genes on a chromosome.
 He assumed that crossing over is a random event, and that the chance of crossing over is
approximately equal at all points on a chromosome.
 Sturtevant predicted that the farther apart two genes are, the higher the probability that a
crossover will occur between them, and therefore, the higher the recombination
frequency.
 The greater the distance between two genes, the more points there are between them
where crossing over can occur.
 Sturtevant used recombination frequencies from fruit fly crosses to map the relative
position of genes along chromosomes.
 A genetic map based on recombination frequencies is called a linkage map.
 Sturtevant used the testcross design to map the relative position of three fruit fly genes,
body color (b), wing size (vg), and eye color (cn).
 The recombination frequency between cn and b is 9%.
 The recombination frequency between cn and vg is 9.5%.
 The recombination frequency between b and vg is 17%.
 The only possible arrangement of these three genes places the eye color gene between
the other two.
 Sturtevant expressed the distance between genes, the recombination frequency, as map
units.
 One map unit (called a centimorgan) is equivalent to a 1% recombination frequency.
 You may notice that the three recombination frequencies in our mapping example are not
quite additive: 9% (b-cn) + 9.5% (cn-vg) > 17% (b-vg).
 This results from multiple crossing over events.
 A second crossing over “cancels out” the first and reduces the observed number of
recombinant offspring.
 Genes father apart (for example, b-vg) are more likely to experience multiple crossing
over events.
 Some genes on a chromosome are so far apart that a crossover between them is virtually
certain.
 In this case, the frequency of recombination reaches its maximum value of 50% and the
genes behave as if found on separate chromosomes.
 In fact, two genes studied by Mendel—for seed color and flower color—are located on
the same chromosome but still assort independently.
 Genes located far apart on a chromosome are mapped by adding the recombination
frequencies between the distant genes and the intervening genes.
 Sturtevant and his colleagues were able to map the linear positions of genes in Drosophila
into four groups, one for each chromosome.
Biology Chapter Notes
 A linkage map provides an imperfect picture of a chromosome.
 Map units indicate relative distance and order, not precise locations of genes.
 The frequency of crossing over is not actually uniform over the length of a
chromosome.
 A linkage map does portray the order of genes along a chromosome, but does not
accurately portray the precise location of those genes.
 Combined with other methods like chromosomal banding, geneticists can develop
cytogenetic maps of chromosomes.
 These indicate the positions of genes with respect to chromosomal features.
 Recent techniques show the physical distances between gene loci in DNA nucleotides.

Concept 15.3 Sex-linked genes exhibit unique patterns of inheritance

The chromosomal basis of sex varies with the organism.
 Although the anatomical and physiological differences between women and men are
numerous, the chromosomal basis of sex is rather simple.
 In humans and other mammals, there are two varieties of sex chromosomes, X and Y.
 An individual who inherits two X chromosomes usually develops as a female.
 An individual who inherits an X and a Y chromosome usually develops as a male.
 Other animals have different methods of sex determination.
 The X-0 system is found in some insects. Females are XX, males are X.
 In birds, some fishes, and some insects, females are ZW and males are ZZ.
 In bees and ants, females are diploid and males are haploid.
 In the X-Y system, the Y chromosome is much smaller than the X chromosome.
 Only relatively short segments at either end of the Y chromosome are homologous with
the corresponding regions of the X chromosome.
 The X and Y rarely cross over.
 In both testes (XY) and ovaries (XX), the two sex chromosomes segregate during meiosis,
and each gamete receives one.
 Each ovum receives an X chromosome.
 Half the sperm cells receive an X chromosome, and half receive a Y chromosome.
 Because of this, each conception has about a fifty-fifty chance of producing a particular
sex.
 If a sperm cell bearing an X chromosome fertilizes an ovum, the resulting zygote is
female (XX).
 If a sperm cell bearing a Y chromosome fertilizes an ovum, the resulting zygote is
male (XY).
 In humans, the anatomical signs of sex first appear when the embryo is about two months
old.
 In 1990, a British research team identified a gene on the Y chromosome required for the
development of testes.
 They named the gene SRY (sex-determining region of the Y chromosome).
 In individuals with the SRY gene, the generic embryonic gonads develop into testes.
Biology Chapter Notes
  Activity of the SRY gene triggers a cascade of biochemical, physiological, and
anatomical features because it regulates many other genes.
 Other genes on the Y chromosome are necessary for the production of functional
sperm.
 In the absence of these genes, an XY individual is male but does not produce normal
sperm.
 In individuals lacking the SRY gene, the generic embryonic gonads develop into ovaries.
Sex-linked genes have unique patterns of inheritance.
 In addition to their role in determining sex, the sex chromosomes, especially the X
chromosome, have genes for many characters unrelated to sex.
 A gene located on either sex chromosome is called a sex-linked gene.
 In humans, the term refers to a gene on the X chromosome.
 Human sex-linked genes follow the same pattern of inheritance as Morgan’s white-eye
locus in Drosophila.
 Fathers pass sex-linked alleles to all their daughters but none of their sons.
 Mothers pass sex-linked alleles to both sons and daughters.
 If a sex-linked trait is due to a recessive allele, a female will express this phenotype only
if she is homozygous.
 Heterozygous females are carriers for the recessive trait.
 Because males have only one X chromosome (hemizygous), any male receiving the
recessive allele from his mother will express the recessive trait.
 The chance of a female inheriting a double dose of the mutant allele is much less than
the chance of a male inheriting a single dose.
 Therefore, males are far more likely to exhibit sex-linked recessive disorders than are
females.
 For example, color blindness is a mild disorder inherited as a sex-linked trait.
 A color-blind daughter may be born to a color-blind father whose mate is a carrier.
 However, the odds of this are fairly low.
 Several serious human disorders are sex-linked.
 Duchenne muscular dystrophy affects one in 3,500 males born in the United States.
 Affected individuals rarely live past their early 20s.
 This disorder is due to the absence of an X-linked gene for a key muscle protein called
dystrophin.
 The disease is characterized by a progressive weakening of the muscles and a loss of
coordination.
 Hemophilia is a sex-linked recessive disorder defined by the absence of one or more
proteins required for blood clotting.
 These proteins normally slow and then stop bleeding.
 Individuals with hemophilia have prolonged bleeding because a firm clot forms
slowly.
 Bleeding in muscles and joints can be painful and can lead to serious damage.
 Today, people with hemophilia can be treated with intravenous injections of the missing
protein.

Biology Chapter Notes

 Although female mammals inherit two X chromosomes, only one X chromosome is
active.
 Therefore, males and females have the same effective dose (one copy) of genes on the X
chromosome.
 During female development, one X chromosome per cell condenses into a compact
object called a Barr body.
 Most of the genes on the Barr-body chromosome are not expressed.
 The condensed Barr-body chromosome is reactivated in ovarian cells that produce ova.
 Mary Lyon, a British geneticist, demonstrated that selection of which X chromosome will
form the Barr body occurs randomly and independently in embryonic cells at the time of
X inactivation.
 As a consequence, females consist of a mosaic of two types of cells, some with an active
paternal X chromosome, others with an active maternal X chromosome.
 After an X chromosome is inactivated in a particular cell, all mitotic descendants of
that cell will have the same inactive X.
 If a female is heterozygous for a sex-linked trait, approximately half her cells will
express one allele, and the other half will express the other allele.
 In humans, this mosaic pattern is evident in women who are heterozygous for an X-linked
mutation that prevents the development of sweat glands.
 A heterozygous woman will have patches of normal skin and skin patches lacking
sweat glands.
 Similarly, the orange-and-black pattern on tortoiseshell cats is due to patches of cells
expressing an orange allele while other patches have a nonorange allele.
 X inactivation involves modification of the DNA by attachment of methyl (—CH3)
groups to cytosine nucleotides on the X chromosome that will become the Barr body.
 Researchers have discovered a gene called XIST (X-inactive specific transcript).
 This gene is active only on the Barr-body chromosome and produces multiple copies of
an RNA molecule that attach to the X chromosome on which they were made.
 This initiates X inactivation.
 The mechanism that connects XIST RNA and DNA methylation is unknown.
 What determines which of the two X chromosomes has an active XIST gene is also
unknown.

Concept 15.4 Alterations of chromosome number or structure cause some genetic

disorders
 Physical and chemical disturbances can damage chromosomes in major ways.
 Errors during meiosis can alter chromosome number in a cell.
 Plants tolerate genetic defects to a greater extent that do animals.
 Nondisjunction occurs when problems with the meiotic spindle cause errors in daughter
cells.
 This may occur if tetrad chromosomes do not separate properly during meiosis I.
 Alternatively, sister chromatids may fail to separate during meiosis II.

Biology Chapter Notes

 As a consequence of nondisjunction, one gamete receives two of the same type of
chromosome, and another gamete receives no copy.
 Offspring resulting from fertilization of a normal gamete with one produced by
nondisjunction will have an abnormal chromosome number, a condition known as
aneuploidy.
 Trisomic cells have three copies of a particular chromosome type and have 2n + 1
total chromosomes.
 Monosomic cells have only one copy of a particular chromosome type and have 2n − 1
chromosomes.
 If the organism survives, aneuploidy typically leads to a distinct phenotype.
 Aneuploidy can also occur during failures of the mitotic spindle.
 If this happens early in development, the aneuploid condition will be passed along by
mitosis to a large number of cells.
 This is likely to have a substantial effect on the organism.
 Organisms with more than two complete sets of chromosomes are polyploid.
 This may occur when a normal gamete fertilizes another gamete in which there has been
nondisjunction of all its chromosomes.
 The resulting zygote would be triploid (3n).
 Alternatively, if a 2n zygote failed to divide after replicating its chromosomes, a
tetraploid (4n) embryo would result from subsequent successful cycles of mitosis.
 Polyploidy is relatively common among plants and much less common among animals,
although it is known to occur in fishes and amphibians.
 The spontaneous origin of polyploid individuals plays an important role in the
evolution of plants.
 Both fishes and amphibians have polyploid species.
 Recently, researchers in Chile have identified a new rodent species that may be
tetraploid.
 Polyploids are more nearly normal in phenotype than aneuploids.
 One extra or missing chromosome apparently upsets the genetic balance during
development more than does an entire extra set of chromosomes.
 Breakage of a chromosome can lead to four types of changes in chromosome structure.
 A deletion occurs when a chromosome fragment lacking a centromere is lost during
cell division.
 This chromosome will be missing certain genes.
 A duplication occurs when a fragment becomes attached as an extra segment to a
sister chromatid.
 Alternatively, a detached fragment may attach to a nonsister chromatid of a
homologous chromosome.
 In this case, the duplicated segments will not be identical if the homologues carry
different alleles.
 An inversion occurs when a chromosomal fragment reattaches to the original
chromosome, but in the reverse orientation.
 In translocation, a chromosomal fragment joins a nonhomologous chromosome.
 Deletions and duplications are especially likely to occur during meiosis.

Biology Chapter Notes

  Homologous chromatids may break and rejoin at incorrect places during crossing over,
so that one chromatid loses more genes than it receives.
 The products of such a nonreciprocal crossover are one chromosome with a deletion
and one chromosome with a duplication.
 A diploid embryo that is homozygous for a large deletion or a male with a large deletion
to its single X chromosome is usually missing many essential genes.
 This is usually lethal.
 Duplications and translocations are typically harmful.
 Reciprocal translocation or inversion can alter phenotype because a gene’s expression is
influenced by its location among neighboring genes.
Human disorders are due to chromosome alterations.
 Several serious human disorders are due to alterations of chromosome number and
structure.
 Although the frequency of aneuploid zygotes may be quite high in humans, most of these
alterations are so disastrous to development that the embryos are spontaneously aborted
long before birth.
 Severe developmental problems result from an imbalance among gene products.
 Certain aneuploid conditions upset the balance less, making survival to birth and beyond
possible.
 Surviving individuals have a set of symptoms—a syndrome—characteristic of the type
of aneuploidy.
 Genetic disorders caused by aneuploidy can be diagnosed before birth by fetal testing.
 One aneuploid condition, Down syndrome, is due to three copies of chromosome 21 or
trisomy 21.
 It affects one in 700 children born in the United States.
 Although chromosome 21 is the smallest human chromosome, trisomy 21 severely alters
an individual’s phenotype in specific ways.
 Individuals with Down syndrome have characteristic facial features, short stature, heart
defects, susceptibility to respiratory infection, mental retardation, and increased risk of
developing leukemia and Alzheimer’s disease.
 Most are sexually underdeveloped and sterile.
 Most cases of Down syndrome result from nondisjunction during gamete production in
one parent.
 The frequency of Down syndrome increases with the age of the mother.
 This may be linked to some age-dependent abnormality in the spindle checkpoint
during meiosis I, leading to nondisjunction.
 Trisomies of other chromosomes also increase in incidence with maternal age, but it is
rare for infants with these autosomal trisomies to survive for long.
 Nondisjunction of sex chromosomes produces a variety of aneuploid conditions in
humans.
 This aneuploidy upsets the genetic balance less severely that autosomal aneuploidy.
 This may be because the Y chromosome contains relatively few genes and because
extra copies of the X chromosome become inactivated as Barr bodies in somatic cells.
 An XXY male has Klinefelter’s syndrome, which occurs once in every 2,000 live births.
Biology Chapter Notes
  These individuals have male sex organs, but have abnormally small testes and are
sterile.
 Although the extra X is inactivated, some breast enlargement and other female
characteristics are common.
 Affected individuals have normal intelligence.
 Males with an extra Y chromosome (XYY) tend to be somewhat taller than average.
 Trisomy X (XXX), which occurs once in every 2,000 live births, produces healthy
females.
 Monosomy X or Turner syndrome (X0) occurs once in every 5,000 births.
 This is the only known viable monosomy in humans.
 X0 individuals are phenotypically female but are sterile because their sex organs do
not mature.
 When provided with estrogen replacement therapy, girls with Turner syndrome
develop secondary sex characteristics.
 Most are of normal intelligence.
 Structural alterations of chromosomes can also cause human disorders.
 Deletions, even in a heterozygous state, can cause severe problems.
 One syndrome, cri du chat, results from a specific deletion in chromosome 5.
 These individuals are mentally retarded, have small heads with unusual facial features,
and have a cry like the mewing of a distressed cat.
 This syndrome is fatal in infancy or early childhood.
 Chromosomal translocations between nonhomologous chromosomes are also associated
with human disorders.
 Chromosomal translocations have been implicated in certain cancers, including chronic
myelogenous leukemia (CML).
 CML occurs when a large fragment of chromosome 22 switches places with a small
fragment from the tip of chromosome 9.
 The resulting short, easily recognized chromosome 22 is called the Philadelphia
chromosome.

Concept 15.5 Some inheritance patterns are exceptions to the standard chromosome
theory
The phenotypic effects of some mammalian genes depend on whether they are inherited
from the mother or the father.
 For most genes, it is a reasonable assumption that a specific allele will have the same
effect regardless of whether it is inherited from the mother or father.
 However, for a few dozen mammalian traits, phenotype varies depending on which parent
passed along the alleles for those traits.
 The genes involved are not necessarily sex linked and may or may not lie on the X
chromosome.
 Variation in phenotype depending on whether an allele is inherited from the male or
female parent is called genomic imprinting.
 Genomic imprinting occurs during formation of gametes and results in the silencing of
certain genes.
Biology Chapter Notes
  Imprinted genes are not expressed.
 Because different genes are imprinted in sperm and ova, some genes in a zygote are
maternally imprinted, and others are paternally imprinted.
 These maternal and paternal imprints are transmitted to all body cells during
development.
 For a maternally imprinted gene, only the paternal allele is expressed.
 For a paternally imprinted gene, only the maternal allele is expressed.
 Patterns of imprinting are characteristic of a given species.
 The gene for insulin-like growth factor 2 (Igf2) is one of the first imprinted genes to be
identified.
 Although the growth factor is required for normal prenatal growth, only the paternal allele
is expressed.
 Evidence that the Igf2 allele is imprinted initially came from crosses between wild-type
mice and dwarf mice homozygous for a recessive mutation in the Igf2 gene.
 The phenotypes of heterozygous offspring differ, depending on whether the mutant
allele comes from the mother or the father.
 The Igf2 allele is imprinted in eggs, turning off expression of the imprinted allele.
 In sperm, the Igf2 allele is not imprinted and functions normally.
 What exactly is a genomic imprint?
 In many cases, it consists of methyl (—CH3) groups that are added to the cytosine
nucleotides of one of the alleles.
 The hypothesis that methylation directly silences an allele is consistent with the evidence
that heavily methylated genes are usually inactive.
 Other mechanisms may lead to silencing of imprinted genes.
 Most of the known imprinted genes are critical for embryonic development.
 In experiments with mice, embryos engineered to inherit both copies of certain
chromosomes from the same parent die before birth, whether their lone parent is male or
female.
 Normal development requires that embryonic cells have one active copy of certain genes.
 Aberrant imprinting is associated with abnormal development and certain cancers.
Extranuclear genes exhibit a non-Mendelian pattern of inheritance.
 Not all of a eukaryote cell’s genes are located on nuclear chromosomes, or even in the
nucleus.
 Extranuclear genes are found in small circles of DNA in mitochondria and chloroplasts.
 These organelles reproduce themselves and transmit their genes to daughter organelles.
 Their cytoplasmic genes do not display Mendelian inheritance, because they are not
distributed to offspring according to the same rules that direct distribution of nuclear
chromosomes during meiosis.
 Karl Correns first observed cytoplasmic genes in plants in 1909 when he studied the
inheritance of patches of yellow or white on the leaves of an otherwise green plant.
 He determined that the coloration of the offspring was determined by only the maternal
parent.

Biology Chapter Notes

  These coloration patterns are due to genes in the plastids that are inherited only via the
ovum, not via the sperm nucleus in the pollen.
 Because a zygote inherits all its mitochondria from the ovum, all mitochondrial genes in
mammals demonstrate maternal inheritance.
 Several rare human disorders are produced by mutations to mitochondrial DNA.
 These primarily impact ATP supply by producing defects in the electron transport
chain or ATP synthase.
 Tissues that require high energy supplies (the nervous system and muscles) may suffer
energy deprivation from these defects.
 For example, a person with mitochondrial myopathy suffers weakness, intolerance of
exercise, and muscle deterioration.
 Other mitochondrial mutations may contribute to diabetes, heart disease, and other
diseases of aging.

Biology Chapter Notes

 Chapter 16 The Molecular Basis of Inheritance
Chapter Notes

Overview: Life’s Operating Instructions

 In April 1953, James Watson and Francis Crick shook the scientific world with an elegant
double-helical model for the structure of deoxyribonucleic acid, or DNA.
 Your genetic endowment is the DNA you inherited from your parents.
 Nucleic acids are unique in their ability to direct their own replication.
 The resemblance of offspring to their parents depends on the precise replication of DNA
and its transmission from one generation to the next.
 It is this DNA program that directs the development of your biochemical, anatomical,
physiological, and (to some extent) behavioral traits.

Concept 16.1 DNA is the genetic material

The search for genetic material led to DNA.
 Once T. H. Morgan’s group showed that genes are located on chromosomes, the two
constituents of chromosomes—proteins and DNA—were the candidates for the genetic
material.
 Until the 1940s, the great heterogeneity and specificity of function of proteins seemed to
indicate that proteins were the genetic material.
 However, this was not consistent with experiments with microorganisms, such as bacteria
and viruses.
 The discovery of the genetic role of DNA began with research by Frederick Griffith in
1928.
 He studied Streptococcus pneumoniae, a bacterium that causes pneumonia in mammals.
 One strain, the R strain, was harmless.
 The other strain, the S strain, was pathogenic.
 Griffith mixed heat-killed S strain with live R strain bacteria and injected this into a
mouse.
 The mouse died, and he recovered the pathogenic strain from the mouse’s blood.
 Griffith called this phenomenon transformation, a phenomenon now defined as a change
in genotype and phenotype due to the assimilation of foreign DNA by a cell.
 For the next 14 years, scientists tried to identify the transforming substance.
 Finally in 1944, Oswald Avery, Maclyn McCarty, and Colin MacLeod announced that the
transforming substance was DNA.
 Still, many biologists were skeptical.
 Proteins were considered better candidates for the genetic material.
 There was also a belief that the genes of bacteria could not be similar in composition
and function to those of more complex organisms.
Biology Chapter Notes
 Further evidence that DNA was the genetic material was derived from studies that tracked
the infection of bacteria by viruses.
 Viruses consist of DNA (or sometimes RNA) enclosed by a protective coat of protein.
 To replicate, a virus infects a host cell and takes over the cell’s metabolic machinery.
 Viruses that specifically attack bacteria are called bacteriophages or just phages.
 In 1952, Alfred Hershey and Martha Chase showed that DNA was the genetic material of
the phage T2.
 The T2 phage, consisting almost entirely of DNA and protein, attacks Escherichia coli (E.
coli), a common intestinal bacteria of mammals.
 This phage can quickly turn an E. coli cell into a T2-producing factory that releases
phages when the cell ruptures.
 To determine the source of genetic material in the phage, Hershey and Chase designed an
experiment in which they could label protein or DNA and then track which entered the E.
coli cell during infection.
 They grew one batch of T2 phage in the presence of radioactive sulfur, marking the
proteins but not DNA.
 They grew another batch in the presence of radioactive phosphorus, marking the DNA
but not proteins.
 They allowed each batch to infect separate E. coli cultures.
 Shortly after the onset of infection, they spun the cultured infected cells in a blender,
shaking loose any parts of the phage that remained outside the bacteria.
 The mixtures were spun in a centrifuge, which separated the heavier bacterial cells in
the pellet from lighter free phages and parts of phage in the liquid supernatant.
 They then tested the pellet and supernatant of the separate treatments for the presence
of radioactivity.
 Hershey and Chase found that when the bacteria had been infected with T2 phages that
contained radiolabeled proteins, most of the radioactivity was in the supernatant that
contained phage particles, not in the pellet with the bacteria.
 When they examined the bacterial cultures with T2 phage that had radiolabeled DNA,
most of the radioactivity was in the pellet with the bacteria.
 Hershey and Chase concluded that the injected DNA of the phage provides the genetic
information that makes the infected cells produce new viral DNA and proteins to
assemble into new viruses.
 The fact that cells double the amount of DNA in a cell prior to mitosis and then distribute
the DNA equally to each daughter cell provided some circumstantial evidence that DNA
was the genetic material in eukaryotes.
 Similar circumstantial evidence came from the observation that diploid sets of
chromosomes have twice as much DNA as the haploid sets in gametes of the same
organism.
 By 1947, Erwin Chargaff had developed a series of rules based on a survey of DNA
composition in organisms.
 He already knew that DNA was a polymer of nucleotides consisting of a nitrogenous
base, deoxyribose, and a phosphate group.
 The bases could be adenine (A), thymine (T), guanine (G), or cytosine (C).
 Chargaff noted that the DNA composition varies from species to species.

Biology Chapter Notes

 In any one species, the four bases are found in characteristic, but not necessarily equal,
ratios.
 He also found a peculiar regularity in the ratios of nucleotide bases that are known as
Chargaff’s rules.
 In all organisms, the number of adenines was approximately equal to the number of
thymines (%T = %A).
 The number of guanines was approximately equal to the number of cytosines (%G = %C).
 Human DNA is 30.9% adenine, 29.4% thymine, 19.9% guanine, and 19.8% cytosine.
 The basis for these rules remained unexplained until the discovery of the double helix.
Watson and Crick discovered the double helix by building models to conform to X-ray
data.
 By the beginnings of the 1950s, the race was on to move from the structure of a single
DNA strand to the three-dimensional structure of DNA.
 Among the scientists working on the problem were Linus Pauling in California and
Maurice Wilkins and Rosalind Franklin in London.
 Maurice Wilkins and Rosalind Franklin used X-ray crystallography to study the structure
of DNA.
 In this technique, X-rays are diffracted as they passed through aligned fibers of
purified DNA.
 The diffraction pattern can be used to deduce the three-dimensional shape of
molecules.
 James Watson learned from their research that DNA was helical in shape, and he deduced
the width of the helix and the spacing of nitrogenous bases.
 The width of the helix suggested that it was made up of two strands, contrary to a
three-stranded model that Linus Pauling had recently proposed.
 Watson and his colleague Francis Crick began to work on a model of DNA with two
strands, the double helix.
 Using molecular models made of wire, they placed the sugar-phosphate chains on the
outside and the nitrogenous bases on the inside of the double helix.
 This arrangement put the relatively hydrophobic nitrogenous bases in the molecule’s
interior.
 The sugar-phosphate chains of each strand are like the side ropes of a rope ladder.
 Pairs of nitrogenous bases, one from each strand, form rungs.
 The ladder forms a twist every ten bases.
 The nitrogenous bases are paired in specific combinations: adenine with thymine and
guanine with cytosine.
 Pairing like nucleotides did not fit the uniform diameter indicated by the X-ray data.
 A purine-purine pair is too wide, and a pyrimidine-pyrimidine pairing is too short.
 Only a pyrimidine-purine pairing produces the 2-nm diameter indicated by the X-ray
data.
 In addition, Watson and Crick determined that chemical side groups of the nitrogenous
bases would form hydrogen bonds, connecting the two strands.
 Based on details of their structure, adenine would form two hydrogen bonds only with
thymine, and guanine would form three hydrogen bonds only with cytosine.
Biology Chapter Notes
  This finding explained Chargaff’s rules.
 The base-pairing rules dictate the combinations of nitrogenous bases that form the “rungs”
of DNA.
 However, this does not restrict the sequence of nucleotides along each DNA strand.
 The linear sequence of the four bases can be varied in countless ways.
 Each gene has a unique order of nitrogenous bases.
 In April 1953, Watson and Crick published a succinct, one-page paper in Nature reporting
their double helix model of DNA.

Concept 16.2 Many proteins work together in DNA replication and repair
 The specific pairing of nitrogenous bases in DNA was the flash of inspiration that led
Watson and Crick to the correct double helix.
 The possible mechanism for the next step, the accurate replication of DNA, was clear to
Watson and Crick from their double helix model.
During DNA replication, base pairing enables existing DNA strands to serve as templates
for new complementary strands.
 In a second paper, Watson and Crick published their hypothesis for how DNA replicates.
 Essentially, because each strand is complementary to the other, each can form a
template when separated.
 The order of bases on one strand can be used to add complementary bases and
therefore duplicate the pairs of bases exactly.
 When a cell copies a DNA molecule, each strand serves as a template for ordering
nucleotides into a new complementary strand.
 One at a time, nucleotides line up along the template strand according to the base-
pairing rules.
 The nucleotides are linked to form new strands.
 Watson and Crick’s model, semiconservative replication, predicts that when a double
helix replicates, each of the daughter molecules will have one old strand and one newly
made strand.
 Other competing models, the conservative model and the dispersive model, were also
proposed.
 Experiments in the late 1950s by Matthew Meselson and Franklin Stahl supported the
semiconservative model proposed by Watson and Crick over the other two models.
 In their experiments, 15they labeled the nucleotides of the old strands with a heavy
isotope of nitrogen ( N), while any new nucleotides were indicated by a lighter
isotope (14N).
 Replicated strands could be separated by density in a centrifuge.
 Each model—the semiconservative model, the conservative model, and the dispersive
model—made specific predictions about the density of replicated DNA strands.
 The first replication in the 14N medium produced a band of hybrid (15N-14N) DNA,
eliminating the conservative model.
 A second replication produced both light and hybrid DNA, eliminating the dispersive
model and supporting the semiconservative model.
Biology Chapter Notes
 A large team of enzymes and other proteins carries out DNA replication.
 It takes E. coli 25 minutes to copy each of the 5 million base pairs in its single
chromosome and divide to form two identical daughter cells.
 A human cell can copy its 6 billion base pairs and divide into daughter cells in only a few
hours.
 This process is remarkably accurate, with only one error per ten billion nucleotides.
 More than a dozen enzymes and other proteins participate in DNA replication.
 Much more is known about replication in bacteria than in eukaryotes.
 The process appears to be fundamentally similar for prokaryotes and eukaryotes.
 The replication of a DNA molecule begins at special sites, origins of replication.
 In bacteria, this is a specific sequence of nucleotides that is recognized by the replication
enzymes.
 These enzymes separate the strands, forming a replication “bubble.”
 Replication proceeds in both directions until the entire molecule is copied.
 In eukaryotes, there may be hundreds or thousands of origin sites per chromosome.
 At the origin sites, the DNA strands separate, forming a replication “bubble” with
replication forks at each end.
 The replication bubbles elongate as the DNA is replicated, and eventually fuse.
 DNA polymerases catalyze the elongation of new DNA at a replication fork.
 As nucleotides align with complementary bases along the template strand, they are added
to the growing end of the new strand by the polymerase.
 The rate of elongation is about 500 nucleotides per second in bacteria and 50 per
second in human cells.
 In E. coli, two different DNA polymerases are involved in replication: DNA polymerase
III and DNA polymerase I.
 In eukaryotes, at least 11 different DNA polymerases have been identified so far.
 Each nucleotide that is added to a growing DNA strand is a nucleoside triphosphate.
 Each has a nitrogenous base, deoxyribose, and a triphosphate tail.
 ATP is a nucleoside triphosphate with ribose instead of deoxyribose.
 Like ATP, the triphosphate monomers used for DNA synthesis are chemically reactive,
partly because their triphosphate tails have an unstable cluster of negative charge.
 As each nucleotide is added to the growing end of a DNA strand, the last two phosphate
groups are hydrolyzed to form pyrophosphate.
 The exergonic hydrolysis of pyrophosphate to two inorganic phosphate molecules
drives the polymerization of the nucleotide to the new strand.
 The strands in the double helix are antiparallel.
 The sugar-phosphate backbones run in opposite directions.
 Each DNA strand has a 3’ end with a free hydroxyl group attached to deoxyribose and
a 5’ end with a free phosphate group attached to deoxyribose.
 The 5’  3’ direction of one strand runs counter to the 3’  5’ direction of the other
strand.
 DNA polymerases can only add nucleotides to the free 3’ end of a growing DNA strand.
 A new DNA strand can only elongate in the 5’  3’ direction.
Biology Chapter Notes
 Along one template strand, DNA polymerase III can synthesize a complementary strand
continuously by elongating the new DNA in the mandatory 5’  3’ direction.
 The DNA strand made by this mechanism is called the leading strand.
 The other parental strand (5’  3’ into the fork), the lagging strand, is copied away from
the fork.
 Unlike the leading strand, which elongates continuously, the lagging stand is
synthesized as a series of short segments called Okazaki fragments.
 Okazaki fragments are about 1,000–2,000 nucleotides long in E. coli and 100–200
nucleotides long in eukaryotes.
 Another enzyme, DNA ligase, eventually joins the sugar-phosphate backbones of the
Okazaki fragments to form a single DNA strand.
 DNA polymerases cannot initiate synthesis of a polynucleotide.
 They can only add nucleotides to the 3’ end of an existing chain that is base-paired
with the template strand.
 The initial nucleotide chain is called a primer.
 In the initiation of the replication of cellular DNA, the primer is a short stretch of RNA
with an available 3’ end.
 The primer is 5–10 nucleotides long in eukaryotes.
 Primase, an RNA polymerase, links ribonucleotides that are complementary to the DNA
template into the primer.
 RNA polymerases can start an RNA chain from a single template strand.
 After formation of the primer, DNA pol III adds a deoxyribonucleotide to the 3’ end of
the RNA primer and continues adding DNA nucleotides to the growing DNA strand
according to the base-pairing rules.
 Returning to the original problem at the replication fork, the leading strand requires the
formation of only a single primer as the replication fork continues to separate.
 For synthesis of the lagging strand, each Okazaki fragment must be primed separately.
 Another DNA polymerase, DNA polymerase I, replaces the RNA nucleotides of the
primers with DNA versions, adding them one by one onto the 3’ end of the adjacent
Okazaki fragment.
 The primers are converted to DNA before DNA ligase joins the fragments together.
 In addition to primase, DNA polymerases, and DNA ligases, several other proteins have
prominent roles in DNA synthesis.
 Helicase untwists the double helix and separates the template DNA strands at the
replication fork.
 This untwisting causes tighter twisting ahead of the replication fork, and
topoisomerase helps relieve this strain.
 Single-strand binding proteins keep the unpaired template strands apart during
replication.
 To summarize, at the replication fork, the leading strand is copied continuously into the
fork from a single primer.
 The lagging strand is copied away from the fork in short segments, each requiring a
new primer.
 It is conventional and convenient to think of the DNA polymerase molecules as moving
along a stationary DNA template.
Biology Chapter Notes
 In reality, the various proteins involved in DNA replication form a single large complex, a
DNA replication “machine.”
 Many protein-protein interactions facilitate the efficiency of this machine.
 For example, helicase works much more rapidly when it is in contact with primase.
 The DNA replication machine is probably stationary during the replication process.
 In eukaryotic cells, multiple copies of the machine may anchor to the nuclear matrix, a
framework of fibers extending through the interior of the nucleus.
 The DNA polymerase molecules “reel in” the parental DNA and “extrude” newly made
daughter DNA molecules.
Enzymes proofread DNA during its replication and repair damage in existing DNA.
 Mistakes during the initial pairing of template nucleotides and complementary nucleotides
occur at a rate of one error per 100,000 base pairs.
 DNA polymerase proofreads each new nucleotide against the template nucleotide as soon
as it is added.
 If there is an incorrect pairing, the enzyme removes the wrong nucleotide and then
resumes synthesis.
 The final error rate is only one per ten billion nucleotides.
 DNA molecules are constantly subject to potentially harmful chemical and physical
agents.
 Reactive chemicals, radioactive emissions, X-rays, and ultraviolet light can change
nucleotides in ways that can affect encoded genetic information.
 DNA bases may undergo spontaneous chemical changes under normal cellular
conditions.
 Mismatched nucleotides that are missed by DNA polymerase or mutations that occur after
DNA synthesis is completed can often be repaired.
 Each cell continually monitors and repairs its genetic material, with 100 repair
enzymes known in E. coli and more than 130 repair enzymes identified in humans.
 In mismatch repair, special enzymes fix incorrectly paired nucleotides.
 A hereditary defect in one of these enzymes is associated with a form of colon cancer.
 In nucleotide excision repair, a nuclease cuts out a segment of a damaged strand.
 DNA polymerase and ligase fill in the gap.
 The importance of the proper functioning of repair enzymes is clear from the inherited
disorder xeroderma pigmentosum.
 These individuals are hypersensitive to sunlight.
 Ultraviolet light can produce thymine dimers between adjacent thymine nucleotides.
 This buckles the DNA double helix and interferes with DNA replication.
 In individuals with this disorder, mutations in their skin cells are left uncorrected and
cause skin cancer.
The ends of DNA molecules are replicated by a special mechanism.
 Limitations of DNA polymerase create problems for the linear DNA of eukaryotic
chromosomes.
 The usual replication machinery provides no way to complete the 5’ ends of daughter
DNA strands.
Biology Chapter Notes
  Repeated rounds of replication produce shorter and shorter DNA molecules.
 Prokaryotes do not have this problem because they have circular DNA molecules without
ends.
 The ends of eukaryotic chromosomal DNA molecules, the telomeres, have special
nucleotide sequences.
 Telomeres do not contain genes. Instead, the DNA typically consists of multiple
repetitions of one short nucleotide sequence.
 In human telomeres, this sequence is typically TTAGGG, repeated between 100 and
1,000 times.
 Telomeres protect genes from being eroded through multiple rounds of DNA replication.
 Telomeric DNA tends to be shorter in dividing somatic cells of older individuals and
in cultured cells that have divided many times.
 It is possible that the shortening of telomeres is somehow connected with the aging
process of certain tissues and perhaps to aging in general.
 Telomeric DNA and specific proteins associated with it also prevents the staggered ends
of the daughter molecule from activating the cell’s system for monitoring DNA damage.
 Eukaryotic cells have evolved a mechanism to restore shortened telomeres in germ cells,
which give rise to gametes.
 If the chromosomes of germ cells became shorter with every cell cycle, essential genes
would eventually be lost.
 An enzyme called telomerase catalyzes the lengthening of telomeres in eukaryotic germ
cells, restoring their original length.
 Telomerase uses a short molecule of RNA as a template to extend the 3’ end of the
telomere.
 There is now room for primase and DNA polymerase to extend the 5’ end.
 It does not repair the 3’-end “overhang,” but it does lengthen the telomere.
 Telomerase is not present in most cells of multicellular organisms.
 Therefore, the DNA of dividing somatic cells and cultured cells tends to become shorter.
 Telomere length may be a limiting factor in the life span of certain tissues and of the
organism.
 Normal shortening of telomeres may protect organisms from cancer by limiting the
number of divisions that somatic cells can undergo.
 Cells from large tumors often have unusually short telomeres, because they have gone
through many cell divisions.
 Active telomerase has been found in some cancerous somatic cells.
 This overcomes the progressive shortening that would eventually lead to self-
destruction of the cancer.
 Immortal strains of cultured cells are capable of unlimited cell division.
 Telomerase may provide a useful target for cancer diagnosis and chemotherapy.

Biology Chapter Notes

 Chapter 17 From Gene to Protein
Chapter Notes

Overview: The Flow of Genetic Information

 The information content of DNA is in the form of specific sequences of nucleotides along
the DNA strands.
 The DNA inherited by an organism leads to specific traits by dictating the synthesis of
proteins.
 Gene expression, the process by which DNA directs protein synthesis, includes two stages
called transcription and translation.
 Proteins are the links between genotype and phenotype.
 For example, Mendel’s dwarf pea plants lack a functioning copy of the gene that
specifies the synthesis of a key protein, gibberellin.
 Gibberellins stimulate the normal elongation of stems.

Concept 17.1 Genes specify proteins via transcription and translation

The study of metabolic defects provided evidence that genes specify proteins.
 In 1909, Archibald Gerrod was the first to suggest that genes dictate phenotype through
enzymes that catalyze specific chemical reactions in the cell.
 He suggested that the symptoms of an inherited disease reflect a person’s inability to
synthesize a particular enzyme.
 He referred to such diseases as “inborn errors of metabolism.”
 Gerrod speculated that alkaptonuria, a hereditary disease, was caused by the absence of an
enzyme that breaks down a specific substrate, alkapton.
 Research conducted several decades later supported Gerrod’s hypothesis.
 Progress in linking genes and enzymes rested on the growing understanding that cells
synthesize and degrade most organic molecules in a series of steps, a metabolic pathway.
 In the 1930s, George Beadle and Boris Ephrussi speculated that each mutation affecting
eye color in Drosophila blocks pigment synthesis at a specific step by preventing
production of the enzyme that catalyzes that step.
 However, neither the chemical reactions nor the enzymes that catalyze them were
known at the time.
 Beadle and Edward Tatum were finally able to establish the link between genes and
enzymes in their exploration of the metabolism of a bread mold, Neurospora crassa.
 They bombarded Neurospora with X-rays and screened the survivors for mutants that
differed in their nutritional needs.
 Wild-type Neurospora can grow on a minimal medium of agar, inorganic salts,
glucose, and the vitamin biotin.
 Beadle and Tatum identified mutants that could not survive on minimal medium, because
they were unable to synthesize certain essential molecules from the minimal ingredients.

Biology Chapter Notes

  However, most of these nutritional mutants can survive on a complete growth medium
that includes all 20 amino acids and a few other nutrients.
 One type of mutant required only the addition of arginine to the minimal growth medium.
 Beadle and Tatum concluded that this mutant was defective somewhere in the
biochemical pathway that normally synthesizes arginine.
 They identified three classes of arginine-deficient mutants, each apparently lacking a
key enzyme at a different step in the synthesis of arginine.
 They demonstrated this by growing these mutant strains in media that provided
different intermediate molecules.
 Their results provided strong evidence for the one gene–one enzyme hypothesis.
 Later research refined the one gene–one enzyme hypothesis.
 First, not all proteins are enzymes.
 Keratin, the structural protein of hair, and insulin, a hormone, both are proteins and
gene products.
 This tweaked the hypothesis to one gene–one protein.
 Later research demonstrated that many proteins are composed of several polypeptides,
each of which has its own gene.
 Therefore, Beadle and Tatum’s idea has been restated as the one gene–one polypeptide
hypothesis.
 Some genes code for RNA molecules that play important roles in cells although they are
never translated into protein.
Transcription and translation are the two main processes linking gene to protein.
 Genes provide the instructions for making specific proteins.
 The bridge between DNA and protein synthesis is the nucleic acid RNA.
 RNA is chemically similar to DNA, except that it contains ribose as its sugar and
substitutes the nitrogenous base uracil for thymine.
 An RNA molecule almost always consists of a single strand.
 In DNA or RNA, the four nucleotide monomers act like the letters of the alphabet to
communicate information.
 The specific sequence of hundreds or thousands of nucleotides in each gene carries the
information for the primary structure of proteins, the linear order of the 20 possible amino
acids.
 To get from DNA, written in one chemical language, to protein, written in another,
requires two major stages: transcription and translation.
 During transcription, a DNA strand provides a template for the synthesis of a
complementary RNA strand.
 Just as a DNA strand provides a template for the synthesis of each new complementary
strand during DNA replication, it provides a template for assembling a sequence of
RNA nucleotides.
 Transcription of many genes produces a messenger RNA (mRNA) molecule.
 During translation, there is a change of language.
 The site of translation is the ribosome, complex particles that facilitate the orderly
assembly of amino acids into polypeptide chains.

Biology Chapter Notes

 Why can’t proteins be translated directly from DNA?
 The use of an RNA intermediate provides protection for DNA and its genetic
information.
 Using an RNA intermediate allows more copies of a protein to be made
simultaneously, since many RNA transcripts can be made from one gene.
 Also, each gene transcript can be translated repeatedly.
 The basic mechanics of transcription and translation are similar in eukaryotes and
prokaryotes.
 Because bacteria lack nuclei, their DNA is not segregated from ribosomes and other
protein-synthesizing equipment.
 This allows the coupling of transcription and translation.
 Ribosomes attach to the leading end of an mRNA molecule while transcription is still
in progress.
 In a eukaryotic cell, transcription occurs in the nucleus, and translation occurs at
ribosomes in the cytoplasm.
 The transcription of a protein-coding eukaryotic gene results in pre-mRNA.
 The initial RNA transcript of any gene is called a primary transcript.
 RNA processing yields the finished mRNA.
 To summarize, genes program protein synthesis via genetic messages in the form of
messenger RNA.
 The molecular chain of command in a cell is DNA  RNA  protein.
In the genetic code, nucleotide triplets specify amino acids.
 If the genetic code consisted of a single nucleotide or even pairs of nucleotides per amino
acid, there would not be enough combinations (4 and 16, respectively) to code for all 20
amino acids.
 Triplets of nucleotide bases are the smallest units of uniform length that can code for all
the amino acids.
 With a triplet code, three consecutive bases specify an amino acid, creating 4 3 (64)
possible code words.
 The genetic instructions for a polypeptide chain are written in DNA as a series of
nonoverlapping three-nucleotide words.
 During transcription, one DNA strand, the template strand, provides a template for
ordering the sequence of nucleotides in an RNA transcript.
 A given DNA strand can be the template strand for some genes along a DNA
molecule, while for other genes in other regions, the complementary strand may
function as the template.
 The complementary RNA molecule is synthesized according to base-pairing rules, except
that uracil is the complementary base to adenine.
 Like a new strand of DNA, the RNA molecule is synthesized in an antiparallel direction
to the template strand of DNA.
 The mRNA base triplets are called codons, and they are written in the 5’  3’ direction.
 During translation, the sequence of codons along an mRNA molecule is translated into a
sequence of amino acids making up the polypeptide chain.
 During translation, the codons are read in the 5’  3’ direction along the mRNA.
Biology Chapter Notes
  Each codon specifies which one of the 20 amino acids will be incorporated at the
corresponding position along a polypeptide.
 Because codons are base triplets, the number of nucleotides making up a genetic message
must be three times the number of amino acids making up the protein product.
 It takes at least 300 nucleotides to code for a polypeptide that is 100 amino acids long.
 The task of matching each codon to its amino acid counterpart began in the early 1960s.
 Marshall Nirenberg determined the first match: UUU coded for the amino acid
phenylalanine.
 He created an artificial mRNA molecule entirely of uracil and added it to a test tube
mixture of amino acids, ribosomes, and other components for protein synthesis.
 This “poly-U” translated into a polypeptide containing a single amino acid,
phenylalanine, in a long chain.
 AAA, GGG, and CCC were solved in the same way.
 Other more elaborate techniques were required to decode mixed triplets such as AUA and
CGA.
 By the mid-1960s the entire code was deciphered.
 Sixty-one of 64 triplets code for amino acids.
 The codon AUG not only codes for the amino acid methionine, but also indicates the
“start” of translation.
 Three codons do not indicate amino acids but are “stop” signals marking the
termination of translation.
 There is redundancy in the genetic code but no ambiguity.
 Several codons may specify the same amino acid, but no codon specifies more than
one amino acid.
 The redundancy in the code is not random. In many cases, codons that are synonyms
for a particular amino acid differ only in the third base of the triplet.
 To extract the message from the genetic code requires specifying the correct starting
point.
 This establishes the reading frame; subsequent codons are read in groups of three
nucleotides.
 The cell’s protein-synthesizing machinery reads the message as a series of
nonoverlapping three-letter words.
 In summary, genetic information is encoded as a sequence of nonoverlapping base
triplets, or codons, each of which is translated into a specific amino acid during protein
synthesis.
The genetic code must have evolved very early in the history of life.
 The genetic code is nearly universal, shared by organisms from the simplest bacteria to
the most complex plants and animals.
 In laboratory experiments, genes can be transcribed and translated after they are
transplanted from one species to another.
 This has permitted bacteria to be programmed to synthesize certain human proteins
after insertion of the appropriate human genes.
 Such applications are exciting developments in biotechnology.
 Exceptions to the universality of the genetic code exist in certain unicellular eukaryotes
and in the organelle genes of some species.
Biology Chapter Notes
  Some prokaryotes can translate stop codons into one of two amino acids not found in
most organisms.
 The evolutionary significance of the near universality of the genetic code is clear.
 A language shared by all living things arose very early in the history of life—early
enough to be present in the common ancestors of all modern organisms.
 A shared genetic vocabulary is a reminder of the kinship that bonds all life on Earth.

Concept 17.2 Transcription is the DNA-directed synthesis of RNA: a closer look

 Messenger RNA, the carrier of information from DNA to the cell’s protein-synthesizing
machinery, is transcribed from the template strand of a gene.
 RNA polymerase separates the DNA strands at the appropriate point and bonds the RNA
nucleotides as they base-pair along the DNA template.
 Like DNA polymerases, RNA polymerases can only assemble a polynucleotide in its
5’  3’ direction.
 Unlike DNA polymerases, RNA polymerases are able to start a chain from scratch;
they don’t need a primer.
 Specific sequences of nucleotides along the DNA mark where gene transcription begins
and ends.
 RNA polymerase attaches and initiates transcription at the promoter.
 In prokaryotes, the sequence that signals the end of transcription is called the
terminator.
 Molecular biologists refer to the direction of transcription as “downstream” and the other
direction as “upstream.”
 The stretch of DNA that is transcribed into an RNA molecule is called a transcription
unit.
 Bacteria have a single type of RNA polymerase that synthesizes all RNA molecules.
 In contrast, eukaryotes have three RNA polymerases (I, II, and III) in their nuclei.
 RNA polymerase II is used for mRNA synthesis.
 Transcription can be separated into three stages: initiation, elongation, and termination of
the RNA chain.
 The presence of a promoter sequence determines which strand of the DNA helix is the
template.
 Within the promoter is the starting point for the transcription of a gene.
 The promoter also includes a binding site for RNA polymerase several dozen
nucleotides “upstream” of the start point.
 In prokaryotes, RNA polymerase can recognize and bind directly to the promoter region.
 In eukaryotes, proteins called transcription factors mediate the binding of RNA
polymerase and the initiation of transcription.
 Only after certain transcription factors are attached to the promoter does RNA polymerase
II bind to it.
 The completed assembly of transcription factors and RNA polymerase II bound to a
promoter is called a transcription initiation complex.
 A crucial promoter DNA sequence is called a TATA box.
Biology Chapter Notes
 RNA polymerase then starts transcription.
 As RNA polymerase moves along the DNA, it untwists the double helix, 10 to 20 bases at
time.
 The enzyme adds nucleotides to the 3’ end of the growing strand.
 Behind the point of RNA synthesis, the double helix re-forms and the RNA molecule
peels away.
 Transcription progresses at a rate of 60 nucleotides per second in eukaryotes.
 A single gene can be transcribed simultaneously by several RNA polymerases at a time.
 A growing strand of RNA trails off from each polymerase.
 The length of each new strand reflects how far along the template the enzyme has
traveled from the start point.
 The congregation of many polymerase molecules simultaneously transcribing a single
gene increases the amount of mRNA transcribed from it.
 This helps the cell make the encoded protein in large amounts.
 Transcription proceeds until after the RNA polymerase transcribes a terminator sequence
in the DNA.
 In prokaryotes, RNA polymerase stops transcription right at the end of the terminator.
 Both the RNA and DNA are then released.
 In eukaryotes, the pre-mRNA is cleaved from the growing RNA chain while RNA
polymerase II continues to transcribe the DNA.
 Specifically, the polymerase transcribes a DNA sequence called the
polyadenylation signal sequence that codes for a polyadenylation sequence
(AAUAAA) in the pre-mRNA.
 At a point about 10 to 35 nucleotides past this sequence, the pre-mRNA is cut from
the enzyme.
 The polymerase continues transcribing for hundreds of nucleotides.
 Transcription is terminated when the polymerase eventually falls off the DNA.

Concept 17.3 Eukaryotic cells modify RNA after transcription

 Enzymes in the eukaryotic nucleus modify pre-mRNA before the genetic messages are
dispatched to the cytoplasm.
 During RNA processing, both ends of the primary transcript are usually altered.
 Certain interior parts of the molecule are cut out and the remaining parts spliced
together.
 At the 5’ end of the pre-mRNA molecule, a modified form of guanine is added, the 5’
cap.
 At the 3’ end, an enzyme adds 50 to 250 adenine nucleotides, the poly-A tail.
 These modifications share several important functions.
 They seem to facilitate the export of mRNA from the nucleus.
 They help protect mRNA from hydrolytic enzymes.
 They help the ribosomes attach to the 5’ end of the mRNA.
 The most remarkable stage of RNA processing occurs during the removal of a large
portion of the RNA molecule in a cut-and-paste job of RNA splicing.
Biology Chapter Notes
 Most eukaryotic genes and their RNA transcripts have long noncoding stretches of
nucleotides.
 Noncoding segments of nucleotides called intervening regions, or introns, lie between
coding regions.
 The final mRNA transcript includes coding regions, exons, which are translated into
amino acid sequences, plus the leader and trailer sequences.
 RNA splicing removes introns and joins exons to create an mRNA molecule with a
continuous coding sequence.
 This splicing is accomplished by a spliceosome.
 Spliceosomes consist of a variety of proteins and several small nuclear
ribonucleoproteins (snRNPs) that recognize the splice sites.
 snRNPs are located in the cell nucleus and are composed of RNA and protein
molecules.
 Each snRNP has several protein molecules and a small nuclear RNA molecule
(snRNA).
 Each snRNA is about 150 nucleotides long.
 The spliceosome interacts with certain sites along an intron, releasing the introns and
joining together the two exons that flanked the introns.
 snRNAs appear to play a major role in catalytic processes, as well as spliceosome
assembly and splice site recognition.
 The idea of a catalytic role for snRNA arose from the discovery of ribozymes, RNA
molecules that function as enzymes.
 In some organisms, splicing occurs without proteins or additional RNA molecules.
 The intron RNA functions as a ribozyme and catalyzes its own excision.
 For example, in the protozoan Tetrahymena, self-splicing occurs in the production of
ribosomal RNA (rRNA), a component of the organism’s ribosomes.
 The pre-rRNA actually removes its own introns.
 The discovery of ribozymes rendered obsolete the statement, “All biological catalysts are
proteins.”
 The fact that RNA is single-stranded plays an important role in allowing certain RNA
molecules to function as ribozymes.
 A region of the RNA molecule may base-pair with a complementary region elsewhere in
the same molecule, thus giving the RNA a specific 3-D structure that is key to its ability
to catalyze reactions.
 Introns and RNA splicing appear to have several functions.
 Some introns play a regulatory role in the cell. These introns contain sequences that
control gene activity in some way.
 Splicing itself may regulate the passage of mRNA from the nucleus to the cytoplasm.
 One clear benefit of split genes is to enable one gene to encode for more than one
polypeptide.
 Alternative RNA splicing gives rise to two or more different polypeptides, depending on
which segments are treated as exons.
 Sex differences in fruit flies may be due to differences in splicing RNA transcribed
from certain genes.
 Early results of the Human Genome Project indicate that this phenomenon may be
common in humans, and may explain why we have a relatively small number of genes.
Biology Chapter Notes
 Proteins often have a modular architecture with discrete structural and functional regions
called domains.
 The presence of introns in a gene may facilitate the evolution of new and potentially
useful proteins as a result of a process known as exon shuffling.
 In many cases, different exons code for different domains of a protein.
 The presence of introns increases the probability of potentially beneficial crossing over
between genes.
 Introns increase the opportunity for recombination between two alleles of a gene.
 This raises the probability that a crossover will switch one version of an exon for
another version found on the homologous chromosome.
 There may also be occasional mixing and matching of exons between completely
different genes.
 Either way, exon shuffling can lead to new proteins through novel combinations of
functions.

Concept 17.4 Translation is the RNA-directed synthesis of a polypeptide: a closer look

 In the process of translation, a cell interprets a series of codons along an mRNA molecule
and builds a polypeptide.
 The interpreter is transfer RNA (tRNA), which transfers amino acids from the
cytoplasmic pool to a ribosome.
 A cell has all 20 amino acids available in its cytoplasm, either by synthesizing them
from scratch or by taking them up from the surrounding solution.
 The ribosome adds each amino acid carried by tRNA to the growing end of the
polypeptide chain.
 During translation, each type of tRNA links an mRNA codon with the appropriate amino
acid.
 Each tRNA arriving at the ribosome carries a specific amino acid at one end and has a
specific nucleotide triplet, an anticodon, at the other.
 The anticodon base-pairs with a complementary codon on mRNA.
 If the codon on mRNA is UUU, a tRNA with an AAA anticodon and carrying
phenylalanine will bind to it.
 Codon by codon, tRNAs deposit amino acids in the prescribed order, and the ribosome
joins them into a polypeptide chain.
 The tRNA molecule is a translator, because it can read a nucleic acid word (the mRNA
codon) and translate it to a protein word (the amino acid).
 Like other types of RNA, tRNA molecules are transcribed from DNA templates in the
nucleus.
 Once it reaches the cytoplasm, each tRNA is used repeatedly, picking up its designated
amino acid in the cytosol, depositing the amino acid at the ribosome, and returning to the
cytosol to pick up another copy of that amino acid.
 A tRNA molecule consists of a strand of about 80 nucleotides that folds back on itself to
form a three-dimensional structure.
 It includes a loop containing the anticodon and an attachment site at the 3’ end for an
amino acid.
Biology Chapter Notes
 If each anticodon had to be a perfect match to each codon, we would expect to find 61
types of tRNA, but the actual number is about 45.
 The anticodons of some tRNAs recognize more than one codon.
 This is possible because the rules for base pairing between the third base of the codon and
anticodon are relaxed (called wobble).
 At the wobble position, U on the anticodon can bind with A or G in the third position
of a codon.
 Wobble explains why the synonymous codons for a given amino acid can differ in
their third base, but not usually in their other bases.
 Each amino acid is joined to the correct tRNA by aminoacyl-tRNA synthetase.
 The 20 different synthetases match the 20 different amino acids.
 Each has active sites for only a specific tRNA-and-amino-acid combination.
 The synthetase catalyzes a covalent bond between them in a process driven by ATP
hydrolysis.
 The result is an aminoacyl-tRNA or activated amino acid.
 Ribosomes facilitate the specific coupling of the tRNA anticodons with mRNA codons
during protein synthesis.
 Each ribosome is made up of a large and a small subunit.
 The subunits are composed of proteins and ribosomal RNA (rRNA), the most
abundant RNA in the cell.
 In eukaryotes, the subunits are made in the nucleolus.
 After rRNA genes are transcribed to rRNA in the nucleus, the rRNA and proteins are
assembled to form the subunits with proteins from the cytoplasm.
 The subunits exit the nucleus via nuclear pores.
 The large and small subunits join to form a functional ribosome only when they attach to
an mRNA molecule.
 While very similar in structure and function, prokaryotic and eukaryotic ribosomes have
enough differences that certain antibiotic drugs (like tetracycline) can paralyze
prokaryotic ribosomes without inhibiting eukaryotic ribosomes.
 Each ribosome has a binding site for mRNA and three binding sites for tRNA molecules.
 The P site holds the tRNA carrying the growing polypeptide chain.
 The A site carries the tRNA with the next amino acid to be added to the chain.
 Discharged tRNAs leave the ribosome at the E (exit) site.
 The ribosome holds the tRNA and mRNA in close proximity and positions the new amino
acid for addition to the carboxyl end of the growing polypeptide.
 It then catalyzes the formation of the peptide bond.
 As the polypeptide becomes longer, it passes through an exit tunnel in the ribosome’s
large unit and is released to the cytosol.
 Recent advances in our understanding of the structure of the ribosome strongly support
the hypothesis that rRNA, not protein, carries out the ribosome’s functions.
 RNA is the main constituent at the interphase between the two subunits and of the A
and P sites.
 It is the catalyst for peptide bond formation.
 A ribosome can be regarded as one colossal ribozyme.
Biology Chapter Notes
 Translation can be divided into three stages: initiation, elongation, and termination.
 All three phases require protein “factors” that aid in the translation process.
 Both initiation and chain elongation require energy provided by the hydrolysis of GTP.
 Initiation brings together mRNA, a tRNA with the first amino acid, and the two
ribosomal subunits.
 First, a small ribosomal subunit binds with mRNA and a special initiator tRNA, which
carries methionine and attaches to the start codon.
 The small subunit then moves downstream along the mRNA until it reaches the start
codon, AUG, which signals the start of translation.
 This establishes the reading frame for the mRNA.
 The initiator tRNA, already associated with the complex, then hydrogen-bonds with
the start codon.
 Proteins called initiation factors bring in the large subunit so that the initiator tRNA
occupies the P site.
 Elongation involves the participation of several protein elongation factors, and consists of
a series of three-step cycles as each amino acid is added to the proceeding one.
 During codon recognition, an elongation factor assists hydrogen bonding between the
mRNA codon under the A site with the corresponding anticodon of tRNA carrying the
appropriate amino acid.
 This step requires the hydrolysis of two GTP.
 During peptide bond formation, an rRNA molecule catalyzes the formation of a
peptide bond between the polypeptide in the P site with the new amino acid in the A
site.
 This step separates the tRNA at the P site from the growing polypeptide chain and
transfers the chain, now one amino acid longer, to the tRNA at the A site.
 During translocation, the ribosome moves the tRNA with the attached polypeptide
from the A site to the P site.
 Because the anticodon remains bonded to the mRNA codon, the mRNA moves
along with it.
 The next codon is now available at the A site.
 The tRNA that had been in the P site is moved to the E site and then leaves the
ribosome.
 Translocation is fueled by the hydrolysis of GTP.
 Effectively, translocation ensures that the mRNA is “read” 5’  3’ codon by
codon.
 • The three steps of elongation continue to add amino acids codon by codon until
the polypeptide chain is completed.
 Termination occurs when one of the three stop codons reaches the A site.
 A release factor binds to the stop codon and hydrolyzes the bond between the
polypeptide and its tRNA in the P site.
 This frees the polypeptide, and the translation complex disassembles.
 Typically a single mRNA is used to make many copies of a polypeptide simultaneously.
 Multiple ribosomes, polyribosomes, may trail along the same mRNA.
 Polyribosomes can be found in prokaryotic and eukaryotic cells.
 A ribosome requires less than a minute to translate an average-sized mRNA into a
polypeptide.
Biology Chapter Notes
 During and after synthesis, a polypeptide coils and folds to its three-dimensional shape
spontaneously.
 The primary structure, the order of amino acids, determines the secondary and tertiary
structure.
 Chaperone proteins may aid correct folding.
 In addition, proteins may require posttranslational modifications before doing their
particular job.
 This may require additions such as sugars, lipids, or phosphate groups to amino acids.
 Enzymes may remove some amino acids or cleave whole polypeptide chains.
 Two or more polypeptides may join to form a protein.
Signal peptides target some eukaryotic polypeptides to specific destinations in the cell.
 Two populations of ribosomes, free and bound, are active participants in protein synthesis.
 Free ribosomes are suspended in the cytosol and synthesize proteins that reside in the
cytosol.
 Bound ribosomes are attached to the cytosolic side of the endoplasmic reticulum.
 They synthesize proteins of the endomembrane system as well as proteins secreted
from the cell.
 While bound and free ribosomes are identical in structure, their location depends on the
type of protein that they are synthesizing.
 Translation in all ribosomes begins in the cytosol, but a polypeptide destined for the
endomembrane system or for export has a specific signal peptide region at or near the
leading end.
 This consists of a sequence of about 20 amino acids.
 A signal recognition particle (SRP) binds to the signal peptide and attaches it and its
ribosome to a receptor protein in the ER membrane.
 The SRP consists of a protein-RNA complex.
 After binding, the SRP leaves and protein synthesis resumes with the growing polypeptide
snaking across the membrane into the cisternal space via a protein pore.
 An enzyme usually cleaves the signal polypeptide.
 Secretory proteins are released entirely into the cisternal space, but membrane proteins
remain partially embedded in the ER membrane.
 Other kinds of signal peptides are used to target polypeptides to mitochondria,
chloroplasts, the nucleus, and other organelles that are not part of the endomembrane
system.
 In these cases, translation is completed in the cytosol before the polypeptide is
imported into the organelle.
 While the mechanisms of translocation vary, each of these polypeptides has a “ZIP
code” that ensures its delivery to the correct cellular location.
 Prokaryotes also employ signal sequences to target proteins for secretion.

Concept 17.5 RNA plays multiple roles in the cell: a review

 The cellular machinery of protein synthesis and ER targeting is dominated by various
kinds of RNA.
Biology Chapter Notes
  In addition to mRNA, these include tRNA; rRNA; and in eukaryotes, snRNA and SRP
RNA.
 A type of RNA called small nucleolar RNA (snoRNA) aids in processing pre-rRNA
transcripts in the nucleolus, a process necessary for ribosome formation.
 Recent research has also revealed the presence of small, single-stranded and double-
stranded RNA molecules that play important roles in regulating which genes get
expressed.
 These types of RNA include small interfering RNA (siRNA) and microRNA
(miRNA).
 The diverse functions of RNA are based, in part, on its ability to form hydrogen bonds
with other nucleic acid molecules (DNA or RNA).
 It can also assume a specific three-dimensional shape by forming hydrogen bonds
between bases in different parts of its polynucleotide chain.
 DNA may be the genetic material of all living cells today, but RNA is much more
versatile.
 The diverse functions of RNA range from structural to informational to catalytic.

Concept 17.6 Comparing gene expression in prokaryotes and eukaryotes reveals key
differences
 Although prokaryotes and eukaryotes carry out transcription and translation in very
similar ways, they do have differences in cellular machinery and in details of the
processes.
 Eukaryotic RNA polymerases differ from those of prokaryotes and require
transcription factors.
 They differ in how transcription is terminated.
 Their ribosomes also are different.
 One major difference is that prokaryotes can transcribe and translate the same gene
simultaneously.
 The new protein quickly diffuses to its operating site.
 In eukaryotes, the nuclear envelope segregates transcription from translation.
 In addition, extensive RNA processing is carried out between these processes.
 This provides additional steps whose regulation helps coordinate the elaborate
activities of a eukaryotic cell.
 Eukaryotic cells also have complicated mechanisms for targeting proteins to the
appropriate organelle.

Concept 17.7 Point mutations can affect protein structure and function
 Mutations are changes in the genetic material of a cell (or virus).
 These include large-scale mutations in which long segments of DNA are affected (for
example, translocations, duplications, and inversions).
 A chemical change in just one base pair of a gene causes a point mutation.
 If these occur in gametes or cells producing gametes, they may be transmitted to future
generations.

Biology Chapter Notes

 For example, sickle-cell disease is caused by a mutation of a single base pair in the gene
that codes for one of the polypeptides of hemoglobin.
 A change in a single nucleotide from T to A in the DNA template leads to an abnormal
protein.
 A point mutation that results in the replacement of a pair of complementary nucleotides
with another nucleotide pair is called a base-pair substitution.
 Some base-pair substitutions have little or no impact on protein function.
 In silent mutations, altered nucleotides still code for the same amino acids because of
redundancy in the genetic code.
 Other changes lead to switches from one amino acid to another with similar properties.
 Still other mutations may occur in a region where the exact amino acid sequence is not
essential for function.
 Other base-pair substitutions cause a readily detectable change in a protein.
 These are usually detrimental but can occasionally lead to an improved protein or one
with novel capabilities.
 Changes in amino acids at crucial sites, especially active sites, are likely to impact
function.
 Missense mutations are those that still code for an amino acid but a different one.
 Nonsense mutations change an amino acid codon into a stop codon, nearly always
leading to a nonfunctional protein.
 Insertions and deletions are additions or losses of nucleotide pairs in a gene.
 These have a disastrous effect on the resulting protein more often than substitutions do.
 Unless insertion or deletion mutations occur in multiples of three, they cause a frameshift
mutation.
 All the nucleotides downstream of the deletion or insertion will be improperly grouped
into codons.
 The result will be extensive missense, ending sooner or later in nonsense—premature
termination.
 Mutations can occur in a number of ways.
 Errors can occur during DNA replication, DNA repair, or DNA recombination.
 These can lead to base-pair substitutions, insertions, or deletions, as well as mutations
affecting longer stretches of DNA.
 These are called spontaneous mutations.
 Rough estimates suggest that about 1 nucleotide in every 10 10 is altered and inherited by
daughter cells.
 Mutagens are chemical or physical agents that interact with DNA to cause mutations.
 Physical agents include high-energy radiation like X-rays and ultraviolet light.
 Chemical mutagens fall into several categories.
 Some chemicals are base analogues that may be substituted into DNA, but they pair
incorrectly during DNA replication.
 Other mutagens interfere with DNA replication by inserting into DNA and distorting
the double helix.
 Still others cause chemical changes in bases that change their pairing properties.

Biology Chapter Notes

 Researchers have developed various methods to test the mutagenic activity of different
chemicals.
 These tests are often used as a preliminary screen of chemicals to identify those that
may cause cancer.
 This makes sense because most carcinogens are mutagenic and most mutagens are
carcinogenic.
What is a gene? We revisit the question.
 The Mendelian concept of a gene views it as a discrete unit of inheritance that affects
phenotype.
 Morgan and his colleagues assigned genes to specific loci on chromosomes.
 We can also view a gene as a specific nucleotide sequence along a region of a DNA
molecule.
 We can define a gene functionally as a DNA sequence that codes for a specific
polypeptide chain.
 All these definitions are useful in certain contexts.
 Even the one gene–one polypeptide definition must be refined and applied selectively.
 Most eukaryotic genes contain large introns that have no corresponding segments in
polypeptides.
 Promoters and other regulatory regions of DNA are not transcribed either, but they
must be present for transcription to occur.
 Our molecular definition must also include the various types of RNA that are not
translated into polypeptides, such as rRNA, tRNA, and other RNAs.
 This is our definition of a gene: A gene is a region of DNA whose final product is either a
polypeptide or an RNA molecule.

Biology Chapter Notes

 Chapter 18 The Genetics of Viruses and Bacteria
Chapter Notes

Overview: Microbial Model Systems

 Viruses and bacteria are the simplest biological systems—microbial models in which
scientists find life’s fundamental molecular mechanisms in their most basic, accessible
forms.
 Molecular biology was born in the laboratories of microbiologists studying viruses and
bacteria.
 Microbes such as E. coli and its viruses are called model systems because of their use
in studies that reveal broad biological principles.
 Microbiologists provided most of the evidence that genes are made of DNA, and they
worked out most of the major steps in DNA replication, transcription, and translation.
 Techniques enabling scientists to manipulate genes and transfer them from one
organism to another were developed in microbes.
 In addition, viruses and bacteria have unique genetic features with implications for
understanding the diseases that they cause.
 Bacteria are prokaryotic organisms, with cells that are much smaller and more simply
organized than those of eukaryotes, such as plants and animals.
 Viruses are smaller and simpler still, lacking the structure and metabolic machinery of
cells.
 Most viruses are little more than aggregates of nucleic acids and protein—genes in a
protein coat.

Concept 18.1 A virus has a genome but can reproduce only within a host cell
Researchers discovered viruses by studying a plant disease.
 The story of how viruses were discovered begins in 1883 with research on the cause of
tobacco mosaic disease by Adolf Mayer.
 This disease stunts tobacco plant growth and mottles plant leaves.
 Mayer concluded that the disease was infectious when he found that he could transmit
the disease by rubbing sap from diseased leaves onto healthy plants.
 He concluded that the disease must be caused by an extremely small bacterium.
 Ten years later, Dimitri Ivanovsky demonstrated that the sap was still infectious even
after passing through a filter designed to remove bacteria.
 In 1897, Martinus Beijerinck ruled out the possibility that the disease was due to a
filterable toxin produced by a bacterium by demonstrating that the infectious agent could
reproduce.
 The sap from one generation of infected plants could be used to infect a second
generation of plants that could infect subsequent generations.
 Beijerinck also determined that the pathogen could reproduce only within the host,
could not be cultivated on nutrient media, and was not inactivated by alcohol,
generally lethal to bacteria.
Biology Chapter Notes
 In 1935, Wendell Stanley crystallized the pathogen, the tobacco mosaic virus (TMV).
A virus is a genome enclosed in a protective coat.
 Stanley’s discovery that some viruses could be crystallized was puzzling because not even
the simplest cells can aggregate into regular crystals.
 However, viruses are not cells.
 They are infectious particles consisting of nucleic acid encased in a protein coat and, in
some cases, a membranous envelope.
 The tiniest viruses are only 20 nm in diameter—smaller than a ribosome.
 The genome of viruses may consist of double-stranded DNA, single-stranded DNA,
double-stranded RNA, or single-stranded RNA, depending on the kind of virus.
 A virus is called a DNA virus or an RNA virus, according to the kind of nucleic acid
that makes up its genome.
 The viral genome is usually organized as a single linear or circular molecule of nucleic
acid.
 The smallest viruses have only four genes, while the largest have several hundred.
 The capsid is the protein shell enclosing the viral genome.
 Capsids are built of a large number of protein subunits called capsomeres.
 The number of different kinds of proteins making up the capsid is usually small.
 The capsid of the tobacco mosaic virus has more than 1,000 copies of the same protein.
 Adenoviruses have 252 identical proteins arranged into a polyhedral capsid—as an
icosahedron.
 Some viruses have accessory structures to help them infect their hosts.
 A membranous envelope surrounds the capsids of flu viruses.
 These viral envelopes are derived from the membrane of the host cell.
 They also have some host cell viral proteins and glycoproteins, as well as molecules of
viral origin.
 Some viruses carry a few viral enzyme molecules within their capsids.
 The most complex capsids are found in viruses that infect bacteria, called bacteriophages
or phages.
 The T-even phages (T2, T4, T6) that infect Escherichia coli have elongated icosahedral
capsid heads that enclose their DNA and a protein tailpiece that attaches the phage to the
host and injects the phage DNA inside.
Viruses can reproduce only within a host cell.
 Viruses are obligate intracellular parasites.
 They can reproduce only within a host cell.
 An isolated virus is unable to reproduce—or do anything else, except infect an appropriate
host.
 Viruses lack the enzymes for metabolism and the ribosomes for protein synthesis.
 An isolated virus is merely a packaged set of genes in transit from one host cell to
another.
 Each type of virus can infect and parasitize only a limited range of host cells, called its
host range.
Biology Chapter Notes
  This host specificity depends on the evolution of recognition systems by the virus.
 Viruses identify host cells by a “lock and key” fit between proteins on the outside of
the virus and specific receptor molecules on the host’s surface (which evolved for
functions that benefit the host).
 Some viruses have a broad enough host range to infect several species, while others infect
only a single species.
 West Nile virus can infect mosquitoes, birds, horses, and humans.
 Measles virus can infect only humans.
 Most viruses of eukaryotes attack specific tissues.
 Human cold viruses infect only the cells lining the upper respiratory tract.
 The AIDS virus binds only to certain white blood cells.
 A viral infection begins when the genome of the virus enters the host cell.
 Once inside, the viral genome commandeers its host, reprogramming the cell to copy viral
nucleic acid and manufacture proteins from the viral genome.
 The host provides nucleotides, ribosomes, tRNAs, amino acids, ATP, and other
components for making the viral components dictated by viral genes.
 Most DNA viruses use the DNA polymerases of the host cell to synthesize new genomes
along the templates provided by the viral DNA.
 RNA viruses use special virus-encoded polymerases that can use RNA as a template.
 The nucleic acid molecules and capsomeres then self-assemble into viral particles and exit
the cell.
 Tobacco mosaic virus RNA and capsomeres can be assembled to form complete
viruses if the components are mixed together under the right conditions.
 The simplest type of viral reproductive cycle ends with the exit of many viruses from the
infected host cell, a process that usually damages or destroys the host cell.
Phages reproduce using lytic or lysogenic cycles.
 While phages are the best understood of all viruses, some of them are also among the
most complex.
 Research on phages led to the discovery that some double-stranded DNA viruses can
reproduce by two alternative mechanisms: the lytic cycle and the lysogenic cycle.
 In the lytic cycle, the phage reproductive cycle culminates in the death of the host.
 In the last stage, the bacterium lyses (breaks open) and releases the phages produced
within the cell to infect others.
 Each of these phages can infect a healthy cell.
 Virulent phages reproduce only by a lytic cycle.
 While phages have the potential to wipe out a bacterial colony in just hours, bacteria have
defenses against phages.
 Natural selection favors bacterial mutants with receptor sites that are no longer
recognized by a particular type of phage.
 Bacteria produce restriction endonucleases, or restriction enzymes, that recognize and
cut up foreign DNA, including certain phage DNA.
 Chemical modifications to the bacteria’s own DNA prevent its destruction by
restriction nucleases.
 Natural selection also favors phage mutants that are resistant to restriction enzymes.
Biology Chapter Notes
 In the lysogenic cycle, the phage genome replicates without destroying the host cell.
 Temperate phages, like phage lambda, use both lytic and lysogenic cycles.
 The lambda phage that infects E. coli demonstrates the cycles of a temperate phage.
 Infection of an E. coli by phage lambda begins when the phage binds to the surface of the
cell and injects its DNA.
 What happens next depends on the reproductive mode: lytic or lysogenic cycle.
 During a lytic cycle, the viral genes turn the host cell into a lambda phage-producing
factory, and the cell lyses and releases its viral products.
 During a lysogenic cycle, the viral DNA molecule is incorporated by genetic
recombination into a specific site on the host cell’s chromosome.
 In this prophage stage, one of the viral genes codes for a protein that represses most other
prophage genes.
 As a result, the phage genome is largely silent.
 A few other prophage genes may also be expressed during lysogenic cycles.
 Expression of these genes may alter the host’s phenotype, which can have medical
significance.
 Every time the host divides, it copies the phage DNA and passes the copies to daughter
cells.
 The viruses propagate without killing the host cells on which they depend.
 The term lysogenic implies that prophages are capable of giving rise to active phages that
lyse their host cells.
 That happens when the viral genome exits the bacterial chromosome and initiates a lytic
cycle.
Animal viruses are diverse in their modes of infection and replication.
 Many variations on the basic scheme of viral infection and reproduction are represented
among animal viruses.
 One key variable is the type of nucleic acid that serves as a virus’s genetic material.
 Another variable is the presence or absence of a membranous envelope derived from
the host cell membrane.
 Most animal viruses with RNA genomes have an envelope, as do some with DNA
genomes.
 Viruses equipped with an outer envelope use the envelope to enter the host cell.
 Glycoproteins on the envelope bind to specific receptors on the host’s membrane.
 The envelope fuses with the host’s membrane, transporting the capsid and viral
genome inside.
 The viral genome duplicates and directs the host’s protein synthesis machinery to
synthesize capsomeres with free ribosomes and glycoproteins with bound ribosomes.
 After the capsid and viral genome self-assemble, they bud from the host cell covered
with an envelope derived from the host’s plasma membrane, including viral
glycoproteins.
 The viral envelope is thus derived from the host’s plasma membrane, although viral genes
specify some of the molecules in the membrane.
 These enveloped viruses do not necessarily kill the host cell.
 Some viruses have envelopes that are not derived from plasma membrane.
Biology Chapter Notes
  The envelope of the herpesvirus is derived from the nuclear envelope of the host.
 These double-stranded DNA viruses reproduce within the cell nucleus using viral and
cellular enzymes to replicate and transcribe their DNA.
 In some cases, copies of the herpesvirus DNA remain behind as minichromosomes in
the nuclei of certain nerve cells.
 There they remain for life until triggered by physical or emotional stress to leave the
genome and initiate active viral production.
 The infection of other cells by these new viruses causes cold or genital sores.
 The viruses that use RNA as the genetic material are quite diverse, especially those that
infect animals.
 In some with single-stranded RNA (class IV), the genome acts as mRNA and is
translated directly.
 In others (class V), the RNA genome serves as a template for complementary RNA
strands, which function both as mRNA and as templates for the synthesis of additional
copies of genome RNA.
 All viruses that require RNA  RNA synthesis to make mRNA use a viral enzyme
that is packaged with the genome inside the capsid.
 Retroviruses (class VI) have the most complicated life cycles.
 These carry an enzyme called reverse transcriptase that transcribes DNA from an
RNA template.
 This provides RNA  DNA information flow.
 The newly made DNA is inserted as a provirus into a chromosome in the animal cell.
 The host’s RNA polymerase transcribes the viral DNA into more RNA molecules.
 These can function both as mRNA for the synthesis of viral proteins and as
genomes for new virus particles released from the cell.
 Human immunodeficiency virus (HIV), the virus that causes AIDS (acquired
immunodeficiency syndrome) is a retrovirus.
 The reproductive cycle of HIV illustrates the pattern of infection and replication in a
retrovirus.
 The viral particle includes an envelope with glycoproteins for binding to specific types of
red blood cells, a capsid containing two identical RNA strands as its genome, and two
copies of reverse transcriptase.
 After HIV enters the host cell, reverse transcriptase molecules are released into the
cytoplasm and catalyze synthesis of viral DNA.
 The host’s polymerase transcribes the proviral DNA into RNA molecules that can
function both as mRNA for the synthesis of viral proteins and as genomes for new virus
particles released from the cell.
 Transcription produces more copies of the viral RNA that are translated into viral
proteins, which self-assemble into a virus particle and leave the host.
Viruses may have evolved from other mobile genetic elements.
 Viruses do not fit our definition of living organisms.
 An isolated virus is biologically inert, and yet it has a genetic program written in the
universal language of life.
 Although viruses are obligate intracellular parasites that cannot reproduce independently,
it is hard to deny their evolutionary connection to the living world.
Biology Chapter Notes
 Because viruses depend on cells for their own propagation, it is reasonable to assume that
they evolved after the first cells appeared.
 Most molecular biologists favor the hypothesis that viruses originated from fragments of
cellular nucleic acids that could move from one cell to another.
 A viral genome usually has more in common with the genome of its host than with
those of viruses infecting other hosts.
 However, some viruses have genetic sequences that are quite similar to seemingly
distantly related viruses.
 This genetic similarity may reflect the persistence of groups of viral genes that were
evolutionarily successful during the early evolution of viruses and their eukaryotic
host cells.
 Perhaps the earliest viruses were naked bits of nucleic acids that passed between cells via
injured cell surfaces.
 The evolution of capsid genes may have facilitated the infection of undamaged cells.
 Candidates for the original sources of viral genomes include plasmids and transposable
elements.
 Plasmids are small, circular DNA molecules that are separate from chromosomes.
 Plasmids, found in bacteria and in eukaryote yeast, can replicate independently of the
rest of the cell and are occasionally transferred between cells.
 Transposable elements are DNA segments that can move from one location to another
within a cell’s genome.
 Both plasmids and transposable elements are mobile genetic elements.
 The ongoing evolutionary relationship between viruses and the genomes of their hosts is
an association that makes viruses very useful model systems in molecular biology.

Concept 18.2 Viruses, viroids, and prions are formidable pathogens in animals and
plants
 The link between viral infection and the symptoms it produces is often obscure.
 Some viruses damage or kill cells by triggering the release of hydrolytic enzymes from
lysosomes.
 Some viruses cause the infected cell to produce toxins that lead to disease symptoms.
 Others have molecular components, such as envelope proteins, that are toxic.
 In some cases, viral damage is easily repaired (respiratory epithelium after a cold), but in
others, infection causes permanent damage (nerve cells after polio).
 Many of the temporary symptoms associated with a viral infection result from the body’s
own efforts at defending itself against infection.
 The immune system is a complex and critical part of the body’s natural defense
mechanism against viral and other infections.
 Modern medicine has developed vaccines, harmless variants or derivatives of pathogenic
microbes that stimulate the immune system to mount defenses against the actual pathogen.
 Vaccination has eradicated smallpox.
 Effective vaccines are available against polio, measles, rubella, mumps, hepatitis B,
and a number of other viral diseases.
 Medical technology can do little to cure viral diseases once they occur.
Biology Chapter Notes
 Antibiotics, which can kill bacteria by inhibiting enzymes or processes specific to
bacteria, are powerless against viruses, which have few or no enzymes of their own.
 Most antiviral drugs resemble nucleosides and interfere with viral nucleic acid
synthesis.
 An example is acyclovir, which impedes herpesvirus reproduction by inhibiting the
viral polymerase that synthesizes viral DNA.
 Azidothymidine (AZT) curbs HIV reproduction by interfering with DNA synthesis by
reverse transcriptase.
 Currently, multidrug “cocktails” are the most effective treatment for HIV.
New viral diseases are emerging.
 In recent years, several emerging viruses have risen to prominence.
 HIV, the AIDS virus, seemed to appear suddenly in the early 1980s.
 Each year new strains of influenza virus cause millions to miss work or class, and
deaths are not uncommon.
 The deadly Ebola virus has caused hemorrhagic fevers in central Africa periodically
since 1976.
 West Nile virus appeared for the first time in North America in 1999.
 A more recent viral disease is severe acute respiratory syndrome (SARS).
 Researchers identified the disease agent causing SARS as a coronavirus, a class IV
virus with a single-stranded RNA genome.
 The emergence of these new viral diseases is due to three processes: mutation; spread of
existing viruses from one species to another; and dissemination of a viral disease from a
small, isolated population.
 Mutation of existing viruses is a major source of new viral diseases.
 RNA viruses tend to have high mutation rates because replication of their nucleic acid
lacks proofreading.
 Some mutations create new viral strains with sufficient genetic differences from earlier
strains that they can infect individuals who had acquired immunity to these earlier
strains.
 This is the case in flu epidemics.
 Another source of new viral diseases is the spread of existing viruses from one host
species to another.
 It is estimated that about three-quarters of new human diseases originated in other
animals.
 For example, hantavirus, which killed dozens of people in 1993, normally infects
rodents, especially deer mice.
 In 1993, unusually wet weather in the southwestern United States increased the mice’s
food, exploding the population.
 Humans acquired hantavirus when they inhaled dust-containing traces of urine and
feces from infected mice.
 The source of the SARS-causing virus is still undetermined, but candidates include the
exotic animal markets in China.
 In early 2004, the first cases of a new bird flu were reported in southeast Asia.
 If this disease evolves to spread from person to person, the potential for a major
human outbreak is great.

Biology Chapter Notes

 Finally, a viral disease can spread from a small, isolated population to a widespread
epidemic.
 For example, AIDS went unnamed and virtually unnoticed for decades before
spreading around the world.
 Technological and social factors, including affordable international travel, blood
transfusion technology, sexual promiscuity, and the abuse of intravenous drugs
allowed a previously rare disease to become a global scourge.
 These emerging viruses are generally not new. Rather, they are existing viruses that
mutate, spread to new host species, or expand their host territory.
 Changes in host behavior and environmental changes can increase the viral traffic
responsible for emerging disease.
 Destruction of forests to expand cropland may bring humans into contact with other
animals that may host viruses that can infect humans.
Plant viruses are serious agricultural pests.
 More than 2,000 types of viral diseases of plants are known.
 These diseases account for an annual loss of $15 billion worldwide.
 Plant viruses can stunt plant growth and diminish crop yields.
 Most are RNA viruses with rod-shaped or polyhedral capsids.
 Plant viral diseases are spread by two major routes.
 In horizontal transmission, a plant is infected with the virus by an external source.
 Plants are more susceptible if their protective epidermis is damaged, perhaps by wind,
chilling, injury, or insects.
 Insects are often carriers of viruses, transmitting disease from plant to plant.
 In vertical transmission, a plant inherits a viral infection from a parent.
 This may occur by asexual propagation or in sexual reproduction via infected seeds.
 Once a virus starts reproducing inside a plant cell, viral particles can spread throughout
the plant by passing through plasmodesmata.
 These cytoplasmic connections penetrate the walls between adjacent cells.
 Proteins encoded by viral genes can alter the diameter of plasmodesmata to allow
passage of viral proteins or genomes.
 Agricultural scientists have focused their efforts largely on reducing the incidence and
transmission of viral disease and in breeding resistant plant varieties.
Viroids and prions are the simplest infectious agents.
 Viroids, smaller and simpler than even viruses, consist of tiny molecules of naked circular
RNA that infect plants.
 Their several hundred nucleotides do not encode for proteins but can be replicated by the
host’s cellular enzymes.
 These small RNA molecules can disrupt plant metabolism and stunt plant growth, perhaps
by causing errors in the regulatory systems that control plant growth.
 Viroids show that molecules can act as infectious agents to spread disease.
 Prions are infectious proteins that spread disease.
 They appear to cause several degenerative brain diseases including scrapie in sheep,
“mad cow disease,” and Creutzfeldt-Jakob disease in humans.
Biology Chapter Notes
 Prions are likely transmitted in food.
 They have two alarming characteristics.
 They are very slow-acting agents. The incubation period is around ten years.
 Prions are virtually indestructible. They are not destroyed or deactivated by heating to
normal cooking temperatures.
 How can a nonreplicating protein be a transmissible pathogen?
 According to the leading hypothesis, a prion is a misfolded form of a normal brain
protein.
 When the prion gets into a cell with the normal form of the protein, the prion can convert
the normal protein into the prion version, creating a chain reaction that increases their
numbers.

Concept 18.3 Rapid reproduction, mutation, and genetic recombination contribute to

the genetic diversity of bacteria
 Bacteria are very valuable as microbial models in genetics research.
 As prokaryotes, bacteria allow researchers to study molecular genetics in simple
organisms.
 With the advent of large-scale genome sequencing, information about many
prokaryotes has accumulated.
 The best-studied bacterium is Escherichia coli, “the laboratory rat of molecular
biology.”
 The major component of the bacterial genome is one double-stranded, circular DNA
molecule that is associated with a small amount of protein.
 For E. coli, the chromosomal DNA consists of about 4.6 million nucleotide pairs with
about 4,400 genes.
 This is 100 times more DNA than in a typical virus and 1,000 times less than in a
typical eukaryote cell.
 Tight coiling of DNA results in a dense region of DNA, called the nucleoid, which is
not bound by a membrane.
 In addition, many bacteria have plasmids, much smaller circles of DNA.
 Each plasmid has only a small number of genes, from just a few to several dozen.
 Bacterial cells divide by binary fission.
 This is preceded by replication of the bacterial chromosome from a single origin of
replication.
 Bacteria proliferate very rapidly in a favorable natural or laboratory environment.
 Under optimal laboratory conditions, E. coli can divide every 20 minutes, producing a
colony of 107 to 108 bacteria in as little as 12 hours.
 In the human colon, E. coli grows more slowly and can double every 12 hours.
 It does reproduce rapidly enough to replace the 2 × 10 10 bacteria lost each day in feces.
 Through binary fission, most of the bacteria in a colony are genetically identical to the
parent cell.
 However, the spontaneous mutation rate of E. coli is 1 × 10−7 mutations per gene per
cell division.

Biology Chapter Notes

  This produces about 2,000 bacteria per day in the human colon that have a mutation in
any one gene.
 About 9 million mutant E. coli are produced in the human gut each day.
 New mutations, though individually rare, can have a significant impact on genetic
diversity when reproductive rates are very high because of short generation spans.
 Individual bacteria that are genetically well equipped for the local environment clone
themselves more prolifically than do less fit individuals.
 In contrast, organisms with slower reproduction rates (like humans) create genetic
variation not by novel alleles produced through new mutations, but primarily by sexual
recombination of existing alleles.
Genetic recombination produces new bacterial strains.
 In addition to mutation, genetic recombination generates diversity within bacterial
populations.
 Here, recombination is defined as the combining of DNA from two individuals into a
single genome.
 Bacterial recombination occurs through three processes: transformation, transduction, and
conjugation.
 Recombination can be observed when two mutant E. coli strains are combined.
 If each is unable to synthesize one of its required amino acids, neither can grow on a
minimal medium.
 However, if they are combined, numerous colonies will be created that started from
cells that acquired the missing genes for amino acid synthesis from the other strain.
 Some of these capable cells may have resulted from mutation. However, most acquired
the missing genes by genetic recombination.
 Transformation is the alteration of a bacterial cell’s genotype by the uptake of naked,
foreign DNA from the surrounding environment.
 For example, harmless Streptococcus pneumoniae bacteria can be transformed to
pneumonia-causing cells.
 This occurs when a live nonpathogenic cell takes up a piece of DNA that happens to
include the allele for pathogenicity from dead, broken-open pathogenic cells.
 The foreign allele replaces the native allele in the bacterial chromosome by genetic
recombination.
 The resulting cell is now recombinant, with DNA derived from two different cells.
 Years after transformation was discovered in laboratory cultures, most biologists believed
that the process was too rare and haphazard to play an important role in natural bacterial
populations.
 Researchers have since learned that many bacterial species have surface proteins that are
specialized for the uptake of naked DNA.
 These proteins recognize and transport DNA from closely related bacterial species into
the cell, which can then incorporate the foreign DNA into the genome.
 While E. coli lacks this specialized mechanism, it can be induced to take up small
pieces of DNA if cultured in a medium with a relatively high concentration of calcium
ions.
 In biotechnology, this technique has been used to introduce foreign DNA into E. coli.
 Transduction occurs when a phage carries bacterial genes from one host cell to another
as a result of aberrations in the phage reproductive cycle.
Biology Chapter Notes
 In generalized transduction, bacterial genes are randomly transferred from one bacterial
cell to another.
 Occasionally, a small piece of the host cell’s degraded DNA, rather than the phage
genome, is packaged within a phage capsid.
 When this phage attaches to another bacterium, it will inject this foreign DNA into its
new host.
 Some of this DNA can subsequently replace the homologous region of the second cell.
 This type of transduction transfers bacterial genes at random.
 Specialized transduction occurs via a temperate phage.
 When the prophage viral genome is excised from the chromosome, it sometimes takes
with it a small region of adjacent bacterial DNA.
 These bacterial genes are injected along with the phage’s genome into the next host
cell.
 Specialized transduction only transfers those genes near the prophage site on the
bacterial chromosome.
 Both generalized and specialized transduction use phage as a vector to transfer genes
between bacteria.
 Sometimes known as bacterial “sex,” conjugation transfers genetic material between two
bacterial cells that are temporarily joined.
 The transfer is one-way. One cell (“male”) donates DNA and its “mate” (“female”)
receives the genes.
 A sex pilus from the male initially joins the two cells and creates a cytoplasmic mating
bridge between cells.
 “Maleness,” the ability to form a sex pilus and donate DNA, results from an F (for
fertility) factor as a section of the bacterial chromosome or as a plasmid.
 Plasmids, including the F plasmid, are small, circular, self-replicating DNA
molecules.
 A genetic element that can replicate either as part of the bacterial chromosome or
independently of it is called an episome.
 Episomes such as the F plasmid can undergo reversible incorporation into the cell’s
chromosome.
 Temperate viruses are also episomes.
 Plasmids usually have only a few genes, which are not required for normal survival and
reproduction of the bacterium.
 However, plasmid genes may be advantageous in stressful conditions.
 The F plasmid facilitates genetic recombination when environmental conditions no
longer favor existing strains.
 The F factor or its F plasmid consists of about 25 genes, most required for the production
of sex pili.
 Cells with either the F factor or the F plasmid are called F+ and they pass this condition
to their offspring.
 Cells lacking either form of the F factor, are called F−, and they function as DNA
recipients.
 When an F+ and F− cell meet, the F+ cell passes a copy of the F plasmid to the F − cell,
converting it.

Biology Chapter Notes

 The plasmid form of the F factor can become integrated into the bacterial chromosome.
 A cell with the F factor built into its chromosome is called an Hfr cell (for High frequency
of recombination).
 Hfr cells function as males during conjugation.
 The Hfr cell initiates DNA replication at a −point on the F factor DNA and begins to
transfer the DNA copy from that point to its F partner.
 Random movements almost always disrupt conjugation long before an entire copy of the
Hfr chromosome can be passed to the F− cell.
 In the partially diploid cell, the newly acquired DNA aligns with the homologous region
of the F− chromosome.
 Recombination exchanges segments of DNA.
 The resulting recombinant bacterium has genes from two different cells.
 In the 1950s, Japanese physicians began to notice that some bacterial strains had evolved
antibiotic resistance.
 Mutations may reduce the ability of the pathogen’s cell-surface proteins to transport
antibiotics into the bacterial cell.
 Some of these genes code for enzymes that specifically destroy certain antibiotics, like
tetracycline or ampicillin.
 The genes conferring resistance are carried by plasmids, specifically the R plasmid (R for
resistance).
 When a bacterial population is exposed to an antibiotic, individuals with the R plasmid
will survive and increase in the overall population.
 Because R plasmids also have genes that encode for sex pili, they can be transferred from
one cell to another by conjugation.
 The DNA of a single cell can also undergo recombination due to movement of
transposable genetic elements or transposable elements within the cell’s genome.
 Unlike plasmids or prophages, transposable elements never exist independently but are
always part of chromosomal or plasmid DNA.
 During transposition, the transposable element moves from one location to another in a
cell’s genome.
 In bacteria, the movement may be within the chromosome, from a plasmid to a
chromosome (or vice versa), or between plasmids.
 Transposable elements may move by a “copy and paste” mechanism, in which the
transposable element replicates at its original site, and the copy inserts elsewhere.
 In other words, the transposable element is added at a new site without being lost from
the old site.
 Most transposable elements can move to many alternative locations in the DNA,
potentially moving genes to a site where genes of that sort have never before existed.
 The simplest transposable elements, called insertion sequences, exist only in bacteria.
 An insertion sequence contains a single gene that codes for transposase, an enzyme that
catalyzes movement of the insertion sequence from one site to another within the genome.
 The insertion sequence consists of the transposase gene, flanked by a pair of inverted
repeat sequences.
 The 20 to 40 nucleotides of the inverted repeat on one side are repeated in reverse
along the opposite DNA strand at the other end of the transposable element.
Biology Chapter Notes
 The transposase enzyme recognizes the inverted repeats as the edges of the transposable
element.
 Transposase cuts the transposable elements from its initial site and inserts it into the target
site.
 Insertion sequences cause mutations when they happen to land within the coding sequence
of a gene or within a DNA region that regulates gene expression.
 Insertion sequences account for 1.5% of the E. coli genome, but a mutation in a particular
gene by transposition is rare, occurring about once in every 10 million generations.
 This is about the same rate as spontaneous mutations from external factors.
 Transposable elements longer and more complex than insertion sequences, called
transposons, also move about in the bacterial genome.
 In addition to the DNA required for transposition, transposons include extra genes that
“go along for the ride,” such as genes for antibiotic resistance.
 In some bacterial transposons, the extra genes are sandwiched between two insertion
sequences.
 While insertion sequences may not benefit bacteria in any specific way, transposons may
help bacteria adapt to new environments.
 For example, a single R plasmid may carry several genes for resistance to different
antibiotics.
 This is explained by transposons, which can add a gene for antibiotic resistance to a
plasmid already carrying genes for resistance to other antibiotics.
 The transmission of this composite plasmid to other bacterial cells by cell division or
conjugation can spread resistance to a variety of antibiotics throughout a bacterial
population.
 In an antibiotic-rich environment, natural selection factors bacterial clones that have
built up R plasmids with multiple antibiotic resistance through a series of
transpositions.
 Transposable elements are also important components of eukaryotic genomes.

Concept 18.4 Individual bacteria respond to environmental change by regulating their

gene expression
 An individual bacterium, locked into the genome that it has inherited, can cope with
environmental fluctuations by exerting metabolic control.
 First, cells can vary the number of specific enzyme molecules they make by regulating
gene expression.
 Second, cells can adjust the activity of enzymes already present (for example, by
feedback inhibition).
 The tryptophan biosynthesis pathway demonstrates both levels of control.
 If tryptophan levels are high, some of the tryptophan molecules can inhibit the first
enzyme in the pathway.
 If the abundance of tryptophan continues, the cell can stop synthesizing additional
enzymes in this pathway by blocking transcription of the genes for these enzymes.
 The basic mechanism for this control of gene expression in bacteria, the operon model,
was discovered in 1961 by François Jacob and Jacques Monod.

Biology Chapter Notes

 E. coli synthesizes tryptophan from a precursor molecule in a series of steps, with each
reaction catalyzed by a specific enzyme.
 The five genes coding for these enzymes are clustered together on the bacterial
chromosome, served by a single promoter.
 Transcription gives rise to one long mRNA molecule that codes for all five enzymes in
the tryptophan pathway.
 The mRNA is punctuated with start and stop codons that signal where the coding
sequence for each polypeptide begins and ends.
 A key advantage of grouping genes of related functions into one transcription unit is that a
single “on-off switch” can control a cluster of functionally related genes.
 When an E. coli cell must make tryptophan for itself, all the enzymes are synthesized at
one time.
 The switch is a segment of DNA called an operator.
 The operator, located between the promoter and the enzyme-coding genes, controls the
access of RNA polymerase to the genes.
 The operator, the promoter, and the genes they control constitute an operon.
 By itself, an operon is on and RNA polymerase can bind to the promoter and transcribe
the genes.
 However, if a repressor protein, a product of a regulatory gene, binds to the operator, it
can prevent transcription of the operon’s genes.
 Each repressor protein recognizes and binds only to the operator of a certain operon.
 Regulatory genes are transcribed continuously at low rates.
 Binding by the repressor to the operator is reversible.
 The number of active repressor molecules available determines the on or off mode of
the operator.
 Repressors contain allosteric sites that change shape depending on the binding of other
molecules.
 In the case of the trp, or tryptophan, operon, when concentrations of tryptophan in the
cell are high, some tryptophan molecules bind as a corepressor to the repressor
protein.
 This activates the repressor and turns the operon off.
 At low levels of tryptophan, most of the repressors are inactive, and the operon is
transcribed.
 The trp operon is an example of a repressible operon, one that is inhibited when a specific
small molecule binds allosterically to a regulatory protein.
 In contrast, an inducible operon is stimulated when a specific small molecule interacts
with a regulatory protein.
 In inducible operons, the regulatory protein is active (inhibitory) as synthesized, and
the operon is off.
 Allosteric binding by an inducer molecule makes the regulatory protein inactive, and
the operon is turned on.
 The lac operon contains a series of genes that code for enzymes that play a major role in
the hydrolysis and metabolism of lactose (milk sugar).
 In the absence of lactose, this operon is off, as an active repressor binds to the operator
and prevents transcription.
Biology Chapter Notes
 Lactose metabolism begins with hydrolysis of lactose into its component
monosaccharides, glucose and galactose.
 This reaction is catalyzed by the enzyme ß-galactosidase.
 Only a few molecules of this enzyme are present in an E. coli cell grown in the
absence of lactose.
 If lactose is added to the bacterium’s environment, the number of ß-galactosidase
increases by a thousandfold within 15 minutes.
 The gene for ß-galactosidase is part of the lac operon, which includes two other genes
coding for enzymes that function in lactose metabolism.
 The regulatory gene, lacI, located outside the operon, codes for an allosteric repressor
protein that can switch off the lac operon by binding to the operator.
 Unlike the trp operon, the lac repressor is active all by itself, binding to the operator and
switching the lac operon off.
 An inducer inactivates the repressor.
 When lactose is present in the cell, allolactose, an isomer of lactose, binds to the
repressor.
 This inactivates the repressor, and the lac operon can be transcribed.
 Repressible enzymes generally function in anabolic pathways, synthesizing end products
from raw materials.
 When the end product is present in sufficient quantities, the cell can allocate its
resources to other uses.
 Inducible enzymes usually function in catabolic pathways, digesting nutrients to simpler
molecules.
 By producing the appropriate enzymes only when the nutrient is available, the cell
avoids making proteins that have nothing to do.
 Both repressible and inducible operons demonstrate negative control because active
repressors switch off the active form of the repressor protein.
 Positive gene control occurs when an activator molecule interacts directly with the
genome to switch transcription on.
 Even if the lac operon is turned on by the presence of allolactose, the degree of
transcription depends on the concentrations of other substrates.
 If glucose levels are low, then cyclic AMP (cAMP) accumulates.
 The regulatory protein catabolite activator protein (CAP) is an activator of transcription.
 When cAMP is abundant, it binds to CAP, and the regulatory protein assumes its
active shape and can bind to a specific site at the upstream end of the lac promoter.
 The attachment of CAP to the promoter directly stimulates gene expression.
 Thus, this mechanism qualifies as positive regulation.
 The cellular metabolism is biased toward the use of glucose.
 If glucose levels are sufficient and cAMP levels are low (lots of ATP), then the CAP
protein has an inactive shape and cannot bind upstream of the lac promoter.
 The lac operon will be transcribed but at a low level.
 For the lac operon, the presence/absence of lactose (allolactose) determines if the operon
is on or off.

Biology Chapter Notes

 Overall energy levels in the cell determine the level of transcription, a “volume” control,
through CAP.
 CAP works on several operons that encode enzymes used in catabolic pathways.
 If glucose is present and CAP is inactive, then the synthesis of enzymes that catabolize
other compounds is slowed.
 If glucose levels are low and CAP is active, then the genes that produce enzymes that
catabolize whichever other fuel is present will be transcribed at high levels.

Biology Chapter Notes

 Chapter 19 Eukaryotic Genomes
Chapter Notes

Overview: How Eukaryotic Genomes Work and Evolve

 Two features of eukaryotic genomes present a major information-processing challenge.

 First, the typical multicellular eukaryotic genome is much larger than that of a
prokaryotic cell.
 Second, cell specialization limits the expression of many genes to specific cells.
 The estimated 25,000 genes in the human genome include an enormous amount of DNA
that does not code for RNA or protein.
 This DNA is elaborately organized.
 Not only is the DNA associated with protein, but also this DNA-protein complex
called chromatin is organized into higher structural levels than the DNA-protein
complex in prokaryotes.

Concept 19.1 Chromatin structure is based on successive levels of DNA packing

 While the single circular chromosome of bacteria is coiled and looped in a complex but
orderly manner, eukaryotic chromatin is far more complex.
 Eukaryotic DNA is precisely combined with large amounts of protein.
 The resulting chromatin undergoes striking changes in the course of the cell cycle.
 During interphase of the cell cycle, chromatin fibers are usually highly extended within
the nucleus.
 As a cell prepares for meiosis, its chromatin condenses, forming a characteristic number
of short, thick chromosomes that can be distinguished with a light microscope.
 Eukaryotic chromosomes contain an enormous amount of DNA relative to their
condensed length.
 Each human chromosome averages about 1.5 × 108 nucleotide pairs.
 If extended, each DNA molecule would be about 4 cm long, thousands of times longer
than the cell diameter.
 This chromosome and 45 other human chromosomes fit into the nucleus.
 This occurs through an elaborate, multilevel system of DNA packing.
 Histone proteins are responsible for the first level of DNA packaging.
 The mass of histone in chromatin is approximately equal to the mass of DNA.
 Their positively charged amino acids bind tightly to negatively charged DNA.
 The five types of histones are very similar from one eukaryote to another, and similar
proteins are found in prokaryotes.
 The conservation of histone genes during evolution reflects their pivotal role in
organizing DNA within cells.
 Unfolded chromatin has the appearance of beads on a string.
 In this configuration, a chromatin fiber is 10 nm in diameter (the 10-nm fiber).
 Each bead of chromatin is a nucleosome, the basic unit of DNA packing.
Biology Chapter Notes
  The “string” between the beads is called linker DNA.
 A nucleosome consists of DNA wound around a protein core composed of two molecules
each of four types of histone: H2A, H2B, H3, and H4.
 The amino acid (N-terminus) of each histone protein (the histone tail) extends outward
from the nucleosome.
 A molecule of a fifth histone, H1, attaches to the DNA near the nucleosome.
 The beaded string seems to remain essentially intact throughout the cell cycle.
 Histones leave the DNA only transiently during DNA replication.
 They stay with the DNA during transcription.
 By changing shape and position, nucleosomes allow RNA-synthesizing polymerases to
move along the DNA.
 The next level of packing is due to the interactions between the histone tails of one
nucleosome and the linker DNA and nucleosomes to either side.
 With the aid of histone H1, these interactions cause the 10-nm to coil to form the 30-
nm chromatin fiber.
 This fiber forms looped domains attached to a scaffold of nonhistone proteins to make up
a 300-nm fiber.
 In a mitotic chromosome, the looped domains coil and fold to produce the characteristic
metaphase chromosome.
 These packing steps are highly specific and precise, with particular genes located in the
same places on metaphase chromosomes.
 Interphase chromatin is generally much less condensed than the chromatin of mitotic
chromosomes, but it shows several of the same levels of higher-order packing.
 Much of the chromatin is present as a 10-nm fiber, and some is compacted into a 30-
nm fiber, which in some regions is folded into looped domains.
 An interphase chromosome lacks an obvious scaffold, but its looped domains seem to
be attached to the nuclear lamina on the inside of the nuclear envelope, and perhaps
also to fibers of the nuclear matrix.
 The chromatin of each chromosome occupies a specific restricted area within the
interphase nucleus.
 Interphase chromosomes have highly condensed areas, heterochromatin, and less
compacted areas, euchromatin.
 Heterochromatin DNA is largely inaccessible to transcription enzymes.
 Looser packing of euchromatin makes its DNA accessible to enzymes and available
for transcription.

Concept 19.2 Gene expression can be regulated at any stage, but the key step is
transcription
 Like unicellular organisms, the tens of thousands of genes in the cells of multicellular
eukaryotes are continually turned on and off in response to signals from their internal and
external environments.
 Gene expression must be controlled on a long-term basis during cellular differentiation,
the divergence in form and function as cells in a multicellular organism specialize.
 A typical human cell probably expresses about 20% of its genes at any given time.
Biology Chapter Notes
  Highly specialized cells, such as nerves or muscles, express only a tiny fraction of
their genes.
 Although all the cells in an organism contain an identical genome, the subset of
genes expressed in the cells of each type is unique.
 The differences between cell types are due to differential gene expression, the
expression of different genes by cells with the same genome.
 The genomes of eukaryotes may contain tens of thousands of genes.
 For quite a few species, only a small amount of the DNA—1.5% in humans—codes
for protein.
 Of the remaining DNA, a very small fraction consists of genes for rRNA and tRNA.
 Most of the rest of the DNA seems to be largely noncoding, although researchers have
found that a significant amount of it is transcribed into RNAs of unknown function.
 Problems with gene expression and control can lead to imbalance and diseases, including
cancers.
 Our understanding of the mechanisms controlling gene expression in eukaryotes has been
enhanced by new research methods, including advances in DNA technology.
 In all organisms, the expression of specific genes is most commonly regulated at
transcription, often in response to signals coming from outside the cell.
 The term gene expression is often equated with transcription.
 With their greater complexity, eukaryotes have opportunities for controlling gene
expression at additional stages.
 Each stage in the entire process of gene expression provides a potential control point
where gene expression can be turned on or off, sped up or slowed down.
 A web of control connects different genes and their products.
 These levels of control include chromatin packing, transcription, RNA processing,
translation, and various alterations to the protein product.
Chromatin modifications affect the availability of genes for transcription.
 In addition to its role in packing DNA inside the nucleus, chromatin organization
regulates gene expression.
 Genes of densely condensed heterochromatin are usually not expressed, presumably
because transcription proteins cannot reach the DNA.
 A gene’s location relative to nucleosomes and to attachment sites to the chromosome
scaffold or nuclear lamina can affect transcription.
 Chemical modifications of chromatin play a key role in chromatin structure and gene
expression.
 Chemical modifications of histones play a direct role in the regulation of gene
transcription.
 The N-terminus of each histone molecule in a nucleosome protrudes outward from the
nucleosome.
 These histone tails are accessible to various modifying enzymes, which catalyze the
addition or removal of specific chemical groups.
 Histone acetylation (addition of an acetyl group —COCH3) and deacetylation appear to
play a direct role in the regulation of gene transcription.
 Acetylated histones grip DNA less tightly, providing easier access for transcription
proteins in this region.
Biology Chapter Notes
  Some of the enzymes responsible for acetylation or deacetylation are associated with
or are components of transcription factors that bind to promoters.
 Thus histone acetylation enzymes may promote the initiation of transcription not only
by modifying chromatin structure, but also by binding to and recruiting components of
the transcription machinery.
 DNA methylation is the attachment by specific enzymes of methyl groups (—CH3) to
DNA bases after DNA synthesis.
 Inactive DNA is generally highly methylated compared to DNA that is actively
transcribed.
 For example, the inactivated mammalian X chromosome in females is heavily
methylated.
 Genes are usually more heavily methylated in cells where they are not expressed.
 Demethylating certain inactive genes turns them on.
 However, there are exceptions to this pattern.
 DNA methylation proteins recruit histone deacetylation enzymes, providing a mechanism
by which DNA methylation and histone deacetylation cooperate to repress transcription.
 In some species, DNA methylation is responsible for long-term inactivation of genes
during cellular differentiation.
 Once methylated, genes usually stay that way through successive cell divisions.
 Methylation enzymes recognize sites on one strand that are already methylated and
correctly methylate the daughter strand after each round of DNA replication.
 This methylation patterns accounts for genomic imprinting in which methylation turns
off either the maternal or paternal alleles of certain genes at the start of development.
 The chromatin modifications just discussed do not alter DNA sequence, and yet they may
be passed along to future generations of cells.
 Inheritance of traits by mechanisms not directly involving the nucleotide sequence is
called epigenetic inheritance.
 Researchers are amassing more and more evidence for the importance of epigenetic
information in the regulation of gene expression.
 Enzymes that modify chromatin structure are integral parts of the cell’s machinery for
regulating transcription.
Transcription initiation is controlled by proteins that interact with DNA and with each
other.
 Chromatin-modifying enzymes provide initial control of gene expression by making a
region of DNA either more available or less available for transcription.
 A cluster of proteins called a transcription initiation complex assembles on the promoter
sequence at the “upstream” end of the gene.
 One component, RNA polymerase II, transcribes the gene, synthesizing a primary
RNA transcript or pre-mRNA.
 RNA processing includes enzymatic addition of a 5’ cap and a poly-A tail, as well as
splicing out of introns to yield a mature mRNA.
 Multiple control elements are associated with most eukaryotic genes.
 Control elements are noncoding DNA segments that regulate transcription by binding
certain proteins.

Biology Chapter Notes

  These control elements and the proteins they bind are critical to the precise regulation
of gene expression in different cell types.
 To initiate transcription, eukaryotic RNA polymerase requires the assistance of proteins
called transcription factors.
 General transcription factors are essential for the transcription of all protein-coding
genes.
 Only a few general transcription factors independently bind a DNA sequence such as
the TATA box within the promoter.
 Others in the initiation complex are involved in protein-protein interactions, binding
each other and RNA polymerase II.
 The interaction of general transcription factors and RNA polymerase II with a promoter
usually leads to only a low rate of initiation and production of few RNA transcripts.
 In eukaryotes, high levels of transcription of particular genes depend on the interaction of
control elements with specific transcription factors.
 Some control elements, named proximal control elements, are located close to the
promoter.
 Distant control elements, enhancers, may be thousands of nucleotides away from the
promoter or even downstream of the gene or within an intron.
 A given gene may have multiple enhancers, each active at a different time or in a different
cell type or location in the organism.
 An activator is a protein that binds to an enhancer to stimulate transcription of a gene.
 Protein-mediated bending of DNA brings bound activators in contact with a group of
mediator proteins that interact with proteins at the promoter.
 This helps assemble and position the initiation complex on the promoter.
 Eukaryotic genes also have repressor proteins to inhibit expression of a gene.
 Eukaryotic repressors can cause inhibition of gene expression by blocking the binding
of activators to their control elements or to components of the transcription machinery
or by turning off transcription even in the presence of activators.
 Some activators and repressors act indirectly to influence chromatin structure.
 Some activators recruit proteins that acetylate histones near the promoters of specific
genes, promoting transcription.
 Some repressors recruit proteins that deacetylate histones, reducing transcription or
silencing the gene.
 Recruitment of chromatin-modifying proteins seems to be the most common
mechanism of repression in eukaryotes.
 The number of nucleotide sequences found in control elements is surprisingly small.
 For many genes, the particular combination of control elements associated with the gene
may be more important than the presence of a single unique control element in regulating
transcription of the gene.
 Even with only a dozen control element sequences, a large number of combinations are
possible.
 A particular combination of control elements will be able to activate transcription only
when the appropriate activator proteins are present, such as at a precise time during
development or in a particular cell type.
 The use of different combinations of control elements allows fine regulation of
transcription with a small set of control elements.
Biology Chapter Notes
 In prokaryotes, coordinately controlled genes are often clustered into an operon with a
single promoter and other control elements upstream.
 The genes of the operon are transcribed into a single mRNA and translated together.
 In contrast, very few eukaryotic genes are organized this way.
 Recent studies of the genomes of several eukaryotic species have found that some
coexpressed genes are clustered near each other on the same chromosome.
 Each eukaryotic gene in these clusters has its own promoter and is individually
transcribed.
 The coordinate regulation of clustered genes in eukaryotic cells is thought to involve
changes in the chromatin structure that makes the entire group of genes either available
or unavailable for transcription.
 More commonly, genes coding for the enzymes of a metabolic pathway are scattered over
different chromosomes.
 Coordinate gene expression in eukaryotes depends on the association of a specific control
element or combination of control elements with every gene of a dispersed group.
 A common group of transcription factors binds to all the genes in the group, promoting
simultaneous gene transcription.
 For example, a steroid hormone enters a cell and binds to a specific receptor protein in
the cytoplasm or nucleus, forming a hormone-receptor complex that serves as a
transcription activator.
 Every gene whose transcription is stimulated by that steroid hormone has a control
element recognized by that hormone-receptor complex.
 Other signal molecules control gene expression indirectly by triggering signal-
transduction pathways that lead to activation of transcription.
 Systems for coordinating gene regulation probably arose early in evolutionary history and
evolved by the duplication and distribution of control elements within the genome.
Post-transcriptional mechanisms play supporting roles in the control of gene expression.
 Gene expression may be blocked or stimulated by any posttranscriptional step.
 By using regulatory mechanisms that operate after transcription, a cell can rapidly fine-
tune gene expression in response to environmental changes without altering its
transcriptional patterns.
 RNA processing in the nucleus and the export of mRNA to the cytoplasm provide
opportunities for gene regulation that are not available in bacteria.
 In alternative RNA splicing, different mRNA molecules are produced from the same
primary transcript, depending on which RNA segments are treated as exons and which as
introns.
 Regulatory proteins specific to a cell type control intron-exon choices by binding to
regulatory sequences within the primary transcript.
 The life span of an mRNA molecule is an important factor in determining the pattern of
protein synthesis.
 Prokaryotic mRNA molecules may be degraded after only a few minutes.
 Eukaryotic mRNAs typically last for hours, days, or weeks.
 In red blood cells, mRNAs for hemoglobin polypeptides are unusually stable and are
translated repeatedly.

Biology Chapter Notes

 A common pathway of mRNA breakdown begins with enzymatic shortening of the poly-
A tail.
 This triggers the enzymatic removal of the 5’ cap.
 This is followed by rapid degradation of the mRNA by nucleases.
 Nucleotide sequences in the untranslated trailer region at the 3’ end affect mRNA
stability.
 Transferring such a sequence from a short-lived mRNA to a normally stable mRNA
results in quick mRNA degradation.
 During the past few years, researchers have found small single-stranded RNA molecules
called microRNAs, or miRNAs, that bind to complementary sequences in mRNA
molecules.
 miRNAs are formed from longer RNA precursors that fold back on themselves,
forming a long hairpin structure stabilized by hydrogen bonding.
 An enzyme called Dicer cuts the double-stranded RNA into short fragments.
 One of the two strands is degraded. The other miRNA strand associates with a protein
complex and directs the complex to any mRNA molecules with a complementary
sequence.
 The miRNA-protein complex then degrades the target mRNA or blocks its translation.
 The phenomenon of inhibition of gene expression by RNA molecules is called RNA
interference (RNAi).
 Small interfering RNAs (siRNAs) are similar in size and function to miRNAs and are
generated by similar mechanisms in eukaryotic cells.
 Cellular RNAi pathways lead to the destruction of RNAs and may have originated as a
natural defense against infection by RNA viruses.
 Whatever their origin, RNAi plays an important role in regulating gene expression in
the cell.
 Translation of specific mRNAs can be blocked by regulatory proteins that bind to specific
sequences or structures within the 5’ leader region of mRNA.
 This prevents attachment of ribosomes.
 mRNAs may be stored in egg cells without poly-A tails of sufficient size to allow
translation initiation.
 At the appropriate time during development, a cytoplasmic enzyme adds more A
residues, allowing translation to begin.
 Protein factors required to initiate translation in eukaryotes offer targets for
simultaneously controlling translation of all mRNAs in a cell.
 This allows the cell to shut down translation if environmental conditions are poor (for
example, shortage of a key constituent) or until the appropriate conditions exist (for
example, after fertilization in an egg or during daylight in plants).
 Finally, eukaryotic polypeptides must often be processed to yield functional proteins.
 This may include cleavage, chemical modifications, and transport to the appropriate
destination.
 The cell limits the lifetimes of normal proteins by selective degradation.
 Many proteins, like the cyclins in the cell cycle, must be short-lived to function
appropriately.
 Proteins intended for degradation are marked by the attachment of ubiquitin proteins.

Biology Chapter Notes

 Giant protein complexes called proteasomes recognize the ubiquitin and degrade the
tagged protein.
 Mutations making cell cycle proteins impervious to proteasome degradation can lead
to cancer.

Concept 19.3 Cancer results from genetic changes that affect cell cycle control
 Cancer is a disease in which cells escape the control methods that normally regulate cell
growth and division.
 The gene regulation systems that go wrong during cancer are the very same systems
that play important roles in embryonic development, the immune response, and other
biological processes.
 The genes that normally regulate cell growth and division during the cell cycle include
genes for growth factors, their receptors, and the intracellular molecules of signaling
pathways.
 Mutations altering any of these genes in somatic cells can lead to cancer.
 The agent of such changes can be random spontaneous mutations or environmental
influences such as chemical carcinogens, X-rays, or certain viruses.
 In 1911, Peyton Rous discovered a virus that causes cancer in chickens.
 Since then, scientists have recognized a number of tumor viruses that cause cancer in
various animals, including humans.
 All tumor viruses transform cells into cancer cells through the integration of viral
nucleic acid into host cell DNA.
 Cancer-causing genes, oncogenes, were initially discovered in retroviruses, but close
counterparts, proto-oncogenes, have been found in other organisms.
 The products of proto-oncogenes are proteins that stimulate normal cell growth and
division and play essential functions in normal cells.
 A proto-oncogene becomes an oncogene following genetic changes that lead to an
increase in the proto-oncogene’s protein production or the activity of each protein
molecule.
 These genetic changes include movements of DNA within the genome, amplification
of the proto-oncogene, and point mutations in the control element of the proto-
oncogene.
 Cancer cells frequently have chromosomes that have been broken and rejoined
incorrectly.
 This may translocate a fragment to a location near an active promoter or other control
element.
 Movement of transposable elements may also place a more active promoter near a
proto-oncogene, increasing its expression.
 Amplification increases the number of copies of the proto-oncogene in the cell.
 A point mutation in the promoter or enhancer of a proto-oncogene may increase its
expression.
 A point mutation in the coding sequence may lead to translation of a protein that is
more active or longer-lived.
 Mutations to tumor-suppressor genes, whose normal products inhibit cell division, also
contribute to cancer.
Biology Chapter Notes
 Any decrease in the normal activity of a tumor-suppressor protein may contribute to
cancer.
 Some tumor-suppressor proteins normally repair damaged DNA, preventing the
accumulation of cancer-causing mutations.
 Others control the adhesion of cells to each other or to an extracellular matrix, crucial
for normal tissues and often absent in cancers.
 Still others are components of cell-signaling pathways that inhibit the cell cycle.
Oncogene proteins and faulty tumor-suppressor proteins interfere with normal signaling
pathways.
 The proteins encoded by many proto-oncogenes and tumor-suppressor genes are
components of cell-signaling pathways.
 Mutations in the products of two key genes, the ras proto-oncogene, and the p53 tumor
suppressor gene occur in 30% and 50% of human cancers, respectively.
 Both the Ras protein and the p53 protein are components of signal-transduction pathways
that convey external signals to the DNA in the cell’s nucleus.
 Ras, the product of the ras gene, is a G protein that relays a growth signal from a growth
factor receptor on the plasma membrane to a cascade of protein kinases.
 At the end of the pathway is the synthesis of a protein that stimulates the cell cycle.
 Many ras oncogenes have a point mutation that leads to a hyperactive version of the
Ras protein that can issue signals on its own, resulting in excessive cell division.
 The p53 gene, named for its 53,000-dalton protein product, is often called the “guardian
angel of the genome.”
 Damage to the cell’s DNA acts as a signal that leads to expression of the p53 gene.
 The p53 protein is a transcription factor for several genes.
 It can activate the p21 gene, which halts the cell cycle.
 It can turn on genes involved in DNA repair.
 When DNA damage is irreparable, the p53 protein can activate “suicide genes” whose
protein products cause cell death by apoptosis.
 A mutation that knocks out the p53 gene can lead to excessive cell growth and cancer.
Multiple mutations underlie the development of cancer.
 More than one somatic mutation is generally needed to produce the changes characteristic
of a full-fledged cancer cell.
 If cancer results from an accumulation of mutations, and if mutations occur throughout
life, then the longer we live, the more likely we are to develop cancer.
 Colorectal cancer, with 135,000 new cases and 60,000 deaths in the United States each
year, illustrates a multistep cancer path.
 The first sign is often a polyp, a small benign growth in the colon lining.
 The cells of the polyp look normal but divide unusually frequently.
 Through gradual accumulation of mutations that activate oncogenes and knock out tumor-
suppressor genes, the polyp can develop into a malignant tumor.
 About a half dozen DNA changes must occur for a cell to become fully cancerous.
 These usually include the appearance of at least one active oncogene and the mutation or
loss of several tumor-suppressor genes.
Biology Chapter Notes
  Since mutant tumor-suppressor alleles are usually recessive, mutations must knock out
both alleles.
 Most oncogenes behave as dominant alleles and require only one mutation.
 In many malignant tumors, the gene for telomerase is activated, removing a natural limit
on the number of times the cell can divide.
 Viruses, especially retroviruses, play a role in about 15% of human cancer cases
worldwide.
 These include some types of leukemia, liver cancer, and cancer of the cervix.
 Viruses promote cancer development by integrating their DNA into that of infected cells.
 By this process, a retrovirus may donate an oncogene to the cell.
 Alternatively, insertion of viral DNA may disrupt a tumor-suppressor gene or convert a
proto-oncogene to an oncogene.
 Some viruses produce proteins that inactivate p53 and other tumor-suppressor proteins,
making the cell more prone to becoming cancerous.
 The fact that multiple genetic changes are required to produce a cancer cell helps explain
the predispositions to cancer that run in some families.
 An individual inheriting an oncogene or a mutant allele of a tumor-suppressor gene
will be one step closer to accumulating the necessary mutations for cancer to develop.
 Geneticists are devoting much effort to finding inherited cancer alleles so that
predisposition to certain cancers can be detected early in life.
 About 15% of colorectal cancers involve inherited mutations, especially to DNA repair
genes or to the tumor-suppressor gene adenomatous polyposis coli, or APC.
 Normal functions of the APC gene include regulation of cell migration and
adhesion.
 Even in patients with no family history of the disease, APC is mutated in about 60%
of colorectal cancers.
 Between 5–10% of breast cancer cases show an inherited predisposition.
 This is the second most common type of cancer in the United States, striking more
than 180,000 women annually and leading to 40,000 annual deaths.
 Mutations to one of two tumor-suppressor genes, BRCA1 and BRCA2, increase the
risk of breast and ovarian cancer.
 A woman who inherits one mutant BRCA1 allele has a 60% probability of developing
breast cancer before age 50 (versus a 2% probability in an individual with two normal
alleles).
 BRCA1 and BRCA2 are considered tumor-suppressor genes because their wild-type
alleles protect against breast cancer and because their mutant alleles are recessive.
 Recent evidence suggests that the BRCA2 protein is directly involved in repairing
breaks that occur in both strands of DNA.

Concept 19.4 Eukaryotic genomes can have many noncoding DNA sequences in
addition to genes
 Several trends are evident when we compare the genomes of prokaryotes to those of
eukaryotes.
 There is a general trend from smaller to larger genomes, but with fewer genes in a given
length of DNA.
Biology Chapter Notes
  Humans have 500 to 1,500 times as many base pairs in their genome as most
prokaryotes, but only 5 to 15 times as many genes.
 Most of the DNA in a prokaryote genome codes for protein, tRNA, or rRNA.
 The small amount of noncoding DNA consists mainly of regulatory sequences.
 In eukaryotes, most of the DNA (98.5% in humans) does not code for protein or RNA.
 Gene-related regulatory sequences and introns account for 24% of the human genome.
 Introns account for most of the difference in average length of eukaryotic (27,000
base pairs) and prokaryotic genes (1,000 base pairs).
 Most intergenic DNA is repetitive DNA, present in multiple copies in the genome.
 Transposable elements and related sequences make up 44% of the entire human
genome.
 The first evidence for transposable elements came from geneticist Barbara McClintock’s
breeding experiments with Indian corn (maize) in the 1940s and 1950s.
 Eukaryotic transposable elements are of two types: transposons, which move within a
genome by means of a DNA intermediate, and retrotransposons, which move by means of
an RNA intermediate, a transcript of the retrotransposon DNA.
 Transposons can move by a “cut and paste” mechanism, which removes the element
from its original site, or by a “copy and paste” mechanism, which leaves a copy
behind.
 Retrotransposons always leave a copy at the original site, since they are initially
transcribed into an RNA intermediate.
 Most transposons are retrotransposons, in which the transcribed RNA includes the code
for an enzyme that catalyzes the insertion of the retrotransposon and may include a gene
for reverse transcriptase.
 Reverse transcriptase uses the RNA molecule originally transcribed from the
retrotransposon as a template to synthesize a double-stranded DNA copy.
 Multiple copies of transposable elements and related sequences are scattered throughout
eukaryotic genomes.
 A single unit is hundreds or thousands of base pairs long, and the dispersed “copies”
are similar but not identical to one another.
 Some of the copies are transposable elements and some are related sequences that have
lost the ability to move.
 Transposable elements and related sequences make up 25–50% of most mammalian
genomes, and an even higher percentage in amphibians and angiosperms.
 In primates, a large portion of transposable element–related DNA consists of a family of
similar sequences called Alu elements.
 These sequences account for approximately 10% of the human genome.
 Alu elements are about 300 nucleotides long, shorter than most functional transposable
elements, and they do not code for protein.
 Many Alu elements are transcribed into RNA molecules.
 However, their cellular function is unknown.
 Repetitive DNA that is not related to transposable elements probably arose by mistakes
that occurred during DNA replication or recombination.
 Repetitive DNA accounts for about 15% of the human genome.

Biology Chapter Notes

  Five percent of the human genome consists of large-segment duplications in which
10,000 to 300,000 nucleotide pairs seem to have been copied from one chromosomal
location to another.
 Simple sequence DNA contains many copies of tandemly repeated short sequences of 15–
500 nucleotides.
 There may be as many as several hundred thousand repetitions of a nucleotide
sequence.
 Simple sequence DNA makes up 3% of the human genome.
 Much of the genome’s simple sequence DNA is located at chromosomal telomeres and
centromeres, suggesting that it plays a structural role.
 The DNA at centromeres is essential for the separation of chromatids in cell
division and may also help to organize the chromatin within the interphase nucleus.
 Telomeric DNA prevents gene loss as DNA shortens with each round of replication
and also binds proteins that protect the ends of a chromosome from degradation or
attachment to other chromosomes.
Gene families have evolved by duplication of ancestral genes.
 Sequences coding for proteins and structural RNAs compose a mere 1.5% of the human
genome.
 If introns and regulatory sequences are included, gene-related DNA makes up 25% of
the human genome.
 In humans, solitary genes present in one copy per haploid set of chromosomes make up
only half of the total coding DNA.
 The rest occurs in multigene families, collections of identical or very similar genes.
 Some multigene families consist of identical DNA sequences that may be clustered
tandemly.
 These code for RNA products or for histone proteins.
 For example, the three largest rRNA molecules are encoded in a single transcription
unit that is repeated tandemly hundreds to thousands of times.
 This transcript is cleaved to yield three rRNA molecules that combine with proteins
and one other kind of rRNA to form ribosomal subunits.
 Two related families of nonidentical genes encode globins, a group of proteins that

 The different versions of each globin subunit are expressed at different times in
development, allowing hemoglobin to function effectively in the changing environment of
the developing animal.

embryonic, fetal, and/or adult stage of development.
 In humans, the embryonic and fetal hemoglobins have higher affinity for oxygen than
do adult forms, ensuring transfer of oxygen from mother to developing fetus.
 Also found in the globin gene family clusters are several pseudogenes, DNA
sequences similar to real genes that do not yield functional proteins.

Biology Chapter Notes

Concept 19.5 Duplications, rearrangements, and mutations of DNA contribute to
genome evolution
 The earliest forms of life likely had a minimal number of genes, including only those
necessary for survival and reproduction.
 The size of genomes has increased over evolutionary time, with the extra genetic material
providing raw material for gene diversification.
 An accident in meiosis can result in one or more extra sets of chromosomes, a condition
known as polyploidy.
 In a polyploid organism, one complete set of genes can provide essential functions for
the organism.
 The genes in the extra set may diverge by accumulating mutations.
 These variations may persist if the organism carrying them survives and
reproduces.
 In this way, genes with novel functions may evolve.
 Errors during meiosis due to unequal crossing over during Prophase I can lead to
duplication of individual genes.
 Slippage during DNA replication can result in deletion or duplication of DNA regions.
 Such errors can lead to regions of repeats, such as simple sequence DNA.
 Major rearrangements of at least one set of genes occur during immune system
differentiation.
 Duplication events can lead to the evolution of genes with related functions, such as the
- -globin gene families.
 A comparison of gene sequences within a multigene family indicates that they all
evolved from one common ancestral globin gene, which was duplicated and diverged
about 450–500 million years ago.
 After the duplication events, the differences between the genes in the globin family arose
from mutations that accumulated in the gene copies over many generations.
 -globin protein was fulfilled by one gene,
while other copies of -globin gene accumulated random mutations.
 Some mutations may have altered the function of the protein product in ways that were
beneficial to the organism without changing its oxygen-carrying function.
 The similarity in the amino acid sequences of th - -globin proteins
supports this model of gene duplication and mutation.
 Random mutations accumulating over time in the pseudogenes have destroyed their
function.
 In other gene families, one copy of a duplicated gene can undergo alterations that lead
to a completely new function for the protein product.
 -lactalbumin are good examples.
 Lysozyme is an enzyme that helps prevent infection by hydrolyzing bacterial cell
walls.
 -lactalbumin is a nonenzymatic protein that plays a role in mammalian
milk production.
 Both genes are found in mammals, while only lysozyme is found in birds.
 The two proteins are similar in their amino acids sequences and 3-D structures.

Biology Chapter Notes

  These findings suggest that at some time after the bird and mammalian lineage had
separated, the lysozyme gene underwent a duplication event in the mammalian lineage
but not in the avian lineage.
 Subsequently, one copy of the duplicated lysozyme gene evolved into a gene
-lactalbumin, a protein with a completely different function.
 Rearrangement of existing DNA sequences has also contributed to genome evolution.
 The presence of introns in eukaryotic genes may have promoted the evolution of
new and potentially useful proteins by facilitating the duplication or repositioning
of exons in the genome.
 A particular exon within a gene could be duplicated on one chromosome and
deleted from the homologous chromosome.
 The gene with the duplicated exon would code for a protein with a second copy of
the encoded domain.
 This change in the protein’s structure could augment its function by increasing its
stability or altering its ability to bind a particular ligand.
 Mixing and matching of different exons within or between genes owing to errors in
meiotic recombination is called exon shuffling and could lead to new proteins with
novel combinations of functions.
 The persistence of transposable elements as a large percentage of eukaryotic genomes
suggests that they play an important role in shaping a genome over evolutionary time.
 These elements can contribute to evolution of the genome by promoting
recombination, disrupting cellular genes or control elements, and carrying entire genes
or individual exons to new locations.
 The presence of homologous transposable element sequences scattered throughout the
genome allows recombination to take place between different chromosomes.
 Most of these alterations are likely detrimental, causing chromosomal
translocations and other changes in the genome that may be lethal to the organism.
 Over the course of evolutionary time, an occasional recombination may be
advantageous.
 The movement of transposable elements around the genome can have several direct
consequences.
 If a transposable element “jumps” into the middle of a coding sequence of a
protein-coding gene, it prevents the normal functioning of that gene.
 If a transposable element inserts within a regulatory sequence, it may increase or
decrease protein production.
 During transposition, a transposable element may transfer genes to a new position
on the genome or may insert an exon from one gene into another gene.
 Transposable elements can lead to new coding sequences when an Alu element
hops into introns to create a weak alternative splice site in the RNA transcript.
 Splicing will usually occur at the regular splice sites, producing the original
protein.
 Occasionally, splicing will occur at the new weak site.
 In this way, alternative genetic combinations can be “tried out” while the function
of the original gene product is retained.
 These processes produce no effect or harmful effects in most individual cases.
 However, over long periods of time, the generation of genetic diversity provides
more raw material for natural selection to work on during evolution.

Biology Chapter Notes

 Chapter 20 DNA Technology and Genomics
Chapter Notes

Overview: Understanding and Manipulating Genomes

 One of the great achievements of modern science has been the sequencing of the human
genome, which was largely completed by 2003.
 Progress began with the development of techniques for making recombinant DNA, in
which genes from two different sources—and often different species—are combined in
vitro into the same molecule.
 The methods for making recombinant DNA are central to genetic engineering, the direct
manipulation of genes for practical purposes.
 Applications include the introduction of a desired gene into the DNA of a host that will
produce the desired protein.
 DNA technology has launched a revolution in biotechnology, the manipulation of
organisms or their components to make useful products.
 Practices that go back centuries, such as the use of microbes to make wine and cheese
and the selective breeding of livestock, are examples of biotechnology.
 These techniques exploit naturally occurring mutations and genetic recombination.
 Biotechnology based on the manipulation of DNA in vitro differs from earlier
practices by enabling scientists to modify specific genes and move them between
organisms as distinct as bacteria, plants, and animals.
 DNA technology is now applied in areas ranging from agriculture to criminal law, but its
most important achievements are in basic research.

Concept 20.1 DNA cloning permits production of multiple copies of a specific gene or
other DNA segment
 To study a particular gene, scientists needed to develop methods to isolate the small, well-
defined portion of a chromosome containing the gene of interest.
 Techniques for gene cloning enable scientists to prepare multiple identical copies of
gene-sized pieces of DNA.
 One basic cloning technique begins with the insertion of a foreign gene into a bacterial
plasmid.
 E. coli and its plasmids are commonly used.
 First, a foreign gene is inserted into a bacterial plasmid to produce a recombinant DNA
molecule.
 The plasmid is returned to a bacterial cell, producing a recombinant bacterium, which
reproduces to form a clone of identical cells.
 Every time the bacterium reproduces, the recombinant plasmid is replicated as well.
 Under suitable conditions, the bacterial clone will make the protein encoded by the
foreign gene.
 The potential uses of cloned genes fall into two general categories.
 First, the goal may be to produce a protein product.
Biology Chapter Notes
  For example, bacteria carrying the gene for human growth hormone can produce
large quantities of the hormone.
 Alternatively, the goal may be to prepare many copies of the gene itself.
 This may enable scientists to determine the gene’s nucleotide sequence or provide
an organism with a new metabolic capability by transferring a gene from another
organism.
 Most protein-coding genes exist in only one copy per genome, so the ability to clone
rare DNA fragments is very valuable.
Restriction enzymes are used to make recombinant DNA.
 Gene cloning and genetic engineering were made possible by the discovery of restriction
enzymes that cut DNA molecules at specific locations.
 In nature, bacteria use restriction enzymes to cut foreign DNA, to protect themselves
against phages or other bacteria.
 They work by cutting up the foreign DNA, a process called restriction.
 Most restriction enzymes are very specific, recognizing short DNA nucleotide sequences
and cutting at specific points in these sequences.
 Bacteria protect their own DNA by methylating the sequences recognized by these
enzymes.
 Each restriction enzyme cleaves a specific sequence of bases or restriction site.
 These are often a symmetrical series of four to eight bases on both strands running in
opposite directions.
 If the restriction site on one strand is 3’-CTTAAG-5’, the complementary strand is
5’-GAATTC-3’.
 Because the target sequence usually occurs (by chance) many times on a long DNA
molecule, an enzyme will make many cuts.
 Copies of a DNA molecule will always yield the same set of restriction fragments
when exposed to a specific enzyme.
 Restriction enzymes cut covalent sugar-phosphate backbones of both strands, often in a
staggered way that creates single-stranded sticky ends.
 These extensions can form hydrogen-bonded base pairs with complementary single-
stranded stretches (sticky ends) on other DNA molecules cut with the same restriction
enzyme.
 These DNA fusions can be made permanent by DNA ligase, which seals the strand by
catalyzing the formation of covalent bonds to close up the sugar-phosphate backbone.
 Restriction enzymes and DNA ligase can be used to make a stable recombinant DNA
molecule, with DNA that has been spliced together from two different organisms.
Eukaryotic genes can be cloned in bacterial plasmids.
 Recombinant plasmids are produced by splicing restriction fragments from foreign DNA
into plasmids.
 The original plasmid used to produce recombinant DNA is called a cloning vector,
defined as a DNA molecule that can carry foreign DNA into a cell and replicate there.
 Bacterial plasmids are widely used as cloning vectors for several reasons.
 They can be easily isolated from bacteria, manipulated to form recombinant plasmids
by in vitro insertion of foreign DNA, and then reintroduced into bacterial cells.

Biology Chapter Notes

 Bacterial cells carrying the recombinant plasmid reproduce rapidly, replicating the
inserted foreign DNA.
 The process of cloning a human gene in a bacterial plasmid can be divided into six steps.
o The first step is the isolation of vector and gene-source DNA.
 The source DNA comes from human tissue cells grown in lab culture.
 The source of the plasmid is typically E. coli.
 This plasmid carries two useful genes, ampR, conferring resistance to the antibiotic
ampicillin and lacZ, encoding the enzyme ß-galactosidase that catalyzes the hydrolysis
of sugar.
 The plasmid has a single recognition sequence, within the lacZ gene, for the restriction
enzyme used.
o DNA is inserted into the vector.
 Both the plasmid and human DNA are digested with the same restriction enzyme. The
enzyme cuts the plasmid DNA at its single restriction site within the lacZ gene. It cuts
the human DNA at many sites, generating thousands of fragments. One fragment
carries the human gene of interest. All the fragments—bacterial and human—have
complementary sticky ends.
o The human DNA fragments are mixed with the cut plasmids, and base-pairing takes
place between complementary sticky ends.
 DNA ligase is added to permanently join the base-paired fragments.
 Some of the resulting recombinant plasmids contain human DNA fragments.
o The recombinant plasmids are mixed with bacteria that are lacZ−, unable to hydrolyze
lactose.
 This creates a diverse pool of bacteria: some bacteria that have taken up the desired
recombinant plasmid DNA, and other bacteria that have taken up other DNA, both
recombinant and nonrecombinant.
o The transformed bacteria are plated on a solid nutrient medium containing ampicillin
and a molecular mimic of lactose called X-gal.
 Only bacteria that have the ampicillin-resistance (ampR) plasmid will grow.
 Each reproducing bacterium forms a clone by repeating cell divisions, generating a
colony of cells on the agar.
 The lactose mimic in the medium is used to identify plasmids that carry foreign DNA.
 Bacteria with plasmids lacking foreign DNA stain blue when ß-galactosidase from
the intact lacZ gene hydrolyzes X-gal.
 Bacteria with plasmids containing foreign DNA inserted into the lacZ gene are
white because they lack ß-galactosidase.
o Cell clones with the right gene are identified.
 In the final step, thousands of bacterial colonies with foreign DNA must be sorted
through to find those containing the gene of interest.
 One technique, nucleic acid hybridization, depends on base-pairing between the gene
and a complementary sequence, a nucleic acid probe, on another nucleic acid
molecule.
 The sequence of the RNA or DNA probe depends on knowledge of at least part of
the sequence of the gene of interest.
 A radioactive or fluorescent tag is used to label the probe.
 The probe will hydrogen-bond specifically to complementary single strands of the
desired gene.

Biology Chapter Notes

  After denaturating (separating) the DNA strands in the bacterium, the probe will
bind with its complementary sequence, tagging colonies with the targeted gene.
Cloned genes are stored in DNA libraries.
 In the “shotgun” cloning approach described above, a mixture of fragments from the
entire genome is included in thousands of different recombinant plasmids.
 A complete set of recombinant plasmid clones, each carrying copies of a particular
segment from the initial genome, forms a genomic library.
 The library can be saved and used as a source of other genes or for gene mapping.
 In addition to plasmids, certain bacteriophages are also common cloning vectors for
making genomic libraries.
 Fragments of foreign DNA can be spliced into a phage genome using a restriction
enzyme and DNA ligase.
 An advantage of using phage as vectors is that phage can carry larger DNA inserts than
plasmids can.
 The recombinant phage DNA is packaged in a capsid in vitro and allowed to infect a
bacterial cell.
 Infected bacteria produce new phage particles, each with the foreign DNA.
 A more limited kind of gene library can be developed by starting with mRNA extracted
from cells.
 The enzyme reverse transcriptase is used to make single-stranded DNA transcripts of the
mRNA molecules.
 The mRNA is enzymatically digested, and a second DNA strand complementary to the
first is synthesized by DNA polymerase.
 This double-stranded DNA, called complementary DNA (cDNA), is modified by the
addition of restriction sites at each end.
 Finally, the cDNA is inserted into vector DNA.
 A cDNA library represents that part of a cell’s genome that was transcribed in the
starting cells.
 This is an advantage if a researcher wants to study the genes responsible for
specialized functions of a particular kind of cell.
 By making cDNA libraries from cells of the same type at different times in the life
of an organism, one can trace changes in the patterns of gene expression.
 If a researcher wants to clone a gene but is unsure in what cell type it is expressed or
unable to obtain that cell type, a genomic library will likely contain the gene.
 A researcher interested in the regulatory sequences or introns associated with a gene will
need to obtain the gene from a genomic library.
 These sequences are missing from the processed mRNAs used in making a cDNA
library.
Eukaryote genes can be expressed in prokaryotic host cells.
 A clone can sometimes be screened for a desired gene based on detection of its encoded
protein.
 Inducing a cloned eukaryotic gene to function in a prokaryotic host can be difficult.
 One way around this is to insert an expression vector, a cloning vector containing a
highly active prokaryotic promoter, upstream of the restriction site.

Biology Chapter Notes

  The prokaryotic host will then recognize the promoter and proceed to express the
foreign gene that has been linked to it.
 Such expression vectors allow the synthesis of many eukaryotic proteins in prokaryotic
cells.
 The presence of long noncoding introns in eukaryotic genes may prevent correct
expression of these genes in prokaryotes, which lack RNA-splicing machinery.
 This problem can be surmounted by using a cDNA form of the gene inserted in a
vector containing a bacterial promoter.
 Molecular biologists can avoid incompatibility problems by using eukaryotic cells as
hosts for cloning and expressing eukaryotic genes.
 Yeast cells, single-celled fungi, are as easy to grow as bacteria and, unlike most
eukaryotes, have plasmids.
 Scientists have constructed yeast artificial chromosomes (YACs) that combine the
essentials of a eukaryotic chromosome (an origin site for replication, a centromere, and
two telomeres) with foreign DNA.
 These chromosome-like vectors behave normally in mitosis and can carry more DNA
than a plasmid.
 Another advantage of eukaryotic hosts is that they are capable of providing the
posttranslational modifications that many proteins require.
 Such modifications may include adding carbohydrates or lipids.
 For some mammalian proteins, the host must be an animal cell to perform the
necessary modifications.
 Many eukaryotic cells can take up DNA from their surroundings, but inefficiently.
 Several techniques facilitate entry of foreign DNA into eukaryotic cells.
 In electroporation, brief electrical pulses create a temporary hole in the plasma
membrane through which DNA can enter.
 Alternatively, scientists can inject DNA into individual cells using microscopically
thin needles.
 Once inside the cell, the DNA is incorporated into the cell’s DNA by natural genetic
recombination.
The polymerase chain reaction (PCR) amplifies DNA in vitro.
 DNA cloning is the best method for preparing large quantities of a particular gene or other
DNA sequence.
 When the source of DNA is scanty or impure, the polymerase chain reaction (PCR) is
quicker and more selective.
 This technique can quickly amplify any piece of DNA without using cells.
 The DNA is incubated in a test tube with special DNA polymerase, a supply of
nucleotides, and short pieces of single-stranded DNA as a primer.
 PCR can make billions of copies of a targeted DNA segment in a few hours.
 This is faster than cloning via recombinant bacteria.
 In PCR, a three-step cycle—heating, cooling, and replication—brings about a chain
reaction that produces an exponentially growing population of identical DNA molecules.
 The reaction mixture is heated to denature the DNA strands.

Biology Chapter Notes

  The mixture is cooled to allow hydrogen-bonding of short, single-stranded DNA
primers complementary to sequences on opposite sides at each end of the target
sequence.
 A heat-stable DNA polymerase extends the primers in the 5’  3’ direction.
 If a standard DNA polymerase were used, the protein would be denatured along with the
DNA during the heating step.
 The key to easy PCR automation was the discovery of an unusual DNA polymerase,
isolated from prokaryotes living in hot springs, which can withstand the heat needed to
separate the DNA strands at the start of each cycle.
 PCR is very specific.
 By their complementarity to sequences bracketing the targeted sequence, the primers
determine the DNA sequence that is amplified.
 PCR can make many copies of a specific gene before cloning in cells, simplifying the
task of finding a clone with that gene.
 PCR is so specific and powerful that only minute amounts of partially degraded DNA
need be present in the starting material.
 Occasional errors during PCR replication impose limits to the number of good copies that
can be made when large amounts of a gene are needed.
 Increasingly, PCR is used to make enough of a specific DNA fragment to clone it
merely by inserting it into a vector.
 Devised in 1985, PCR has had a major impact on biological research and technology.
 PCR has amplified DNA from a variety of sources:
 Fragments of ancient DNA from a 40,000-year-old frozen woolly mammoth.
 DNA from footprints or tiny amounts of blood or semen found at the scenes of
violent crimes.
 DNA from single embryonic cells for rapid prenatal diagnosis of genetic disorders.
 DNA of viral genes from cells infected with HIV.

Concept 20.2 Restriction fragment analysis detects DNA differences that affect
restriction sites
 Once we have prepared homogeneous samples of DNA, each containing a large number
of identical segments, we can begin to ask some interesting questions about specific genes
and their functions.
 Does a particular gene differ from person to person?
 Are certain alleles associated with a hereditary disorder?
 Where in the body and when during development is a gene expressed?
 What is the location of a gene in the genome?
 Is expression of a particular gene related to expression of other genes?
 How has a gene evolved, as revealed by interspecific comparisons?
 To answer these questions, we need to know the nucleotide sequence of the gene and its
counterparts in other individuals and species, as well as its expression pattern.
 One indirect method of rapidly analyzing and comparing genomes is gel electrophoresis.
 Gel electrophoresis separates macromolecules—nucleic acids or proteins—on the basis
of their rate of movement through a gel in an electrical field.
Biology Chapter Notes
  Rate of movement depends on size, electrical charge, and other physical properties
of the macromolecules.
 In restriction fragment analysis, the DNA fragments produced by restriction enzyme
digestion of a DNA molecule are sorted by gel electrophoresis.
 When the mixture of restriction fragments from a particular DNA molecule undergoes
electrophoresis, it yields a band pattern characteristic of the starting molecule and the
restriction enzyme used.
 The relatively small DNA molecules of viruses and plasmids can be identified simply
by their restriction fragment patterns.
 The separated fragments can be recovered undamaged from gels, providing pure
samples of individual fragments.
 We can use restriction fragment analysis to compare two different DNA molecules
representing, for example, different alleles of a gene.
 Because the two alleles differ slightly in DNA sequence, they may differ in one or
more restriction sites.
 If they do differ in restriction sites, each will produce different-sized fragments when
digested by the same restriction enzyme.
 In gel electrophoresis, the restriction fragments from the two alleles will produce
different band patterns, allowing us to distinguish the two alleles.
 Restriction fragment analysis is sensitive enough to distinguish between two alleles of a
gene that differ by only one base pair in a restriction site.
 A technique called Southern blotting combines gel electrophoresis with nucleic acid
hybridization.
 Although electrophoresis will yield too many bands to distinguish individually, we can
use nucleic acid hybridization with a specific probe to label discrete bands that derive
from our gene of interest.
 The probe is a radioactive single-stranded DNA molecule that is complementary to the
gene of interest.
 Southern blotting reveals not only whether a particular sequence is present in the
sample of DNA, but also the size of the restriction fragments that contain the sequence.
 One of its many applications is to identify heterozygous carriers of mutant alleles
associated with genetic disease.
 In the example below, we compare genomic DNA samples from three individuals: an
individual who is homozygous for the normal ß-globin allele, a homozygote for sickle-cell
allele, and a heterozygote.
 We combine several molecular techniques to compare DNA samples from three
individuals.
o We start by adding the same restriction enzyme to each of the three samples to produce
restriction fragments.
o We then separate the fragments by gel electrophoresis.
o We transfer the DNA fragments from the gel to a sheet of nitrocellulose paper, still
separated by size.
 This also denatures the DNA fragments.
o Bathing the sheet in a solution containing a radioactively labeled probe allows the
probe to attach by base-pairing to the DNA sequence of interest.
o We can visualize bands containing the label with autoradiography.

Biology Chapter Notes

 The band pattern for the heterozygous individual will be a combination of the patterns for
the two homozygotes.
Restriction fragment length differences are useful as genetic markers.
 Restriction fragment analysis can be used to examine differences in noncoding DNA as
well.
 Differences in DNA sequence on homologous chromosomes that produce different
restriction fragment patterns are scattered abundantly throughout genomes, including the
human genome.
 A restriction fragment length polymorphism (RFLP or Rif-lip) can serve as a genetic
marker for a particular location (locus) in the genome.
 RFLPs are detected and analyzed by Southern blotting, frequently using the entire genome
as the DNA starting material.
 The probe is complementary to the sequence under consideration.
 Because RFLP markers are inherited in a Mendelian fashion, they can serve as genetic
markers for making linkage maps.
 The frequency with which two RFPL markers—or an RFLP marker and a certain allele
for a gene—are inherited together is a measure of the closeness of the two loci on a
chromosome.

Concept 20.3 Entire genomes can be mapped at the DNA level

 The field of genomics is based on comparisons among whole sets of genes and their
interactions.
 As early as 1980, Daniel Botstein and his colleagues proposed that the DNA variations
reflected in RFLPs could serve as the basis of an extremely detailed map of the entire
human genome.
 Since then, researchers have used such markers in conjunction with the tools and
techniques of DNA technology to develop detailed maps of the genomes of a number
of species.
 The most ambitious research project made possible by DNA technology has been the
sequencing of the human genome, officially begun as the Human Genome Project in
1990.
 This effort was largely completed in 2003 when the nucleotide sequence of the vast
majority of DNA in the human genome was obtained.
 An international, publicly funded consortium of researchers at universities and
research institutes has taken this project through three stages that provided
progressively more detailed views of the human genome: genetic (linkage) mapping,
physical mapping, and DNA sequencing.
 In addition to mapping human DNA, the genomes of other organisms important to
biological research are also being mapped.
 Completed sequences include those of E. coli and other prokaryotes, Saccharomyces
cerevisiae (yeast), Drosophila melanogaster (fruit fly), Mus musculus (mouse), and
others.
 These genomes are providing important insights of general biological significance.
 In mapping a large genome, cytogenetic maps based on karyotyping and fluorescence
hybridization provide a starting point for more detailed mapping.
Biology Chapter Notes
  The first stage is to construct a linkage map of several thousand markers spaced
throughout the chromosomes.
 The order of the markers and the relative distances between them on such a map are
based on recombination frequencies.
 The markers can be genes or any other identifiable sequences in DNA, such as RFLPs
or simple sequence DNA.
 The human map with 5,000 genetic markers enabled researchers to locate other markers,
including genes, by testing for genetic linkage with the known markers.
 The next step was converting the relative distances to some physical measure, usually the
number of nucleotides along the DNA.
 For whole-genome mapping, a physical map is made by cutting the DNA of each
chromosome into identifiable restriction fragments and then determining the original
order of the fragments.
 The key is to make fragments that overlap and then use probes or automated nucleotide
sequencing of the ends to find the overlaps.
 When working with large genomes, researchers carry out several rounds of DNA cutting,
cloning, and physical mapping.
 The first cloning vector is often a yeast artificial chromosome (YAC), which can carry
inserted fragments up to a million base pairs long, or a bacterial artificial
chromosome (BAC), which can carry inserts of 100,000 to 500,000 base pairs.
 After the order of these long fragments has been determined, each fragment is cut into
pieces that are cloned in plasmids or phages, ordered, and finally sequenced.
 The complete nucleotide sequence of a genome is the ultimate map.
 Starting with a pure preparation of many copies of a relatively short DNA fragment,
the nucleotide sequence of the fragment can be determined by a sequencing machine.
 The usual sequencing technique combines DNA labeling, DNA synthesis with special
chain-terminating nucleotides, and high-resolution gel electrophoresis.
 A major thrust of the Human Genome Project has been the development of technology
for faster sequencing and more sophisticated computer software for analyzing and
assembling the partial sequences.
 One common method of sequencing DNA, the Sanger or dideoxyribonucleotide chain-
termination method, is similar to PCR.
 Inclusion of special dideoxyribonucleotides in the reaction mix ensures that rather than
copying the whole template, fragments of various lengths will be synthesized.
 These dideoxyribonucleotides, marked radioactively or fluorescently, terminate
elongation when they are incorporated randomly into the growing strand because they
lack a 3’-OH to attach the next nucleotide.
 The order of these fragments via gel electrophoresis can be interpreted as the nucleotide
sequence.
 While the public consortium followed a hierarchical, three-stage approach for sequencing
an entire genome, J. Craig Venter decided in 1992 to try a whole-genome shotgun
approach.
 This used powerful computers to assemble sequences from random fragments,
skipping the first two steps.
 The worth of his approach was demonstrated in 1995 when he and colleagues reported the
complete sequence of a bacterium.

Biology Chapter Notes

 His private company, Celera Genomics, finished the sequence of Drosophila
melanogaster in 2000.
 In February 2001, Celera and the public consortium separately announced sequencing
more than 90% of the human genome.
 Sequencing of the human genome is now virtually complete, although some gaps remain
to be mapped.
 Areas with repetitive DNA and certain parts of the chromosomes of multicellular
organisms resist detailed mapping by the usual methods.
 On one level, genome sequences of humans and other organisms are simply lists of
nucleotide bases.
 On another level, analyses of these sequences and comparisons between species are
leading to exciting discoveries.

Concept 20.4 Genome sequences provide clues to important biological questions

 Genomics, the study of genomes and their interactions, is yielding new insights into
fundamental questions about genome organization, the regulation of gene expression,
growth and development, and evolution.
 Rather than inferring genotype from phenotype as classical geneticists did, molecular
geneticists can study genes directly.
 This approach poses the challenge of determining phenotype from genotype.
 Starting with a long DNA sequence, how does a researcher recognize genes and
determine their function?
 DNA sequences are collected in computer data banks that are available via the Internet to
researchers everywhere.
 Special software scans the sequences for the telltale signs of protein-coding genes,
looking for start and stop signals, RNA-splicing sites, and other features.
 The software also looks for expressed sequence tags (ESTs), sequences similar to those in
known genes.
 From these clues, researchers collect a list of gene candidates.
 Although genome size increases from prokaryotes to eukaryotes, it does not always
correlate with biological complexity among eukaryotes.
 One flowering plant has a genome 40 times the size of the human genome.
 An organism may have fewer genes than expected from the size of its genome.
 The estimated number of human genes is 25,000 or fewer, only about one-and-a-half
times the number found in the fruit fly.
 This is surprising, given the great diversity of cell types in humans.
 Genes account for only a small fraction of the human genome.
 Much of the enormous amount of noncoding DNA in the human genome consists of
repetitive DNA and unusually long introns.
 By doing more mixing and matching of modular elements, humans—and vertebrates in
general—reach greater complexity than flies or worms.
 Gene expression is regulated in more subtle and complicated ways in vertebrates than
in other organisms.

Biology Chapter Notes

  The typical human gene specifies several different polypeptides by using different
combinations of exons.
 Nearly all human genes contain multiple exons, and an estimated 75% of these
multiexon genes are alternatively spliced.
 Along with this is additional polypeptide diversity via posttranslational processing.
 There are a much greater number of possible interactions between gene products as
a result of greater polypeptide diversity.
 About half of the human genes were already known before the Human Genome Project.
 To determine what the others are and what they may do, scientists compare the sequences
of new gene candidates with those of known genes.
 In some cases, the sequence of a new gene candidate will be similar in part to that of a
known gene, suggesting similar function.
 In other cases, the new sequences will be similar to a sequence encountered before, but
of unknown function.
 In still other cases, the sequence is entirely unlike anything ever seen before.
 About 30% of the E. coli genes are new to us.
 How can scientists determine the function of new genes identified by genome sequencing
and comparative analysis?
 One way to determine their function is to disable the gene and observe the consequences.
 Using in vitro mutagenesis, specific mutations are introduced into a cloned gene,
altering or destroying its function.
 When the mutated gene is returned to the cell, it may be possible to determine the
function of the normal gene by examining the phenotype of the mutant.
 Researchers may put a mutated gene into cells from the early embryo of an organism
to study the role of the gene in development and functioning of the whole organisms.
 In nonmammalian organisms, a simpler and faster method, RNA interference (RNAi),
has been applied to silence the expression of selected genes.
 This method uses synthetic double-stranded RNA molecules matching the sequences
of a particular gene to trigger breakdown of the gene’s mRNA.
 The RNAi technique has had limited success in mammalian cells but has been valuable
in analyzing the functions of genes in nematodes and fruit flies.
 In one study, RNAi was used to prevent expression of 86% of the genes in early
nematode embryos, one gene at a time.
 Analysis of the phenotypes of the worms that developed from these embryos allowed
the researchers to group most of the genes into functional groups.
 A major goal of genomics is to learn how genes act together to produce a functioning
organism.
 Part of the explanation for how humans get along with so few genes probably lies in
the unusual complexity of networks of interactions among genes and their products.
 As the sequences of entire genomes of several organisms neared completion, some
researchers began to investigate which genes are transcribed under different situations.
 They also looked for groups of genes that are expressed in a coordinated pattern to
identify global patterns or networks of expression.
 The basic strategy in global expression is to isolate mRNAs from particular cells and use
the mRNA as a template to build cDNA by reverse transcription.
 Each cDNA can be compared to other collections of DNA by hybridization.
Biology Chapter Notes
  This will reveal which genes are active at different developmental stages, in different
tissues, or in tissues in different states of health.
 Automation has allowed scientists to detect and measure the expression of thousands of
genes at one time using DNA microarray assays.
 Tiny amounts of a large number of single-stranded DNA fragments representing
different genes are fixed on a glass slide in a tightly spaced grid (array).
 The array is called a DNA chip.
 The fragments, sometimes representing all the genes of an organism, are tested for
hybridization with various samples of fluorescently labeled cDNA molecules.
 Spots where any of the cDNA hybridizes fluoresce with an intensity indicating the relative
amount of the mRNA that was in the tissue.
 Ultimately, information from microarray assays should provide us a grander view: how
ensembles of genes interact to form a living organism.
 DNA microarray assays are being used to compare cancerous versus noncancerous
tissues.
 This may lead to new diagnostic techniques and biochemically targeted treatments,
as well as a fuller understanding of cancer.
 The genomes of about 150 species have been completely or almost completely sequenced
by the spring of 2004, with many more in progress.
 Most of these are prokaryotes, including 20 archaean genomes.
 Among the 20 eukaryotic species are vertebrates, invertebrates, and plants.
 Comparisons of genome sequences from different species allow us to determine the
evolutionary relationships even between distantly related organisms.
 The more similar the nucleotide sequences between two species, the more closely related
these species are in their evolutionary history.
 Comparisons of the complete genome sequences of bacteria, archaea, and eukarya support
the theory that these are the three fundamental domains of life.
 Comparative genome studies confirm the relevance of research on simpler organisms to
our understanding of human biology.
 The yeast genome is proving useful in helping us to understand the human genome.
 Comparisons of noncoding sequences in the human genome to those in the much
smaller yeast genome revealed regions with highly conserved sequences that are
important regulatory sequences in both species.
 Several yeast protein-coding genes are so similar to certain human disease genes
that researchers have figured out the functions of the disease genes by studying
their normal yeast counterparts.
 The genomes of two closely related species are likely to be similarly organized.
 Once the sequence and organization of one genome is known, it can greatly accelerate
the mapping of a related genome.
 For example, the mouse genome can be mapped quickly, with the human genome
serving as a guide.
 The small number of gene differences between closely related species makes it easier to
correlate phenotypic differences between species with particular genetic differences.
 One gene that is clearly different in chimps and humans appears to function in speech.
 Researchers may determine what a human disease gene does by studying its normal
counterpart in mice, who share 80% of our genes.
Biology Chapter Notes
 The next step after mapping and sequencing genomes is proteomics, the systematic study
of full protein sets (proteomes) encoded by genomes.
 One challenge is the sheer number of proteins in humans and our close relatives
because of alternative RNA splicing and posttranslational modifications.
 Collecting all the proteins produced by an organism will be difficult because a cell’s
proteins differ with cell type and its state.
 Unlike DNA, proteins are extremely varied in structure and chemical and physical
properties.
 Because proteins are the molecules that actually carry out cell activities, we must study
them to learn how cells and organisms function.
 Complete catalogs of genes and proteins will change the discipline of biology
dramatically.
 With such catalogs in hand, researchers are turning their attention to the functional
integration of individual components in biological systems.
 Advances in bioinformatics, the application of computer science and mathematics to
genetic and other biological information, will play a crucial role in dealing with the
enormous mass of data.
 These analyses will provide understanding of the spectrum of genetic variation in humans.
 Because we are all probably descended from a small population living in Africa
150,000 to 200,000 years ago, the amount of DNA variation in humans is small.
 Most of our diversity is in the form of single nucleotide polymorphisms (SNPs),
single base-pair variations.
 In humans, SNPs occur about once in 1,000 bases, meaning that any two humans
are 99.9% identical.
 The locations of the human SNP sites will provide useful markers for studying human
evolution, the differences between human populations, and the migratory routes of
human populations throughout history.
 SNPs and other polymorphisms will be valuable markers for identifying disease genes
and genes that influence our susceptibility to diseases, toxins, or drugs.
 This will change the practice of 21st-century medicine.

Concept 20.5 The practical applications of DNA technology affect our lives in many
ways
DNA technology is reshaping medicine and the pharmaceutical industry.
 Modern biotechnology is making enormous contributions both to the diagnosis of diseases
and in the development of pharmaceutical products.
 The identification of genes whose mutations are responsible for genetic diseases may
lead to ways to diagnose, treat, or even prevent these conditions.
 Susceptibility to many “nongenetic” diseases, from arthritis to AIDS, is influenced by
a person’s genes.
 Diseases of all sorts involve changes in gene expression within the affected genes and
within the patient’s immune system.
 DNA technology can identify these changes and lead to the development of targets for
prevention or therapy.
 PCR and labeled nucleic acid probes can track down the pathogens responsible for
infectious diseases.
Biology Chapter Notes
  For example, PCR can amplify and thus detect HIV DNA in blood and tissue samples,
detecting an otherwise elusive infection.
 RNA cannot be directly amplified by PCR.
 The RNA genome is first converted to double-stranded cDNA by a technique called
RT-PCR, using a probe specific for one of the HIV genes.
 Medical scientists can use DNA technology to identify individuals with genetic diseases
before the onset of symptoms, even before birth.
 Genetic disorders are diagnosed by using PCR and primers corresponding to cloned
disease genes, and then sequencing the amplified product to look for the disease-
causing mutation.
 Cloned disease genes include those for sickle-cell disease, hemophilia, cystic
fibrosis, Huntington’s disease, and Duchenne muscular dystrophy.
 It is even possible to identify symptomless carriers of these diseases.
 It is possible to detect abnormal allelic forms of genes, even in cases in which the gene
has not yet been cloned.
 The presence of an abnormal allele can be diagnosed with reasonable accuracy if a
closely linked RFLP marker has been found.
 The closeness of the marker to the gene makes crossing over between them unlikely,
and the marker and gene will almost always be inherited together.
 Techniques for gene manipulation hold great potential for treating disease by gene
therapy, the alteration of an afflicted individual’s genes.
 A normal allele is inserted into somatic cells of a tissue affected by a genetic disorder.
 For gene therapy of somatic cells to be permanent, the cells that receive the normal
allele must be ones that multiply throughout the patient’s life.
 Bone marrow cells, which include the stem cells that give rise to blood and immune
system cells, are prime candidates for gene therapy.
 A normal allele can be inserted by a retroviral vector into bone marrow cells removed
from the patient.
 If the procedure succeeds, the returned modified cells will multiply throughout the
patient’s life and express the normal gene, providing missing proteins.
 This procedure was used in a 2000 trial involving ten young children with SCID (severe
combined immunodeficiency disease), a genetic disease in which bone marrow cells do
not produce a vital enzyme because of a single defective gene.
 Nine of the children showed significant improvement after two years.
 However, two of the children developed leukemia.
 It was discovered that the retroviral vector used to carry the normal allele into bone
marrow cells had inserted near a gene involved in proliferation and development of
blood cells, causing leukemia.
 The trial has been suspended until researchers learn how to control the location of
insertion of the retroviral vectors.
 Gene therapy poses many technical questions.
 These include regulation of the activity of the transferred gene to produce the
appropriate amount of the gene product at the right time and place.
 In addition, the insertion of the therapeutic gene must not harm other necessary cell
functions.
 Gene therapy raises some difficult ethical and social questions.

Biology Chapter Notes

  Some critics suggest that tampering with human genes, even for those with life-
threatening diseases, is wrong.
 They argue that this will lead to the practice of eugenics, a deliberate effort to control
the genetic makeup of human populations.
 The most difficult ethical question is whether we should treat human germ-line cells to
correct the defect in future generations.
 In laboratory mice, transferring foreign genes into egg cells is now a routine procedure.
 Once technical problems relating to similar genetic engineering in humans are solved,
we will have to face the question of whether it is advisable, under any circumstances,
to alter the genomes of human germ lines or embryos.
 Should we interfere with evolution in this way?
 From a biological perspective, the elimination of unwanted alleles from the gene pool
could backfire.
 Genetic variation is a necessary ingredient for the survival of a species as
environmental conditions change with time.
 Genes that are damaging under some conditions could be advantageous under other
conditions, as in the example of the sickle-cell allele.
 DNA technology has been used to create many useful pharmaceuticals, mostly proteins.
 By transferring the gene for a protein into a host that is easily grown in culture, one can
produce large quantities of normally rare proteins.
 By including highly active promoters (and other control elements) into vector DNA,
the host cell can be induced to make large amounts of the product of a gene.
 In addition, host cells can be engineered to secrete a protein, simplifying the task of
purification.
 One of the first practical applications of gene splicing was the production of mammalian
hormones and other mammalian regulatory proteins in bacteria.
 These include human insulin, human growth factor (HGF), and tissue plasminogen
activator.
 Human insulin, produced by bacteria, is superior for the control of diabetes to the older
treatment of pig or cattle insulin.
 Human growth hormone benefits children with hypopituitarism, a form of dwarfism.
 Tissue plasminogen activator (TPA) helps dissolve blood clots and reduce the risk of
future heart attacks.
 Like many such drugs, it is expensive.
 New pharmaceutical products are responsible for novel ways of fighting diseases that do
not respond to traditional drug treatments.
 One approach is to use genetically engineered proteins that either block or mimic
surface receptors on cell membranes.
 For example, one experimental drug mimics a receptor protein that HIV bonds to when
entering white blood cells. HIV binds to the drug instead and fails to enter the blood
cells.
 DNA technology can also be used to produce vaccines, which stimulate the immune
system to defend against specific pathogens.
 A vaccine is a harmless variant or derivative of a pathogen that stimulates the immune
system.
 Traditional vaccines are either killed microbes or attenuated microbes that do not cause
disease.
Biology Chapter Notes
  Both are similar enough to the active pathogen to trigger an immune response.
 Recombinant DNA techniques can generate large amounts of a specific protein molecule
normally found on the pathogen’s surface.
 If this protein triggers an immune response against the intact pathogen, then it can be
used as a vaccine.
 Alternatively, genetic engineering can modify the genome of the pathogen to attenuate
it.
 These attenuated microbes are often more effective than a protein vaccine because
they usually trigger a greater response by the immune system.
 Pathogens attenuated by gene-splicing techniques may be safer than the natural
mutants traditionally used.
DNA technology offers forensic, environmental, and agricultural applications.
 In violent crimes, blood, semen, or traces of other tissues may be left at the scene or on
the clothes or other possessions of the victim or assailant.
 If enough tissue is available, forensic laboratories can determine blood type or tissue type
by using antibodies for specific cell surface proteins.
 However, these tests require relatively large amounts of fresh tissue.
 Also, this approach can only exclude a suspect.
 DNA testing can identify the guilty individual with a much higher degree of certainty,
because the DNA sequence of every person is unique (except for identical twins).
 RFPL analysis by Southern blotting can detect similarities and differences in DNA
samples and requires only a tiny amount of blood or other tissue.
 Radioactive probes mark electrophoresis bands that contain certain RFLP markers.
 As few as five markers from an individual can be used to create a DNA fingerprint.
 The probability that two people who are not identical twins have the same DNA
fingerprint is very small.
 DNA fingerprints can be used forensically to present evidence to juries in murder trials.
 An autoradiograph of RFLP bands of samples from a murder victim, the defendant,
and the defendant’s clothes may be consistent with the conclusion that the blood on the
clothes is from the victim, not the defendant.
 The forensic use of DNA fingerprinting extends beyond violent crimes.
 For instance, DNA fingerprinting can be used to settle conclusively questions of
paternity.
 DNA fingerprinting recently provided strong evidence that Thomas Jefferson fathered
at lease one of the children of his slave Sally Hemings.
 These techniques can also be used to identify the remains of individuals killed in
natural or man-made disasters.
 Variations in the lengths of repeated base sequences are increasingly used as markers in
DNA fingerprinting.
 Such polymorphic genetic loci have repeating units of only a few base pairs and are
highly variable from person to person.
 Individuals may vary in the numbers of simple tandem repeats (STRs) at a locus.
 Restriction fragments with STRs vary in size among individuals because of differences
in STR lengths.
 PCR is often used to amplify selectively particular STRs or other markers before
electrophoresis, especially if the DNA is poor or in minute quantities.
Biology Chapter Notes
 The DNA fingerprint of an individual would be truly unique if it were feasible to perform
restriction fragment analysis on the entire genome.
 In practice, forensic DNA tests focus on only about five tiny regions of the genome.
 The probability that two people will have identical DNA fingerprints in these highly
variable regions is typically between one in 100,000 and one in a billion.
 The exact figure depends on the number of markers and the frequency of those
markers in the population.
 Despite problems that might arise from insufficient statistical data, human error, or
flawed evidence, DNA fingerprinting is now accepted as compelling evidence.
 Increasingly, genetic engineering is being applied to environmental work.
 Scientists are engineering the metabolism of microorganisms to help cope with some
environmental problems.
 For example, genetically engineered microbes that can extract heavy metals from their
environments and incorporate the metals into recoverable compounds may become
important both in mining materials and cleaning up highly toxic mining wastes.
 In addition to the normal microbes that participate in sewage treatment, new microbes
that can degrade other harmful compounds are being engineered.
 Bacterial strains have been developed that can degrade some of the chemicals released
during oil spills.
 For many years, scientists have been using DNA technology to improve agricultural
productivity.
 DNA technology is now routinely used to make vaccines and growth hormones for
farm animals.
 Transgenic organisms are made by introducing genes from one species into the genome
of another organism.
 An egg cell is removed from a female animal and fertilized in vitro.
 Meanwhile, the desired gene is obtained from another organism and cloned.
 The cloned DNA is injected directly into the nuclei of the fertilized egg.
 Some of the cells integrate the transgene into their genomes and express the foreign
gene.
 The engineered embryos are surgically implanted in a surrogate mother.
 Transgenic animals may be created to exploit the attributes of new genes (for example,
genes for faster growth or larger muscles).
 Other transgenic organisms are pharmaceutical “factories”—producers of large amounts
of otherwise rare substances for medical use.
 Transgenic farm mammals may secrete the gene product of interest in their milk.
 Researchers have engineered transgenic chickens that express large quantities of the
transgene’s product in their eggs.
 The human proteins produced by farm animals may or may not be structurally identical to
natural human proteins.
 Therefore, they have to be tested very carefully to ensure that they will not cause
allergic reactions or other adverse effects in patients receiving them.
 In addition, the health and welfare of transgenic farm animals are important issues, as
they often suffer from lower fertility or increased susceptibility to disease.
 Agricultural scientists have engineered a number of crop plants with genes for desirable
traits.
Biology Chapter Notes
  These include delayed ripening and resistance to spoilage and disease.
 Because a single transgenic plant cell can be grown in culture to generate an adult
plant, plants are easier to engineer than most animals.
 The Ti plasmid, from the soil bacterium Agrobacterium tumefaciens, is often used to
introduce new genes into plant cells.
 The Ti plasmid normally integrates a segment of its DNA into its host plant and
induces tumors.
 Foreign genes can be inserted into the Ti plasmid (a version that does not cause disease)
using recombinant DNA techniques.
 The recombinant plasmid can be put back into Agrobacterium, which then infects plant
cells, or introduced directly into plant cells.
 Genetic engineering is quickly replacing traditional plant-breeding programs, especially
for useful traits determined by one or a few genes, like herbicide or pest resistance.
 Use of genetically modified crops has reduced the need for chemical insecticides.
 Scientists are using gene transfer to improve the nutritional value of crop plants.
 For example, a transgenic rice plant has been developed that produces yellow grains
containing beta-carotene, which our bodies use to make vitamin A.
 Large numbers of young people in southeast Asia are deficient in vitamin A,
leading to vision impairment and increased disease rates.
 DNA technology has led to new alliances between the pharmaceutical industry and
agriculture.
 Plants can be engineered to produce human proteins for medical use and viral proteins
for use as vaccines.
 Several such “pharm” products are in clinical trials, including vaccines for hepatitis B
and an antibody that blocks the bacteria that cause tooth decay.
 The advantage of pharm plants is that large amounts of proteins might be made more
economically by plants than by cultured cells.
DNA technology raises important safety and ethical questions.
 The power of DNA technology has led to worries about potential dangers.
 Early concerns focused on the possibility that recombinant DNA technology might
create hazardous new pathogens.
 In response, scientists developed a set of guidelines that have become formal government
regulations in the United States and some other countries.
 Strict laboratory procedures are designed to protect researchers from infection by
engineered microbes and to prevent their accidental release.
 Some strains of microorganisms used in recombinant DNA experiments are genetically
crippled to ensure that they cannot survive outside the laboratory.
 Finally, certain obviously dangerous experiments have been banned.
 Today, most public concern centers on genetically modified (GM) organisms used in
agriculture.
 GM organisms have acquired one or more genes (perhaps from another species) by
artificial means.
 Salmon have been genetically modified by addition of a more active salmon growth
hormone gene.
 However, the majority of GM organisms in our food supply are not animals but crop
plants.
Biology Chapter Notes
 In 1999, the European Union suspended the introduction of new GM crops pending new
legislation.
 Early in 2000, negotiators from 130 countries, including the United States, agreed on a
Biosafety Protocol that requires exporters to identify GM organisms present in bulk
food shipments.
 Advocates of a cautious approach fear that GM crops might somehow be hazardous to
human health or cause ecological harm.
 In particular, transgenic plants might pass their new genes to close relatives in nearby
wild areas through pollen transfer.
 Transference of genes for resistance to herbicides, diseases, or insect pests may lead to
the development of wild “superweeds” that would be difficult to control.
 To date there is little good data either for or against any special health or environmental
risks posed by genetically modified crops.
 Today, governments and regulatory agencies are grappling with how to facilitate the use
of biotechnology in agriculture, industry, and medicine while ensuring that new products
and procedures are safe.
 In the United States, all projects are evaluated for potential risks by various regulatory
agencies, including the Food and Drug Administration, Environmental Protection
Agency, the National Institutes of Health, and the Department of Agriculture.
 These agencies are under increasing pressures from some consumer groups.
 As with all new technologies, developments in DNA technology have ethical overtones.
 Who should have the right to examine someone else’s genes?
 How should that information be used?
 Should a person’s genome be a factor in suitability for a job or eligibility for life
insurance?
 The power of DNA technology and genetic engineering demands that we proceed with
humility and caution.

Biology Chapter Notes

 Chapter 21 The Genetic Basis of Development
Chapter Notes

Overview: From Single Cell to Multicellular Organism

 The application of genetic analysis and DNA technology to the study of development has
brought about a revolution in our understanding of how a complex multicellular organism
develops from a single cell.
 In 1995, Swiss researchers identified a gene that functions as a master switch to trigger
the development of the eye in Drosophila.
 A similar gene triggers eye development in mammals.
 Developmental biologists are discovering remarkable similarities in the mechanisms
that shape diverse organisms.
 While geneticists were advancing from Mendel’s laws to an understanding of the
molecular basis of inheritance, developmental biologists were focusing on embryology.
 Embryology is the study of the stages of development leading from fertilized egg to
fully formed organism.
 In recent years, the concepts and tools of molecular genetics have reached a point where a
real synthesis of genetics and developmental biology has been possible.
 When the primary research goal is to understand broad biological principles, the organism
chosen for study is called a model organism.
 Researchers select model organisms that are representative of a larger group, suitable
for the questions under investigation, and easy to grow in the lab.
 For study of the connections between genes and development, suitable model organisms
have short generation times and small genomes that are suitable for genetic analysis.
 Model organisms used in developmental genetics include the fruit fly Drosophila
melanogaster, the nematode Caenorhabditis elegans, the mouse Mus musculus, the
zebra fish Danio rerio, and the plant Arabidopsis thaliana.
 The fruit fly Drosophila melanogaster was first chosen as a model organism by geneticist
T. H. Morgan and intensively studied by generations of geneticists after him.
 The fruit fly is small and easily grown in the laboratory.
 It has a generation time of only two weeks and produces many offspring.
 Embryos develop outside the mother’s body.
 There are vast amounts of information on its genes and other aspects of its biology.
 However, because first rounds of mitosis occur without cytokinesis, parts of its
development are superficially quite different from that of other organisms.
 Sequencing of the Drosophila genome was completed in 2000.
 It has 180 × 106 base pairs (180 Mb) and contains about 13,700 genes.
 The nematode Caenorhabditis elegans normally lives in the soil but is easily grown in
petri dishes.
 Only a millimeter long, it has a simple, transparent body with only a few cell types and
grows from zygote to mature adult in only three and a half days.
 Its genome has been sequenced. It is 97 Mb long and contains an estimated 19,000
genes.
 Because individuals are hermaphrodites, it is easy to detect recessive mutations.
Biology Chapter Notes
  Self-fertilization of heterozygotes produces some homozygous recessive offspring
with mutant phenotypes.
 Every adult C. elegans has exactly 959 somatic cells.
 These arise from the zygote in virtually the same way for every individual.
 By following all cell divisions with a microscope, biologists have constructed the
organism’s complete cell lineage, showing the ancestry of every cell in the adult
body.
 The mouse Mus musculus has a long history as a mammalian model of development.
 Much is known about its biology.
 The mouse genome is about 2,600 Mb long with about 25,000 genes, about the same
as the human genome.
 Researchers are adept at manipulating mouse genes to make transgenic mice and mice
in which particular genes are “knocked out” by mutation.
 Mice are complex animals with a genome as large as ours.
 Their embryos develop in the mother’s uterus, hidden from view.
 A second vertebrate model, the zebra fish Danio rerio, has some unique advantages.
 These small fish (2–4 cm long) are easy to breed in the laboratory in large numbers.
 The transparent embryos develop outside the mother’s body.
 Although generation time is two to four months, the early stages of development
proceed quickly.
 By 24 hours after fertilization, most tissues and early versions of the organs have
formed.
 After two days, the fish hatches out of the egg case.
 The zebra fish genome is estimated to be 1,700 Mb, and is still being mapped and
sequenced.
 For studying the molecular genetics of plant development, researchers are focusing on a
small weed, Arabidopsis thaliana (a member of the mustard family).
 One plant can grow and produce thousands of progeny after eight to ten weeks.
 A hermaphrodite, each flower makes eggs and sperm.
 For gene manipulation research, scientists can induce cultured cells to take up foreign
DNA (genetic transformation).
 Its relatively small genome, about 118 Mb, contains an estimated 25,500 genes.
 In the development of most multicellular organisms, a single-celled zygote gives rise to
cells of many different types.
 Each type has a different structure and corresponding function.
 Cells of similar types are organized into tissues, tissues into organs, organs into organ
systems, and organ systems into the whole organism.
 Thus, the process of embryonic development must give rise not only to cells of different
types, but also to higher-level structures arranged in a particular way in three dimensions.

Concept 21.1 Embryonic development involves cell division, cell differentiation, and
morphogenesis
 An organism arises from a fertilized egg cell as the result of three interrelated processes:
cell division, cell differentiation, and morphogenesis.

Biology Chapter Notes

 Through a succession of mitotic cell divisions, the zygote gives rise to a large number of
cells.
 Cell division alone would produce only a great ball of identical cells.
 During development, cells become specialized in structure and function, undergoing cell
differentiation.
 Different kinds of cells are organized into tissues and organs.
 The physical processes that give an organism its shape constitute morphogenesis, the
“creation of form.”
 The processes of cell division, differentiation, and morphogenesis overlap during
development.
 Early events of morphogenesis lay out the basic body plan very early in embryonic
development.
 These include establishing the head of an animal embryo or the roots of a plant
embryo.
 Later morphogenetic events establish relative locations within smaller regions of the
embryo, such as the digits on a vertebrate limb.
 The overall schemes of morphogenesis in animals and plants are very different.
 In animals, but not in plants, movements of cells and tissues are necessary to transform
the embryo into the characteristic 3-D form of the organism.
 In plants, morphogenesis and growth in overall size are not limited to embryonic and
juvenile periods but occur throughout the life of the plant.
 Apical meristems, perpetually embryonic regions in the tips of shoots and roots, are
responsible for the plant’s continual growth and formation of new organs, such as leaves
and roots.
 In animals, ongoing development in adults is restricted to the generation of cells, such as
blood cells, that must be continually replenished.

Concept 21.2 Different cell types result from differential gene expression in cells with
the same DNA
 During differentiation and morphogenesis, embryonic cells behave and function in ways
different from one another, even though all of them have arisen from the same zygote.
 The differences between cells in a multicellular organism come almost entirely from
differences in gene expression, not differences in the cell’s genomes.
 These differences arise during development, as regulatory mechanisms turn specific genes
off and on.
Different types of cells in an organism have the same DNA.
 Much evidence supports the conclusion that nearly all the cells of an organism have
genomic equivalence—that is, they all have the same genes.
 An important question that emerges is whether genes are irreversibly inactivated during
differentiation.
 One experimental approach to the question of genomic equivalence is to try to generate a
whole organism from differentiated cells of a single type.
 In many plants, whole new organisms can develop from differentiated somatic cells.
Biology Chapter Notes
  During the 1950s, F. C. Steward and his students found that differentiated root cells
removed from the root could grow into normal adult plants when placed in a medium
culture.
 These cloning experiments produced genetically identical individuals, popularly called
clones.
 The fact that a mature plant cell can dedifferentiate (reverse its function) and give rise to
all the different kinds of specialized cells of a new plant shows that differentiation does
not necessarily involve irreversible changes in the DNA.
 In plants, at least, cells can remain totipotent.
 They retain the zygote’s potential to form all parts of the mature organism.
 Plant cloning is now used extensively in agriculture.
 Differentiated cells from animals often fail to divide in culture, much less develop into a
new organism.
 Animal researchers have approached the genomic equivalence question by replacing the
nucleus of an unfertilized egg or zygote with the nucleus of a differentiated cell.
 The pioneering experiments in nuclear transplantation were carried out by Robert
Briggs and Thomas King in the 1950s and extended later by John Gordon in the 1980s.
 They destroyed or removed the nucleus of a frog egg and transplanted a nucleus from
an embryonic or tadpole cell from the same species into an enucleated egg.
 The ability of the transplanted nucleus to support normal development is inversely related
to the donor’s age.
 Transplanted nuclei from relatively undifferentiated cells from an early embryo lead to
the development of most eggs into tadpoles.
 Transplanted nuclei from fully differentiated intestinal cells lead to fewer than 2% of
the cells developing into normal tadpoles.
 Most of the embryos failed to make it through even the earliest stages of
development.
 Developmental biologists agree on several conclusions about these results.
 First, nuclei do change in some ways as cells differentiate.
 While the DNA sequences do not change, histones may be modified or DNA may
be methylated.
 In frogs and most other animals, nuclear “potency” tends to be restricted more and
more as embryonic development and cell differentiation progress.
 However, chromatin changes are sometimes reversible, and the nuclei of most
differentiated animal cells probably have all the genes required for making an entire
organism.
 The ability to clone mammals using nuclei or cells from early embryos has long been
possible.
 In 1997, Scottish researchers announced the birth of Dolly, a lamb cloned from an adult
sheep by nuclear transplantation from a differentiated mammary cell.
 The mammary cells were fused with sheep egg cells whose nuclei had been removed.
 The resulting cells divided to form early embryos, which were implanted into surrogate
mothers.
 One of several hundred implanted embryos completed normal development.

Biology Chapter Notes

 In 2003, Dolly developed a lung disease usually seen in much older sheep and was
euthanized.
 Dolly’s premature death as well as her arthritis led to speculation that her cells were
older than those of a normal sheep, possibly reflecting incomplete reprogramming of
the original transplanted nucleus.
 Since 1997, cloning has been demonstrated in numerous mammals, including mice, cats,
cows, horses, and pigs.
 The possibility of cloning humans raises unprecedented ethical issues.
 In most cases, the goal is to produce new individuals.
 This is known as reproductive cloning.
 These experiments have led to some interesting results.
 Cloned animals in the same species do not look or behave identically.
 Clearly, environmental influences and random phenomena can play a significant role
during development.
 The successful cloning of various mammals raised interest in human cloning.
 In early 2004, South Korean researchers reported success in the first step of
reproductive cloning of humans.
 Nuclei from differentiated human cells were transplanted into unfertilized enucleated
eggs.
 The eggs divided, and some embryos reached the blastocyst stage before
development was halted.
 In most nuclear transplantation studies, only a small percentage of cloned embryos
develop normally to birth.
 Like Dolly, many cloned animals have various defects, such as obesity, pneumonia,
liver failure, and premature death.
 In the nuclei of fully differentiated cells, a small subset of genes is turned on and the
expression of the rest is repressed.
 This regulation is often the result of epigenetic changes in chromatin, such as the
acetylation of histones or the methylation of DNA.
 Many of these changes must be reversed in the nucleus of the donor animal in order for
genes to be expressed or repressed appropriately for early stages of development.
 Researchers have found that the DNA in embryonic cells from cloned embryos, like
that of differentiated cells, often has more methyl groups than does the DNA in
equivalent cells from uncloned embryos of the same species.
 Because DNA methylation helps regulate gene expression, methylated DNA of donor
nuclei may interfere with the pattern of gene expression necessary for normal
embryonic development.
 Another hot research area involves stem cells.
 A stem cell is a relatively unspecialized cell that can reproduce itself and, under
appropriate conditions, differentiate into specialized cell types.
 In addition to contributing to the study of differentiation, stem cell research has enormous
potential in medicine.
 The ultimate goal is to supply cells for the repair of damaged or diseased organs.
 For example, providing insulin-producing pancreatic cells to diabetics or certain brain
cells to individuals with Parkinson’s disease could cure these diseases.

Biology Chapter Notes

 Many early animal embryos contain totipotent stem cells, which can give rise to
differentiated cells of any type.
 In culture, these embryonic stem cells reproduce indefinitely and can differentiate into
various specialized cells.
 The adult body has various kinds of stem cells, which replace nonreproducing specialized
cells.
 Adult stem cells are said to be pluripotent, able to give rise to many, but not all, cell
types.
 For example, stem cells in the bone marrow give rise to all the different kinds of
blood cells.
 The adult brain contains stem cells that continue to produce certain kinds of nerve
cells.
 Although adult animals have only tiny numbers of stem cells, scientists are learning to
identify, isolate, and culture these cells from various tissues.
 Under some culture conditions, with the addition of specific growth factors,
cultured adult stem cells can differentiate into multiple types of specialized cells.
 Stem cells from early embryos are somewhat easier to culture than those from adults
and can produce differentiated cells of any type.
 Embryonic stem cells are currently obtained from embryos donated by parents
undergoing fertility treatments, or from long-term cell cultures originally
established with cells isolated from donated embryos.
 Because the cells are derived from human embryos, their use raises ethical and
political issues.
 With the recent cloning of human embryos to the blastocyst stage, scientists might
be able to use these clones as the source of embryonic stem cells in the future.
 When the major aim of cloning is to produce embryonic stem cells to treat disease,
the process is called therapeutic cloning.
 Opinions vary about the morality of therapeutic cloning.

Different cell types make different proteins, usually as a result of transcriptional

regulation.
 During embryonic development, cells become visibly different in structure and function
as they differentiate.
 The earliest changes that set a cell on a path to specialization show up only at the
molecular level.
 Molecular changes in the embryo drive the process, termed determination, which leads
up to observable differentiation of a cell.
 At the end of this process, an embryonic cell is irreversibly committed to its final fate.
 If a determined cell is experimentally placed in another location in the embryo, it will
differentiate as if it were in its original position.
 The outcome of determination—cell differentiation—is caused by the expression of genes
that encode tissue-specific proteins.
 These give a cell its characteristic structure and function.
 Differentiation begins with the appearance of mRNA and is finally observable in the
microscope as changes in cellular structure.
 In most cases, the pattern of gene expression in a differentiated cell is controlled at the
level of transcription.

Biology Chapter Notes

 Cells produce the proteins that allow them to carry out their specialized roles in the
organism.
 For example, lens cells, and only lens cells, devote 80% of their capacity for protein
synthesis to making just one type of protein, crystallin proteins.
 These form transparent fibers that allow the lens to transmit and focus light.
 Similarly, skeletal muscle cells have high concentrations of proteins specific to muscle
tissues, such as a muscle-specific version of the contractile protein myosin and the
structural protein actin.
 They also have membrane receptor proteins that detect signals from nerve cells.
 Muscle cells develop from embryonic precursors that have the potential to develop into a
number of alternative cell types, including cartilage cells, fat cells, or multinucleate
muscle cells.
 As the muscle cells differentiate, they become myoblasts and begin to synthesize
muscle-specific proteins.
 They fuse to form mature, elongated, multinucleate skeletal muscle cells.
 Researchers developed the hypothesis that certain muscle-specific regulatory genes are
active in myoblasts, leading to muscle cell determination.
 To test this, researchers isolated mRNA from cultured myoblasts and used reverse
transcriptase to prepare a cDNA library containing all the genes that are expressed in
cultured myoblasts.
 Transplanting these cloned genes into embryonic precursor cells led to the
identification of several “master regulatory genes” that, when transcribed and
translated, commit the cells to become skeletal muscle.
 One of these master regulatory genes is called myoD, a transcription factor.
 myoD encodes MyoD protein, which binds to specific control elements and stimulates
the transcription of various genes, including some that encode for other muscle-
specific transcription factors.
 These secondary transcription factors activate the muscle protein genes.
 MyoD also stimulates expression of the myoD gene itself, perpetuating its effect in
maintaining the cell’s differentiated state.
 MyoD protein is capable of changing fully differentiated nonmuscle cells into muscle
cells.
 However, not all cells will transform.
 Nontransforming cells may lack a combination of regulatory proteins, in addition to
MyoD.
Transcriptional regulation is directed by maternal molecules in the cytoplasm and signals
from other cells.
 Two sources of information “tell” a cell, such as a myoblast or even the zygote, which
genes to express at any given time.
 One source of information is the cytoplasm of the unfertilized egg cell, which contains
RNA and protein molecules encoded by the mother’s DNA.
 Messenger RNA, proteins, other substances, and organelles are distributed unevenly in
the unfertilized egg.
 This impacts embryonic development in many species.
 Maternal substances that influence the course of early development are called
cytoplasmic determinants.
Biology Chapter Notes
  These substances regulate the expression of genes that affect the developmental fate of
the cell.
 After fertilization, the cell nuclei resulting from mitotic division of the zygote are
exposed to different cytoplasmic environments.
 The set of cytoplasmic determinants a particular cell receives helps determine its
developmental fate by regulating expression of the cell’s genes during the course of
cell differentiation.
 The other important source of developmental information is the environment around the
cell, especially signals impinging on an embryonic cell from other nearby embryonic
cells.
 In animals, these include contact with cell-surface molecules on neighboring cells and
the binding of growth factors secreted by neighboring cells.
 In plants, the cell-cell junctions known as plasmodesmata allow signal molecules to
pass from one cell to another.
 The synthesis of these signals is controlled by the embryo’s own genes.
 These signal molecules cause induction, triggering observable cellular changes by
causing a change in gene expression in the target cell.

Concept 21.3 Pattern formation in animals and plants results from similar genetic and
cellular mechanisms
 Before morphogenesis can shape an animal or plant, the organism’s body plan must be
established.
 Cytoplasmic determinants and inductive signals contribute to pattern formation, the
development of spatial organization in which the tissues and organs of an organism are
all in their characteristic places.
 Pattern formation continues throughout the life of a plant in the apical meristems.
 In animals, pattern formation is mostly limited to embryos and juveniles.
 Pattern formation begins in the early embryo, when the major axes of an animal and the
root-shoot axis of the plant are established.
 The molecular cues that control pattern formation, positional information, tell a cell
its location relative to the body axes and to neighboring cells.
 They also determine how the cells and their progeny will respond to future molecular
signals.
Drosophila development is controlled by a cascade of gene activations.
 Pattern formation has been most extensively studied in Drosophila melanogaster, where
genetic approaches have had spectacular success.
 These studies have established that genes control development and have identified the
key roles that specific molecules play in defining position and directing differentiation.
 Combining anatomical, genetic, and biochemical approaches in the study of
Drosophila development, researchers have discovered developmental principles
common to many other species, including humans.
 Fruit flies and other arthropods have a modular construction, an ordered series of
segments.
 These segments make up the three major body parts: the head, thorax (with wings and
legs), and abdomen.
Biology Chapter Notes
  Like other bilaterally symmetrical animals, Drosophila has an anterior-posterior axis
and a dorsal-ventral axis.
 Cytoplasmic determinants in the unfertilized egg provide positional information for
the two developmental axes before fertilization.
 After fertilization, positional information establishes a specific number of correctly
oriented segments and finally triggers the formation of each segment’s characteristic
structures.
 The Drosophila egg cell develops in the female’s ovary, surrounded by ovarian cells
called nurse cells and follicle cells that supply the egg cell with nutrients, mRNAs, and
other substances needed for development.
 Development of the fruit fly from egg cell to adult fly occurs in a series of discrete stages.
o Mitosis follows fertilization and egg laying.
 Early mitosis occurs without growth of the cytoplasm and without cytokinesis,
producing one big multinucleate cell.
o At the tenth nuclear division, the nuclei begin to migrate to the periphery of the
embryo.
o At division 13, the cytoplasm partitions the 6,000 or so nuclei into separate cells.
 The basic body plan—including body axes and segment boundaries—has already been
determined by this time.
 A central yolk nourishes the embryo, and the eggshell continues to protect it.
o Subsequent events in the embryo create clearly visible segments, which at first look
very much alike.
o Some cells move to new positions, organs form, and a wormlike larva hatches from the
shell.
 During three larval stages, the larva eats, grows, and molts.
o During the third larval stage, the larva transforms into the pupa enclosed in a case.
o Metamorphosis, the change from larva to adult fly, occurs in the pupal case, and the fly
emerges.
 Each segment is anatomically distinct, with characteristic appendages.
 The results of detailed anatomical observations of development in several species and
experimental manipulations of embryonic tissues laid the groundwork for understanding
the mechanisms of development.
 In the 1940s, Edward B. Lewis demonstrated that the study of mutants could be used to
investigate Drosophila development.
 He studied bizarre developmental mutations and located the mutations on the fly’s genetic
map.
 This research provided the first concrete evidence that genes somehow direct the
developmental process.
 In the late 1970s, Christiane Nüsslein-Volhard and Eric Weischaus pushed the
understanding of early pattern formation to the molecular level.
 Their goal was to identify all the genes that affect segmentation in Drosophila, but they
faced three problems.
 Because Drosophila has about 13,700 genes, there could be only a few genes affecting
segmentation or so many that the pattern would be impossible to discern.
 Mutations that affect segmentation are likely to be embryonic lethals, leading to death
at the embryonic or larval stage.

Biology Chapter Notes

  Because flies with embryonic lethal mutations never reproduce, they cannot be bred
for study.
 Because of maternal effects on axis formation in the egg, researchers also need to
study maternal genes.
 Nüsslein-Volhard and Wieschaus focused on recessive mutations that could be propagated
in heterozygous flies.
 After mutating flies, they looked for dead embryos and larvae with abnormal
segmentation among the fly’s descendents.
 Through appropriate crosses, they could identify living heterozygotes carrying
embryonic lethal mutations.
 They hoped that the segmental abnormalities would suggest how the affected genes
normally functioned.
 Nüsslein-Volhard and Wieschaus identified 1,200 genes essential for embryonic
development.
 About 120 of these were essential for pattern formation leading to normal
segmentation.
 After several years, they were able to group the genes by general function, map them,
and clone many of them.
 Their results, combined with Lewis’s early work, created a coherent picture of Drosophila
development.
 In 1995, Nüsslein-Volhard, Wieschaus, and Lewis were awarded the Nobel Prize.
Gradients of maternal molecules in the early embryo control axis formation.
 Cytoplasmic determinants establish the axes of the Drosophila body.
 Substances are produced under the direction of maternal effect genes that are
deposited in the unfertilized egg.
 When a maternal effect gene is mutated, the offspring has an abnormal mutant
phenotype.
 In fruit fly development, maternal effect genes encode proteins or mRNA that are placed
in the egg while it is still in the ovary.
 When the mother has a mutated gene, she makes a defective gene product (or none at
all), and her eggs will not develop properly when fertilized.
 These maternal effect genes are also called egg-polarity genes, because they control the
orientation of the egg and consequently the fly.
 One group of genes sets up the anterior-posterior axis, while a second group
establishes the dorsal-ventral axis.
 One of these, the bicoid gene, affects the front half of the body.
 An embryo whose mother has a mutant bicoid gene lacks the front half of its body and has
duplicate posterior structures at both ends.
 This suggests that the product of the mother’s bicoid gene is essential for setting up the
anterior end of the fly.
 It also suggests that the gene’s products are concentrated at the future anterior end.
 This is a specific version of a general gradient hypothesis, in which gradients of
morphogens establish an embryo’s axes and other features.
 Using DNA technology and biochemical methods, researchers were able to clone the
bicoid gene and use it as a probe for bicoid mRNA in the egg.
Biology Chapter Notes
  As predicted, the bicoid mRNA is concentrated at the extreme anterior end of the egg
cell.
 After the egg is fertilized, bicoid mRNA is transcribed into bicoid protein, which diffuses
from the anterior end toward the posterior, resulting in a gradient of proteins in the early
embryo.
 Injections of pure bicoid mRNA into various regions of early embryos results in the
formation of anterior structures at the injection sites as the mRNA is translated into
protein.
 The bicoid research is important for three reasons.
o It identified a specific protein required for some of the earliest steps in pattern
formation.
o It increased our understanding of the mother’s role in development of an embryo.
 As one developmental biologist put it, “Mom tells Junior which way is up.”
o It demonstrated a key developmental principle that a gradient of molecules can
determine polarity and position in the embryo.
 Gradients of specific proteins determine the posterior end as well as the anterior and also
are responsible for establishing the dorsal-ventral axis.
A cascade of gene activations sets up the segmentation pattern in Drosophila.
 The bicoid protein and other morphogens are transcription factors that regulate the
activity of some of the embryo’s own genes.
 Gradients of these morphogens bring about regional differences in the expression of
segmentation genes, the genes that direct the actual formation of segments after the
embryo’s major axes are defined.
 In a cascade of gene activations, sequential activation of three sets of segmentation genes
provides the positional information for increasingly fine details of the body plan.
 The three sets are called gap genes, pair-rule genes, and segment polarity genes.
 The products of many segmentation genes are transcription factors that directly activate
the next set of genes in the hierarchical scheme of pattern formation.
 Other segmentation proteins operate more indirectly.
 Some are components of cell-signaling pathways, including signal molecules used in
cell-cell communication and the membrane receptors that recognize them.
 Working together, the products of egg-polarity genes such as bicoid regulate the regional
expression of gap genes, which control the localized expression of pair-rule genes, which
in turn activate specific segment polarity genes in different parts of each segment.
 The boundaries and axes of segments are set by this hierarchy of genes (and their
products).
Homeotic genes direct the identity of body parts.
 In a normal fly, structures such as antennae, legs, and wings develop on the appropriate
segments.
 The anatomical identity of the segments is controlled by master regulatory genes, the
homeotic genes.
 Discovered by Edward Lewis, these genes specify the types of appendages and other
structures that each segment will form.

Biology Chapter Notes

 Mutations to homeotic genes produce flies with such strange traits as legs growing from
the head in place of antennae.
 Structures characteristic of a particular part of the animal arise in the wrong place.
 Like other developmental genes, the homeotic genes encode transcription factors that
control the expression of genes responsible for specific anatomical structures.
 For example, a homeotic protein made in a thoracic segment may activate genes that
bring about leg development, while a homeotic protein in a certain head segment
activates genes for antennal development.
 A mutant version of this protein may label a segment as “thoracic” instead of “head,”
causing legs to develop in place of antennae.
 Scientists are now working to identify the genes activated by the homeotic proteins—the
genes specifying the proteins that actually build the fly structures.
 Amazingly, many of the molecules and mechanisms that regulate development in the
Drosophila embryo have close counterparts throughout the animal kingdom.
Neighboring cells instruct other cells to form particular structures: cell signaling and
induction in the nematode.
 The development of a multicellular organism requires close communication among cells.
 Signals generated by neighboring nurse cells trigger the localization of bicoid mRNA
in the egg of the Drosophila.
 Once the embryo is truly multicellular, cells signal nearby cells to change in a specific
way, in a process called induction.
 Induction brings about cell differentiation through transcriptional regulation of specific
genes.
 The nematode C. elegans has proved to be a very useful model organism for investigating
the roles of cell signaling, induction, and programmed cell death in development.
 Researchers know the entire ancestry of every cell in the body of an adult C. elegans—the
organism’s complete cell lineage.
 As early as the four-cell stage in C. elegans, cell signaling helps direct daughter cells
down appropriate pathways.
 Researchers have combined genetic, biochemical, and embryological approaches to study
the development of the vulva, through which the worm lays its eggs.
 The pathway from fertilized egg to adult nematode involves four larval stages (during
which the larvae look much like smaller versions of the adult) during which this structure
develops.
 Already present on the ventral surface of the second-stage larva are six cells from
which the vulva will arise.
 A single cell in the embryonic gonad, the anchor cell, initiates a cascade of signals that
establishes the fate of the six vulval precursor cells.
 If an experimenter destroys the anchor cell with a laser beam, the vulva fails to form
and the precursor cells simply become part of the worm’s epidermis.
 Secreted factors or cell-surface proteins bind to receptors on the recipient cell, initiating
intracellular signal transduction pathways.
 This example illustrates a number of important concepts that apply to development of C.
elegans and many other animals.
 In the developing embryo, sequential inductions drive organ formation.
Biology Chapter Notes
  The effect of an inducer can depend on its concentration.
 Inducers produce their effects via signal transduction pathways similar to those
operating in adult cells.
 The induced cell’s response is often the activation of genes—transcriptional
regulation—that, in turn, establishes a pattern of gene activity characteristic of a
particular kind of differentiated cell.
 Lineage analysis of C. elegans highlights another outcome of cell signaling, programmed
cell death, or apoptosis.
 The timely suicide of cells occurs exactly 131 times in the course of C. elegans’s
normal development.
 At precisely the same points in development, signals trigger the activation of a cascade
of “suicide” proteins in the cells destined to die.
 During apoptosis, a cell shrinks and becomes lobed (called “blebbing”), the nucleus
condenses, and the DNA is fragmented.
 Neighboring cells quickly engulf and digest the membrane-bound remains, leaving no
trace.
 Genetic screening of C. elegans has revealed two key apoptosis genes, ced-3 and ced-4
(ced stands for cell death), which encode proteins (Ced-3 and Ced-4) that are essential for
apoptosis.
 In C. elegans, a protein in the outer mitochondrial membrane called Ced-9 (the product of
ced-9) is a master regulator of apoptosis.
 ced-9 acts as a brake in the absence of a signal promoting apoptosis.
 When the cell receives an external death signal, Ced-9 is inactivated, allowing both Ced-4
and Ced-3 to be active.
 The apoptosis pathway activates proteases and nucleases to cut up the proteins and
DNA of the cell.
 The main proteases of apoptosis are called caspases.
 In nematodes, Ced-3 is the chief caspase—the main protease of apoptosis.
 Apoptosis is regulated not at the level of transcription or translation, but through changes
in the activity of proteins that are continually present in the cell.
 Apoptosis pathways in humans and other mammals are more complicated.
 Research on mammals has revealed a prominent role for mitochondria in apoptosis.
 Signals from apoptosis pathways or others somehow cause the outer mitochondrial
membrane to leak, releasing proteins that promote apoptosis.
 Surprisingly, these proteins include cytochrome c, which functions in mitochondrial
electron transport in healthy cells but acts as a cell death factor when released from
mitochondria.
 Still controversial is whether mitochondria play a central role in apoptosis or only a
subsidiary role.
 A cell must make a life-or-death “decision” by somehow integrating both the “death” and
“life” (growth factor) signals that it receives.
 A built-in cell suicide mechanism is essential to development in all animals.
 Similarities between the apoptosis genes in mammals and nematodes, as well as the
observation that apoptosis occurs in multicellular fungi and unicellular yeast, indicate
that the basic mechanism evolved early in animal evolution.

Biology Chapter Notes

  The timely activation of apoptosis proteins in some cells functions during normal
development and growth in both embryos and adults.
 It is part of the normal development of the nervous system, normal operation of the
immune system, and normal morphogenesis of human hands and feet.
 A low level of apoptosis in developing limbs accounts for the webbed feet of ducks.
 Problems with the cell suicide mechanism may have health consequences, ranging from
minor to serious.
 Failure of normal cell death during morphogenesis of the hands and feet can result in
webbed fingers and toes.
 Researchers are also investigating the possibility that certain degenerative diseases of
the nervous system result from inappropriate activation of the apoptosis genes.
 Others are investigating the possibility that some cancers result from a failure of cell
suicide that normally occurs if the cell has suffered irreparable damage, especially
DNA damage.
 Damaged cells normally generate internal signals that trigger apoptosis.
Plant development depends on cell signaling and transcriptional regulation.
 The genetic analysis of plant development, using model organisms such as Arabidopsis,
has lagged behind that of animal models.
 Biologists are just beginning to understand the molecular basis of plant development.
 In general, cell linage is less important for pattern formation in plants than in animals.
 Many plant cells are totipotent, and their fates depend more on positional information
than on cell lineage.
 Plant development, like that of animals, depends on cell signaling (induction) and
transcriptional regulation.
 The embryonic development of most plants occurs in seeds that are relatively inaccessible
to study.
 However, other important aspects of plant development are observable in plant meristems,
particularly the apical meristems at the tips of shoots.
 These give rise to new organs, such as leaves or the petals of flowers.
 Environmental signals (such as day length or temperature) trigger signal transduction
pathways that convert ordinary shoot meristems to floral meristems.
 A floral meristem is a “bump” with three cell layers, all of which participate in the
formation of a flower with four types of organs: carpels (containing egg cells), petals,
stamens (containing sperm-bearing pollen), and sepals (leaflike structures outside the
petals).
 To examine induction of the floral meristem, researchers grafted stems from a mutant
tomato plant onto a wild-type plant and then grew new plants from the shoots at the graft
sites.
 Plants homozygous for the mutant allele fasciated (f) produce flowers with an
abnormally large number of organs.
 The new plants were chimeras, organisms with a mixture of genetically different cells.
 Some of the chimeras produced floral meristems in which the three cell layers did not all
come from the same “parent.”
 The number of organs per flower depends on genes of the L3 (innermost) cell layer.
 This induces the L2 and L1 layers to form that number of organs.
Biology Chapter Notes
 In contrast to genes controlling organ number in flowers, genes controlling organ identity
(organ identity genes) determine the types of structure that will grow from a meristem.
 In Arabidopsis and other plants, organ identity genes are analogous to homeotic genes in
animals and are often referred to as plant homeotic genes.
 Mutations cause plant structures to grow in unusual places, such as carpels in the place
of sepals.
 Researchers have identified and cloned a number of floral identity genes, and they are
beginning to determine how they act.
 In plants with a “homeotic” mutation, specific organs are missing or repeated.
 Like the homeotic genes of animals, the organ identity genes of plants encode
transcription factors that regulate specific target genes by binding to their enhancers in
the DNA.

Concept 21.4 Comparative studies help explain how the evolution of development leads
to morphological diversity
 Biologists in the field of evolutionary developmental biology, or “evo-devo,” compare
developmental processes of different multicellular organisms.
 Their aim is to understand how developmental processes have evolved and how
changes in the processes can modify existing organismal features or lead to new ones.
 Biologists are finding that the genomes of related species with strikingly different
forms may have only minor differences in gene sequence or regulation.
 All homeotic genes of Drosophila include a 180-nucleotide sequence called the
homeobox, which specifies a 60-amino-acid homeodomain.
 An identical, or very similar, sequence of nucleotides (often called Hox genes) is found
in many other animals, including humans.
 The vertebrate genes homologous to the homeotic genes of fruit flies have even kept
their chromosomal arrangement.
 Related sequences have been found in the regulatory genes of plants, yeasts, and even
prokaryotes.
 The homeobox DNA sequence must have evolved very early in the history of life and is
sufficiently valuable that it has been conserved virtually unchanged in animals and plants
for hundreds of millions of years.
 Most, but not all, homeobox-containing genes are homeotic genes that are associated with
development.
 For example, in Drosophila, homeoboxes are present not only in the homeotic genes,
but also in the egg-polarity gene bicoid, in several segmentation genes, and in the
master regulatory gene for eye development.
 The homeobox-encoded homeodomain is part of a protein that binds to DNA when the
protein functions as a transcriptional regulator.
 However, the shape of the homeodomain allows it to bind to any DNA segment.
 Other, more variable, domains of the overall protein determine which genes it will
regulate.
 Interaction of these latter domains with still other transcription factors helps a
homeodomain-protein recognize specific enhancers in the DNA.
 Proteins with homeodomains probably regulate development by coordinating the
transcription of batteries of developmental genes.
Biology Chapter Notes
  In Drosophila, different combinations of homeobox genes are active in different parts
of the embryo and at different times, leading to pattern formation.
 Many other genes involved in development are highly conserved from species to species.
 These include numerous genes encoding components of signaling pathways.
 How can the same genes be involved in the development of so many different animals?
 In some cases, small changes in regulatory sequences of particular genes can lead to
major changes in body form.
 For example, varying expression of the Hox genes along the body axis produce
different numbers of leg-bearing segments in insects and crustaceans.
 Plants also have homeobox-containing genes.
 However, they do not appear to function as master regulatory switches in plants.
 Other genes appear to be responsible for pattern formation in plants.
There are some basic similarities—and many differences—in the development of plants
and animals.
 The last common ancestor of plants and animals was a single-celled microbe living
hundreds of millions of years ago, so the processes of development evolved independently
in the two lineages.
 Plants have rigid cell walls that prevent cell movement, while morphogenetic
movements are very important in animals.
 Morphogenesis in plants is dependent on differing planes of cell division and selective
cell enlargement.
 Nevertheless, there are some basic similarities of development.
 In both plants and animals, development relies on a cascade of transcriptional
regulators turning on or off genes in a finely tuned series.
 The genes that direct these processes are very different in plants and animals.
 Quite a few of the master regulatory switches in Drosophila are homeobox-containing
Hox genes.
 Those in Arabidopsis belong to the Mads-box family of genes.
 Although homeobox-containing genes can be found in plants and Mads-box genes can be
found in animals, they do not play the same major roles in development in plants and
animals.
 The unity of life is reflected in the similarity of biological mechanisms used to establish
body pattern, although the exact genes directing develop may differ.
 The similarities reflect the common ancestry of life on Earth, while the differences have
created the diversity of living organisms.

Biology Chapter Notes

Chapter 22 Descent with Modification: Darwinian View
of Life
Chapter Notes

Overview: Darwin Introduces a Revolutionary Theory

 On November 24, 1859, Charles Darwin published On the Origin of Species by Means of
Natural Selection.
 Darwin’s book drew a cohesive picture of life by connecting what had once seemed a
bewildering array of unrelated facts.
 Darwin made two major points in The Origin of Species:
o Today’s organisms descended from ancestral species that were different from modern
species.
o Natural selection provided a mechanism for this evolutionary change.
 The basic idea of natural selection is that a population can change over time if
individuals that possess certain heritable traits leave more offspring than other
individuals.
 Natural selection results in evolutionary adaptation, an accumulation of inherited
characteristics that increase the ability of an organism to survive and reproduce in its
environment.
 Eventually, a population may accumulate enough change that it constitutes a new species.
 In modern terms, we can define evolution as a change over time in the genetic
composition of a population.
 Evolution also refers to the gradual appearance of all biological diversity.
 Evolution is such a fundamental concept that its study is relevant to biology at every level,
from molecules to ecosystems.
 Evolutionary perspectives continue to transform medicine, agriculture, biotechnology,
and conservation biology.

Concept 22.1 The Darwinian revolution challenged traditional views of a young Earth
inhabited by unchanging species
Western culture resisted evolutionary views of life.
 Darwin’s view of life contrasted with the traditional view of an Earth that was a few
thousand years old, populated by life forms that were created at the beginning and had
remained fundamentally unchanged.
 The Origin of Species challenged a worldview that had been long accepted.
 The Greek philosopher Aristotle (384–322 B.C.E.) opposed any concept of evolution and
viewed species as fixed and unchanging.
 Aristotle believed that all living forms could be arranged on a ladder of increasing
complexity (scala naturae) with perfect, permanent species on every rung.
 The Old Testament account of creation held that species were individually designed by
God and, therefore, perfect.
Biology Chapter Notes
 In the 1700s, natural theology viewed the adaptations of organisms as evidence that the
Creator had designed each species for a purpose.
 Carolus Linnaeus (1707–1778), a Swedish physician and botanist, founded taxonomy, a
system for naming species and classifying species into a hierarchy of increasingly
complex categories.
 Linnaeus developed the binomial system of naming organisms according to genus and
species.
 In contrast to the linear hierarchy of the scala naturae, Linnaeus adopted a nested
classification system, grouping similar species into increasingly general categories.
 For Linnaeus, similarity between species did not imply evolutionary kinship but rather
the pattern of their creation.
 Darwin’s views were influenced by fossils, remains or traces of organisms from the past
mineralized in sedimentary rocks.
 Sedimentary rocks form when mud and sand settle to the bottom of seas, lakes, and
marshes.
 New layers of sediment cover older ones, creating layers of rock called strata.
 Erosion may later carve through sedimentary rock to expose older strata at the surface.
 Fossils within layers of sedimentary rock show that a succession of organisms have
populated Earth throughout time.
 Paleontology, the study of fossils, was largely developed by the French anatomist
Georges Cuvier (1769–1832).
 In examining rock strata in the Paris Basin, Cuvier noted that the older the strata, the more
dissimilar the fossils from modern life.
 Cuvier recognized that extinction had been a common occurrence in the history of life.
 Instead of evolution, Cuvier advocated catastrophism, speculating that boundaries
between strata were due to local floods or droughts that destroyed the species then
present.
 He suggested that the denuded areas were later repopulated by species immigrating
from unaffected areas.
Theories of geologic gradualism prepared the path for evolutionary biologists.
 In contrast to Cuvier’s catastrophism, Scottish geologist James Hutton (1726–1797)
proposed a theory of gradualism that held that profound geological changes took place
through the cumulative effect of slow but continuous processes identical to those currently
operating.
 Thus, valleys were formed by rivers flowing through rocks and sedimentary rocks
were formed from soil particles that eroded from land and were carried by rivers to the
sea.
 Later, geologist Charles Lyell (1797–1875) proposed a theory of uniformitarianism,
which held that geological processes had not changed throughout Earth’s history.
 Hutton’s and Lyell’s observations and theories had a strong influence on Darwin.
 First, if geologic changes result from slow, continuous processes rather than sudden
events, then the Earth must be far older than the 6,000 years estimated by theologians
from biblical inference.
 Second, slow and subtle processes persisting for long periods of time can also act on
living organisms, producing substantial change over a long period of time.
Lamarck placed fossils in an evolutionary context.
Biology Chapter Notes
 In 1809, French biologist Jean-Baptiste de Lamarck (1744–1829) published a theory of
evolution based on his observations of fossil invertebrates in the collections of the Natural
History Museum of Paris.
 By comparing fossils and current species, Lamarck found what appeared to be several
lines of descent.
 Each was a chronological series of older to younger fossils, leading to a modern
species.
 He explained his observations with two principles: use and disuse of parts and the
inheritance of acquired characteristics.
 Use and disuse was the concept that body parts that are used extensively become larger
and stronger, while those that are not used deteriorate.
 The inheritance of acquired characteristics stated that modifications acquired during
the life of an organism could be passed to offspring.
 A classic example is the long neck of the giraffe. Lamarck reasoned that the long,
muscular neck of the modern giraffe evolved over many generations as the ancestors of
giraffes reached for leaves on higher branches and passed this characteristic to their
offspring.
 Lamarck thought that evolutionary change was driven by the innate drive of organisms to
increasing complexity.
 Lamarck’s theory was a visionary attempt to explain the fossil record and the current
diversity of life with recognition of gradual evolutionary change.
 However, modern genetics has provided no evidence that acquired characteristics can
be inherited.
 Acquired traits such as a body builder’s bigger biceps do not change the genes
transmitted through gametes to offspring.

Concept 22.2 In The Origin of Species, Darwin proposed that species change through
natural selection
 Charles Darwin (1809–1882) was born in western England.
 As a boy, he developed a consuming interest in nature.
 When Darwin was 16, his father sent him to the University of Edinburgh to study
medicine.
 Darwin left Edinburgh without a degree and enrolled at Cambridge University with the
intent of becoming a clergyman.
 At that time, most naturalists and scientists belonged to the clergy and viewed the
world in the context of natural theology.
 Darwin received his B.A. in 1831.
 After graduation Darwin joined the survey ship HMS Beagle as ship naturalist and
conversation companion to Captain Robert FitzRoy.
 FitzRoy chose Darwin because of his education, and because his age and social class
were similar to that of the captain.
Field research helped Darwin frame his view of life.
 The primary mission of the five-year voyage of the Beagle was to chart poorly known
stretches of the South American coastline.

Biology Chapter Notes

 Darwin had the freedom to explore extensively on shore while the crew surveyed the
coast.
 He collected thousands of specimens of the exotic and diverse flora and fauna of South
America.
 Darwin explored the Brazilian jungles, the grasslands of the Argentine pampas, the
desolation of Tierra del Fuego near Antarctica, and the heights of the Andes.
 Darwin noted that the plants and animals of South America were very distinct from those
of Europe.
 Organisms from temperate regions of South America more closely resembled those
from the tropics of South America than those from temperate regions of Europe.
 Further, South American fossils, though different from modern species, more closely
resembled modern species from South America than those from Europe.
 While on the Beagle, Darwin read Lyell’s Principles of Geology.
 He experienced geological change firsthand when a violent earthquake rocked the
coast of Chile, causing the coastline to rise by several feet.
 He found fossils of ocean organisms high in the Andes and inferred that the rocks
containing the fossils had been raised there by a series of similar earthquakes.
 These observations reinforced Darwin’s acceptance of Lyell’s ideas and led him to
doubt the traditional view of a young and static Earth.
 Darwin’s interest in the geographic distribution of species was further stimulated by the
Beagle’s visit to the Galapagos, a group of young volcanic islands 900 km west of the
South American coast.
 Darwin was fascinated by the unusual organisms found there.
 After his return to England, Darwin noted that while most of the animal species on the
Galapagos lived nowhere else, they resembled species living on the South American
mainland.
 He hypothesized that the islands had been colonized by plants and animals from the
mainland that had subsequently diversified on the different islands.
 After his return to Great Britain in 1836, Darwin began to perceive that the origin of new
species and adaptation of species to their environment were closely related processes.
 For example, clear differences in the beaks among the 13 species of finches that
Darwin collected in the Galapagos are adaptations to the specific foods available on
their home islands.
 By the early 1840s, Darwin had developed the major features of his theory of natural
selection as the mechanism for evolution.
 In 1844, he wrote a long essay on the origin of species and natural selection, but he was
reluctant to publish and continued to compile evidence to support his theory.
 In June 1858, Alfred Russel Wallace (1823–1913), a young naturalist working in the East
Indies, sent Darwin a manuscript containing a theory of natural selection essentially
identical to Darwin’s.
 Later that year, both Wallace’s paper and extracts of Darwin’s essay were presented to the
Linnaean Society of London.
 Darwin quickly finished The Origin of Species and published it the next year.
 While both Darwin and Wallace developed similar ideas independently, the theory of
evolution by natural selection is attributed to Darwin because he developed his ideas
earlier and supported the theory much more extensively.
Biology Chapter Notes
  The theory of evolution by natural selection was presented in The Origin of Species
with immaculate logic and an avalanche of supporting evidence.
 Within a decade, The Origin of Species had convinced most biologists that biological
diversity was the product of evolution.
The Origin of Species developed two main ideas: that evolution explains life’s unity and
diversity and that natural selection is the mechanism of adaptive evolution.
 Darwin scarcely used the word evolution in The Origin of Species.
 Instead he used the phrase descent with modification.
 All organisms are related through descent from a common ancestor that lived in the
remote past.
 Over evolutionary time, the descendents of that common ancestor have
accumulated diverse modifications, or adaptations, that allow them to survive and
reproduce in specific habitats.
 Viewed from the perspective of descent with modification, the history of life is like a tree
with multiple branches from a common trunk.
 Closely related species, the twigs on a common branch of the tree, shared the same line
of descent until their recent divergence from a common ancestor.
 Linnaeus recognized that some organisms resemble each other more closely than others,
but he did not explain these similarities by evolution.
 However, his taxonomic scheme fit well with Darwin’s theory.
 To Darwin, the Linnaean hierarchy reflected the branching history of the tree of life.
 Organisms at various taxonomic levels are united through descent from common
ancestors.
 How does natural selection work, and how does it explain adaptation?
 Evolutionary biologist Ernst Mayr has dissected the logic of Darwin’s theory into three
inferences based on five observations.
 Observation #1: All species have such great potential fertility that their population size
would increase exponentially if all individuals that are born reproduced successfully.
 Observation #2: Populations tend to remain stable in size, except for seasonal
fluctuations.
 Observation #3: Environmental resources are limited.
 Inference #1: Production of more individuals than the environment can support
leads to a struggle for existence among the individuals of a population, with only a
fraction of the offspring surviving each generation.
 Observation #4: Individuals of a population vary extensively in their characteristics; no
two individuals are exactly alike.
 Observation #5: Much of this variation is heritable.
 Inference #2: Survival in the struggle for existence is not random, but depends in
part on inherited traits. Those individuals whose inherited traits are best suited for
survival and reproduction in their environment are likely to leave more offspring
than less fit individuals.
 Inference #3: This unequal ability of individuals to survive and reproduce will lead
to a gradual change in a population, with favorable characteristics accumulating
over generations.
 A 1798 essay on human population by Thomas Malthus heavily influenced Darwin’s
views on “overreproduction.”
Biology Chapter Notes
  Malthus contended that much human suffering—disease, famine, homelessness, war—
was the inescapable consequence of the potential for human populations to increase
faster than food supplies and other resources.
 The capacity to overproduce seems to be a characteristic of all species.
 Only a tiny fraction of offspring produced complete their development and reproduce
successfully to leave offspring of their own.
 In each generation, environmental factors filter heritable variations, favoring some over
others.
 Differential reproductive success—whereby organisms with traits favored by the
environment produce more offspring than do organisms without those traits—results in
the favored traits being disproportionately represented in the next generation.
 This increasing frequency of the favored traits in a population is evolutionary change.
 Darwin’s views on the role of environmental factors in the screening of heritable variation
were heavily influenced by artificial selection.
 Humans have modified a variety of domesticated plants and animals over many
generations by selecting individuals with the desired traits as breeding stock.
 If artificial selection can achieve so much change in a relatively short period of time,
Darwin reasoned, then natural selection should be capable of considerable
modification of species over thousands of generations.
 Darwin’s main ideas can be summarized in three points.
 Natural selection is differential success in reproduction (unequal ability of individuals
to survive and reproduce) that results from individuals that vary in heritable traits and
their environment.
 The product of natural selection is the increasing adaptation of organisms to their
environment.
 If an environment changes over time, or if individuals of a species move to a new
environment, natural selection may result in adaptation to the new conditions,
sometimes giving rise to a new species in the process.
 Three important points need to be emphasized about evolution through natural
selection.
o Although natural selection occurs through interactions between individual organisms
and their environment, individuals do not evolve. A population (a group of
interbreeding individuals of a single species that share a common geographic area) is
the smallest group that can evolve. Evolutionary change is measured as changes in
relative proportions of heritable traits in a population over successive generations.
o Natural selection can act only on heritable traits, traits that are passed from organisms
to their offspring. Characteristics acquired by an organism during its lifetime may
enhance its survival and reproductive success, but there is no evidence that such
characteristics can be inherited by offspring.
o Environmental factors vary from place to place and from time to time. A trait that is
favorable in one environment may be useless or even detrimental in another
environment.
 Darwin envisioned the diversity of life as evolving by a gradual accumulation of minute
changes through the actions of natural selection operating over vast spans of time.

Concept 22.3 Darwin’s theory explains a wide range of observations

Biology Chapter Notes

 The power of evolution by natural selection as a unifying theory is its versatility as a
natural explanation for diverse data from many fields of biology.
 We will consider two examples of natural selection as a mechanism of evolution in
populations.
 Our first example concerns differential predation and guppy populations.
 Guppies (Poecilia reticulata) live in the wild in pools in the Aripo River system in
Trinidad.
 John Endler and David Reznick have been studying these small fish for more than a
decade.
 The researchers observed significant differences between populations of guppies that live
in different pools in the river system.
 Populations varied in the average age and size of sexual maturity.
 These variations were correlated to the type of predator present in each pool.
 In some pools, the main predator is the small killifish, which eats juvenile guppies.
 In other pools, the major predator is the large pike-cichlid, which eats adult guppies.
 Guppies in populations preyed on by pike-cichlids begin reproducing at a younger age
and are smaller at maturity than guppies in populations preyed on by killifish.
 To test whether these differences are due to natural selection, Reznick and Endler
introduced guppies from pike-cichlid locations to new pools that contained killifish but no
guppies.
 After eleven years, the transplanted guppies were, on average, 14% heavier at maturity
than the nontransplanted populations.
 Their average age at maturity had also increased.
 These results support the hypothesis that natural selection caused the changes in the
transplanted population.
 Because pike-cichlids prey mainly on reproductively mature adults, the chance that a
guppy will survive to reproduce several times is low.
 The guppies with the greatest reproductive success in ponds with pike-cichlid
predators are those that mature at a young age and small size, enabling them to
produce at least one brood before growing to a size preferred by pike-cichlids.
 In ponds with killifish predators, guppies that survive early predation can grow slowly
and produce many broods of young.
 A second example of ongoing natural selection is the evolution of drug-resistant HIV
(human immunodeficiency virus).
 Researchers have developed numerous drugs to combat HIV, but using these medications
selects for viruses resistant to the drugs.
 A few drug-resistant viruses may be present by chance at the beginning of treatment.
 The drug-resistant pathogens are more likely to survive treatment and pass on the
genes that enable them to resist the drug to their offspring.
 As a result, the frequency of drug resistance in the viral population rapidly increases.
 Scientists designed the drug 3TC to interfere with reverse transcriptase, the enzyme that
HIV uses to copy its RNA genome into the DNA of the host cell.
 Because 3TC is similar in shape to the cytosine nucleotide of DNA, HIV’s reverse
transcriptase incorporates 3TC into its growing DNA chain instead of cytosine. This
error terminates elongation of DNA and thus prevents HIV reproduction.

Biology Chapter Notes

  3TC-resistant varieties of HIV have a form of reverse transcriptase that can
discriminate between cytosine and 3TC.
 These viruses have no advantage in the absence of 3TC. In fact, they replicate more
slowly than viruses with normal reverse transcriptase.
 Once 3TC is added to their environment, it becomes a powerful selective agent,
favoring reproduction of resistant individuals.
 The examples of the guppies and HIV highlight two important points about natural
selection.
 First, natural selection is an editing mechanism, not a creative force. It can only act on
existing variation in the population; it cannot create favorable traits.
 Second, natural selection favors traits that increase fitness in the current, local
environment. What is adaptive in one situation is not adaptive in another.
 For example, guppies that mature at an early age and small size are at an advantage
in a pool with pike-cichlids, but at a disadvantage in a pool with killifish.
 In the absence of 3TC, HIV with the modified form of reverse transcriptase grows
more slowly than HIV with normal reverse transcriptase.
Evidence of evolution pervades biology.
 In the cases described, natural selection brought about change rapidly enough that it could
be observed directly.
 Darwin’s theory also provides a cohesive explanation for observations in the fields of
anatomy, embryology, molecular biology, biogeography, and paleontology.
 Descent with modification can explain why certain traits in related species have an
underlying similarity even if they have very different functions.
 Similarity in characteristic traits from common ancestry is known as homology.
 For example, the forelimbs of human, cats, whales, and bats share the same skeletal
elements, even though the appendages have very different functions.
 These forelimbs are homologous structures that represent variations on the ancestral
tetrapod forelimb.
 Homologies that are not obvious in adult organisms may become evident when we look at
embryonic development.
 For example, all vertebrate embryos have structures called pharyngeal pouches in their
throat at some stage in their development.
 These embryonic structures develop into very different, but still homologous, adult
structures, such as the gills of fish or the Eustacian tubes that connect the middle ear
with the throat in mammals.
 Some of the most interesting homologous structures are vestigial organs, structures that
have marginal, if any, importance to a living organism, but which had important functions
in the organism’s ancestors.
 For example, the skeletons of some snakes and of fossil whales retain vestiges of the
pelvis and leg bones of walking ancestors.
 Comparative anatomy confirms that evolution is a remodeling process, an alteration of
existing structures.
 Because evolution can only modify existing structures and functions, it may produce
structures that are less than perfect.
 For example, the back and knee problems of bipedal humans are an unsurprising
outcome of adapting structures originally evolved to support four-legged mammals.
Biology Chapter Notes
 Similarities among organisms can also be seen at the molecular level.
 For example, all species of life have the same basic genetic machinery of RNA and
DNA, and the genetic code is essentially universal.
 The ubiquity of the genetic code provides evidence of a single origin of life.
 It is likely that the language of the genetic code has been passed along through all the
branches of the tree of life ever since its inception in an early life form.
 Homologies mirror the taxonomic hierarchy of the tree of life.
 Some homologies, such as the genetic code, are shared by all living things because
they arose in the deep ancestral past.
 Other homologies that evolved more recently are shared only by smaller branches of
the tree of life.
 For example, all tetrapods (amphibians, reptiles, birds, and mammals) share the
same five-digit limb structure.
 Thus homologies are found in a nested pattern, with all life sharing the deepest layer
and each smaller group adding new homologies to those they share with the larger
group.
 This hierarchical pattern of homology is exactly what we would expect if life evolved
and diversified from a common ancestor.
 Anatomical resemblances among species are generally reflected in their genes (DNA) and
gene products (proteins).
 If hierarchies of homology reflect evolutionary history, then we should expect to find
similar patterns whether we are comparing molecules or bones.
 Different kinds of homologies will coincide because they have followed the same
branching pattern through evolutionary history.
 The geographical distribution of species—biogeography—first suggested evolution to
Darwin.
 Species tend to be more closely related to other species from the same area than to
other species with the same way of life that live in different areas.
 Consider Australia, home to a unique group of marsupial mammals, which
complete their development in an external pouch.
 Some marsupial mammals superficially resemble eutherian mammals (which
complete their development in the uterus) from other continents.
 For example, the Australian sugar glider and North American flying squirrel are
adapted to the same mode of life and look somewhat similar.
 However, the sugar glider shares more characteristics with other Australian
marsupials than with the flying squirrel.
 The resemblance between the two gliders is an example of convergent evolution.

 Islands and island archipelagos have provided strong evidence of evolution.

 Islands generally have many species of plants and animals that are endemic, found
nowhere else in the world.
 As Darwin observed when he reassessed his collections from the Beagle’s voyage, these
endemic species are typically more closely related to species living on the nearest
mainland (despite different environments) than to species from other island groups.
 In island chains, or archipelagos, individual islands may have different, but related,
species. The first mainland invaders reached one island and then evolved into several new
species as they colonized other islands in the archipelago.

Biology Chapter Notes

  Several well-investigated examples of this phenomenon include the diversification of
finches on the Galapagos Islands and fruit flies (Drosophila) on the Hawaiian
Archipelago.
 The succession of fossil forms is consistent with what is known from other types of
evidence about the major branches of descent in the tree of life.
 For example, considerable evidence suggests that prokaryotes are the ancestors of all
life and should precede all eukaryotes in the fossil record. In fact, the oldest known
fossils are prokaryotes.
 Fossil fishes predate all other vertebrates, with amphibians next, followed by reptiles,
then mammals and birds.
 This is consistent with the history of vertebrate descent supported by many other types
of evidence.
 The Darwinian view of life also predicts that evolutionary transitions should leave signs in
the fossil record.
 Paleontologists have discovered fossils of many such transitional forms that link ancient
organisms to modern species.
 For example, fossil evidence documents the origin of birds from one branch of
dinosaurs.
 Recent discoveries include fossilized whales that link these aquatic mammals to their
terrestrial ancestors.
What is theoretical about the Darwinian view of life?
 Some people dismiss the Darwinian view as “just a theory.”
 As we have seen, Darwin’s explanation makes sense of large amounts of data.
 The effects of natural selection can be observed in nature.
 What is theoretical about evolution?
 The term theory has a very different meaning in science than in everyday use.
 The word theory in colloquial use is closer to the concept of a hypothesis in science.
 In science, a theory is more comprehensive than a hypothesis, accounting for many
observations and data and attempting to explain and integrate a great variety of
phenomena.
 A unifying theory does not become widely accepted unless its predictions stand up to
thorough and continual testing by experiments and additional observation.
 That has certainly been the case with the theory of evolution by natural selection.
 Scientists continue to test this theory.
 For example, many evolutionary biologists now question whether natural selection is
the only mechanism responsible for evolutionary history.
 Other factors may have played an important role, particularly in the evolution of genes
and proteins.
 By attributing the diversity of life to natural causes, Darwin gave biology a sound
scientific basis.
 As Darwin said, “There is grandeur in this view of life.”

Biology Chapter Notes

 Chapter 23 The Evolution of Populations
Chapter Notes

Overview: The Smallest Unit of Evolution

 One common misconception about evolution is that organisms evolve, in a Darwinian

sense, during their lifetimes.
 Natural selection does act on individuals. Each individual’s combination of inherited
traits affects its survival and its reproductive success relative to other individuals in the
population.
 However, the evolutionary impact of natural selection is only apparent in the changes
in a population of organisms over time.
 It is the population, not the individual, that evolves.
 Consider the example of bent grass (Agrostis tenuis) growing on the tailings of an
abandoned mine. These tailings are rich in toxic heavy metals.
 While many bent grass seeds land on the mine tailings each year, the only plants that
germinate, grow, and reproduce are those that possess genes enabling them to tolerate
metallic soils.
 These plants tend to produce metal-tolerant offspring.
 Individual plants do not evolve to become more metal-tolerant during their lifetimes.
Concept 23.1 Population genetics provides a foundation for studying evolution
 Darwin proposed a mechanism for change in species over time.
 What was missing from Darwin’s explanation was an understanding of inheritance that
could explain how chance variations arise in a population while also accounting for the
precise transmission of these variations from parents to offspring.
 The widely accepted hypothesis of the time—that the traits of parents are blended in
their offspring—would eliminate the differences in individuals over time.
 Just a few years after Darwin published On the Origin of Species, Gregor Mendel
proposed a model of inheritance that supported Darwin’s theory.
 Mendel’s particulate hypothesis of inheritance stated that parents pass on discrete
heritable units (genes) that retain their identities in offspring.
 Although Gregor Mendel and Charles Darwin were contemporaries, Darwin never saw
Mendel’s paper, and its implications were not understood by the few scientists who did
read it at the time.
 Mendel’s contribution to evolutionary theory was not appreciated until half a century
later.
The modern evolutionary synthesis integrated Darwinian selection and Mendelian
inheritance.
 When Mendel’s research was rediscovered in the early 20th century, many geneticists
believed that his laws of inheritance conflicted with Darwin’s theory of natural selection.
 Darwin emphasized quantitative characters, those that vary along a continuum.
 These characters are influenced by multiple loci.
 Mendel and later geneticists investigated discrete “either-or” traits.
 It was not obvious that there was a genetic basis to quantitative characters.
Biology Chapter Notes
 Within a few decades, geneticists determined that quantitative characters are influenced
by multiple genetic loci and that the alleles at each locus follow Mendelian laws of
inheritance.
 These discoveries helped reconcile Darwin’s and Mendel’s ideas and led to the birth of
population genetics, the study of how populations change genetically over time.
 A comprehensive theory of evolution, the modern synthesis, took form in the early
1940s.
 It integrated discoveries and ideas from paleontology, taxonomy, biogeography, and
population genetics.
 The first architects of the modern synthesis included statistician R. A. Fisher, who
demonstrated the rules by which Mendelian characters are inherited, and biologist J. B. S.
Haldane, who explored the rules of natural selection. Later contributors included
geneticists Theodosius Dobzhansky and Sewall Wright, biogeographer and taxonomist
Ernst Mayr, paleontologist George Gaylord Simpson, and botanist G. Ledyard Stebbins.
 The modern synthesis emphasizes:
 The importance of populations as the units of evolution.
 The central role of natural selection as the most important mechanism of adaptive
evolution.
 The idea of gradualism to explain how large changes can evolve as an accumulation of
small changes over long periods of time.
 While many evolutionary biologists are now challenging some of the assumptions of the
modern synthesis, it has shaped our ideas about how populations evolve.
A population’s gene pool is defined by its allele frequencies.
 A population is a localized group of individuals that belong to the same species.
 One definition of a species is a group of natural populations whose individuals have the
potential to interbreed and produce fertile offspring.
 Populations of a species may be isolated from each other and rarely exchange genetic
material.
 Members of a population are far more likely to breed with members of the same
population than with members of other populations.
 Individuals near the population’s center are, on average, more closely related to one
another than to members of other populations.
 The total aggregate of genes in a population at any one time is called the population’s
gene pool.
 It consists of all alleles at all gene loci in all individuals of a population.
 If only one allele exists at a particular locus in a population, that allele is said to be
fixed in the gene pool, and all individuals will be homozygous for that gene.
 If there are two or more alleles for a particular locus, then individuals can be either
homozygous or heterozygous for that gene.
 Each allele has a frequency in the population’s gene pool.
 For example, imagine a population of 500 wildflower plants with two alleles (C R and CW)
at a locus that codes for flower pigment.
 Suppose that in the imaginary population of 500 plants, 20 (4%) are homozygous for
the CW allele (CWCW) and have white flowers.

Biology Chapter Notes

  Of the remaining plants, 320 (64%) are homozygous for the C R allele (CRCR) and have
red flowers.
 These alleles show incomplete dominance. 160 (32%) of the plants are heterozygous
(CRCW) and produce pink flowers.
 Because these plants are diploid, the population of 500 plants has 1,000 copies of the gene
for flower color.
 The R W
dominant allele (CR) accounts for 800 copies (320 × 2 for CRCR + 160 × 1 for
C C ).
 The frequency of the CR allele in the gene pool of this population is 800/1,000 = 0.8, or
80%.
 The CW allele must have a frequency of 1.0 − 0.8 = 0.2, or 20%.
 When there are two alleles at a locus, the convention is to use p to represent the frequency
of one allele and q to represent the frequency of the other.
 Thus p, the frequency of the CR allele in this population, is 0.8.
 The frequency of the CW allele, represented by q, is 0.2.
The Hardy-Weinberg Theorem describes a nonevolving population.
 The Hardy-Weinberg theorem describes the gene pool of a nonevolving population.
 This theorem states that the frequencies of alleles and genotypes in a population’s gene
pool will remain constant over generations unless acted upon by agents other than
Mendelian segregation and recombination of alleles.
 The shuffling of alleles by meiosis and random fertilization has no effect on the overall
gene pool of a population.
 In our imaginary wildflower population of 500 plants, 80% (0.8) of the flower color
alleles are CR, and 20% (0.2) are CW.
 How will meiosis and sexual reproduction affect the frequencies of the two alleles in the
next generation?
 We assume that fertilization is completely random and all male-female mating
combinations are equally likely.
 Because each gamete has only one allele for flower color, we expect that a gamete drawn
from the geneW pool at random has a 0.8 chance of bearing an C R allele and a 0.2 chance of
bearing an C allele.
 Suppose that the individuals in a population not only donate gametes to the next
generation at random, but also mate at random. In other words, all male-female matings
are equally likely.
 The allele frequencies in this population will not change from one generation to the
next. Its genotype frequencies, which can be predicted from the allele frequencies, will
also remain unchanged.
 For the flower-color locus, the population’s genetic structure is in a state of Hardy-
Weinberg equilibrium.
 Using the rule of multiplication, we can determine the frequencies of the three possible
genotypes in the next generation.
 The probability of picking two CR alleles (to obtain a CRCR genotype) is 0.8 × 0.8 =
0.64, or 64%.
 The probability of picking two CW alleles (to obtain a CWCW genotype) is 0.2 × 0.2 =
0.04, or 4%.

Biology Chapter Notes

  Heterozygous individuals are either C RCW or CWCR, depending on whether the CR
allele arrived via sperm or egg.
 The probability of being heterozygous (with a C RCW genotype) is 0.8 ×R0.2 = 0.16 for
C C , 0.2 × 0.8 = 0.16 for C C , and 0.16 + 0.16 = 0.32, or 32%, for C CW + CWCR.
R W W R

 As you can see, the processes of meiosis and random fertilization have maintained the
same allele and genotype frequencies that existed in the previous generation.
 The Hardy-Weinberg theorem states that the repeated shuffling of a population’s gene
pool over generations does not increase the frequency of one allele over another.
 Theoretically, the allele frequencies in our flower population should remain at 0.8 for
CR and 0.2 for CW forever.
 To generalize the example, in a population with two alleles with frequencies of p and q,
the combined frequencies must add to 100%.
 Therefore p + q = 1.
 If p + q = 1, then p = 1 − q and q = 1 − p.
 In the wildflower W
example, p is the frequency of red alleles (CR) and q is the frequency of
white alleles (C ).
 The probability of generating an CRCR offspring is p2 (an application of the rule of
multiplication).
 In our example, p = 0.8 and p2 = 0.64.
 The probability of generating a CWCW offspring is q2.
 In our example, q = 0.2 and q2 = 0.04.
 The probability of generating a CRCW offspring is 2pq.
 In our example, 2 × 0.8 × 0.2 = 0.32.
 The genotype frequencies must add up to 1.0:
 p2 + 2pq + q2 = 1.0
 For the wildflowers, 0.64 + 0.32 + 0.04 = 1.0.
 This general formula is the Hardy-Weinberg equation.
 Using this formula, we can calculate frequencies of alleles in a gene pool if we know the
frequency of genotypes, or the frequency of genotypes if we know the frequencies of
alleles.
Five conditions must be met for a population to remain in Hardy-Weinberg equilibrium.
 The Hardy-Weinberg theorem describes a hypothetic population that is not evolving.
However, real populations do evolve, and their allele and genotype frequencies do change
over time.
 That is because the five conditions for nonevolving populations are rarely met for long in
nature.
 A population must satisfy five conditions if it is to remain in Hardy-Weinberg
equilibrium:
o Extremely large population size. In small populations, chance fluctuations in the gene
pool can cause genotype frequencies to change over time. These random changes are
called genetic drift.
o No gene flow. Gene flow, the transfer of alleles due to the migration of individuals or
gametes between populations, can change the proportions of alleles.
o No mutations. Introduction, loss, or modification of genes will alter the gene pool.
Biology Chapter Notes
 o Random mating. If individuals pick mates with certain genotypes, or if inbreeding is
common, the mixing of gametes will not be random.
o No natural selection. Differential survival or reproductive success among genotypes
will alter their frequencies.
 Evolution usually results when any of these five conditions are not met.
 Although natural populations are rarely, if ever, in true Hardy-Weinberg equilibrium, the
rate of evolutionary change in many populations is so slow that they appear to be close to
equilibrium.
 In such cases, we can use the Hardy-Weinberg equation to estimate genotype and
allele frequencies.
 We can use the theorem to estimate the percentage of the human population that carries
the allele for the inherited disease phenylketonuria (PKU).
 About 1 in 10,000 babies born in the United States is born with PKU, a metabolic
condition that results in mental retardation and other problems if left untreated.
 The disease is caused by a recessive allele.
 Is the U.S. population in Hardy-Weinberg equilibrium with respect to the PKU gene?
o The U.S. population is very large.
o Populations outside the United States have PKU allele frequencies similar to those
seen in the United States, so gene flow will not alter allele frequencies significantly.
o The mutation rate for the PKU gene is very low.
o People do not choose their partners based on whether or not they carry the PKU allele,
and inbreeding (marriage to close relatives) is rare in the United States.
o Selection against PKU only acts against the rare heterozygous recessive individuals.
 From the epidemiological data, we know that frequency of homozygous recessive
individuals (q2 in the Hardy-Weinberg theorem) = 1 in 10,000, or 0.0001.
 The frequency of the recessive allele (q) is the square root of 0.0001 = 0.01.
 The frequency of the dominant allele (p) is p = 1 − q, or 1 − 0.01 = 0.99.
 The frequency of carriers (heterozygous individuals) is 2pq = 2 × 0.99 × 0.01 =
0.0198, or about 2%.
 Thus, about 2% of the U.S. population carries the PKU allele.

Concept 23.2 Mutation and sexual recombination produce the variation that makes
evolution possible
New genes and new alleles originate only by mutation.
 A mutation is a change in the nucleotide sequence of an organism’s DNA.
 Most mutations occur in somatic cells and are lost when the individual dies.
 Only mutations in cell lines that form gametes can be passed on to offspring, and only a
small fraction of these spread through populations and become fixed.
 A new mutation that is transmitted in a gamete to an offspring can immediately change
the gene pool of a population by introducing a new allele.
 A point mutation is a change of a single base in a gene.
Biology Chapter Notes
 Point mutations can have a significant impact on phenotype, as in the case of sickle-cell
disease.
 However, most point mutations are harmless.
 Much of the DNA in eukaryotic genomes does not code for protein products.
 However, some noncoding regions of DNA do regulate gene expression.
 Changes in these regulatory regions of DNA can have profound effects.
 Because the genetic code is redundant, some point mutations in genes that code for
proteins may not alter the protein’s amino acid composition.
 On rare occasions, a mutant allele may actually make its bearer better suited to the
environment, increasing reproductive success.
 This is more likely when the environment is changing.
 Some mutations alter gene number or sequence.
 Chromosomal mutations that delete or rearrange many gene loci at once are almost
always harmful.
 In rare cases, chromosomal rearrangements may be beneficial.
 For example, the translocation of part of one chromosome to a different
chromosome could link genes that act together to positive effect.
 Gene duplication is an important source of new genetic variation.
 Small pieces of DNA can be introduced into the genome through the activity of
transposons.
 Such duplicated segments can persist over generations and provide new loci that may
eventually take on new functions by mutation and subsequent selection.
 New genes may also arise when the coding subsections of genes known as exons are
shuffled within the genome, within a single locus or between loci.
 Such beneficial increases in gene number appear to have played a major role in evolution.
 For example, mammalian ancestors carried a single gene for detecting odors that has been
duplicated though various mutational mechanisms.
 Modern humans have close to 1,000 olfactory receptor genes.
 60% of these genes have been inactivated in humans, due to mutations.
 Mice, who rely more on their sense of smell, have lost only 20% of their olfactory
receptor genes.
 Mutation rates vary from organism to organism.
 Mutation rates are low in animals and plants, averaging about 1 mutation in every
100,000 genes per generation.
 In microorganisms and viruses with short generation spans, mutation rates are much
higher and can rapidly generate genetic variation.
Sexual recombination also produces genetic variation.
 On a generation-to-generation timescale, sexual recombination is far more important than
mutation in producing the genetic differences that make adaptation possible.
 Sexual reproduction rearranges alleles into novel combinations every generation.
 Bacteria and viruses can also undergo recombination, but they do so less regularly than
animals and plants.
 Bacterial and viral recombination may cross species barriers.

Biology Chapter Notes

Concept 23.3 Natural selection, genetic drift, and gene flow can alter a population’s
genetic composition
 Although new mutations can modify allele frequencies, the change from generation to
generation is very small.
 Recombination reshuffles alleles but does not change their frequency.
 Three major factors alter allele frequencies to bring about evolutionary change: natural
selection, genetic drift, and gene flow.
Natural selection is based on differential reproductive success.
 Individuals in a population vary in their heritable traits.
 Those with variations better suited to the environment tend to produce more offspring
than those with variations that are less well suited.
 As a result of selection, alleles are passed on to the next generation in frequencies
different from their relative frequencies in the present population.
 Imagine that in our imaginary wildflower population, white flowers are more visible to
herbivorous insects and thus have lower survival. Imagine that red flowers are more
visible to pollinators.
 Such differences in survival and reproductive W
success would disturb the Hardy-
Weinberg equilibrium. The frequency of the C allele would decline and the frequency
of the CR allele would increase.
Genetic drift results from chance fluctuations in allele frequencies in small populations.
 Genetic drift occurs when changes in gene frequencies from one generation to another
occur because of chance events (sampling errors) that occur in small populations.
 For example, you would not be too surprised if a thrown coin produced seven heads
and three tails in ten tosses, but you would be surprised if you saw 700 heads and 300
tails in 1,000 tosses—you would expect close to 500 of each.
 The smaller the sample, the greater the chance of deviation from the expected result.
 In a large population, allele frequencies will not change from generation to generation by
chance alone.
 However, in a small wildflower population with a stable size of only ten plants, genetic
drift can completely eliminate some alleles.
 Genetic drift at small population sizes may occur as a result of two situations: the
bottleneck effect or the founder effect.
 The bottleneck effect occurs when the numbers of individuals in a large population are
drastically reduced by a disaster.
 By chance, some alleles may be overrepresented and others underrepresented among
the survivors.
 Some alleles may be eliminated altogether.
 Genetic drift will continue to change the gene pool until the population is large enough
to eliminate the effect of chance fluctuations.
 The bottleneck effect is an important concept in conservation biology of endangered
species.
 Populations that have suffered bottleneck incidents have lost genetic variation from the
gene pool.
Biology Chapter Notes
  This reduces individual variation and may reduce adaptation.
 For example, in the 1890s, hunters reduced the population of northern elephant
seals in California to 20 individuals.
 Now that it is a protected species, the population has increased to more than 30,000.
 However, a study of 24 gene loci in a representative sample of seals showed no
variation. One allele had been fixed for each gene.
 Populations of the closely related southern elephant seal, which did not go through
a bottleneck, show abundant genetic variation.
 The founder effect occurs when a new population is started by only a few individuals
who do not represent the gene pool of the larger source population.
 At an extreme, a population could be started by a single pregnant female or single seed
with only a tiny fraction of the genetic variation of the source population.
 Genetic drift would continue from generation to generation until the population grew
large enough for sampling errors to be minimal.
 Founder effects have been demonstrated in human populations that started from a
small group of colonists.
A population may lose or gain alleles by gene flow.
 Gene flow is genetic exchange due to migration of fertile individuals or gametes between
populations.
 For example, if a nearby wildflower population consisted entirely of white flowers, its
pollen (CW alleles only) could be carried into our target population.
 This would increase the frequency of CW alleles in the target population in the next
generation.
 Gene flow tends to reduce differences between populations.
 If extensive enough, gene flow can amalgamate neighboring populations into a single
population with a common gene pool.
 Humans today migrate much more freely than in the past, and gene flow has become
an important agent of evolutionary change in human populations that were previously
isolated.

Concept 23.4 Natural selection is the primary mechanism of adaptive evolution

 Of all the factors that can change a gene pool, only natural selection leads to adaptation of
an organism to its environment.
 Natural selection accumulates and maintains favorable genotypes in a population.
 Most populations have extensive genetic variation.
 Not all variation is heritable. For example, body builders alter their phenotypes but do not
pass on their huge muscles to their children.
 Only the genetic component of variation can have evolutionary consequences as a result
of natural selection.
 This is because only heritable traits pass from generation to generation.
Genetic variation occurs within and between populations.
 Both quantitative and discrete characters contribute to variation within a population.
 Quantitative characters are those that vary along a continuum within a population.
Biology Chapter Notes
  For example, plant height in a wildflower population ranges from short to tall.
 Quantitative variation is usually due to polygenic inheritance in which the additive
effects of two or more genes influence a single phenotypic character.
 Discrete characters, such as flower color, are usually determined by a single locus with
different alleles that produce distinct phenotypes.
 Phenotypic polymorphism occurs when two or more discrete phenotypes are represented
in high enough frequencies to be noticeable in a population.
 The contrasting forms are called morphs, as in the red-flowered and white-flowered
morphs in our wildflower population.
 Human populations are polymorphic for a variety of physical (e.g., freckles) and
biochemical (e.g., blood types) characters.
 Polymorphism applies only to discrete characters, not quantitative characters.
 Human height, which varies in a continuum, is not a phenotypic polymorphism.
 Population geneticists measure genetic variation by determining the amount of
heterozygosity at the level of whole genes (gene variability) and at the molecular level of
DNA (nucleotide variability).
 Average heterozygosity measures gene variability, the average percent of gene loci that
are heterozygous.
 In the fruit fly (Drosophila), about 86% of their 13,000 gene loci are homozygous
(fixed).
 About 14% (1,800 genes) are heterozygous.
 Nucleotide variability measures the mean level of difference in nucleotide sequences
(base pair differences) among individuals in a population.
 In fruit flies, about 1% of the bases differ between two individuals.
 Two individuals differ, on average, at 1.8 million of the 180 million nucleotides in the
fruit fly genome.
 Why does average heterozygosity tend to be greater than nucleotide diversity?
 This is because a gene can consist of thousands of bases of DNA. A difference at only
one of these bases is sufficient to make two alleles of that gene different and count
toward average heterozygosity.
 Humans have relatively little genetic variation.
 Nucleotide diversity is only 0.1%.
 You and your neighbor probably have the same nucleotide at 999 out of every 1,000
nucleotide sites in your DNA.
 Geographic variation results from differences in phenotypes or genotypes between
populations or between subgroups of a single population that inhabit different areas.
 Natural selection contributes to geographic variation by modifying gene frequencies in
response to differences in local environmental factors.
 Genetic drift can also lead to variation among populations through the cumulative
effect of random fluctuations in allele frequencies.
 Geographic variation can occur on a local scale, within a population, if the environment is
patchy or if dispersal of individuals is limited, producing subpopulations. This is termed
spatial variation.
 Geographic variation in the form of graded change in a trait along a geographic axis is
called a cline.

Biology Chapter Notes

  Clines may represent intergrade zones where individuals from neighboring, genetically
different, populations interbreed.
 Alternatively, clines may reflect the influence of natural selection based on gradation
in some environmental variable.
 For example, the average body size of many North American species of birds and
mammals increases gradually with increasing latitude, allowing Northern
populations to conserve heat in cold environments by decreasing the ratio of surface
area to volume.
Let’s take a closer look at natural selection.
 The terms “struggle for existence” and “survival of the fittest” are misleading because
they suggest that individuals compete directly in contests.
 In some animal species, males do compete directly for mates.
 Reproductive success is generally subtler and depends on factors other than battle for
mates.
 For example, a barnacle may produce more eggs than its neighbors because it is more
efficient at filtering food from the water.
 Wildflowers may be successful because they attract more pollinators.
 These examples of adaptive advantage are all components of evolutionary fitness.
 Fitness is defined as the contribution an individual makes to the gene pool of the next
generation, relative to the contributions of other individuals.
 Population geneticists define relative fitness as the contribution of a genotype to the next
generation compared to the contribution of alternative genotypes for the same locus.
 Consider our wildflower population.
 Let’s assume that individuals with red flowers produce fewer offspring than those with
white or pink flowers, which produce equal numbers of offspring.
 The relative fitness of the most successfulWvariants is set at 1.0 as a basis for
comparison, so the relative fitness of white (C CW) and pink (CRCW) plants is 1.0.
 If plants with red flowers (CRCR) produce only 80% as many offspring, their relative
fitness is 0.8.
 Although population geneticists measure the relative fitness of a genotype, it is important
to remember that natural selection acts on phenotypes, not genotypes.
 The whole organism is subjected to natural selection.
 The relative fitness of an allele depends on the entire genetic and environmental context in
which it is expressed.
 Survival alone does not guarantee reproductive success.
 Relative fitness is zero for a sterile organism, even if it is robust and long-lived.
 On the other hand, longevity may increase fitness if long-lived individuals leave more
offspring than short-lived individuals.
 In many species, individuals that mature quickly, become fertile at an early age, and live
for a short time have greater relative fitness than individuals that live longer but mature
later.
There are three modes of selection: directional, disruptive, and stabilizing.
 Natural selection can alter the frequency distribution of heritable traits in three ways,
depending on which phenotypes in a population are favored.
Biology Chapter Notes
 The three modes of selection are called directional, disruptive, and stabilizing selection.
 Directional selection is most common during periods of environmental change or when
members of a population migrate to a new habitat with different environmental
conditions.
 Directional selection shifts the frequency curve for a phenotypic character in one direction
by favoring individuals who deviate from the average.
 For example, fossil evidence indicates that the average size of black bears in Europe
increased during each glacial period, only to decrease again during the warmer interglacial
periods.
 Large bears have a smaller surface-to-volume ratio and are better at conserving body
heat during periods of extreme cold.
 Disruptive selection occurs when environmental conditions favor individuals at both
extremes of the phenotypic range over those with intermediate phenotypes.
 For example, two distinct bill types are present in Cameroon’s black-bellied
seedcrackers. Larger-billed birds are more efficient in feeding on hard seeds and
smaller-billed birds are more efficient in feeding on soft seeds.
 Birds with intermediate bills are relatively inefficient at cracking both types of seeds
and thus have lower relative fitness.
 Disruptive selection can be important in the early stages of speciation.
 Stabilizing selection favors intermediate variants and acts against extreme phenotypes.
 Stabilizing selection reduces variation and maintains the status quo for a trait.
 Human birth weight is subject to stabilizing selection.
 Babies much larger or smaller than 3–4 kg have higher infant mortality than average-
sized babies.
Diploidy and balancing selection preserve genetic variation.
 The tendency for natural selection to reduce variation is countered by mechanisms that
preserve or restore variation, including diploidy and balanced polymorphisms.
 Diploidy in eukaryotes prevents the elimination of recessive alleles via selection because
recessive alleles do not affect the phenotype in heterozygotes.
 Even recessive alleles that are unfavorable can persist in a population through their
propagation by heterozygous individuals.
 Recessive alleles are only exposed to selection when both parents carry the same recessive
allele and combine two recessive alleles in one zygote.
 This happens only rarely when the frequency of the recessive allele is very low.
 The rarer the recessive allele, the greater the degree of protection it has from natural
selection.
 Heterozygote protection maintains a huge pool of alleles that may not be suitable under
the present conditions but may become beneficial when the environment changes.
 Natural selection itself preserves variation at some gene loci.
 Balancing selection occurs when natural selection maintains stable frequencies of two or
more phenotypes in a population, a state called balanced polymorphism.
 One mechanism producing balanced polymorphism is heterozygote advantage.
 In some situations, individuals who are heterozygous at a particular locus have greater
fitness than homozygotes.
Biology Chapter Notes
  In these cases, natural selection will maintain multiple alleles at that locus.
 Heterozygous advantage maintains genetic diversity at the human gene for one chain of
hemoglobin.
 Homozygous recessive individuals suffer from sickle-cell disease.
 Homozygous dominant individuals are vulnerable to malaria.
 Heterozygous individuals are resistant to malaria.
 The frequency of the sickle-cell allele is highest in areas where the malarial parasite is
common.
 In some African tribes, it accounts for 20% of the gene pool, a very high frequency for
such a harmful allele.
 Even at this high frequency, only 4% of the population suffers from sickle-cell disease
(q2 = 0.2 × 0.2 = 0.04), while 32% of the population is resistant to malaria (2pq = 2 ×
0.8 × 0.2 = 0.32).
 The aggregate benefit of the sickle-cell allele in the population balances its aggregate
harm.
 A second mechanism promoting balanced polymorphism is frequency-dependent
selection.
 Frequency-dependent selection occurs when the fitness of any one morph declines if it
becomes too common in the population.
 Predators may develop “search images” of the most common forms of prey. A prey
morph that becomes too common may become disproportionately vulnerable to
predation.
 Frequency-dependent selection has been observed in a number of predator-prey
interactions in the wild.
 Some genetic variations, neutral variations, have negligible impact on fitness, and thus
natural selection does not affect these alleles.
 For example, the diversity of human fingerprints seems to confer no selective
advantage to some individuals over others.
 Most of the base differences between humans that are found in untranslated parts of
the genome appear to confer no selective advantage.
 Pseudogenes, genes that have become inactivated by mutations, accumulate genetic
variations.
 Over time, some neutral alleles will increase and others will decrease by the chance
effects of genetic drift.
 There is no consensus among biologists on how much genetic variation can be classified
as neutral or even if any variation can be considered truly neutral.
 It is almost impossible to demonstrate that an allele brings no benefit at all to an
organism.
 Also, variant alleles may be neutral in one environment but not in another.
 Even if only a fraction of the extensive variation in a gene pool significantly affects an
organism, there is still an enormous reservoir of raw material for natural selection and
adaptive evolution.
Sexual selection may lead to pronounced secondary differences between the sexes.
 Charles Darwin was the first scientist to investigate sexual selection, which is natural
selection for mating success.

Biology Chapter Notes

 Sexual selection results in sexual dimorphism, marked differences between the sexes in
secondary sexual characteristics not directly associated with reproduction.
 Males and females may differ in size, coloration, and ornamentation.
 In vertebrates, males are usually the larger and showier sex.
 It is important to distinguish between intrasexual and intersexual selection.
 Intrasexual selection is direct competition among individuals of one sex (usually males)
for mates of the opposite sex.
 Competition may take the form of direct physical battles between individuals.
 The stronger individuals gain status.
 More commonly, ritualized displays discourage lesser competitors and determine
dominance.
 Evidence is growing that intrasexual selection can take place between females as well.
 Intersexual selection or mate choice occurs when members of one sex (usually females)
are choosy in selecting their mates from individuals of the other sex.
 Because females invest more in eggs and parental care, they are choosier about their
mates than males.
 A female tries to select a mate that will confer a fitness advantage on their mutual
offspring.
 In many cases, the female chooses a male based on his showy appearance or behavior.
 Some male showiness does not seem to be adaptive except in attracting mates and may
put the male at considerable risk.
 For example, bright plumage may make male birds more visible to predators.
 Even if these extravagant features have some costs, individuals that possess them
will have enhanced fitness if they help an individual gain a mate.
 Every time a female chooses a mate based on appearance or behavior, she
perpetuates the alleles that caused her to make that choice.
 She also allows a male with that particular phenotype to perpetuate his alleles.
 How do female preferences for certain male characteristics evolve? Are there fitness
benefits to showy traits?
 Several researchers are testing the hypothesis that females use male sexual
advertisements to measure the male’s overall health.
 Males with serious parasitic infections may have dull, disheveled plumage.
 These individuals are unlikely to win many females.
 If a female chooses a showy mate, she may be choosing a healthy one, and her benefit
is a greater probability of having healthy offspring.
Sex is an evolutionary enigma.
 As a mechanism of rapid population growth, sex is far inferior to asexual reproduction.
 Consider a population in which half the females reproduce only asexually and half the
females reproduce only sexually.
 Assume that both types of females produce equal numbers of offspring each
generation.
 The asexual condition will increase in frequency, because:
 All offspring of asexual females will be reproductive daughters.
 Only half of the offspring of sexual females will be daughters; the other half will
necessarily be males.
Biology Chapter Notes
 Sex is maintained in the vast majority of eukaryotic species, even those that also
reproduce asexually.
 Sex must confer some selective advantage to compensate for the costs of diminished
reproductive output.
 Otherwise, migration of asexual individuals or mutation permitting asexual
reproduction would outcompete sexual individuals and the alleles favoring sex.
 The traditional explanation for the maintenance of sex was that the process of meiosis and
fertilization generate genetic variation on which natural selection can act.
 However, the assumption that sex is maintained in spite of its disadvantages because it
produces future adaptation in a variable world is difficult to defend.
 Natural selection acts in the present, favoring individuals here and now that best fit the
current, local environment.
 Let us instead consider how the genetic variation promoted by sex might be advantageous
in the short term, on a generation-to-generation timescale.
 Genetic variability may be important in resistance to disease.
 Parasites and pathogens recognize and infect their hosts by attaching to receptor
molecules on the host’s cells.
 There should be an advantage to producing offspring that vary in their resistance to
different diseases.
 One offspring may have cellular markers that make it resistant to virus A, while
another is resistant to virus B.
 This hypothesis predicts that gene loci that code for receptors to which pathogens
attack should have many alleles.
 In humans, there are hundreds of alleles for each of two gene loci that give cell
surfaces their molecular fingerprints.
 At the same time, parasites evolve very rapidly in their ability to use specific host
receptors.
 However, sex provides a mechanism for changing the distribution of alleles and
varying them among offspring.
 This coevolution in which host and parasite must evolve quickly to keep up with each
other has been called a “Red Queen race.”
Natural selection cannot fashion perfect organisms.
 There are at least four reasons natural selection cannot produce perfection.
o Evolution is limited by historical constraints.
 Evolution does not scrap ancestral features and build new complex structures or
behavior from scratch.
 Evolution co-opts existing features and adapts them to new situations.
 For example, birds might benefit from having wings plus four legs. However, birds
descended from reptiles that had only two pairs of limbs. Co-opting the forelimbs for
flight left only two hind limbs for movement on the ground.
o Adaptations are often compromises.
 Each organism must do many different things.
 Because the flippers of a seal must allow it to walk on land and also swim efficiently,
their design is a compromise between these environments.
 Similarly, human limbs are flexible and allow versatile movements, but are prone to
injuries, such as sprains, torn ligaments, and dislocations.
Biology Chapter Notes
  Better structural reinforcement would compromise agility.
o Chance and natural selection interact.
 Chance events affect the subsequent evolutionary history of populations.
 For example, founders of new populations may not necessarily be the individuals best
suited to the new environment, but rather those individuals that were carried there by
chance.
o Selection can only edit existing variations.
 Natural selection favors only the fittest variations from those phenotypes that are
available.
 New alleles do not arise on demand.
 Natural selection works by favoring the best variants available.
 The many imperfections of living organisms are evidence for evolution.

Biology Chapter Notes

 Chapter 24 The Origin of Species
Chapter Notes

Overview: That “Mystery of Mysteries”

 Darwin visited the Galápagos Islands and found them filled with plants and animals
that lived nowhere else in the world.
 He realized that he was observing newly emerged species on these young islands.
 Speciation—the origin of new species—is at the focal point of evolutionary theory
because the appearance of new species is the source of biological diversity.
 Microevolution is the study of adaptive change in a population.
 Macroevolution addresses evolutionary changes above the species level.
 It deals with questions such as the appearance of evolutionary novelties (e.g.,
feathers and flight in birds) that can be used to define higher taxa.
 Speciation addresses the question of how new species originate and develop through
the subdivision and subsequent divergence of gene pools.
 The fossil record chronicles two patterns of speciation: anagenesis and cladogenesis.
 Anagenesis, phyletic evolution, is the accumulation of changes associated with the
gradual transformation of one species into another.
 Cladogenesis, branching evolution, is the budding of one or more new species from a
parent species.
 Only cladogenesis promotes biological diversity by increasing the number of
species.

 Concept 24.1 The biological species concept emphasizes reproductive isolation
 Species is a Latin word meaning “kind” or “appearance.”
 Traditionally, morphological differences have been used to distinguish species.
 Today, differences in body function, biochemistry, behavior, and genetic makeup
are also used to differentiate species.
 Are organisms truly divided into the discrete units we called species, or is this
classification an arbitrary attempt to impose order on the natural world?
 In 1942, Ernst Mayr proposed the biological species concept.

Biology Chapter Notes

  A species is defined as a population or group of populations whose members have
the potential to breed with each other in nature to produce viable, fertile
offspring, but who cannot produce viable, fertile offspring with members of other
species.
 A biological species is the largest set of populations in which genetic exchange is
possible and that is genetically isolated from other populations.
 Species are based on interfertility, not physical similarity.
 For example, eastern and western meadowlarks have similar shapes and coloration,
but differences in song help prevent interbreeding between the two species.
 In contrast, humans have considerable diversity, but we all belong to the same
species because of our capacity to interbreed.
 Prezygotic and postzygotic barriers isolate the gene pools of biological species.
 Because the distinction between biological species depends on reproductive
incompatibility, the concept hinges on reproductive isolation, the existence of
biological barriers that prevent members of two species from producing viable,
fertile hybrids.
 A single barrier may not block all genetic exchange between species, but a
combination of several barriers can effectively isolate a species’ gene pool.
 Typically, these barriers are intrinsic to the organisms, not due to simple
geographic separation.
 Reproductive isolation prevents populations belonging to different species from
interbreeding, even if their ranges overlap.
 Reproductive barriers can be categorized as prezygotic or postzygotic, depending on
whether they function before or after the formation of zygotes.
 Prezygotic barriers impede mating between species or hinder fertilization of ova if
members of different species attempt to mate.
 These barriers include habitat isolation, behavioral isolation, temporal isolation,
mechanical isolation, and gametic isolation.
 Habitat isolation. Two organisms that use different habitats (even in the same
geographic area) are unlikely to encounter each other to even attempt mating.
 Two species of garter snakes in the genus Thamnophis occur in the same areas.
Because one lives mainly in water and the other is primarily terrestrial, they
rarely encounter each other.

Biology Chapter Notes

 Behavioral isolation. Many species use elaborate courtship behaviors unique to the
species to attract mates.
 In many species, elaborate courtship displays identify potential mates of the
correct species and synchronize gonadal maturation.
 In the blue-footed booby, males perform a high-step dance that calls the female’s
attention to the male’s bright blue feet.
 Temporal isolation. Two species that breed during different times of day, different
seasons, or different years cannot mix gametes.
 The geographic ranges of the western spotted skunk and the eastern spotted
skunk overlap. However, they do not interbreed because the former mates in late
summer and the latter in late winter.
 Mechanical isolation. Closely related species may attempt to mate but fail because
they are anatomically incompatible and transfer of sperm is not possible.
 For example, mechanical barriers contribute to the reproductive isolation of
flowering plants that are pollinated by insects or other animals.
 With many insects, the male and female copulatory organs of closely related
species do not fit together, preventing sperm transfer.
 Gametic isolation. The gametes of two species do not form a zygote because of
incompatibilities preventing fertilization.
 In species with internal fertilization, the environment of the female reproductive
tract may not be conducive to the survival of sperm from other species.
 For species with external fertilization, gamete recognition may rely on the
presence of specific molecules on the egg’s coat, which adhere only to specific
molecules on sperm cells of the same species.
 A similar molecular recognition mechanism enables a flower to discriminate
between pollen of the same species and pollen of a different species.
 If a sperm from one species does fertilize the ovum of another, postzygotic barriers
may prevent the hybrid zygote from developing into a viable, fertile adult.
 These barriers include reduced hybrid viability, reduced hybrid fertility, and
hybrid breakdown.
 Reduced hybrid viability. Genetic incompatibility between the two species may abort
the development of the hybrid at some embryonic stage or produce frail offspring.
 This is true for the occasional hybrids between frogs in the genus Rana. Most do
not complete development, and those that do are frail.
Biology Chapter Notes
 Reduced hybrid fertility. Even if the hybrid offspring are vigorous, the hybrids may
be infertile, and the hybrid cannot backbreed with either parental species.
 This infertility may be due to problems in meiosis because of differences in
chromosome number or structure.
 For example, while a mule, the hybrid product of mating between a horse and
donkey, is a robust organism, it cannot mate (except very rarely) with either
horses or donkeys.
 Hybrid breakdown. In some cases, first generation hybrids are viable and fertile.
 However, when they mate with either parent species or with each other, the next
generation is feeble or sterile.
 Strains of cultivated rice have accumulated different mutant recessive alleles at
two loci in the course of their divergence from a common ancestor.
 Hybrids between them are vigorous and fertile, but plants in the next generation
that carry too many of these recessive alleles are small and sterile.
 These strains are in the process of speciating.
 Reproductive barriers can occur before mating, between mating and fertilization, or
after fertilization.
 The biological species concept has some major limitations.
 While the biological species concept has had an important impact on evolutionary
theory, it is limited when applied to species in nature.
 For example, one cannot test the reproductive isolation of morphologically similar
fossils, which are separated into species based on morphology.
 Even for living species, we often lack information on interbreeding needed to
apply the biological species concept.
 In addition, many species (e.g., bacteria) reproduce entirely asexually and are
assigned to species based mainly on structural and biochemical characteristics.
 Many bacteria transfer genes by conjugation and other processes, but this
transfer is different from sexual recombination.
 Evolutionary biologists have proposed several alternative concepts of species.
 Several alternative species concepts emphasize the processes that unite the members
of a species.
 The ecological species concept defines a species in terms of its ecological niche, the set
of environmental resources that a species uses and its role in a biological community.
Biology Chapter Notes
  As an example, a species that is a parasite may be defined in part by its
adaptations to a specific organism.
 This concept accommodates asexual and sexual species.
 The paleontological species concept focuses on morphologically discrete species
known only from the fossil record.
 There is little or no information about the mating capability of fossil species, and
the biological species concept is not useful for them.
 The phylogenetic species concept defines a species as a set of organisms with a unique
genetic history.
 Biologists compare the physical characteristics or molecular sequences of species
to those of other organisms to distinguish groups of individuals that are
sufficiently different to be considered separate species.
 Sibling species are species that appear so similar that they cannot be distinguished
on morphological grounds.
 Scientists apply the biological species concept to determine if the phylogenetic
distinction is confirmed by reproductive incompatibility.
 The morphological species concept, the oldest and still most practical, defines a
species by a unique set of structural features.
 The morphological species concept has certain advantages. It can be applied to
asexual and sexual species, and it can be useful even without information about
the extent of gene flow.
 However, this definition relies on subjective criteria, and researchers sometimes
disagree about which structural features identify a species.
 In practice, scientists use the morphological species concept to distinguish most
species.
 Each species concept may be useful, depending on the situation and the types of
questions we are asking.

 Concept 24.2 Speciation can take place with or without geographic separation
 Two general modes of speciation are distinguished by the way gene flow among
populations is initially interrupted.
 In allopatric speciation, geographic separation of populations restricts gene flow.

Biology Chapter Notes

 In sympatric speciation, speciation occurs in geographically overlapping populations
when biological factors, such as chromosomal changes and nonrandom mating,
reduce gene flow.
 Allopatric speciation: geographic barriers can lead to the origin of species.
 Several geological processes can fragment a population into two or more isolated
populations.
 Mountain ranges, glaciers, land bridges, or splintering of lakes may divide one
population into isolated groups.
 Alternatively, some individuals may colonize a new, geographically remote area
and become isolated from the parent population.
 For example, mainland organisms that colonized the Galápagos Islands were
isolated from mainland populations.
 How significant a barrier must be to limit gene exchange depends on the ability of
organisms to move about.
 A geological feature that is only a minor hindrance to one species may be an
impassible barrier to another.
 The valley of the Grand Canyon is a significant barrier for the ground squirrels
that have speciated on opposite sides.
 For birds that can fly across the canyon, it is no barrier.
 Once geographic separation is established, the separated gene pools may begin to
diverge through a number of mechanisms.
 Mutations arise.
 Sexual selection favors different traits in the two populations.
 Different selective pressures in differing environments act on the two populations.
 Genetic drift alters allele frequencies.
 A small, isolated population is more likely to have its gene pool changed substantially
over a short period of time by genetic drift and natural selection.
 For example, less than 2 million years ago, small populations of stray plants and
animals from the South American mainland colonized the Galápagos Islands and
gave rise to the species that now inhabit the islands.
 However, very few small, isolated populations develop into new species; most simply
persist or perish in their new environment.

Biology Chapter Notes

 To confirm that allopatric speciation has occurred, it is necessary to determine
whether the separated populations have become different enough that they can no
longer interbreed and produce fertile offspring when they come back in contact.
 In some cases, researchers bring together members of separated populations in a
laboratory setting.
 Biologists can also assess allopatric speciation in the wild.
 For example, females of the Galápagos ground finch Geospiza difficilis respond
to the songs of males from the same island but ignore the songs of males of the
same species from other islands.
 Sympatric speciation: a new species can originate in the geographic midst of the parent
species.
 In sympatric speciation, new species arise within the range of the parent populations.
 Here reproductive barriers must evolve between sympatric populations.
 In plants, sympatric speciation can result from accidents during cell division that
result in extra sets of chromosomes, a mutant condition known as polyploidy.
 In animals, it may result from gene-based shifts in habitat or mate preference.
 An individual can have more than two sets of chromosomes.
 An autopolyploid mutant is an individual that has more than two chromosome
sets, all derived from a single species.
 For example, a failure of mitosis or meiosis can double a cell’s chromosome
number from diploid (2n) to tetraploid (4n).
 The tetraploid can reproduce with itself (self-pollination) or with other
tetraploids.
 It cannot mate with diploids from the original population, because of abnormal
meiosis by the triploid hybrid offspring.
 A more common mechanism of producing polyploid individuals occurs when
allopolyploid offspring are produced by the mating of two different species.
 While the hybrids are usually sterile, they may be quite vigorous and propagate
asexually.
 In subsequent generations, various mechanisms may transform a sterile hybrid
into a fertile polyploid.
 These polyploid hybrids are fertile with each other but cannot breed with either
parent species.
Biology Chapter Notes
  They thus represent a new biological species.
 The origin of polyploid plant species is common and rapid enough that scientists
have documented several such speciations in historical times.
 For example, two new species of plants called goatsbeard (Tragopodon) appeared
in Idaho and Washington in the early 1900s.
 They are the results of allopolyploidy events between pairs of introduced
European Tragopodon species.
 Many plants important for agriculture are polyploid.
 For example, wheat is an allohexaploid, with six sets of chromosomes from three
different species.
 Oats, cotton, potatoes, and tobacco are polyploid.
 Plant geneticists now use chemicals that induce meiotic and mitotic errors to
create new polyploid plants with special qualities.
 One example is an artificial hybrid combining the high yield of wheat with the
hardiness and disease resistance of rye.
 While polyploid speciation does occur in animals, other mechanisms also contribute
to sympatric speciation in animals.
 Reproductive isolation can result when genetic factors cause individuals to exploit
resources not used by the parent.
 One example is the North American maggot fly, Rhagoletis pomonella.
 The fly’s original habitat was native hawthorn trees.
 About 200 years ago, some populations colonized newly introduced apple trees.
 Because apples mature more quickly than hawthorn fruit, the apple-feeding
flies have been selected for more rapid development and now show temporal
isolation from the hawthorn-feeding maggot flies.
 Speciation is underway.
 Sympatric speciation is one mechanism that has been proposed for the explosive
adaptive radiation of cichlid fishes in Lake Victoria, Africa.
 This vast, shallow lake has filled and dried up repeatedly due to climate changes.
 The current lake is only 12,000 years old but is home to 600 species of cichlid
fishes.

Biology Chapter Notes

  The species are so genetically similar that many have likely arisen since the
lake last filled.
 While these species are clearly specialized for exploiting different food resources
and other resources, nonrandom mating in which females select males based on a
certain appearance has probably contributed, too.
 Individuals of two closely related sympatric cichlid species will not mate under
normal light because females have specific color preferences and males differ in
color.
 However, under light conditions that de-emphasize color differences, females will
mate with males of the other species and produce viable, fertile offspring.
 It seems likely that the ancestral population was polymorphic for color and that
divergence began with the appearance of two ecological niches that divided the
fish into subpopulations.
 Genetic drift resulted in chance differences in the genetic makeup of the
subpopulations, with different male colors and female preferences.
 Sexual selection reinforced the color differences.
 The lack of postzygotic barriers in this case suggests that speciation occurred
relatively recently.
 As pollution clouds the waters of Lake Victoria, it becomes more difficult for
female cichlids to see differences in male color.
 The gene pools of these two closely related species may blend again.
 We will summarize the differences between sympatric and allopatric speciation.
 In allopatric speciation, a new species forms while geographically isolated from its
parent population.
 As the isolated population accumulates genetic differences due to natural
selection and genetic drift, reproductive isolation from the ancestral species may
arise as a by-product of the genetic change.
 Such reproductive barriers prevent breeding with the parent even if the
populations reestablish contact.
 Sympatric speciation requires the emergence of some reproductive barrier that
isolates a subset of the population without geographic separation from the parent
population.
 In plants, the most common mechanism is hybridization between species or errors
in cell division that lead to polyploid individuals.
Biology Chapter Notes
  In animals, sympatric speciation may occur when a subset of the population is
reproductively isolated by a switch in food source or by sexual selection in a
polymorphic population.
 The evolution of many diversely adapted species from a common ancestor when new
environmental opportunities arise is called adaptive radiation.
 Adaptive radiation occurs when a few organisms make their way into new areas or
when extinction opens up ecological niches for the survivors.
 A major adaptive radiation of mammals followed the extinction of the dinosaurs
65 million years ago.
 The Hawaiian archipelago is a showcase of adaptive radiation.
 Located 3,500 km from the nearest continent, the volcanic islands were formed
“naked” and gradually populated by stray organisms that arrived by wind or
ocean currents.
 The islands are physically diverse, with a range of altitudes and rainfall.
 Multiple invasions and allopatric and sympatric speciation events have ignited an
explosion of adaptive radiation of novel species.
 Researchers study the genetics of speciation.
 Researchers have made great strides in understanding the role of genes in particular
speciation events.
 Douglas Schemske and his colleagues at Michigan State University examined two
species of Mimulus.
 The two species are pollinated by bees and hummingbirds respectively, keeping
their gene pools separate through prezygotic isolation.
 The species show no postzygotic isolation and can be mated readily in the
greenhouse to produce hybrids with flowers that vary in color and shape.
 Researchers observed which pollinators visit which flowers and then investigated
the genetic differences between plants.
 Two gene loci have been identified that are largely responsible for pollinator
choice.
 One locus influences flower color; the other affects the amount of nectar flowers
produce.
 By determining attractiveness of the flowers to different pollinators, allelic
diversity at these loci has led to speciation.

Biology Chapter Notes

 The tempo of speciation is important.
 In the fossil record, many species appear as new forms rather suddenly (in geologic
terms), persist essentially unchanged, and then disappear from the fossil record.
 Darwin noted this when he remarked that species appeared to undergo modifications
during relatively short periods of their total existence and then remained essentially
unchanged.
 Paleontologists Niles Eldredge and Stephen Jay Gould coined the term punctuated
equilibrium to describe these periods of apparent stasis punctuated by sudden
change.
 Some scientists suggest that these patterns require an explanation outside the
Darwinian model of descent with modification.
 However, this is not necessarily the case.
 Suppose that a species survived for 5 million years, but most of its morphological
alterations occurred in the first 50,000 years of its existence—just 1% of its total
lifetime.
 Because time periods this short often cannot be distinguished in fossil strata, the
species would seem to have appeared suddenly and then lingered with little or no
change before becoming extinct.
 Even though the emergence of this species actually took tens of thousands of
years, this period of change left no fossil record.
 Stasis can also be explained.
 All species continue to adapt after they arise, but often by changes that do not
leave a fossil record, such as small biochemical modifications.
 Paleontologists base hypotheses of descent almost entirely on external morphology.
 During periods of apparent equilibrium, changes in behavior, internal anatomy,
and physiology may not leave a fossil record.
 If the environment changes, the stasis will be broken by punctuations that leave
visible traces in the fossil record.
Concept 24.3 Macroevolutionary changes can accumulate through many speciation
events
 Speciation is at the boundary between microevolution and macroevolution.
 Microevolution is a change over generations in a population’s allele frequencies,
mainly by genetic drift and natural selection.

Biology Chapter Notes

  Speciation occurs when a population’s genetic divergence from its ancestral
population results in reproductive isolation.
 While the changes after any speciation event may be subtle, the cumulative
change over millions of speciation episodes must account for macroevolution, the
scale of changes seen in the fossil record.
 Most evolutionary novelties are modified versions of older structures.
 The Darwinian concept of descent with modification can account for the major
morphological transformations of macroevolution.
 It may be difficult to believe that a complex organ like the human eye could be the
product of gradual evolution, rather than a finished design created specially for
humans.
 However, the key is to remember is that a very simple eye can be very useful to an
animal.
 The simplest eyes are just clusters of photoreceptors, light-sensitive pigmented cells.
 These simple eyes appear to have had a single evolutionary origin.
 They are now found in a variety of animals, including limpets.
 These simple eyes have no lenses and cannot focus an image, but they do allow the
animal to distinguish light from dark.
 Limpets cling tightly to their rocks when a shadow falls on them, reducing their
risk of predation.
 Complex eyes have evolved several times independently in the animal kingdom.
 Examples of various levels of complexity, from clusters of photoreceptors to
camera-like eyes, can be seen in molluscs.
 The most complex types did not evolve in one quantum leap, but by incremental
adaptation of organs that benefited their owners at each stage.
 Evolutionary novelties can also arise by gradual refinement of existing structures for
new functions.
 Structures that evolve in one context, but become co-opted for another function,
are exaptations.
 It is important to recognize that natural selection can only improve a structure in the
context of its current utility, not in anticipation of the future.
 An example of an exaptation is the changing function of lightweight, honeycombed
bones of birds.
Biology Chapter Notes
  The fossil record indicates that light bones predated flight.
 Therefore, they must have had some function on the ground, perhaps as a light
frame for agile, bipedal dinosaurs.
 Once flight became an advantage, natural selection would have remodeled the
skeleton to better fit their additional function.
 The wing-like forelimbs and feathers that increased the surface area of these
forelimbs were co-opted for flight after functioning in some other capacity, such
as courtship, thermoregulation, or camouflage.
 Genes that control development play a major role in evolution.
 “Evo-devo” is a field of interdisciplinary research that examines how slight genetic
divergences can become magnified into major morphological differences between
species.
 A particular focus is on genes that program development by controlling the rate,
timing, and spatial pattern of changes in form as an organism develops from a zygote
to an adult.
 Heterochrony, an evolutionary change in the rate or timing of developmental events,
has led to many striking evolutionary transformations.
 Allometric growth tracks how proportions of structures change due to different
growth rates during development.
 Change relative rates of growth even slightly, and you can change the adult form
substantially.
 Different allometric patterns contribute to the contrast of adult skull shapes
between humans and chimpanzees, which both developed from fairly similar fetal
skulls.
 Heterochrony appears to be responsible for differences in the feet of tree-dwelling
versus ground-dwelling salamanders.
 The feet of the tree-dwellers are adapted for climbing vertically, with shorter
digits and more webbing.
 This modification may have evolved due to mutations in the alleles that control
the timing of foot development.
 Stunted feet may have resulted if regulatory genes switched off foot growth early.
 In this way, a relatively small genetic change can be amplified into substantial
morphological change.

Biology Chapter Notes

 Another form of heterochrony is concerned with the relative timing of reproductive
development and somatic development.
 If the rate of reproductive development accelerates compared to somatic
development, then a sexually mature stage can retain juvenile structures—a process
called paedomorphosis.
 Some species of salamander have the typical external gills and flattened tail of an
aquatic juvenile, but have functioning gonads.
 Macroevolution can also result from changes in genes that control the placement and
spatial organization of body parts.
 For example, genes called homeotic genes determine such basic features as where
a pair of wings and a pair of legs will develop on a bird or how a plant’s flower
parts are arranged.
 The products of one class of homeotic genes, the Hox genes, provide positional
information in an animal embryo.
 This information prompts cells to develop into structures appropriate for a
particular location.
 One major transition in the evolution of vertebrates is the development of the
walking legs of tetrapods from the fins of fishes.
 A fish fin that lacks external skeletal support evolved into a tetrapod limb that
extends skeletal supports (digits) to the tip of the limb.
 This may be the result of changes in the positional information provided by Hox
genes during limb development, determining how far digits and other bones
should extend from the limb.
 Evolution is not goal oriented.
 The fossil record shows apparent evolutionary trends.
 For example, the evolution of the modern horse can be interpreted to have been a
steady series of changes from a small, browsing ancestor (Hyracotherium) with
four toes to modern horses (Equus) with only one toe per foot and teeth modified
for grazing on grasses.
 It is possible to arrange a succession of animals intermediate between Hyracotherium
and modern horses to show trends toward increased size, reduced number of toes,
and modifications of teeth for grazing.
 If we look at all fossil horses, the illusion of coherent, progressive evolution leading
directly to modern horses vanishes.

Biology Chapter Notes

  Equus is the only surviving twig of an evolutionary bush that included several
adaptive radiations among both grazers and browsers.
 Differences among species in survival can also produce a macroevolutionary trend.
 The species selection model developed by Steven Stanley considers species as
analogous to individuals.
 Speciation is their birth, extinction is their death, and new species are their
offspring.
 In this model, Stanley suggests that just as individual organisms undergo natural
selection, species undergo species selection.
 The species that endure the longest and generate the greatest number of new species
determine the direction of major evolutionary trends.
 The species selection model suggests that “differential speciation success” plays a
role in macroevolution similar to the role of differential reproductive success in
microevolution.
 To the extent that speciation rates and species longevity reflect success, the analogy
to natural selection is even stronger.
 However, qualities unrelated to the overall success of organisms in specific
environments may be equally important in species selection.
 As an example, the ability of a species to disperse to new locations may contribute
to its giving rise to a large number of “daughter species.”
 The appearance of an evolutionary trend does not imply some intrinsic drive toward
a preordained state of being.
 Evolution is a response to interactions between organisms and their current
environments, leading to changes in evolutionary trends as conditions change.

Biology Chapter Notes

 Chapter 25 Phylogeny and Systematics
Chapter Notes

Overview: Investigating the Tree of Life

 Evolutionary biology is about both process and history.

 The processes of evolution are natural selection and other mechanisms that change the
genetic composition of populations and can lead to the evolution of new species.
 A major goal of evolutionary biology is to reconstruct the history of life on earth.
 In this chapter, we will consider how scientists trace phylogeny, the evolutionary history
of a group of organisms.
 To reconstruct phylogeny, scientists use systematics, an analytical approach to
understanding the diversity and relationships of living and extinct organisms.
 Evidence used to reconstruct phylogenies can be obtained from the fossil record and
from morphological and biochemical similarities between organisms.
 In recent decades, systematists have gained a powerful new tool in molecular
systematics, which uses comparisons of nucleotide sequences in DNA and RNA to
help identify evolutionary relationships between individual genes or even entire
genomes.
 Scientists are working to construct a universal tree of life, which will be refined as the
database of DNA and RNA sequences grows.

Concept 25.1 Phylogenies are based on common ancestries inferred from fossil,
morphological, and molecular evidence
Sedimentary rocks are the richest source of fossils.
 Fossils are the preserved remnants or impressions left by organisms that lived in the past.
 In essence, they are the historical documents of biology.
 Sedimentary rocks form from layers of sand and silt that are carried by rivers to seas and
swamps, where the minerals settle to the bottom along with the remains of organisms.
 As deposits pile up, they compress older sediments below them into layers called
strata.
 The fossil record is the ordered array in which fossils appear within sedimentary rock
strata.
 These rocks record the passing of geological time.
 Fossils can be used to construct phylogenies only if we can determine their ages.
 The fossil record is a substantial, but incomplete, chronicle of evolutionary change.
 The majority of living things were not captured as fossils upon their death.
 Of those that formed fossils, later geological processes destroyed many.
 Only a fraction of existing fossils have been discovered.
 The fossil record is biased in favor of species that existed for a long time, were
abundant and widespread, and had hard shells or skeletons that fossilized readily.
Morphological and molecular similarities may provide clues to phylogeny.
Biology Chapter Notes
 Similarities due to shared ancestry are called homologies.
 Organisms that share similar morphologies or DNA sequences are likely to be more
closely related than organisms without such similarities.
 Morphological divergence between closely related species can be small or great.
 Morphological diversity may be controlled by relatively few genetic differences.
 Similarity due to convergent evolution is called analogy.
 When two organisms from different evolutionary lineages experience similar
environmental pressures, natural selection may result in convergent evolution.
 Similar analogous adaptations may evolve in such organisms.
 Analogies are not due to shared ancestry.
 Distinguishing homology from analogy is critical in the reconstruction of phylogeny.
 For example, both birds and bats have adaptations that allow them to fly.
 However, a close examination of a bat’s wing shows a greater similarity to a cat’s
forelimb that to a bird’s wing.
 Fossil evidence also documents that bat and bird wings arose independently from
walking forelimbs of different ancestors.
 Thus a bat’s wing is homologous to other mammalian forelimbs but is analogous in
function to a bird’s wing.
 Analogous structures that have evolved independently are also called homoplasies.
 In general, the more points of resemblance that two complex structures have, the less
likely it is that they evolved independently.
 For example, the skulls of a human and a chimpanzee are formed by the fusion of
many bones.
 The two skulls match almost perfectly, bone for bone.
 It is highly unlikely that such complex structures have separate origins.
 More likely, the genes involved in the development of both skulls were inherited from
a common ancestor.
 The same argument applies to comparing genes, which are sequences of nucleotides.
 Systematists compare long stretches of DNA and even entire genomes to assess
relationships between species.
 If genes in two organisms have closely similar nucleotide sequences, it is highly likely
that the genes are homologous.
 It may be difficult to carry out molecular comparisons of nucleic acids.
 The first step is to align nucleic acid sequences from the two species being studied.
 In closely related species, sequences may differ at only one or a few sites.
 Distantly related species may have many differences or sequences of different length.
 Over evolutionary time, insertions and deletions accumulate, altering the lengths of
the gene sequences.
 Deletions or insertions may shift the remaining sequences, making it difficult to
recognize closely matching nucleotide sequences.
 To deal with this, systematists use computer programs to analyze comparable DNA
sequences of differing lengths and align them appropriately.
 The fact that molecules have diverged between species does not tell us how long ago their
common ancestor lived.
Biology Chapter Notes
  Molecular divergences between lineages with reasonably complete fossil records can
serve as a molecular yardstick to measure the appropriate time span of various degrees
of divergence.
 As with morphological characters, it is necessary to distinguish homology from analogy
to determine the usefulness of molecular similarities for reconstruction of phylogenies.
 Closely similar sequences are most likely homologies.
 In distantly related organisms, identical bases in otherwise different sequences may
simply be coincidental matches or molecular homoplasies.
 Scientists have developed mathematical tools that can distinguish “distant” homologies
from coincidental matches in extremely divergent sequences.
 For example, such molecular analysis has provided evidence that humans share a
distant common ancestor with bacteria.
 Scientists have sequenced more than 20 billion bases worth of nucleic acid data from
thousands of species.

Concept 25.2 Phylogenetic systematics connects classification with evolutionary history

 In 1748, Carolus Linnaeus published Systema naturae, his classification of all plants and
animals known at the time.
 Taxonomy is an ordered division of organisms into categories based on similarities and
differences.
 Linneaus’s classification was not based on evolutionary relationships but simply on
resemblances between organisms.
 Despite this, many features of his system remain useful in phylogenetic systematics.
Taxonomy employs a hierarchical system of classification.
 The Linnaean system, first formally proposed by Linnaeus in Systema naturae in the 18th
century, has two main characteristics.
13.Each species has a two-part name.
14.Species are organized hierarchically into broader and broader groups of organisms.
 Under the binomial system, each species is assigned a two-part Latinized name, a
binomial.
 The first part, the genus, is the closest group to which a species belongs.
 The second part, the specific epithet, refers to one species within each genus.
 The first letter of the genus is capitalized and both names are italicized and Latinized.
 For example, Linnaeus assigned to humans the optimistic scientific name Homo
sapiens, which means “wise man.”
 A hierarchical classification groups species into increasingly broad taxonomic
categories.
 Species that appear to be closely related are grouped into the same genus.
 For example, the leopard, Panthera pardus, belongs to a genus that includes the
African lion (Panthera leo) and the tiger (Panthera tigris).
 Genera are grouped into progressively broader categories: family, order, class, phylum,
kingdom, and domain.
 Each taxonomic level is more comprehensive than the previous one.
Biology Chapter Notes
  As an example, all species of cats are mammals, but not all mammals are cats.
 The named taxonomic unit at any level is called a taxon.
 Example: Panthera is a taxon at the genus level, and Mammalia is a taxon at the class
level that includes all of the many orders of mammals.
 Higher classification levels are not defined by some measurable characteristic, such as the
reproductive isolation that separates biological species.
 As a result, the larger categories are not comparable between lineages.
 An order of snails does not necessarily exhibit the same degree of morphological or
genetic diversity as an order of mammals.
Classification and phylogeny are linked.
 Systematists explore phylogeny by examining various characteristics in living and fossil
organisms.
 They construct branching diagrams called phylogenetic trees to depict their hypotheses
about evolutionary relationships.
 The branching of the tree reflects the hierarchical classification of groups nested within
more inclusive groups.
 Methods for tracing phylogeny began with Darwin, who realized the evolutionary
implications of Linnaean hierarchy.
 Darwin introduced phylogenetic systematics in On the Origin of Species when he wrote:
“Our classifications will come to be, as far as they can be so made, genealogies.”

Concept 25.3 Phylogenetic systematics informs the construction of phylogenetic trees

based on shared characters
 Patterns of shared characteristics can be depicted in a diagram called a cladogram.
 If shared characteristics are homologous and, thus, explained by common ancestry, then
the cladogram forms the basis of a phylogenetic tree.
 A clade is defined as a group of species that includes an ancestral species and all its
descendents.
 The study of resemblances among clades is called cladistics.
 Each branch, or clade, can be nested within larger clades.
 A valid clade is monophyletic, consisting of an ancestral species and all its descendents.
 When we lack information about some members of a clade, the result is a
paraphyletic grouping that consists of some, but not all, of the descendents.
 The result may also be several polyphyletic groupings that lack a common ancestor.
 Such situations call for further reconstruction to uncover species that tie these
groupings together into monophyletic clades.
 Determining which similarities between species are relevant to grouping the species in a
clade is a challenge.
 It is especially important to distinguish similarities that are based on shared ancestry or
homology from those that are based on convergent evolution or analogy.
 Systematists must also sort through homologous features, or characters, to separate shared
derived characters from shared primitive characters.
 A “character” refers to any feature that a particular taxon possesses.
Biology Chapter Notes
  A shared derived character is unique to a particular clade.
 A shared primitive character is found not only in the clade being analyzed, but also
in older clades.
 For example, the presence of hair is a good character to distinguish the clade of mammals
from other tetrapods.
 It is a shared derived character that uniquely identifies mammals.
 However, the presence of a backbone can qualify as a shared derived character, but at a
deeper branch point that distinguishes all vertebrates from other mammals.
 Among vertebrates, the backbone is a shared primitive character because it evolved in
the ancestor common to all vertebrates.
 Shared derived characters are useful in establishing a phylogeny, but shared primitive
characters are not.
 The status of a character shared derived versus shared primitive may depend on the
level at which the analysis is being performed.
 A key step in cladistic analysis is outgroup comparison, which is used to differentiate
shared primitive characters from shared derived ones.
 To do this, we need to identify an outgroup, a species or group of species that is closely
related to the species that we are studying, but known to be less closely related than any
members of the study group are to each other.
 To study the relationships among an ingroup of five vertebrates (a leopard, a turtle, a
salamander, a tuna, and a lamprey) on a cladogram, an animal called the lancelet is a good
choice.
 The lancelet is a small member of the Phylum Chordata that lacks a backbone.
 The species making up the ingroup display a mixture of shared primitive and shared
derived characters.
 In an outgroup analysis, the assumption is that any homologies shared by the ingroup and
outgroup are primitive characters that were present in the common ancestor of both
groups.
 Homologies present in some or all of the ingroup taxa are assumed to have evolved after
the divergence of the ingroup and outgroup taxa.
 In our example, a notochord, present in lancelets and in the embryos of the ingroup, is a
shared primitive character and, thus, not useful for sorting out relationships between
members of the ingroup.
 The presence of a vertebral column, shared by all members of the ingroup but not the
outgroup, is a useful character for the whole ingroup.
 The presence of jaws, absent in lampreys and present in the other ingroup taxa, helps
to identify the earliest branch in the vertebrate cladogram.
 Analyzing the taxonomic distribution of homologies enables us to identify the sequence in
which derived characters evolved during vertebrate phylogeny.
 A cladogram presents the chronological sequence of branching during the evolutionary
history of a set of organisms.
 However, this chronology does not indicate the time of origin of the species that we
are comparing, only the groups to which they belong.
 For example, a particular species in an old group may have evolved more recently than
a second species that belongs to a newer group.
 A cladogram is not a phylogenetic tree.
Biology Chapter Notes
  To convert it to a phylogenetic tree, we need more information from sources such as
the fossil record, which can indicate when and in which groups the characters first
appeared.
 Any chronology represented by the branching pattern of a phylogenetic tree is relative
(earlier versus later) rather than absolute (so many millions of years ago).
 Some kinds of tree diagrams can be used to provide more specific information about
timing.
 In a phylogram, the length of a branch reflects the number of genetic changes that have
taken place in a particular DNA or RNA sequence in a lineage.
 Even though the branches in a phylogram may have different lengths, all the different
lineages that descend from a common ancestor have survived for the same number of
years.
 Humans and bacteria had a common ancestor that lived more than 3 billion years ago.
 This ancestor was a single-celled prokaryote and was more like a modern bacterium
than like a human.
 Even though bacteria have apparently changed little in structure since that common
ancestor, there have nonetheless been 3 billion years of evolution in both the bacterial
and eukaryotic lineages.
 These equal amounts of chronological time are represented in an ultrameric tree.
 In an ultrameric tree, the branching pattern is the same as in a phylogram, but all the
branches that can be traced from the common ancestor to the present are of equal lengths.
 Ultrameric trees do not contain the information about different evolutionary rates that can
be found in phylograms.
 However, they draw on data from the fossil record to place certain branch points in the
context of geological time.
The principles of maximum parsimony and maximum likelihood help systematists
reconstruct phylogeny.
 As available data about DNA sequences increase, it becomes more difficult to draw the
phylogenetic tree that best describes evolutionary history.
 If you are analyzing data for 50 species, there are 3 × 10 76 different ways to form a
tree.
 According to the principle of maximum parsimony, we look for the simplest explanation
that is consistent with the facts.
 In the case of a tree based on morphological characters, the most parsimonious tree is
the one that requires the fewest evolutionary events to have occurred in the form of
shared derived characters.
 For phylograms based on DNA sequences, the most parsimonious tree requires the
fewest base changes in DNA.
 The principle of maximum likelihood states that, given certain rules about how DNA
changes over time, a tree should reflect the most likely sequence of evolutionary events.
 Maximum likelihood methods are designed to use as much information as possible.
 Many computer programs have been developed to search for trees that are parsimonious
and likely:
 “Distance” methods minimize the total of all the percentage differences among all the
sequences.

Biology Chapter Notes

  More complex “character-state” methods minimize the total number of base changes or
search for the most likely pattern of base changes among all the sequences.
 Although we can never be certain precisely which tree truly reflects phylogeny, if they are
based on a large amount of accurate data, the various methods usually yield similar trees.
Phylogenetic trees are hypotheses.
 Any phylogenetic tree represents a hypothesis about how the organisms in the tree are
related.
 The best hypothesis is the one that best fits all the available data.
 A hypothesis may be modified when new evidence compels systematists to revise their
trees.
 Many older phylogenetic hypotheses have been changed or rejected since the
introduction of molecular methods for comparing species and tracing phylogeny.
 Often, in the absence of conflicting information, the most parsimonious tree is also the
most likely.
 Sometimes there is compelling evidence that the best hypothesis is not the most
parsimonious.
 Nature does not always take the simplest course.
 In some cases, the particular morphological or molecular character we are using to sort
taxa actually did evolve multiple times.
 For example, the most parsimonious assumption would be that the four-chambered heart
evolved only once in an ancestor common to birds and mammals but not to lizards,
snakes, turtles, and crocodiles.
 But abundant evidence indicated that birds and mammals evolved from different reptilian
ancestors.
 The hearts of birds and mammals develop differently, supporting the hypothesis that
they evolved independently.
 The most parsimonious tree is not consistent with the above facts, and must be rejected
in favor of a less parsimonious tree.
 The four-chambered hearts of birds and mammals are analogous, not homologous.
 Occasionally misjudging an analogous similarity in morphology or gene sequence as a
shared derived homology is less likely to distort a phylogenetic tree if several derived
characters define each clade in the tree.
 The strongest phylogenetic hypotheses are those supported by multiple lines of
molecular and morphological evidence as well as by fossil evidence.

Concept 25.4 Much of an organism’s evolutionary history is documented in its genome

 Molecular systematics is a valuable tool for tracing an organism’s evolutionary history.
 The molecular approach helps us to understand phylogenetic relationships that cannot be
measured by comparative anatomy and other nonmolecular methods.
 For example, molecular systematics helps us uncover evolutionary relationships
between groups that have no grounds for morphological comparison, such as mammals
and bacteria.
 Molecular systematics enables scientists to compare genetic divergence within a species.

Biology Chapter Notes

  Molecular biology has helped to extend systematics to evolutionary relationships far
above and below the species level.
 Its findings are sometimes inconclusive, as in cases where a number of taxa diverged at
nearly the same time.
 The ability of molecular trees to encompass both short and long periods of time is based
on the fact that different genes evolve at different rates, even in the same evolutionary
lineage.
 For example, the DNA that codes for ribosomal RNA (rRNA) changes relatively
slowly, so comparisons of DNA sequences in these genes can be used to sort out
relationships between taxa that diverged hundreds of millions of years ago.
 In contrast, mitochondrial DNA (mtDNA) evolved relatively recently and can be used to
explore recent evolutionary events, such as relationships between groups within a species.
Gene duplication has provided opportunities for evolutionary change.
 Gene duplication increases the number of genes in the genome, providing opportunities
for further evolutionary change.
 Gene duplication has resulted in gene families, which are groups of related genes within
an organism’s genome.
 Like homologous genes in different species, these duplicated genes have a common
genetic ancestor.
 There are two types of homologous genes: orthologous genes and paralogous genes.
 The term orthologous refers to homologous genes that are found in different gene pools
because of speciation.
 The ß hemoglobin genes in humans and mice are orthologous.
 Paralogous genes result from gene duplication and are found in more than one copy in
the same genome.
 Olfactory receptor genes have undergone many gene duplications in vertebrates.
 Humans and mice each have huge families of more than 1,000 of these paralogous
genes.
 Now that we have compared entire genomes of different organisms, two remarkable facts
have emerged.
 Orthologous genes are widespread and can extend over enormous evolutionary distances.
 Approximately 99% of the genes of humans and mice are demonstrably orthologous,
and 50% of human genes are orthologous with those of yeast.
 All living things share many biochemical and development pathways.
 The number of genes seems not to have increased at the same rate as phenotypic
complexity.
 Humans have only five times as many genes as yeast, a simple unicellular eukaryote,
although we have a large, complex brain and a body that contains more than 200
different types of tissues.
 Many human genes are more versatile than yeast and can carry out a wide variety of
tasks in various body tissues.

Concept 25.5 Molecular clocks help track evolutionary time

 In the past, the timing of evolutionary events has rested primarily on the fossil record.
Biology Chapter Notes
 One of the goals of evolutionary biology is to understand the relationships among all
living organisms, including those for which there is no fossil record.
 Molecular clocks serve as yardsticks for measuring the absolute time of evolutionary
change.
 They are based on the observation that some regions of the genome evolve at constant
rates.
 For these regions, the number of nucleotide substitutions in orthologous genes is
proportional to the time that has elapsed since the two species last shared a common
ancestor.
 In the case of paralogous genes, the number of substitutions is proportional to the time
since the genes became duplicated.
 We can calibrate the molecular clock of a gene by graphing the number of nucleotide
differences against the timing of a series of evolutionary branch points that are known
from the fossil record.
 The slope of the best line through these points represents the evolution rate of that
molecular clock.
 This rate can be used to estimate the absolute date of evolutionary events that have no
fossil record.
 No molecular clock is completely accurate.
 Genes that make good molecular clocks have fairly smooth average rates of change.
 No genes mark time with a precise tick-tock accuracy in the rate of base changes.
 Over time there may be chance deviations above and below the average rate.
 Rates of change of various genes vary greatly.
 Some genes evolve a million times faster than others.
 The molecular clock approach assumes that much of the change in DNA sequences is due
to genetic drift and is selectively neutral.
 The neutral theory suggests that much evolutionary change in genes and proteins has
no effect on fitness and, therefore, is not influenced by Darwinian selection.
 Researchers supporting this theory point out that many new mutations are harmful and
are removed quickly.
 However, if most of the rest are neutral and have little or no effect on fitness, the rate
of molecular change should be clocklike in their regularity.
 Differences in the rates of change of specific genes are a function of the importance of the
gene.
 If the exact sequence of amino acids specified by a gene is essential to survival, most
mutations will be harmful and will be removed by natural selection.
 If the sequence of genes is less critical, more mutations will be neutral, and mutations
will accumulate more rapidly.
 Some DNA changes are favored by natural selection.
 This leads some scientists to question the accuracy and utility of molecular clocks for
timing evolution.
 Evidence suggests that almost 50% of the amino acid differences in proteins of two
Drosophila species have resulted from directional natural selection.
 Over very long periods of time, fluctuations in the rate of accumulation of mutations due
to natural selection may even out.
 Even genes with irregular clocks can mark elapsed time approximately.
Biology Chapter Notes
 Biologists are skeptical of conclusions derived from molecular clocks that have been
extrapolated to time spans beyond the calibration in the fossil record
 Few fossils are older than 550 million years old.
 Estimates for evolutionary divergences prior to that time may assume that molecular
clocks have been constant over billions of years.
 Such estimates have a high degree of uncertainty.
 The molecular clock approach has been used to date the jump of the HIV virus from
related SIV viruses that infect chimpanzees and other primates to humans.
 The virus has spread to humans more than once.
 The multiple origins of HIV are reflected in the variety of strains of the virus.
 HIV-1 M is the most common HIV strain.
 Investigators have calibrated the molecular clock for the virus by comparing samples
of the virus collected at various times.
 From their analysis, they project that the HIV-1 M strain invaded humans in the 1930s.
There is a universal tree of life.
 The genetic code is universal in all forms of life.
 From this, researchers infer that all living things have a common ancestor.
 Researchers are working to link all organisms into a universal tree of life.
 Two criteria identify regions of DNA that can be used to reconstruct the branching pattern
of this tree.
 The regions must be able to be sequenced.
 They must have evolved slowly, so that even distantly related organisms show
evidence of homologies in these regions.
 rRNA genes, coding for the RNA component of ribosomes, meet these criteria.
 Two points have emerged from this effort:
1. The tree of life consists of three great domains: Bacteria, Archaea, and Eukarya.
 Most prokaryotes belong to Bacteria.
 Archaea includes a diverse group of prokaryotes that inhabit many different habitats.
 Eukarya includes all organisms with true nuclei, including many unicellular organisms
as well as the multicellular kingdoms.
2. The early history of these domains is not yet clear.
 Early in the history of life, there were many interchanges of genes between organisms
in the different domains.
 One mechanism for these interchanges was horizontal gene transfer, in which genes
are transferred from one genome to another by mechanisms such as transposable
elements.
 Different organisms fused to produce new, hybrid organisms.
 It is likely that the first eukaryote arose through fusion between an ancestral bacterium
and an ancestral archaean.

Biology Chapter Notes

 Chapter 26 The Tree of Life:
An Introduction to Biological Diversity
Chapter Notes

Overview: Changing Life on a Changing Earth

 Life is a continuum extending from the earliest organisms to the great variety of forms
alive today.
 Organisms interact with their environments.
 Geological events that alter environments change the course of biological history.
 When glaciers recede and the land rebounds, marine creatures can be trapped in
what gradually become freshwater lakes.
 Populations of organisms trapped in these lakes are isolated from parent
populations, and may evolve into new species.
 Life changes the planet it inhabits.
 The evolution of photosynthetic organisms released oxygen into the air, with a
dramatic effect on Earth’s atmosphere.
 The emergence of Homo sapiens has changed the land, water, and air at an
unprecedented rate.
 Historical study of any sort is an inexact discipline that depends on the preservation,
reliability, and interpretation of records.
 The fossil record of past life is generally less and less complete the further into the past
we delve.
 Fortunately, each organism alive today carries traces of its evolutionary history in its
molecules, metabolism, and anatomy.
 Still, the evolutionary episodes of greatest antiquity are generally the most obscure.

Concept 26.1 Conditions on early Earth made the origin of life possible
 Most biologists now think that it is credible that chemical and physical processes on Earth
produced simple cells.
 According to one hypothetical scenario, there were four main stages in this process:
o The abiotic synthesis of small organic molecules (monomers).
o The joining of monomers into polymers.
o The packaging of these molecules into protobionts, droplets with membranes that
maintained a distinct internal chemistry.
o The origin of self-replicating molecules that eventually made inheritance possible.
 The scenario is speculative but does lead to predictions that can be tested in laboratory
experiments.
 Earth and the other planets in the solar system formed about 4.6 billion years ago,
condensing from a vast cloud of dust and rocks surrounding the young sun.
 It is unlikely that life could have originated or survived in the first few hundred million
years after the Earth’s formation.
Biology Chapter Notes
  The planet was bombarded by huge bodies of rock and ice left over from the formation
of the solar system.
 These collisions generated enough heat to vaporize all available water and prevent the
formation of the seas.
 The oldest rocks on the Earth’s surface, located at a site called Isua in Greenland, are 3.8
billion years old.
 It is not clear whether these rocks show traces of life.
The first cells may have originated by chemical evolution on a young Earth.
 It is credible that chemical and physical processes on early Earth produced the first cells.
 According to one hypothesis, there were four main stages to this process:
o Abiotic processes synthesized small organic molecules, such as amino acids and
nucleotides.
o These monomers were joined into polymers, including proteins and nucleic acids.
o Polymers were packaged into “protobionts,” droplets with membranes that maintained
an internal chemistry distinct from their surroundings.
o Self-replicating molecules arose, making inheritance possible.
Abiotic synthesis of organic monomers is a testable hypothesis.
 As the bombardment of early Earth slowed, conditions on the planet were very different
from today.
 The first atmosphere may have been a reducing atmosphere thick with water vapor,
along with nitrogen and its oxides, carbon dioxide, methane, ammonia, hydrogen, and
hydrogen sulfide.
 Similar compounds are released from volcanic eruptions today.
 As Earth cooled, the water vapor condensed into the oceans and much of the hydrogen
was lost into space.
 In the 1920s, Russian chemist A. I. Oparin and British scientist J. B. S. Haldane
independently postulated that conditions on early Earth favored the synthesis of organic
compounds from inorganic precursors.
 They reasoned that this could not happen today because high levels of oxygen in the
atmosphere attack chemical bonds.
 A reducing environment in the early atmosphere would have promoted the joining of
simple molecules to form more complex ones.
 The considerable energy required to make organic molecules could be provided by
lightning and the intense UV radiation that penetrated the primitive atmosphere.
 Young suns emit more UV radiation. The lack of an ozone layer in the early
atmosphere would have allowed this radiation to reach Earth.
 Haldane suggested that the early oceans were a solution of organic molecules, a
“primitive soup” from which life arose.
 In 1953, Stanley Miller and Harold Urey tested the Oparin-Haldane hypothesis by
creating, in the laboratory, the conditions that had been postulated for early Earth.
 They discharged sparks in an “atmosphere” of gases and water vapor.
 The Miller-Urey experiments produced a variety of amino acids and other organic
molecules.
 Other attempts to reproduce the Miller-Urey experiment with other gas mixtures have
also produced organic molecules, although in smaller quantities.
Biology Chapter Notes
 It is unclear whether the atmosphere contained enough methane and ammonia to be
reducing.
 There is growing evidence that the early atmosphere was made up primarily of
nitrogen and carbon dioxide.
 Miller-Urey-type experiments with such atmospheres have not produced organic
molecules.
 It is likely that small “pockets” of the early atmosphere near volcanic openings
were reducing.
 Alternate sites proposed for the synthesis of organic molecules include submerged
volcanoes and deep-sea vents where hot water and minerals gush into the deep ocean.
 These regions are rich in inorganic sulfur and iron compounds, which are important in
ATP synthesis by present-day organisms.
 Some of the organic compounds from which the first life on Earth arose may have come
from space.
 Researchers are looking outside of Earth for clues about the origin of life.
 Evidence is growing that Mars was relatively warm for a brief period, with liquid
water and an atmosphere rich in carbon dioxide.
 During that period, prebiotic chemistry similar to that on early Earth may have
occurred on Mars.
 Did life evolve on Mars and then die out, or did dropping temperatures and a thinning
atmosphere terminate prebiotic chemistry before life evolved?
 Liquid water lies beneath the ice-covered surface of Europa, one of Jupiter’s moons,
raising the possibility that Europa’s hidden ocean may harbor life.
 Detection of free oxygen in the atmosphere of any planets outside our solar system
would be strongly suggestive of oxygenic photosynthesis.
Laboratory simulations of early-Earth conditions have produced organic polymers.
 The abiotic origin hypothesis predicts that monomers should link to form polymers
without enzymes and other cellular equipment.
 Researchers have produced polymers, including polypeptides, after dripping solutions of
monomers onto hot sand, clay, or rock.
 Similar conditions likely existed on early Earth at deep-sea vents or when dilute
solutions of monomers splashed onto fresh lava.
Protobionts can form by self-assembly.
 Life is defined by two properties: accurate replication and metabolism.
 Neither property can exist without the other.
 DNA molecules carry genetic information, including the information needed for accurate
replication.
 The replication of DNA requires elaborate enzymatic machinery, along with a copious
supply of nucleotide building blocks provided by cell metabolism.
 Although Miller-Urey experiments have yielded some of the nitrogenous bases of DNA
and RNA, they have not produced anything like nucleotides.
 Thus, nucleotides were likely not part of the early organic soup.
 Self-replicating molecules and a metabolism-like source of the building blocks must have
appeared together.

Biology Chapter Notes

  The necessary conditions may have been provided by protobionts, aggregates of
abiotically produced molecules surrounded by a membrane or membrane-like
structure.
 Protobionts exhibit some of the properties associated with life, including reproduction
and metabolism, and can maintain an internal chemical environment different from
their surroundings.
 Laboratory experiments show the spontaneous formation of protobionts from abiotically
produced organic compounds.
 For example, droplets of abiotically produced organic compounds called liposomes
form when lipids and other organic molecules are added to water.
 The lipids form a molecular bilayer at the droplet surface, much like the lipid bilayer
of a membrane.
 These droplets can undergo osmotic swelling or shrinking in different salt
concentrations.
 Some liposomes store energy in the form of a membrane potential.
 Liposomes behave dynamically, growing by engulfing smaller liposomes or “giving birth”
to smaller liposomes.
 If similar droplets forming in ponds on early Earth incorporate random polymers of linked
amino acids into their membranes, and if some of these polymers made the membranes
permeable to molecules, then those droplets could have selectively taken up organic
molecules from their environment.
RNA may have been the first genetic material.
 The first genetic material was probably RNA, not DNA.
 Thomas Cech and Sidney Altman found that RNA molecules not only play a central
role in protein synthesis, but also are important catalysts in modern cells.
 RNA catalysts, called ribozymes, remove their own introns and modify tRNA molecules
to make them fully functional.
 Ribozymes also help catalyze the synthesis of new RNA polymers.
 Ribozyme-catalyzed reactions are slow, but the proteins normally associated with
ribozymes can increase the reaction rate more than a thousandfold.
 Laboratory experiments have demonstrated that RNA sequences can evolve under abiotic
conditions.
 Unlike double-stranded DNA, single-stranded RNA molecules can assume a variety of
3-D shapes specified by their nucleotide sequences.
 RNA molecules have both a genotype (nucleotide sequence) and a phenotype (three-
dimensional shape) that interacts with surrounding molecules.
 Under particular conditions, some RNA sequences are more stable and replicate faster
and with fewer errors than other sequences.
 Occasional copying errors create mutations; selection screens these mutations for the
most stable or the best at self-replication.
 Beginning with a diversity of RNA molecules that must compete for monomers to
replicate, the sequence best suited to the temperature, salt concentration, and other
features of the surrounding environment and having the greatest autocatalytic activity
will increase in frequency.
 Its descendents will be a family of closely related RNA sequences, differing due to
copying errors.

Biology Chapter Notes

  Some copying errors will result in molecules that are more stable or more capable of
self-replication.
 Similar selection events may have occurred on early Earth.
 Modern molecular biology may have been preceded by an “RNA world.”
Natural selection could refine protobionts containing hereditary information.
 The first RNA molecules may have been short, virus-like sequences, aided in their
replication by amino acid polymers with rudimentary catalytic capabilities.
 This early replication may have taken place inside protobionts.
 RNA-directed protein synthesis may have begun as weak binding of specific amino
acids to bases along RNA molecules, which functioned as simple templates holding a
few amino acids together long enough for them to be linked.
 This is one function of rRNA today in ribosomes.
 Some RNA molecules may have synthesized short polypeptides that behaved as enzymes
helping RNA replication.
 Early chemical dynamics would include molecular cooperation as well as competition.
 Other RNA sequences might have become embedded in the protobiont membrane,
allowing it to use high-energy inorganic molecules such as hydrogen sulfide to carry out
organic reactions.
 A protobiont with self-replicating, catalytic RNA would differ from others without RNA
or with RNA with fewer capabilities.
 If that protobiont could grow, split, and pass its RNA molecules to its daughters, the
daughters would have some of the properties of their parent.
 The first protobionts must have had limited amounts of genetic information, specifying
only a few properties.
 Because their properties were heritable, they could be acted on by natural selection.
 The most successful of these protobionts would have increased in numbers, because they
could exploit available resources and produce a number of similar daughter protobionts.
 Once RNA sequences that carried genetic information appeared in protobionts, many
further changes were possible.
 One refinement was the replacement of RNA as the repository of genetic information
by DNA.
 Double-stranded DNA is a more stable molecule, and it can be replicated more
accurately.
 Once DNA appeared, RNA molecules would have begun to take on their modern roles
as intermediates in translation of genetic programs.
 The “RNA world” gave way to a “DNA world.”

Concept 26.2 The fossil record chronicles life on Earth

Radiometric dating gives absolute dates for some rock strata.
 The relative sequence of fossils in rock strata tells us the order in which the fossils were
formed, but it does not tell us their ages.
 Geologists have developed methods for obtaining absolute dates for fossils.

Biology Chapter Notes

 One of the most common techniques is radiometric dating, which is based on the decay
of radioactive isotopes.
 An isotope’s half-life, the number of years it takes for 50% of the original sample to
decay, is unaffected by temperature, pressure, or other environmental variables.
 Fossils contain isotopes of elements that accumulated while the organisms were alive.
 For example, the carbon in a living organism contains the most common carbon
isotope, carbon-12, as well as a radioactive isotope, carbon-14.
 When an organism dies, it stops accumulating carbon, and the carbon-14 that it
contained at the time of death slowly decays to nitrogen-14.
 By measuring the ratio of carbon-14 to total carbon or to nitrogen-14 in a fossil, we
can determine the fossil’s age.
 With a half-life of 5,730 years, carbon-13 is useful for dating fossils up to about
75,000 years old.
 Fossils older than that contain too little carbon-14 to be detected by current
techniques.
 Radioactive isotopes with longer half-lives are used to date older fossils.
 Paleontologists can determine the age of fossils sandwiched between layers of volcanic
rocks by measuring the amount of potassium-40 in those layers.
 Potassium-40 decays to the chemically unreactive gas argon-40, which is trapped in
the rock.
 When the rock is heated during a volcanic eruption, the argon is driven out, but the
potassium remains.
 This resets the clock for potassium-40 to zero.
 The current ratio of potassium-40 to argon-40 in a layer of volcanic rock gives an
estimate of when that layer was formed.
 Magnetism of rocks can also be used to date them.
 When volcanic or sedimentary rock forms, iron particles in the rock align themselves
with Earth’s magnetic field.
 When the rock hardens, their orientation is frozen in time.
 Geologists have determined that Earth’s north and south magnetic poles have
reversed repeatedly in the past.
 These magnetic reversals have left their record on rocks throughout the world.
 Patterns of magnetic reversal can be matched with corresponding patterns
elsewhere, allowing rocks to be dated when other methods are not available.
Geologists have established a geologic record of Earth’s history.
 By studying rocks and fossils at many different sites, geologists have established a
geologic record of the history of life on Earth, which is divided into three eons.
 The first two eons—the Archaean and the Proterozoic—lasted approximately four billion
years.
 These two eons are referred to as the Precambrian.
 The Phanerozoic eon covers the last half billion years and encompasses much of the time
that multicellular eukaryotic life has existed on Earth.
 It is divided into three eras: Paleozoic, Mesozoic, and Cenozoic.
 Each age represents a distinct age in the history of Earth and life on Earth.
 The boundaries between eras correspond to times of mass extinction, when many
forms of life disappeared.
Biology Chapter Notes
 Mass extinctions have destroyed the majority of species on Earth.
 A species may become extinct for many reasons.
 Its habitat may have been destroyed, or its environment may have changed in a
direction unfavorable to the species.
 Biological factors may change, as evolutionary changes in one species impact others.
 On a number of occasions, global environmental changes were so rapid and major that the
majority of species went extinct.
 Such mass extinctions are known primarily from the loss of shallow-water, marine,
hard-bodied animals, the organisms for which the fossil record is most complete.
 The Permian mass extinction defines the boundary between the Paleozoic and Mesozoic
eras.
 Ninety-six percent of marine animal species went extinct in less than 5 million years.
 Terrestrial life was also affected.
 The Cretaceous extinction of 65 million years marks the boundary between the Mesozoic
and Cenozoic eras.
 More than half of all marine species and many families of terrestrial plants and
animals, including the dinosaurs, went extinct.
 The Permian mass extinction happened at a time of enormous volcanic eruptions in what
is now in Siberia.
 These eruptions may have produced enough carbon dioxide to warm the global
climate.
 Reduced temperature differences between the equator and the poles would have
slowed the mixing of ocean water.
 The resulting oxygen deficit in the oceans may have played a large role in the Permian
extinction.
 A clue to the Cretaceous mass extinction is a thin layer of clay enriched in iridium that
separates sediments from the Mesozoic and Cenozoic.
 Iridium is a very rare element on Earth that is common in meteorites and other objects
that fall to Earth.
 Walter and Luis Alvarez and their colleagues at the University of California proposed
that this clay is fallout from a huge cloud of debris that was thrown into the
atmosphere when an asteroid or a large comet collided with Earth.
 The cloud would have blocked sunlight and disrupted the global climate for several
months.
 A 65-million-year-old crater scar has been located beneath sediments on the Yucatán
coast of Mexico.
 At 180 km in diameter, it is the right size to have been caused by an object with a
diameter of 10 km.
 Much remains to be learned about the causes of mass extinctions.
 It is clear that they provided life with opportunities for adaptive radiations into newly
vacated ecological niches.

Concept 26.3 As prokaryotes evolved, they exploited and changed young Earth
 The oldest known fossils are 3.5-billion-year-old stromatolites, rocklike structures
composed of layers of cyanobacteria and sediment.
Biology Chapter Notes
 If bacterial communities existed 3.5 billion years ago, it seems reasonable that life
originated much earlier, perhaps 3.9 billion years ago, when Earth first cooled to a
temperature where liquid water could exist.
Prokaryotes dominated evolutionary history from 3.5 to 2.0 billion years ago.
 The early protobionts must have used molecules present in the primitive soup for their
growth and replication.
 Eventually, organisms that could produce all their needed compounds from molecules in
their environment replaced these protobionts.
 A rich variety of autotrophs emerged, some of which could use light energy.
 The diversification of autotrophs allowed the emergence of heterotrophs, which could live
on molecules produced by the autotrophs.
 Prokaryotes were Earth’s sole inhabitants from 3.5 to 2.0 billion years ago.
 These organisms transformed the biosphere of the planet.
 Relatively early, prokaryotes diverged into two main evolutionary branches, the bacteria
and the archaea.
 Representatives from both groups thrive in various environments today.
Metabolism evolved in prokaryotes.
 The chemiosmotic mechanism of ATP synthesis is common to all three domains—
Bacteria, Archaea, and Eukarya.
 This is evidence of a relatively early origin of chemiosmosis.
 Transmembrane proton pumps may have functioned originally to expel H + that
accumulated when fermentation produced organic acids as waste products.
 The cell would have to spend a large portion of its ATP to regulate internal pH by
driving H+ pumps.
 The first electron +transport pumps may have coupled the oxidation of organic acids to
the transport of H out of the cell.
 Finally, in some prokaryotes, electron transport systems efficient enough to expel more H+
than necessary to regulate pH evolved.
 These cells could use the inward gradient of H + to reverse the H+ pump, which now
generated ATP instead of consuming it.
 Such anaerobic respiration persists in some present-day prokaryotes.
 Photosynthesis probably evolved very early in prokaryotic history.
 The metabolism of early versions of photosynthesis did not split water and liberate
oxygen.
 Some living prokaryotes display such nonoxygenic photosynthesis.
 The only living photosynthetic prokaryotes that generate O2 are cyanobacteria.
 Most atmospheric oxygen is of biological origin, from the water-splitting step of
photosynthesis.
 When oxygenic photosynthesis first evolved, the free oxygen it produced likely
dissolved in the surrounding water until the seas and lakes became saturated with O2.
 Additional O2 then reacted with dissolved iron to form the precipitate iron oxide.
 These marine sediments were the source of banded iron formations, red layers of rock
containing iron oxide that are a valuable source of iron ore today.

Biology Chapter Notes

  About 2.7 billion years ago, oxygen began accumulating in the atmosphere and
terrestrial rocks with oxidized iron formed.
 While oxygen accumulation was gradual between 2.7 and 2.2 billion years ago, it shot up
to 10% of current values shortly afterward.
 This oxygen revolution had an enormous impact on life.
 In its free molecular and ionized forms and in compounds such as hydrogen peroxide,
oxygen attacks chemical bonds, inhibits enzymes, and damages cells.
 The increase in atmospheric oxygen likely doomed many prokaryote groups.
 Some species survived in habitats that remained anaerobic, where their descendents
survive as obligate anaerobes.
 Other species evolved mechanisms to use O2 in cellular respiration, which uses oxygen to
help harvest the energy stored in organic molecules.

Concept 26.4 Eukaryotic cells arose from symbioses and genetic exchanges between
prokaryotes
 Eukaryotic cells differ in many respects from the smaller cells of bacteria and archaea.
 Even the simplest single-celled eukaryote is far more complex in structure than any
prokaryote.
 While there is some evidence of earlier eukaryotic fossils, the first clearly identified
eukaryote appeared about 2.1 billion years ago.
 Other fossils that resemble simple, single-celled algae are slightly older (2.2 billion
years) but may not be eukaryotic.
 Traces of molecules similar to cholesterol are found in rocks dating back 2.7 billion
years.
 Such molecules are found only by aerobically respiring eukaryotic cells.
 If confirmed, this would place the earliest eukaryotes at the same time as the
oxygen revolution that changed the Earth’s environment so dramatically.
 Prokaryotes lack internal structures such as the nuclear envelope, endoplasmic reticulum,
and Golgi apparatus.
 They have no cytoskeleton and are unable to change cell shape.
 Eukaryotic cells have a cytoskeleton and can change shape, enabling them to surround
and engulf other cells.
 The first eukaryotes may have been predators of other cells.
 A cytoskeleton enables a eukaryotic cell to move structures within the cell and facilitates
the movement of chromosomes in meiosis and mitosis.
 Mitosis made it possible to reproduce the large eukaryotic genome.
 Meiosis allowed sexual recombination of genes.
 How did the complex organization of the eukaryotic cell evolve from the simpler
prokaryotic condition?
 A process called endosymbiosis probably led to mitochondria and plastids (the general
term for chloroplasts and related organelles).
 The endosymbiotic theory suggests that mitochondria and plastids were formerly small
prokaryotes living within larger cells.
 The term endosymbiont is used for a cell that lives within a host cell.
Biology Chapter Notes
 The proposed ancestors of mitochondria were aerobic heterotrophic prokaryotes.
 The proposed ancestors of plastids were photosynthetic prokaryotes.
 The prokaryotic ancestors of mitochondria and plastids probably gained entry to the host
cell as undigested prey or internal parasites.
 The symbiosis became mutually beneficial.
 A heterotrophic host could use nutrients released from photosynthesis.
 An anaerobic host would have benefited from an aerobic endosymbiont.
 As they became increasingly interdependent, the host and endosymbionts became a single
organism.
 All eukaryotes have mitochondria or their genetic remnants.
 The theory of serial endosymbiosis supposes that mitochondria evolved before
plastids.
 Overwhelming evidence supports an endosymbiotic origin of plastids and mitochondria.
 The inner membranes of both organelles have enzymes and transport systems that are
homologous to those in the plasma membranes of modern prokaryotes.
 Mitochondria and plastids replicate by a splitting process similar to prokaryotic binary
fission.
 Like prokaryotes, each organelle has a single, circular DNA molecule that is not
associated with histone.
 These organelles contain tRNAs, ribosomes, and other molecules needed to transcribe
and translate their DNA into protein.
 Ribosomes of mitochondria and plastids are similar to prokaryotic ribosomes in terms
of size, nucleotide sequence, and sensitivity to antibiotics.
 Which prokaryotic lineages gave rise to mitochondria and plastids?
 Comparisons of small-subunit ribosomal RNA from mitochondria, plastids, and
various living prokaryotes suggest that a group of bacteria called the alpha
proteobacteria are the closest relatives to mitochondria and that cyanobacteria are the
closest relatives to plastids.
 Over time, genes have been transferred from mitochondria and plastids to the nucleus.
 This process may have been accomplished by transposable elements.
 Some mitochondrial and plastic proteins are encoded by the organelle’s DNA, while
others are encoded by nuclear genes.
 Some proteins are combinations of polypeptides encoded by genes in both locations.
 The origins of other aspects of eukaryotic cells are unclear.
 Some researchers have proposed that the nucleus itself evolved from an endosymbiont.
 Nuclear genes with close relatives in both bacteria and archaea have been found.
 The genome of eukaryotic cells may be the product of genetic annealing, in which
horizontal gene transfers occurred between many different bacterial and archaeal lineages.
 These transfers may have taken place during the early evolution of life, or may have
happened repeatedly until the present day.
 The origin of other eukaryotic structures is also the subject of active research.
 The Golgi apparatus and the endoplasmic reticulum may have originated from
infoldings of the plasma membrane.
 The cytoskeletal proteins actin and tubulin have been found in bacteria, where they are
involved in pinching off bacterial cells during cell division.
Biology Chapter Notes
  These bacterial proteins may provide information about the origin of the eukaryotic
cytoskeleton.
 Some investigators have suggested that eukaryotic flagella and cilia evolved from
symbiotic bacteria.
 However, the 9+2 microtubule apparatus of eukaryotic flagella and cilia has not been
found in any prokaryotes.

Concept 26.5 Multicellularity evolved several times in eukaryotes

 A great range of eukaryotic unicellular forms evolved as the diversity of present-day
“protists.”
 Molecular clocks suggest that the common ancestor of multicellular eukaryotes lived 1.5
billion years ago.
 The oldest known fossils of multicellular eukaryotes are 1.2 billion years old.
 Recent fossil finds from China have produced a diversity of algae and animals from
570 million years ago, including beautifully preserved embryos.
 Why were multicellular eukaryotes so limited in size, diversity, and distribution until the
late Proterozoic?
 Geologic evidence suggests that a severe ice age gripped Earth from 750 to 570 million
years ago.
 According to the snowball Earth hypothesis, life would have been confined to deep-
sea vents and hot springs or those few locations where enough ice melted for sunlight
to penetrate the surface waters of the sea.
 The first major diversification of multicellular eukaryotic organisms corresponds to the
time of the thawing of snowball Earth.
 The first multicellular organisms were colonies.
 Some cells in the colonies became specialized for different functions.
 Such specialization can be seen in some prokaryotes.
 For example, certain cells of the filamentous cyanobacterium Nostoc differentiate into
nitrogen-fixing cells called heterocysts, which cannot replicate.
 The evolution of colonies with cellular specialization was carried much further in
eukaryotes.
 A multicellular eukaryote generally develops from a single cell, usually a zygote.
 Cell division and cell differentiation help transform the single cell into a multicellular
organism with many types of specialized cells.
 With increasing cell specialization, specific groups of cells specialized in obtaining
nutrients, sensing the environment, etc.
 This division of function eventually led to the evolution of tissues, organs, and organ
systems.
 Multicellularity evolved several times among early eukaryotes.
Animal diversity exploded during the early Cambrian period.
 Most of the major phyla of animals appear suddenly in the fossil record in the adaptive
radiation known as the Cambrian explosion.
 Cnidarians (the phylum that includes jellies) and poriferans (sponges) were already
present in the late Precambrian.
Biology Chapter Notes
 However, most of the major groups (phyla) of animals make their first fossil appearances
during the relatively short span of the Cambrian period’s first 20 million years.
 Molecular evidence suggests that animal phyla originated and began to diverge between 1
billion and 700 million years ago.
 At the beginning of the Cambrian, these phyla suddenly and simultaneously increased in
diversity and size.
Plants, fungi, and animals colonized the land about 500 million years ago.
 The colonization of land was one of the pivotal milestones in the history of life.
 There is fossil evidence that cyanobacteria and other photosynthetic prokaryotes
coated damp terrestrial surfaces well more than a billion years ago.
 However, macroscopic life in the form of plants, fungi, and animals did not colonize
land until about 500 million years ago, during the early Paleozoic era.
 The gradual evolution from aquatic to terrestrial habitats was associated with adaptations
that allowed organisms to prevent dehydration and to reproduce on land.
 For example, plants evolved a waterproof coating of wax on their photosynthetic
surfaces to slow the loss of water.
 Plants colonized land in association with fungi.
 In the modern world, the roots of most plants are associated with fungi that aid in the
absorption of water and nutrients from the soil.
 The fungi obtain organic nutrients from the plant.
 This ancient symbiotic association is evident in some of the oldest fossilized roots.
 Plants created new opportunities for all life, including herbivorous (plant-eating) animals
and their predators.
 The most widespread and diverse terrestrial animals are arthropods (including insects and
spiders) and vertebrates (including amphibians, reptiles, birds, and mammals).
 Terrestrial vertebrates, which include humans, are called tetrapods because of their
four limbs.
Earth’s continents drift across the planet’s surface on great plates of crust.
 Earth’s continents drift across the planet’s surface on great plates of crust that float on the
hot, underlying mantle.
 Plates may slide along the boundary of other plates, pulling apart or pushing against
each other.
 Continental plates move slowly, but their cumulative effects are dramatic.
 Mountains and islands are built at plate boundaries or at weak points on the plates.
 Plate movements have had a major influence on life.
 About 250 million years ago, near the end of the Paleozoic era, all the continental
landmasses came together into a supercontinent called Pangaea.
 Ocean basins deepened, sea level lowered, and shallow coastal seas drained.
 Many marine species living in shallow waters were driven extinct by the loss of
habitat.
 The interior of the supercontinent was severe, cold, and dry, leading to much terrestrial
extinction.
 During the Mesozoic era, 180 million years ago, Pangaea began to break up.

Biology Chapter Notes

  As the continents drifted apart, each became a separate evolutionary arena with
lineages of plants and animals that diverged from those on other continents.
 Continental drift explains much about the former and current distribution of organisms.
 Australian flora and fauna contrast sharply from that of the rest of the world.
 Marsupial mammals fill ecological roles in Australia analogous to those filled by
placental mammals on other continents.
 Marsupials probably evolved first in what is now North America and reached Australia
via South America and Antarctica while the continents were still joined.
 The breakup of the southern continents set Australia adrift.
 In Australia, marsupials diversified and the few early eutherians became extinct.
 On other continents, marsupials became extinct and eutherians diversified.

Concept 26.6 New information has revised our understanding of the tree of life
 In recent decades, molecular data have provided new insights into the evolutionary
relationships of life’s diverse forms.
 The first taxonomic schemes divided organisms into plant and animal kingdoms.
 In 1969, R. H. Whittaker argued for a five-kingdom system: Monera, Protista, Plantae,
Fungi, and Animalia.
 The five-kingdom system recognized that there are two fundamentally different types
of cells: prokaryotic (the kingdom Monera) and eukaryotic (the other four kingdoms).
 Three kingdoms of multicellular eukaryotes were distinguished by nutrition, in part.
 Plants are autotrophic, making organic food by photosynthesis.
 Most fungi are decomposers with extracellular digestion and absorptive nutrition.
 Most animals ingest food and digest it within specialized cavities.
 In Whittaker’s system, Protista included all eukaryotes that did not fit the definition of
plants, fungi, or animals.
 Most protists are unicellular.
 However, some multicellular organisms, such as seaweeds, were included in Protista
because of their relationships to specific unicellular protists.
 The five-kingdom system prevailed in biology for more than 20 years.
 During the past three decades, systematists applied cladistic analysis to taxonomy,
constructing cladograms based on molecular data.
 These data led to the three-domain system of Bacteria, Archaea, and Eukarya as
“superkingdoms.”
 Bacteria differ from Archaea in many key structural, biochemical, and physiological
characteristics.
 Many microbiologists have divided the two prokaryotic domains into multiple kingdoms
based on cladistic analysis of molecular data.
 A second challenge to the five-kingdom system comes from systematists who are sorting
out the phylogeny of the former members of the kingdom Protista.
 Molecular systematics and cladistics have shown that the Protista is not monophyletic.
 Some of these organisms have been split among five or more new kingdoms.
 Others have been assigned to the Plantae, Fungi, or Animalia.
 Clearly, taxonomy at the highest level is a work in progress.
Biology Chapter Notes
 There will be much more research before there is anything close to a new consensus for
how the three domains of life are related and how many kingdoms should be included in
each domain.
 New data, including the discovery of new groups, will lead to further taxonomic
remodeling.
 Keep in mind that phylogenetic trees and taxonomic groupings are hypotheses that fit
the best available data.

Biology Chapter Notes

 Chapter 27 Prokaryotes
Chapter Notes

Overview: They’re (Almost) Everywhere!

 Prokaryotes were the earliest organisms on Earth.

 Today, they still dominate the biosphere.
 Their collective biomass outweighs all eukaryotes combined at least tenfold.
 More prokaryotes inhabit a handful of fertile soil or the mouth or skin of a human than
the total number of people who have ever lived.
 Prokaryotes are wherever there is life.
 They thrive in habitats that are too cold, too hot, too salty, too acidic, or too alkaline for
any eukaryote.
 Prokaryotes have even been discovered in rocks two miles below the surface of the
Earth.
 Why have these organisms dominated the biosphere since the origin of life on Earth?
 Prokaryotes display diverse adaptations that allow them to inhabit many environments.
 They have great genetic diversity.
 Prokaryotes are classified into two domains, Bacteria and Archaea, which differ in
structure, physiology and biochemistry.

Concept 27.1 Structural, functional, and genetic adaptations contribute to prokaryotic

success
Prokaryotes are small.
 Most prokaryotes are unicellular.
 Some species may aggregate transiently or form true colonies, showing division of
labor between specialized cell types.
 Most prokaryotes have diameters in the range of 1–5 m, compared to 10–100 m for
most eukaryotic cells.
 The largest prokaryote discovered so far has a diameter of 750 m.
 The most common shapes among prokaryotes are spheres (cocci), rods (bacilli), and
helices.
Nearly all prokaryotes have a cell wall external to the plasma membrane.
 In nearly all prokaryotes, a cell wall maintains the shape of the cell, affords physical
protection, and prevents the cell from bursting in a hypotonic environment.
 In a hypertonic environment, most prokaryotes lose water and plasmolyze, like other
walled cells.
 Severe water loss inhibits the reproduction of prokaryotes, which explains why salt can
be used to preserve foods.
 Most bacterial cell walls contain peptidoglycan, a polymer of modified sugars cross-
linked by short polypeptides.
Biology Chapter Notes
  The walls of archaea lack peptidoglycan.
 The Gram stain is a valuable tool for identifying specific bacteria based on differences in
their cell walls.
 Gram-positive bacteria have simple cell walls with large amounts of peptidoglycans.
 Gram-negative bacteria have more complex cell walls with less peptidoglycan.
 An outer membrane on the cell wall of gram-negative cells contains
lipopolysaccharides, carbohydrates bonded to lipids.
 Among pathogenic bacteria, gram-negative species are generally more deadly than gram-
positive species.
 The lipopolysaccharides on the walls of gram-negative bacteria are often toxic, and the
outer membrane protects the pathogens from the defenses of their hosts.
 Gram-negative bacteria are commonly more resistant than gram-positive species to
antibiotics because the outer membrane impedes entry of the drugs.
 Many antibiotics, including penicillin, inhibit the synthesis of cross-links in
peptidoglycans, preventing the formation of a functional wall, especially in gram-positive
species.
 These drugs cripple many species of bacteria, without affecting human and other
eukaryote cells that do not synthesize peptidoglycans.
 Many prokaryotes secrete another sticky protective layer of polysaccharide or protein, the
capsule, outside the cell wall.
 Capsules allow cells to adhere to their substratum.
 They may increase resistance to host defenses.
 They glue together the cells of those prokaryotes that live as colonies.
 Another way for prokaryotes to adhere to one another or to the substratum is by surface
appendages called fimbriae and pili.
 Fimbriae are usually more numerous and shorter than pili.
 These structures can fasten pathogenic bacteria to the mucous membranes of the host.
 Sex pili are specialized for holding two prokaryote cells together long enough to
transfer DNA during conjugation.
Many prokaryotes are motile.
 About half of all prokaryotes are capable of directional movement.
 Some species can move at speeds exceeding 50 m/sec, about 100 times their body
length per second.
 The beating of flagella scattered over the entire surface or concentrated at one or both
ends is the most common method of movement.
 The flagella of prokaryotes differ in structure and function from those of eukaryotes.
 In a heterogeneous environment, many prokaryotes are capable of taxis, movement
toward or away from a stimulus.
 Prokaryotes that exhibit chemotaxis respond to chemicals by changing their movement
patterns.
 Solitary E. coli may exhibit positive chemotaxis toward other members of their
species, enabling the formation of colonies.
The cellular and genomic organization of prokaryotes is fundamentally different from
that of eukaryotes.

Biology Chapter Notes

 The cells of prokaryotes are simpler than those of eukaryotes in both internal structure and
genomic organization.
 Prokaryotic cells lack the complex compartmentalization found in eukaryotic cells.
 Instead, prokaryotes use specialized infolded regions of the plasma membrane to
perform many metabolic functions, including cellular respiration and photosynthesis.
 Prokaryotes have smaller, simpler genomes than eukaryotes.
 On average, a prokaryote has only about one-thousandth as much DNA as a eukaryote.
 In the majority of prokaryotes, the genome consists of a ring of DNA with few associated
proteins.
 The prokaryotic chromosome is located in the nucleoid region.
 Prokaryotes may also have smaller rings of DNA called plasmids, which consist of only a
few genes.
 Prokaryotes can survive in most environments without their plasmids because their
chromosomes program all essential functions.
 Plasmid genes provide resistance to antibiotics, direct metabolism of unusual nutrients,
and other special contingency functions.
 Plasmids replicate independently of the chromosome and can be transferred between
partners during conjugation.
 Although the general processes for DNA replication and translation of mRNA into
proteins are fundamentally alike in eukaryotes and prokaryotes, some of the details differ.
 For example, prokaryotic ribosomes are slightly smaller than the eukaryotic version
and differ in protein and RNA content.
 These differences are great enough that selective antibiotics, including tetracycline and
erythromycin, bind to prokaryotic ribosomes to block protein synthesis in prokaryotes
but not in eukaryotes.
Populations of prokaryotes grow and adapt rapidly.
 Prokaryotes have the potential to reproduce quickly in a favorable environment.
 Prokaryotes reproduce asexually via binary fission, synthesizing DNA almost
continuously.
 While most prokaryotes have generation times of 1–3 hours, some species can produce
a new generation in 20 minutes under optimal conditions.
 A single cell in favorable conditions will produce a large colony of offspring very
quickly.
 Of course, prokaryotic reproduction is limited because cells eventually exhaust their
nutrient supply, accumulate metabolic wastes, or are consumed by other organisms.
 Some bacteria form resistant cells called endospores when an essential nutrient is lacking
in the environment.
 A cell replicates its chromosome and surrounds one chromosome with a durable wall
to form the endospore.
 The original cell then disintegrates to leave the endospore behind.
 An endospore is resistant to all sorts of trauma.
 Endospores can survive lack of nutrients and water, extreme heat or cold, and most
poisons.
 Most endospores can survive in boiling water.
 Endospores may be dormant for centuries or more.
Biology Chapter Notes
  When the environment becomes more hospitable, the endospore absorbs water and
resumes growth.
 Sterilization in an autoclave kills endospores by heating them to 120°C under high
pressure.
 Lacking meiotic sex, mutation is the major source of genetic variation in prokaryotes.
 With generation times of minutes or hours, prokaryotic populations can adapt very rapidly
to environmental changes as natural selection favors gene mutations that confer greater
fitness.
 As a consequence, prokaryotes are important model organisms for scientists who study
evolution in the laboratory.
 Richard Lenski and his colleagues have maintained colonies of E. coli through more than
20,000 generations since 1988.
 The researchers regularly freeze samples of the colonies and later thaw them to
compare their characteristics to those of their descendents.
 Such comparisons have revealed that the colonies in Lenski’s laboratory can grow
60% faster than those that were frozen in 1988.
 Lenski’s team is studying the genetic changes underlying the adaptation of the bacteria
to their environment.
 By measuring RNA production, the researchers found that two separate colonies
showed changes in expression of the same 59 genes, compared to the original colonies.
 The direction of change—increased or decreased expression—was the same for
every gene.
 This is an apparent case of parallel adaptive evolution.
 Horizontal gene transfer also facilitates rapid evolution of prokaryotes.
 Conjugation can permit exchange of a plasmid containing a few genes or large groups
of genes.
 Once the transferred genes are incorporated into the prokaryote’s genome, they are
subject to natural selection.
 Horizontal gene transfer is a major force in the long-term evolution of pathogenic
bacteria.

Concept 27.2 A great diversity of nutritional and metabolic adaptations have evolved in
prokaryotes
 Organisms can be categorized by their nutrition, based on how they obtain energy and
carbon to build the organic molecules that make up their cells.
 Nutritional diversity is greater among prokaryotes than among all eukaryotes.
 Every type of nutrition observed in eukaryotes is found in prokaryotes, along with some
nutritional modes unique to prokaryotes.
 Organisms that obtain energy from light are phototrophs.
 Organisms that obtain energy from chemicals in their environment are chemotrophs.
 Organisms that need only CO2 as a carbon source are autotrophs.
 Organisms that require at least one organic nutrient—such as glucose—as a carbon source
are heterotrophs.

Biology Chapter Notes

 These categories of energy source and carbon source can be combined to group
prokaryotes according to four major modes of nutrition.
o Photoautotrophs are photosynthetic organisms that harness light energy to drive the
synthesis of organic compounds from carbon dioxide.
 Among the photoautotrophic prokaryotes are the cyanobacteria.
 Among the photosynthetic eukaryotes are plants and algae.
o Chemoautotrophs need only CO2 as a carbon source but obtain energy by oxidizing
inorganic substances.
 These substances include hydrogen sulfide (H2S), ammonia (NH3), and ferrous ions
(Fe2+) among others.
 This nutritional mode is unique to prokaryotes.
o Photoheterotrophs use light to generate ATP but obtain their carbon in organic form.
 This mode is restricted to a few marine prokaryotes.
o Chemoheterotrophs must consume organic molecules for both energy and carbon.
 This nutritional mode is found widely in prokaryotes, protists, fungi, animals, and even
some parasitic plants.
 Prokaryotic metabolism also varies with respect to oxygen.
 Obligate aerobes require O2 for cellular respiration.
 Facultative anaerobes will use O2 if present but can also grow by fermentation in an
anaerobic environment.
 Obligate anaerobes are poisoned by O2 and use either fermentation or anaerobic
respiration.
 In anaerobic respiration, inorganic molecules other than O2 accept electrons from
electron transport chains.
 Nitrogen is an essential component of proteins and nucleic acids in all organisms.
 Eukaryotes are limited in the forms of nitrogen they can use.
 In contrast, diverse prokaryotes can metabolize a wide variety of nitrogenous
compounds.
 Nitrogen-fixing prokaryotes convert N2 to NH3, making atmospheric nitrogen available to
themselves (and eventually to other organisms) for incorporation into organic molecules.
 Nitrogen-fixing cyanobacteria are the most self-sufficient of all organisms.
 They require only light energy, CO2, N2, water, and some minerals to grow.
 Prokaryotes were once thought of as single-celled individualists.
 Microbiologists now recognize that cooperation between prokaryotes allows them to use
environmental resources they cannot exploit as individuals.
 Cooperation may involve specialization in cells of a prokaryotic colony.
 For example, the cyanobacterium Anabaena forms filamentous colonies with
specialized cells to carry out nitrogen fixation.
 Photosynthesis produces O2, which inactivates the enzymes involved in nitrogen
fixation.
 Most cells in the filament are photosynthetic, while a few specialized cells called
heterocysts carry out only nitrogen fixation.
 A heterocyst is surrounded by a thickened cell wall that restricts the entry of
oxygen produced by neighboring photosynthetic cells.
 Heterocysts transport fixed nitrogen to neighboring cells in exchange for
carbohydrates.
Biology Chapter Notes
 In some prokaryotic species, metabolic cooperation occurs in surface-coating colonies
known as biofilms.
 Cells in a colony secrete signaling molecules to recruit nearby cells, causing the colony
to grow.
 Once the colony is sufficiently large, the cells begin producing proteins that adhere the
cells to the substrate and to one another.
 Channels in the biofilms allow nutrients to reach cells in the interior and allow wastes
to be expelled.
 In some cases, different species of prokaryotes may cooperate.
 For example, sulfate-consuming bacteria and methane-consuming archaea coexist in
ball-shaped aggregates in the mud of the ocean floor.
 The bacteria use the archaea’s waste products.
 In turn, the bacteria produce compounds that facilitate methane consumption by the
archaea.
 Each year, these archaea consume an estimated 300 billion kg of methane, a major
greenhouse gas.

Concept 27.3 Molecular systematics is illuminating prokaryotic phylogeny

 Until the late 20th century, systematists based prokaryotic taxonomy on criteria such as
shape, motility, nutritional mode, and Gram staining.
 These characteristics may not reflect evolutionary relationships.
 Applying molecular systematics to the investigation of prokaryotic phylogeny has been
very fruitful.
 Microbiologists began comparing sequences of prokaryotic genes in the 1970s.
 Carl Woese and his colleagues used small-subunit ribosomal RNA (SSU-rRNA) as a
marker for evolutionary relationships.
 They concluded that many prokaryotes once classified as bacteria are actually more
closely related to eukaryotes and that they belong in a domain of their own—Archaea.
 Microbiologists have since analyzed larger amounts of genetic data, including whole
genomes of some species.
 They found that a few traditional taxonomic groups, such as cyanobacteria, are
monophyletic.
 Other groups, such as gram-negative bacteria, are scattered throughout several
lineages.
 Two important lessons have already emerged from studies of prokaryotic phylogeny.
 One is that the genetic diversity of prokaryotes is immense.
 When researchers began to sequence the genes of prokaryotes, they could only investigate
those species that can be cultured in the laboratory, a tiny minority of all prokaryotes.
 Norman Price of the University of Colorado pioneered methods that allow researchers
to sample genetic material directly from the environment.
 Every year, new prokaryotes are identified that add major new branches to the tree of
life.
 Some researchers suggest that certain branches represent new kingdoms.

Biology Chapter Notes

 While only 4,500 prokaryotes have been fully characterized, a single handful of soil could
contain 10,000 prokaryotic species, according to some estimates.
 Another important lesson is the significance of horizontal gene transfer in the evolution of
prokaryotes.
 Over hundreds of millions of years, prokaryotes have acquired genes from distantly
related species, and they continue to do so today.
 As a result, significant portions of the genomes of many prokaryotes are actually mosaics
of genes imported from other species.
Researchers are identifying a great diversity of archaea in extreme environments and in
the oceans.
 Early on prokaryotes diverged into two lineages, the domains Archaea and Bacteria.
 The name bacteria was once synonymous with “prokaryotes,” but it now applies to just
one of the two distinct prokaryotic domains.
 However, most known prokaryotes are bacteria.
 Bacteria include the vast majority of familiar prokaryotes, from pathogens causing strep
throat to beneficial species making Swiss cheese.
 Every major mode of nutrition and metabolism is represented among bacteria.
 The major bacterial taxa are now accorded kingdom status by most prokaryotic
systematists.
 Archaea share certain traits with bacteria and other traits with eukaryotes.
 Archaea also have many unique characteristics, as expected for a taxon that has followed
a separate evolutionary path for so long.
 However, much of the research on archaea has focused not on phylogeny, but on their
ecology—their ability to live where no other life can.
 The first prokaryotes to be classified in domain Archaea are species that can live in
environments so extreme that few other organisms can survive there.
 Such organisms are known as extremophiles, or “lovers” of extreme environments.
 Extremophiles include extreme thermophiles, extreme halophiles, and methanogens.
 Extreme thermophiles thrive in hot environments.
 The optimum temperatures for most thermophiles are 60°C–80°C.
 Sulfolobus oxidizes sulfur in hot sulfur springs in Yellowstone National Park.
 Another sulfur-metabolizing thermophile can survive at temperatures as high as 113°C
in water near deep-sea hydrothermal vents.
 Pyrococcus furiosus is an extreme thermophile that is used in biotechnology as the
source of DNA polymerase for the polymerase chain reaction (PCR).
 Extreme halophiles live in such salty places as the Great Salt Lake and the Dead Sea.
 Some species merely tolerate elevated salinity; others require an extremely salty
environment to grow.
 Colonies of certain extreme halophiles form a purple-red scum from
bacteriorhodopsin, a photosynthetic pigment very similar to the visual pigment in the
human retina.
 Methanogens obtain energy by using CO2 to oxidize H2, producing methane as a waste
product.
 Methanogens are among the strictest anaerobes and are poisoned by O 2.
Biology Chapter Notes
  Some species live in swamps and marshes where other microbes have consumed all the
oxygen.
 “Marsh gas” is actually methane produced by the archaea.
 Methanogens are important decomposers in sewage treatment.
 Other methanogens live in the anaerobic guts of animals, playing an important role in
their nutrition.
 They contribute to the greenhouse effect through the production of methane.
 All known extreme halophiles and methanogens, plus a few extreme thermophiles, are
members of a clade called Euryarchaeota.
 Most thermophilic species belong to a second clade, Crenarchaeota.
 Genetic prospecting has revealed that both Euryarchaeota and Crenarchaeota include
many species of archaea that are not extremophiles.
 These species exist in habitats ranging from farm soils to lake sediments to the surface
of the ocean water.
 New findings continue to update our understanding of archaean phylogeny.
 A new clade, Korarchaeota, has been identified that appears to be the oldest lineage in the
domain Archaea.
 In 2002, researchers exploring hydrothermal vents off the cost of Iceland discovered
archaean cells only 0.4 m in diameter attached to a much larger crenarchaeote.
 The genome of this tiny archaean is one of the smallest known of any organisms,
containing only 500,000 base pairs.
 This prokaryote belongs to a fourth archaean clade called Nanoarchaeota.
 Three new nanoarchaeote species have since been found, one from Yellowstone’s hot
springs, one from hot springs in Siberia, and one from a hydrothermal vent in the
Pacific.

Concept 27.4 Prokaryotes play crucial roles in the biosphere

 If humans were to disappear from the planet tomorrow, life on Earth would go on for most
other species.
 But prokaryotes are so important to the biosphere that if they were to disappear, the
prospects for any other life surviving would be dim.
Prokaryotes are indispensable links in the recycling of chemical elements in ecosystems.
 The atoms that make up the organic molecules in all living things were at one time part of
inorganic compounds in the soil, air, and water.
 Life depends on the recycling of chemical elements between the biological and chemical
components of ecosystems.
 Prokaryotes play an important role in this process.
 Chemoheterotrophic prokaryotes function as decomposers, breaking down corpses,
dead vegetation, and waste products and unlocking supplies of carbon, nitrogen, and
other elements essential for life.
 Prokaryotes also mediate the return of elements from the nonliving components of the
environment to the pool of organic compounds.

Biology Chapter Notes

  Autotrophic prokaryotes use carbon dioxide to make organic compounds, which are
then passed up through food chains.
 Prokaryotes have many unique metabolic capabilities.
 They are the only organisms able to metabolize inorganic molecules containing
elements such as iron, sulfur, nitrogen, and hydrogen.
 Cyanobacteria not only synthesize food and restore oxygen to the atmosphere, but they
also fix nitrogen.
 This stocks the soil and water with nitrogenous compounds that other organisms
can use to make proteins.
 When plants and animals die, other prokaryotes return the nitrogen to the atmosphere.
Many prokaryotes are symbiotic.
 Prokaryotes often interact with other species of prokaryotes or eukaryotes with
complementary metabolisms.
 An ecological relationship between organisms that are in direct contact is called
symbiosis.
 If one of the symbiotic organisms is larger than the other, it is termed the host, and the
smaller is known as the symbiont.
 In commensalism, one symbiotic organism benefits while the other is not harmed or
helped by the relationship.
 In parasitism, one symbiotic organism, the parasite, benefits at the expense of the host.
 In mutualism, both symbiotic organisms benefit.
 Human intestines are home to an estimated 500 to 1,000 species of bacteria, which greatly
outnumber all human cells in the body.
 Many of these species are mutualists, digesting food that our own intestines cannot.
 In 2003, scientists at Washington University in St. Louis published the first complete
genome for a gut mutualist, Bacteroides thetaiotaomicron.
 The genome includes a large array of genes involved in synthesizing carbohydrates,
vitamins, and other nutrients needed by humans.
 Signals from the bacterium activate human genes that build the network of intestinal
blood vessels necessary to absorb food.
 Other signals induce human cells to produce antimicrobial compounds to which B.
thetaiotaomicron is not susceptible, protecting the bacterium from its competitors.

Concept 27.5 Prokaryotes have both harmful and beneficial impacts on humans
 Pathogenic prokaryotes represent only a small fraction of prokaryotic species.
 Other prokaryotes serve as essential tools in agriculture and industry.
 Prokaryotes cause about half of human diseases.
 Between 2 and 3 million people a year die of the lung disease tuberculosis, caused by the
bacillus Mycobacterium tuberculosis.
 Another 2 million die from diarrhea caused by other prokaryotes.
 Lyme disease, caused by a bacterium carried by ticks that live on deer and field mice, is
the most widespread pest-carried disease in the United States.

Biology Chapter Notes

  If untreated, Lyme disease can lead to debilitating arthritis, heart disease, and nervous
disorders.
 Pathogens cause illness by producing poisons called exotoxins and endotoxins.
 Exotoxins are proteins secreted by prokaryotes.
 Exotoxins can produce disease symptoms even if the prokaryote is not present.
 An exotoxin produced by Vibrio cholerae causes cholera, a serious disease
characterized by severe diarrhea.
 The exotoxin stimulates intestinal cells to release chloride ions (Cl −) into the gut;
water follows by osmosis.
 Clostridium botulinum, which grows anaerobically in improperly canned foods,
produces an exotoxin that causes botulism.
 Endotoxins are lipopolysaccharide components of the outer membrane of some gram-
negative bacteria.
 In contrast to exotoxins, endotoxins are released only when the bacteria die and their cell
walls break down.
 The endotoxin-producing bacteria in the genus Salmonella are not normally present in
healthy animals.
 Salmonella typhi causes typhoid fever.
 Other Salmonella species, including some that are common in poultry, cause food
poisoning.
 Since the discovery that “germs” cause disease, improved sanitation and improved
treatments have reduced mortality and extended life expectancy in developed countries.
 Antibiotics have greatly reduced the threat of pathogenic prokaryotes and have saved a
great many lives.
 However, resistance to antibiotics is currently evolving in many strains of prokaryotes.
 The rapid reproduction of prokaryotes enables genes conferring resistance to multiply
quickly through prokaryotic populations as a result of natural selection.
 These genes can spread to other species by horizontal gene transfer.
 Horizontal gene transfer can also spread genes associated with virulence, turning harmless
prokaryotes into fatal pathogens.
 E. coli is ordinarily a harmless symbiont in the human intestines.
 Pathogenic strains causing bloody diarrhea have arisen.
 One of the most dangerous strains is called O157:H7.
 Today, it is a global threat, with 75,000 cases annually in the United States alone.
 In 2001, an international team of scientists sequenced the genome of O157:H7 and
compared it with the genome of a harmless strain of E. coli.
 1,387 of the 5,416 genes in O157:H7 have no counterpart in the harmless strain.
 These 1,387 genes must have been incorporated into the genome of O157:H7
through horizontal gene transfer, most likely through the action of bacteriophages.
 Many of the imported genes are associated with the pathogen’s invasion of its host.
 For example, some genes code for exotoxins that enable O157:H7 to attach itself to
the intestinal wall and extract nutrients.
 Pathogenic prokaryotes pose a potential threat as weapons of bioterrorism.

Biology Chapter Notes

 In October 2001, endospores of Bacillus anthracis, the bacterium that causes anthrax,
were mailed to news media and the U.S. Senate.
 Other prokaryotes that could serve as weapons include C. botulinum and Yersinia pestis,
which causes plague.
 This threat has stimulated intense research on pathogenic prokaryotes.
Humans use prokaryotes in research and technology.
 Humans have learned to exploit the diverse metabolic capabilities of prokaryotes for
scientific research and for practical purposes.
 Much of what we know about metabolism and molecular biology has been learned
using prokaryotes, especially E. coli, as simple model systems.
 Increasingly, prokaryotes are used to solve environmental problems.
 The use of organisms to remove pollutants from air, water, and soil is bioremediation.
 The most familiar example is the use of prokaryote decomposers to treat human
sewage.
 Anaerobic bacteria decompose the organic matter into sludge (solid matter in sewage),
while aerobic microbes do the same to liquid wastes.
 Other bioremediation applications include breaking down radioactive waste and
cleaning up oil spills.
 In the mining industry, prokaryotes help recover metals from ores.
 Bacteria assist in extracting more than 30 billion kg of copper from copper sulfides each
year.
 Other prokaryotes can extract gold from ore.
 Through genetic engineering, humans can now modify prokaryotes to produce vitamins,
antibiotics, hormones, and many other products.
 Craig Venter of the Human Genome Project has announced that he and his colleagues are
attempting to build synthetic chromosomes for prokaryotes, producing new species form
scratch.
 Venter hopes to “design” prokaryotes that can perform specific tasks, such as producing
large amounts of hydrogen to reduce dependence on fossil fuels.

Biology Chapter Notes

 Chapter 28 Protists
Chapter Notes

Overview: A World in a Drop of Water

 In the past, taxonomists classified all protists in a single kingdom, Protista.

 However, it is now clear that Protista is in fact paraphyletic.
 Some protists are more closely related to plants, fungi, or animals than they are to other
protists.
 As a result, the kingdom Protista has been abandoned.
 Various lineages are recognized as kingdoms in their own right.
 Scientists still use the convenient term protist informally to refer to eukaryotes that are not
plants, animals, or fungi.

Concept 28.1 Protists are an extremely diverse assortment of eukaryotes

 Protists exhibit more structural and functional diversity than any other group of
organisms.
 Most protists are unicellular, although there are some colonial and multicellular ones.
 At the cellular level, many protists are very complex.
 This is to be expected of a single cell that must carry out the basic functions performed
by all the specialized cells in a multicellular organism.
 Protists are the most nutritionally diverse of all eukaryotes.
 Some are photoautotrophs, containing chloroplasts.
 Some are heterotrophs, absorbing organic molecules or ingesting food particles.
 Some are mixotrophs, combining photosynthesis and heterotrophic nutrition.
 Protists can be divided into three groups, based on their roles in biological communities.
 These groups are not monophyletic.
 Protists include photosynthetic algal protists, ingestive protozoans, and absorptive
protists.
 Protist habitats are also very diverse.
 The life cycles of protists vary greatly.
 Some are exclusively asexual, while most have life cycles including meiosis and
syngamy.
Endosymbiosis has a place in eukaryotic evolution.
 Much of protist diversity is the result of endosymbiosis, a process in which unicellular
organisms engulfed other cells that evolved into organelles in the host cell.
 The earliest eukaryotes acquired mitochondria by engulfing alpha proteobacteria.
 The early origin of mitochondria is supported by the fact that all eukaryotes studied so
far either have mitochondria or had them in the past.

Biology Chapter Notes

 Later in eukaryotic history, one lineage of heterotrophic eukaryotes acquired an additional
endosymbiont—a photosynthetic cyanobacterium—that evolved into plastids.
 This lineage gave rise to red and green algae.
 This hypothesis is supported by the observation that the DNA of plastids in red and
green algae closely resembles the DNA of cyanobacteria.
 Plastids in these algae are surrounded by two membranes, presumably derived from the
cell membranes of host and endosymbiont.
 On several occasions during eukaryotic evolution, red and green algae underwent
secondary endosymbiosis.
 They were ingested in the food vacuole of a heterotrophic eukaryote and became
endosymbionts themselves.
 For example, algae known as chlorarachniophytes evolved when a heterotrophic
eukaryote engulfed a green alga.
 This process likely occurred comparatively early in evolutionary time, because the
engulfed alga still carries out photosynthesis with its plastids and contains a tiny,
vestigial nucleus called a nucleomorph.

Concept 28.2 Diplomads and parabasalids have modified mitochondria

 Most diplomonads and parabasalids are found in anaerobic environments.
 These protists lack plastids, and their mitochondria lack DNA, an electron transport chain,
and the enzymes needed for the citric acid cycle.
 In some species, the mitochondria are very small and produce cofactors for enzymes
involved in ATP production in the cytosol.
 Diplomonads have two equal-sized nuclei and multiple flagella.
 Giardia intestinalis is an infamous diplomonad parasite that lives in the intestines of
mammals.
 The most common method of acquiring Giardia is by drinking water contaminated
with feces containing the parasite in a dormant cyst stage.
 The parabasalids include trichomonads.
 The best-known species, Trichomonas vaginalis, inhabits the vagina of human females.
 If the normal acidity of the vagina is disturbed, T. vaginalis can outcompete beneficial
bacteria and infect the vaginal lining.
 The male urethra may also be infected but without symptoms.
 The infection is sexually transmitted.
 Genetic studies of T. vaginalis suggest that the species became pathogenic after some
individuals acquired a particular gene through horizontal gene transfer from other
vaginal bacteria.
 The gene allows T. vaginalis to feed on epithelial cells.

Concept 28.3 Euglenozoans have flagella with a unique internal structure

 Euglenozoa is a diverse clade that includes predatory heterotrophs, photosynthetic
autotrophs, and pathogenic parasites.
 Members of this group are distinguished by the presence of a spiral or crystalline rod
inside their flagella.
Biology Chapter Notes
 Most euglenozoans have disc-shaped mitochondrial cristae.
 The best-studied groups of euglenozoans are the kinetoplastids and euglenids.
 The kinetoplastids have a single large mitochondrion associated with a unique organelle,
the kinetoplast.
 The kinetoplast houses extranuclear DNA.
 Kinetoplastids are symbiotic and include pathogenic parasites.
 For example, Trypanosoma causes African sleeping sickness, a disease spread by the
African tsetse fly, and Chagas’ disease, which is transmitted by bloodsucking bugs.
 Trypanosomes evade immune detection by switching surface proteins from generation to
generation, preventing the host from developing immunity.
 One-third of Trypanosoma’s genome codes for these surface proteins.
 Euglenids are characterized by an anterior pocket from which one or two flagella emerge.
 They also have a unique glucose polymer, paramylon, as a storage molecule.
 Many species of the euglenid Euglena are autotrophic but can become heterotrophic in
the dark.
 Other euglenids can phagocytose prey.

Concept 28.4 Alveolates have sacs beneath the plasma membrane

 Members of the clade Alveolata have alveoli, small membrane-bound cavities, under the
plasma membrane.
 Their function is not known, but they may help stabilize the cell surface or regulate
water and ion content.
 Alveolata includes flagellated protists (dinoflagellates), parasites (apicomplexans), and
ciliates.
 Dinoflagellates are abundant components of marine and freshwater phytoplankton.
 Dinoflagellates and other phytoplankton form the foundation of most marine and many
freshwater food chains.
 Other species of dinoflagellates are heterotrophic.
 Most dinoflagellates are unicellular, but some are colonial.
 Each dinoflagellate species has a characteristic shape, often reinforced by internal plates
of cellulose.
 Two flagella sit in perpendicular grooves in the “armor” and produce a spinning
movement.
 Dinoflagellate blooms, characterized by explosive population growth, can cause “red
tides” in coastal waters.
 The blooms are brownish red or pinkish orange because of the presence of carotenoids
in dinoflagellate plasmids.
 Toxins produced by some red-tide organisms have produced massive invertebrate and
fish kills.
 These toxins can be deadly to humans as well.

Biology Chapter Notes

 Some dinoflagellates form mutualistic symbioses with coral polyps, the animals that build
coral reefs.
 Photosynthetic products from the dinoflagellates provide the main food resource for
reef communities.
 All apicomplexans are parasites of animals, and some cause serious human diseases.
 The parasites disseminate as tiny infectious cells (sporozoites) with a complex of
organelles specialized for penetrating host cells and tissues at the apex of the
sporozoite cell.
 Apicomplexans have a nonphotosynthetic plasmid called the apicoplast, which carries
out vital functions including the synthesis of fatty acids.
 Most apicomplexans have intricate life cycles with both sexual and asexual stages and
often require two or more different host species for completion.
 Plasmodium, the parasite that causes malaria, spends part of its life in mosquitoes and part
in humans.
 The incidence of malaria was greatly diminished in the 1960s by the use of insecticides
against the Anopheles mosquitoes, which spread the disease, and by drugs that killed the
parasites in humans.
 However, resistant varieties of Anopheles and Plasmodium have caused a malarial
resurgence.
 About 300 million people are infected with malaria in the tropics, and up to 2 million
die each year.
 The search for malarial vaccines has had little success because Plasmodium is evasive.
 It spends most of its time inside human liver and blood cells, and continually changes
its surface proteins, thereby changing its “face” to the human immune system.
 The need for new treatments for malaria led to a major effort to sequence Plasmodium’s
genome.
 By 2003, researchers had identified the expression of most of the parasite’s genes at
specific points in its life cycle.
 This research could help scientists identify potential new targets for vaccines.
 Identification of a gene that may confer resistance to chloroquine, an antimalarial drug,
may lead to ways to block drug resistance in Plasmodium.
 Ciliates are a diverse group of protists, named for their use of cilia to move and feed.
 The cilia may cover the cell surface or be clustered into rows or tufts.
 Some ciliates scurry about on leglike structures constructed from many cilia.
 A submembrane system of microtubules coordinates ciliary movements.
 The cilia are associated with a submembrane system of microtubules that may coordinate
movement.
 Ciliates have two types of nuclei, one or more large macronuclei and tiny micronuclei.
 Each macronucleus has dozens of copies of the ciliate’s genome.
 The genes are not organized into chromosomes but are packaged into small units
with duplicates of a few genes.
 Macronuclear genes control the everyday functions of the cell such as feeding,
waste removal, and water balance.
 Ciliates generally reproduce asexually by binary fission of the macronucleus, rather
than mitotic division.

Biology Chapter Notes

 The sexual shuffling of genes occurs during conjugation, during which two individuals
exchange haploid micronuclei.
 In ciliates, reproduction and conjugation are separate processes.
 In a real sense, ciliates have “sex without reproduction.”
 Conjugation provides an opportunity for ciliates to eliminate transposons and other types
of “selfish” DNA that can replicate within a genome.
 During conjugation, foreign genetic elements are excised when micronuclei develop
from macronuclei.
 Up to 15% of a ciliate’s genome may be removed every time it undergoes conjugation.

Concept 28.5 Stramenopiles have “hairy” and smooth flagella

 The clade Stramenopila includes both heterotrophic and photosynthetic protists.
 The name of this group is derived from the presence of numerous fine, hairlike
projections on the flagella.
 In most cases, a “hairy” flagellum is paired with a smooth flagellum.
 In most stramenopile groups, the only flagellated stages are motile reproductive cells.
 The heterotrophic stramenopiles, the oomycetes, include water molds, white rusts, and
downy mildews.
 Many oomycetes have multinucleate filaments that resemble fungal hyphae.
 However, there are many differences between oomycetes and fungi.
 Oomycetes have cell walls made of cellulose, while fungal walls are made of chitin.
 The diploid condition, reduced in fungi, is dominant in oomycete life cycles.
 Oomycetes have flagellated cells, while almost all fungi lack flagella.
 Molecular systematics has confirmed that oomycetes are not closely related to fungi.
 Their superficial similarity is a case of convergent evolution.
 In both groups, the high surface-to-volume ratio of filamentous hyphae enhances
nutrient uptake.
 Although oomycetes descended from photosynthetic ancestors, they no longer have
plastids.
 Instead, they acquire nutrients as decomposers or parasites.
 Water molds are important decomposers, mainly in fresh water.
 They form cottony masses on dead algae and animals.
 White rusts and downy mildews are parasites of terrestrial plants.
 They are dispersed by windblown spores, and form flagellated zoospores at another
point in their life cycles.
 One species of downy mildew threatened French vineyards in the 1870s.
 Another species causes late potato blight, which contributed to the Irish famine in the
19th century.
 Late blight continues to cause crop losses today.
 Researchers are working to develop resistant potatoes by transferring genes from
wild potatoes that confer resistance to blight.
 Diatoms are unicellular algae with unique glasslike walls composed of hydrated silica
embedded in an organic matrix.
 The wall is divided into two parts that overlap like a shoebox and lid.
Biology Chapter Notes
  These walls allow live diatoms to withstand immense pressure, providing a defense for
them from the crushing jaws of predators.
 Most of the year, diatoms reproduce asexually by mitosis with each daughter cell
receiving half of the cell wall and regenerating a new second half.
 Some species form cysts as resistant stages.
 Sexual stages are not common.
 When it occurs, it involves the formation of eggs and amoeboid or flagellated sperm.
 Diatoms are a highly diverse group of protists, with an estimated 100,000 species.
 They are abundant members of both freshwater and marine plankton.
 Diatoms store food reserves as the glucose polymer laminarin or, in a few diatoms, as oil.
 Massive accumulations of fossilized diatoms are major constituents of diatomaceous
earth.
 Golden algae, or chrysophytes, are named for their yellow and brown carotenoids.
 Their cells are biflagellated, with both flagella attached near one end of the cell.
 Some species are mixotrophic, absorbing organic molecules or ingesting bacteria by
phagocytosis.
 Many chrysophytes live among freshwater and marine plankton.
 While most are unicellular, some are colonial.
 At high densities, they can form resistant cysts that remain viable for decades.
 Brown algae, or phaeophytes, are the largest and most complex protists known.
 All brown algae are multicellular, and most species are marine.
 Brown algae are especially common along temperate coasts in areas of cool water and
adequate nutrients.
 They owe their characteristic brown or olive color to carotenoids in their plastids,
which are homologous to the plastids of golden algae and diatoms.
 The largest marine algae, including brown, red, and green algae, are known collectively as
seaweeds.
 Seaweeds inhabit the intertidal and subtidal zones of coastal waters.
 This environment is characterized by extreme physical conditions, including wave
forces and exposure to sun and drying conditions at low tide.
 Seaweeds have a complex multicellular anatomy, with some differentiated tissues and
organs that resemble those in plants.
 These analogous features include the thallus, or body, of the seaweed.
 The thallus typically consists of a rootlike holdfast and a stemlike stipe, which
supports leaflike photosynthetic blades.
 The term “seaweed” refers to brown algae as well as some species of green and red algae.
 The giant seaweeds known as kelps live in deep water beyond the intertidal zone.
 The stipes of these algae may be as long as 60 m.
 Seaweeds living in the intertidal zone must cope with rough water as well as twice-daily
low tides that expose the algae to hot sun and risk of desiccation.
 Seaweeds are important sources of food and commodities.

Biology Chapter Notes

  Many seaweeds are eaten by coastal people, including Laminaria (“kombu” in Japan)
in soup and Porphyra (Japanese “nori”) for sushi wraps.
 A variety of gel-forming substances are extracted in commercial operations.
 Algin from brown algae and agar and carrageen from red algae are used as thickeners
in food, lubricants in oil drilling, or culture media in microbiology.
Some algae have life cycles with alternating multicellular haploid and diploid generations.
 The multicellular brown, red, and green algae show complex life cycles with alternation
of multicellular haploid and multicellular diploid forms.
 A similar alternation of generations had a convergent evolution in the life cycle of
plants.
 The complex life cycle of the kelp Laminaria provides an example of alternation of
generations.
 The diploid individual, the sporophyte, produces haploid spores (zoospores) by
meiosis.
 The haploid individual, the gametophyte, produces gametes by mitosis that fuse to
form a diploid zygote.
 In Laminaria, the sporophyte and gametophyte are structurally different, or
heteromorphic.
 In other algae, the alternating generations look alike (isomorphic) but differ in the
chromosome number.

Concept 28.6 Cercozoans and radiolarians have threadlike pseudopodia

 A newly recognized clade, Cercozoa, contains the amoebas.
 The term “amoeba” used to refer to protists that move and feed by means of
pseudopodia, cellular extensions that bulge from the cell surface.
 When an amoeba moves, it extends a pseudopodium and anchors the tip.
 Cytoplasm then streams into the pseudopodium.
 It is now clear that amoebas are not a monophyletic group.
 Those that belong to the clade Cercozoa are distinguished by their threadlike pseudopodia.
 Cercozoans include chlorarachniophytes and foraminiferans and are closely related to
radiolarians, which also have threadlike pseudopodia.
 Foraminiferans, or forams, are named for their porous shells, or tests.
 Forams have multichambered, porous shells, consisting of organic materials hardened
with calcium carbonate.
 Pseudopodia extend through the pores for swimming, shell formation, and feeding.
 Many forams form symbioses with algae.
 Forams live in marine and fresh water.
 Most live in sand or attach to rocks or algae.
 Some are abundant in the plankton.
 More than 90% of the described forams are fossils.
 The calcareous skeletons of forams are important components of marine sediments.

Biology Chapter Notes

  Fossil forams are often used as chronological markers to correlate the ages of
sedimentary rocks from different parts of the world.
 Radiolarians are mostly marine protists whose siliceous skeletons are fused into one
delicate piece.
 Pseudopodia known as axopodia radiate from the central body and are reinforced by
microtubules.
 The microtubules are covered by a thin layer of cytoplasm, which phagocytoses
organisms that become attached to the axopodia.
 After death, radiolarian tests accumulate as an ooze that may be hundreds of meters thick
in some seafloor locations.

Concept 28.7 Amoebozoans have lobe-shaped pseudopodia

 Many species of amoebas that have lobe-shaped pseudopodia belong to the clade
Amoebozoans, which includes gymnamoebas, entamoebas, and slime molds.
 Gymnamoebas are a large and varied group of Amoebozoans.
 They are common in soil as well as freshwater and marine environments.
 Most are heterotrophs that actively seek and consume bacteria and protists, while some
feed on detritus.
 Entamoebas include free-living and parasitic species.
 Humans host at least six species of Entamoeba.
 One, E. histolytica, causes amebic dysentery, spread through contaminated drinking
water and food.
 This disease kills 100,000 people each year.
 Slime molds were once thought to be fungi because they produce fruiting bodies that
disperse their spores.
 However, this resemblance is due to evolutionary convergence.
 Molecular systematics places slime molds in the clade Amoebozoa and suggests that they
descended from unicellular, gymnamoeba-like ancestors.
 Slime molds have diverged into two lineages with distinctive life cycles: plasmodial slime
molds and cellular slime molds.
 The plasmodial slime molds are brightly pigmented, heterotrophic organisms.
 The feeding stage is an amoeboid mass, the plasmodium, which may be several
centimeters in diameter.
 The plasmodium is not multicellular, but rather a single mass of cytoplasm with
multiple diploid nuclei.
 The diploid nuclei undergo synchronous mitotic divisions, thousands at a time.
 Because of this characteristic, plasmodial slime molds have been used for studies of
the molecular details of the cell cycle.
 Within the cytoplasm, cytoplasmic streaming distributes nutrients and oxygen throughout
the plasmodium.
 The plasmodium phagocytoses food particles from moist soil, leaf mulch, or rotting logs.

Biology Chapter Notes

 If the habitat begins to dry or if food levels drop, the plasmodium stops growing and
differentiates into a stage of the life cycle that produces fruiting bodies, which function in
sexual reproduction.
 Plasmodial slime molds are primarily diploid.
 Cellular slime molds straddle the line between individuality and multicellularity.
 The feeding stage consists of solitary cells that feed and divide mitotically as
individuals.
 When food is scarce, the cells form an aggregate (“slug”) that functions as a unit.
 Each cell retains its identity in the aggregate.
 The dominant stage in a cellular slime mold is the haploid stage.
 Most cellular slime molds lack flagellated stages.
 Dictyostelium discoideum is a common cellular slime mold that has become a model
organism for addressing the evolution of multicellularity.
 As the fruiting body forms, cells that form the stalk dry out and die, cells at the top
survive, form spores, and have the potential for future reproduction.
 Scientists have found that mutations to a single gene can turn individual Dictyostelium
cells into “cheaters” that never become part of the stalk.
 Since these mutants gain a strong reproductive advantage over noncheaters, why do all
Dictyostelium cells not cheat?
 A group of scientists recently found a possible answer to this puzzle.
 Cheating mutants lack a protein on their cell surface, and noncheating cells can
recognize this difference.
 Noncheaters preferentially aggregate with other noncheaters, depriving cheaters of the
opportunity to exploit them.
 Such recognition systems may have been important in the evolution of multicellular
animals and plants.

Concept 28.8 Red algae and green algae are the closest relatives of land plants
 More than a billion years ago, a heterotrophic protist acquired a cyanobacterial
endosymbiont.
 The photosynthetic descendents of this ancient protist evolved into the red and green
algae.
 At least 475 million years ago, the lineage that produced green algae gave rise to the land
plants.
 Unlike other eukaryotic algae, red algae have no flagellated stages in their life cycle.
 There are more than 6,000 known species of red algae, which are reddish due to the
accessory pigment phycoerythrin.
 Coloration varies among species and depends on the depth that they inhabit.
 Some species lack pigmentation and are parasites on other red algae.
 Red algae are the most common seaweeds in the warm coastal waters of tropical oceans.
 Red algae inhabit deeper waters than other photosynthetic eukaryotes.
 Their photosynthetic pigments, especially phycobilins, allow them to absorb blue and
green wavelengths that penetrate down to deep water.
Biology Chapter Notes
  One red algal species has been discovered off the Bahamas at a depth of more than 260
m.
 Some red algae live in fresh water or on land.
 Most red algae are multicellular, with some reaching a size large enough to be called
“seaweeds.”
 The thalli of many red algal species are filamentous.
 The base of the thallus is usually differentiated into a simple holdfast.
 The life cycles of red algae are especially diverse.
 In the absence of flagella, fertilization depends entirely on water currents to bring
gametes together.
 Alternation of generations is common in red algae.
 Green algae are named for their grass-green chloroplasts.
 These are similar in ultrastructure and pigment composition to those of plants.
 Molecular systematics and cellular morphology provide considerable evidence that green
algae and land plants are closely related.
 In fact, some systematists advocate the inclusion of green algae into an expanded
“plant” kingdom, Viridiplantae.
 Green algae are divided into two main groups, chlorophytes and charophyceans.
 Most of the 7,000 species of chlorophytes have been identified.
 Most live in fresh water, but many are marine inhabitants.
 Some chlorophytes inhabit damp soil, while others are specialized to live on glaciers
and snowfields.
 These snow-dwelling chlorophytes carry out photosynthesis despite subfreezing
temperatures and intense visible and ultraviolet radiation.
 They are protected by radiation-blocking compounds in their cytoplasm and by the
snow itself, which acts as a shield.
 Some chlorophytes live symbiotically with fungi to form lichens, a mutualistic
collective.
 Large size and complexity in chlorophytes has evolved by three different mechanisms:
o Formation of colonies of individual cells (e.g., Volvox).
o The repeated division of nuclei without cytoplasmic division to form multinucleate
filaments (e.g., Caulerpa).
o The formation of true multicellular forms by cell division and cell differentiation (e.g.,
Ulva).
 Some multicellular marine chlorophytes are large and complex enough to qualify as
seaweeds.
 Most green algae have complex life cycles, with both sexual and asexual reproductive
stages.
 Most sexual species have biflagellated gametes with cup-shaped chloroplasts.
 Alternation of generations evolved in the life cycles of some green algae.
 The other main group of green algae is most closely related to land plants.

Biology Chapter Notes

 Chapter 29 Plant Diversity I: How Plants Colonized
Land
Chapter Notes

Overview: The Greening of Earth

 For the first 3 billion years of Earth’s history, the land was lifeless.
 Thin coatings of cyanobacteria existed on land about 1.2 billion years ago.
 About 500 million years ago, plants, fungi, and animals joined them.
 More than 290,000 species of plants inhabit Earth today.
 Most plants live in terrestrial environments, including deserts, grasslands, and forests.
 Some species, such as sea grasses, have returned to aquatic habitats.
 The presence of plants has enabled other organisms to survive on land.
 Plant roots have created habitats for other organisms by stabilizing landscapes.
 Plants are the source of oxygen and the ultimate provider of food for land animals.

Concept 29.1 Land plants evolved from green algae

 Researchers have identified a lineage of green algae called charophyceans as the closest
relatives of land plants.
 Many key characteristics of land plants also appear in a variety of algal clades.
 Plants are multicellular, eukaryotic, photosynthetic autotrophs.
 But red, brown, and some green algae also fit this description.
 Plants have cell walls made of cellulose.
 So do green algae, dinoflagellates, and brown algae.
 Plants have chloroplasts with chlorophyll a and b.
 So do green algae, euglenids, and a few dinoflagellates.
 Land plants share four key features only with the charophyceans.
o The plasma membranes of land plants and charophyceans possess rosette cellulose-
synthesizing complexes that synthesize the cellulose microfibrils of the cell wall.
 These complexes contrast with the linear arrays of cellulose-producing proteins in
noncharophycean algae.
 Also, the cell walls of plants and charophyceans contain a higher percentage of
cellulose than the cell walls of noncharophycean algae.
o A second feature that unites charophyceans and land plants is the presence of
peroxisome enzymes to help minimize the loss of organic products as a result of
photorespiration.
 Peroxisomes of other algae lack these enzymes.
o In those land plants that have flagellated sperm cells, the structure of the sperm
resembles the sperm of charophyceans.

Biology Chapter Notes

 o Finally, certain details of cell division are common only to land plants and the most
complex charophycean algae.
 These include the formation of a phragmoplast, an alignment of cytoskeletal elements
and Golgi-derived vesicles, during the synthesis of new cross-walls during cytokinesis.
 Over the past decade, researchers involved in an international initiative called “Deep
Green” have conducted a large-scale study of the major transitions in plant evolution.
 These researchers have analyzed genes from a wide range of plant and algal
species.
 Comparisons of nuclear and chloroplast genes support the hypothesis that the
charophyceans are the closest living relatives of land plants.
 Many charophycean algae inhabit shallow waters at the edges of ponds and lakes, where
they experience occasional drying.
 In such environments, natural selection favors individuals that can survive periods when
they are not submerged in water.
 A layer of a durable polymer called sporopollenin prevents exposed charophycean
zygotes from drying out until they are in water again.
 This chemical adaptation may have been the precursor to the tough sporopollenin walls
that encase plant spores.
 The accumulation of such traits by at least one population of ancestral charophyceans
enabled their descendents—the first land plants—to live permanently above the waterline.
 The evolutionary novelties of the first land plants opened an expanse of terrestrial habitat
previously occupied only by films of bacteria.
 The new frontier was spacious.
 The bright sunlight was unfiltered by water and plankton.
 The atmosphere had an abundance of carbon dioxide.
 The soil was rich in mineral nutrients.
 At least at first, there were relatively few herbivores or pathogens.

Concept 29.2 Land plants possess a set of derived terrestrial adaptations

 A number of adaptations evolved in plants that allowed them to survive and reproduce on
land.
 What exactly is the line that divides land plants from algae?
 We will adopt the traditional scheme, which equates the kingdom Plantae with
embryophytes (plants with embryos).
 Some botanists now propose that the plant kingdom should be renamed the kingdom
Streptophyta and expanded to include the charophyceans and a few related groups.
 Others suggest the kingdom Viridiplantae, which includes chlorophytes as well as
plants.
 Five key traits appear in nearly all land plants but are absent in the charophyceans.
 We infer that these traits evolved as derived traits of land plants.
 The five traits are:
o Apical meristems.
o Alternation of generations.
o Multicellular embryo that is dependent on the parent plant.
Biology Chapter Notes
 o Sporangia that produce walled spores.
o Gametangia that produce gametes.
Apical meristems
 In terrestrial habitats, the resources that a photosynthetic organism requires are found in
two different places.
 Light and carbon dioxide are mainly aboveground.
 Water and mineral resources are found mainly in the soil.
 Therefore, plants show varying degrees of structural specialization for subterranean and
aerial organs—roots and shoots in most plants.
 The elongation and branching of the shoots and roots maximize their exposure to
environmental resources.
 This growth is sustained by apical meristems, localized regions of cell division at the tips
of shoots and roots.
 Cells produced by meristems differentiate into various tissues, including surface
epidermis and internal tissues.
Alternation of generations
 All land plants show alternation of generations in which two multicellular body forms
alternate.
 This life cycle also occurs in various algae.
 However, alternation of generations does not occur in the charophyceans, the algae
most closely related to land plants.
 In alternation of generations, one of the multicellular bodies is called the gametophyte
and has haploid cells.
 Gametophytes produce gametes, egg and sperm, by mitosis.
 Fusion of egg and sperm during fertilization form a diploid zygote.
 Mitotic division of the diploid zygote produces the other multicellular body, the
sporophyte.
 Meiosis in a mature sporophyte produces haploid reproductive cells called spores.
 A spore is a reproductive cell that can develop into a new organism without fusing
with another cell.
 Mitotic division of a plant spore produces a new multicellular gametophyte.
 Unlike the life cycles of other sexually producing organisms, alternation of generations in
land plants (and some algae) results in both haploid and diploid stages that exist as
multicellular bodies.
 For example, humans do not have alternation of generations because the only haploid
stage in the life cycle is the gamete, which is single-celled.
Walled spores produced by sporangia
 Plant spores are haploid reproductive cells that grow into gametophytes by mitosis.
 Sporopollenin makes the walls of spores very tough and resistant to harsh
environments.
 Multicellular organs called sporangia are found on the sporophyte and produce spores.

Biology Chapter Notes

 Within sporangia, diploid cells called sporocytes undergo meiosis and generate haploid
spores.
 The outer tissues of the sporangium protect the developing spores until they are ready to
be released into the air.
Multicellular gametangia
 Plant gametophytes produce gametes within multicellular organs called gametangia.
 A female gametangium, called an archegonium, produces a single egg cell in a vase-
shaped organ.
 The egg is retained within the base.
 Male gametangia, called antheridia, produce and release sperm into the environment.
 In many major groups of living plants, the sperm have flagella and swim to the eggs
though a water film.
 Each egg is fertilized within an archegonium, where the zygote develops into the embryo.
 The gametophytes of seed plants are so reduced in size that archegonia and antheridia
have been lost in some lineages.
Multicellular, dependent embryos
 Multicellular plant embryos develop from zygotes that are retained within tissues of the
female parent.
 The multicellular, dependent embryo of land plants is such a significant derived trait that
land plants are also known as embryophytes.
 The parent provides nutrients, such as sugars and amino acids, to the embryo.
 The embryo has specialized placental transfer cells that enhance the transfer of
nutrients from parent to embryo.
 These are sometimes present in the adjacent maternal tissues as well.
 This interface is analogous to the nutrient-transferring embryo-mother interface of
placental mammals.
 Additional derived traits have evolved in many plant species.
 The epidermis of many plants has a cuticle consisting of polymers called polyesters and
waxes.
 The cuticle waterproofs the epidermis, preventing excessive water loss, and offers
protection from microbial attack.
 Many land plants produce secondary compounds, so named because they are the products
of secondary metabolic pathways that branch from primary metabolic pathways.
 Alkaloids, terpenes, and tannins defend against herbivores and parasites.
 Flavonoids absorb harmful UV radiation and may act as signals in symbiotic
relationships with beneficial soil microbes.
 Phenolics deter attack by pathogenic microbes.
Land plants have diversified since their origin from algal ancestors.
 Fossils of plant spores have been extracted from 475-million-year-old rocks in Oman.
 These spores were embedded in plant cuticle material that is similar to spore-bearing
tissue in living plants.
 These fossils clearly belong to plants.
Biology Chapter Notes
 A 2001 study of the “molecular clock” of plants suggests that the common ancestor of
living plants existed 700 million years ago.
 A 2003 study suggests a new date of 490 to 425 million years, roughly the same age as the
spores found in Oman.
 Land plants can be informally grouped based on the presence or absence of an extensive
system of vascular tissue, cells joined into tubes that transport water and nutrients
throughout the plant body.
 Plants that do not have an extensive transport system are described as “nonvascular
plants,” although some mosses do have simple vascular tissue.
 Nonvascular plants are informally called bryophytes.
 There is some uncertainty about whether or not bryophytes are monophyletic and
represent a clade.
 Vascular plants form a clade consisting of 93% of all land plants.
 Three smaller clades are found within the vascular plants.
 Lycophytes include club mosses and their relatives.
 Pterophytes include the ferns and their relatives.
 These two clades are called the seedless vascular plants.
 A third clade of vascular plants includes the seed plants, the vast majority of living
plants.
 A seed is an embryo packaged with a supply of nutrients within a protective coat.
 Seed plants can be divided into two groups: gymnosperms and angiosperms.
 Gymnosperms are called “naked seed plants” because their seeds are not enclosed in
chambers.
 Angiosperms are a huge clade including all flowering plants.

Concept 29.3 The life cycles of mosses and other bryophytes are dominated by the
gametophyte stage
 Bryophytes are represented by three phyla:
 Phylum Hepatophyta—liverworts
 Phylum Anthocerophyta—hornworts
 Phylum Bryophyta—mosses
 Note that the name Bryophyta refers only to one phylum, but the informal term bryophyte
refers to all nonvascular plants.
 It has not been established whether the diverse bryophytes form a clade.
 Systematists continue to debate the sequence in which the three phyla of bryophytes
evolved.
 Bryophytes acquired many unique adaptations after their evolutionary split from the
ancestors of modern vascular plants.
 They also possess some ancestral traits characteristic of the earliest plants.
 In bryophytes, gametophytes are the largest and most conspicuous phase of the life cycle.
 Sporophytes are smaller and are present only part of the time.
 Bryophyte spores germinate in favorable habitats and grow into gametophytes by mitosis.
Biology Chapter Notes
 The gametophyte is a mass of green, branched, filaments that are one cell thick, called a
protonema.
 A protonema has a large surface area that enhances absorption of water and minerals.
 In favorable conditions, protonema generate gamete-producing structures, the
gametophores.
 Bryophytes are anchored by tubular cells or filaments of cells, called rhizoids.
 Unlike roots, rhizoids are not composed of tissues, lack specialized conducting cells,
and do not play a primary role in water and mineral absorption.
 Bryophyte gametophytes are generally only one or a few cells thick, placing all cells close
to water and dissolved minerals.
 Most bryophytes lack conducting tissues to distribute water and organic compounds
within the gametophyte.
 Some mosses have conducting tissues in their stems, and a few can grow as tall as 2 m.
 It is not clear if conducting tissues in mosses are analogous or homologous to the
xylem and phloem of vascular plants.
 Lacking support tissues, most bryophytes are only a few centimeters tall.
 The mature gametophores of bryophytes produce gametes in gametangia.
 Each vase-shaped archegonium produces a single egg.
 Elongated antheridia produce many flagellated sperm.
 When plants are coated with a thin film of water, sperm swim toward the archegonia,
drawn by chemical attractants.
 They swim into the archegonia and fertilize the eggs.
 The zygotes and young sporophytes are retained and nourished by the parent
gametophyte.
 Layers of placental nutritive cells transport materials from parent to embryos.
Bryophyte sporophytes disperse enormous numbers of spores.
 While the bryophyte sporophyte does have photosynthetic plastids when young, it cannot
live apart from the maternal gametophyte.
 A bryophyte sporophyte remains attached to its maternal gametophyte throughout the
sporophyte’s lifetime.
 It depends on the gametophyte for sugars, amino acids, minerals, and water.
 Bryophytes have the smallest and simplest sporophytes of all modern plant groups,
consistent with the hypothesis that larger and more complex sporophytes evolved only
later in vascular plants.
 Moss sporophytes consist of a foot, an elongated stalk (the seta), and a sporangium
(the capsule).
 The foot gathers nutrients and water from the parent gametophyte via transfer cells.
 The stalk conducts these materials to the capsule.
 In most mosses, the seta becomes elongated, elevating the capsule and enhancing spore
dispersal.
 The moss capsule (sporangium) is the site of meiosis and spore production.
 One capsule can generate more than 50 million spores.
 When immature, the capsule is covered by a protective cap of gametophyte tissue, the
calyptra.
Biology Chapter Notes
  This is lost when the capsule is ready to release spores.
 The upper part of the capsule, the peristome, is often specialized for gradual spore
release.
 Liverworts have the simplest sporophytes among the bryophytes.
 They consist of a short stalk bearing round sporangia that contain the developing
spores, and a nutritive foot embedded in gametophyte tissues.
 Hornwort and moss sporophytes are larger and more complex.
 Hornwort sporophytes resemble grass blades and have a cuticle.
 The sporophytes of mosses start out green and photosynthetic, but turn tan or brownish
red when ready to release their spores.
 The sporophytes of hornworts and mosses have epidermal stomata, like those of
vascular plants.
 These pores support photosynthesis by allowing the exchange of CO2 and O2
between the outside air and the interior of the sporophyte.
 The fact that stomata are present in mosses and hornworts but absent in liverworts has
led to three hypotheses for their evolution.
o If liverworts are the deepest-branching lineage of land plants, then stomata evolved
once in the ancestor of hornworts, mosses and vascular plants.
o If hornworts are the deepest-branching lineage of land plants, then stomata evolved
once and were lost in the liverwort lineage.
o Perhaps hornworts acquired stomata independently of mosses and vascular plants.
Bryophytes provide many ecological and economic benefits.
 Wind dispersal of lightweight spores has distributed bryophytes around the world.
 They are common and diverse in moist forests and wetlands.
 Some even inhabit extreme environments such as mountaintops, tundra, and deserts.
 Phenolic compounds in moss cell walls absorb damaging levels of radiation present in
deserts and at high altitudes and latitudes.
 Many mosses can exist in very cold or dry habitats because they are able to lose most of
their body water and then rehydrate and reactivate their cells when moisture again
becomes available.
 Few vascular plants can survive the same degree of desiccation.
 Sphagnum, a wetland moss, is especially abundant and widespread.
 It forms extensive deposits of undecayed organic material, called peat.
 Wet regions dominated by Sphagnum or peat moss are known as peat bogs.
 Its organic materials do not decay readily because of resistant phenolic compounds and
acidic secretions that inhibit bacterial activity.
 Peatlands, extensive high-latitude boreal wetlands occupied by Sphagnum, play an
important role as carbon reservoirs, stabilizing atmospheric carbon dioxide levels.
 Sphagnum has been used in the past for diapers and as a natural antiseptic material for
wounds.
 Today, it is harvested for use as a soil conditioner and for packing plants’ roots because of
the water storage capacity of its large, dead cells.
 Worldwide, an estimated 400 billion tons of organic carbon are stored as peat.

Biology Chapter Notes

Concept 29.4 Ferns and other seedless vascular plants formed the first forests
Ferns and other seedless vascular plants flourished in the Carboniferous period.
 Bryophytes were the prevalent vegetation for the first 100 million years that terrestrial
communities existed.
 Then vegetation began to take on a taller profile with the evolution of vascular plants.
 Modern seedless vascular plants provide insights into plant evolution during the
Carboniferous period, when vascular plants began to diversify, but most groups of seed
plants had not yet evolved.
 The sperm of ferns and all other seedless vascular plants are flagellated and must swim
through a film of water to reach eggs.
 Due to the swimming sperm and their fragile gametophytes, modern seedless vascular
plants are most common in damp environments.
 Fossils of the ancestors of today’s vascular plants date back about 420 million years.
 Unlike bryophytes, these plants had branched sporophytes that did not remain dependent
on gametophytes for growth.
Five main traits characterize modern vascular plants.
 Five main traits characterize modern vascular plants:
o Life cycles with dominant sporophytes.
o Transport in xylem and phloem.
o Evolution of roots.
o Evolution of leaves.
o Sporophylls and spore variations.
Life cycles with dominant sporophytes
 Fossils suggest that the ancestors of vascular plants had life cycles characterized by
gametophytes and sporophytes that were about equal in size.
 Among living vascular plants, the sporophyte generation is the larger and more complex
plant.
 For example, the leafy fern plants that you are familiar with are sporophytes.
 The gametophytes are tiny plants that grow on or just below the soil surface.
 This reduction in the size of the gametophytes is even more extreme in seed plants.
Transport in xylem and phloem
 Vascular plants have two types of vascular tissue: xylem and phloem.
 Xylem conducts most of the water and minerals.
 The xylem of all vascular plants includes tracheids, tube-shaped cells that carry water
and minerals up from roots.
 When functioning, these cells are dead, with only their walls providing a system of
microscopic water pipes.
 The water-conducting cells in vascular plants are lignified, strengthened by the
phenolic polymer lignin.
 Phloem is a living tissue in which nutrient-conducting cells are arranged into tubes that
distribute sugars, amino acids, and other organic products.

Biology Chapter Notes

  Lignified vascular tissue permitted vascular plants to grow to greater heights than
bryophytes.
Evolution of roots
 Lignified vascular tissue also allowed the evolution of roots.
 Roots are organs that anchor vascular plants and enable them to absorb water and
nutrients from the soil.
 Roots also allow the shoot system to grow taller.
 Roots may have evolved from the subterranean portions of stems in ancient vascular
plants.
 It is not clear whether roots evolved once in the common ancestor of all vascular plants or
independently in different lineages.
 Studying genes that control root development may resolve this controversy.
Evolution of leaves
 Leaves are organs that increase the surface area of vascular plants, capturing more solar
energy for photosynthesis.
 In terms of size and complexity, leaves can be classified as microphylls and megaphylls.
 All lycophytes have microphylls, small leaves with only a single unbranched vein.
 These leaves probably evolved as small outgrowths on the surface of stems, supported
by single strands of vascular tissue.
 All other vascular plants have megaphylls, leaves with a highly branched vascular
system.
 A branched vascular system can deliver water and minerals to the expanded leaf.
 It can also export larger quantities of sugars from the leaf.
 Megaphylls support more photosynthetic activity.
 The fossil evidence suggests that megaphylls evolved from a series of branches lying
close together on a stem.
 One hypothesis proposes that megaphylls evolved when the branch system flattened
and a tissue webbing developed, joining the branches.
 Under this hypothesis, true, branched stems preceded the origin of large leaves and
roots.
Sporophylls and spore variations
 Vascular plants have sporophylls, modified plants that bear sporangia.
 Sporophylls vary greatly in structure.
 Ferns produce clusters of sporangia called sori, usually on the underside of leaves.
 In gymnosperms, groups of sporophylls form cone or strobili.
 Another key variation among vascular plants is the distinction between homosporous and
heterosporous species.
 Most seedless vascular plants are homosporous, producing a single type of spore.
 This spore develops into a bisexual gametophyte with both archegonia (female sex
organs) and antheridia (male sex organs).
 Most ferns are homosporous.
Biology Chapter Notes
 A heterosporous species produces two kinds of spores.
 Megaspores develop into female gametophytes.
 Microspores develop into male gametophytes.
 All seed plants and a few seedless vascular plants are heterosporous.
Classification of seedless vascular plants.
 Living seedless vascular plants form two clades: lycophytes and pterophytes.
 Lycophytes include club mosses, spike mosses, and quillworts.
 Pterophytes include ferns, horsetails, whisk ferns, and their relatives.
 Phylum Lycophyta: club mosses, spike mosses, and quillworts
 Modern species of lycophytes are relicts of an eminent past.
 By the Carboniferous, there were two evolutionary lineages of lycophytes: small,
herbaceous plants and giant, woody trees standing 40 meters tall.
 The giant lycophytes became extinct as the climate cooled and dried at the end of the
Carboniferous.
 The small lycophytes survived, and are now represented by 1,200 species.
 Phylum Pterophyta: ferns, horsetails, and whisk ferns
 Ferns radiated extensively from their Devonian origins and grew with lycophytes and
horsetails in the Carboniferous swamp forests.
 There are 12,000 species of living ferns.
 They are most diverse in the tropics, thrive in temperate forests, and some can even
survive arid conditions.
 Horsetails grew up to 15 meters in height during the Carboniferous period.
 Today, only 15 species of single genus Equisetum survives.
 Psilotum, the whisk fern, and a close relative form a clade of terrestrial epiphytes.
 Whisk ferns are the only vascular plants lacking true roots and leaves.
 These plants have been considered “living fossils” because their dichotomous
branching and lack of true leaves and roots seemed similar to early vascular plants.
 However, comparisons of DNA sequences and details of sperm ultrastructure indicate
that they are closely related to ferns.
 The whisk fern’s ancestors lost true leaves and roots during evolution.
The significance of seedless vascular plants.
 The ancestors of modern lycophytes and ferns, along with their seedless vascular
relatives, formed the first forests during the Carboniferous.
 With the evolution of vascular tissue, roots, and leaves, these plants accelerated their rate
of photosynthesis and dramatically increased the removal of CO2 in the atmosphere.
 Scientists estimate that CO2 levels dropped by as much as a factor of five during the
Carboniferous, causing global cooling and widespread glacier formation.
 The first forests gave rise to modern-day coal.
 In the stagnant waters of the Carboniferous, dead plants did not fully decay.
 The organic material turned to thick layers of peat. Marine sediments piled up on top, and
over millions of years, heat and pressure converted the peat to coal.
 Humans still burn 6 billion tons of coal each year.

Biology Chapter Notes

 Chapter 30 Plant Diversity II: The Evolution of Seed
Plants
Chapter Notes

Overview: Feeding the World

 The seed arose about 360 million years ago.

 Seed plants, including gymnosperms and angiosperms, have come to dominate modern
landscapes and make up the great majority of plant biodiversity.
 Agriculture, the cultivation and harvest of plants (especially angiosperms), began 13,000
years ago.
 Humans began the cultivation of plants independently in various regions, including the
Near East, East Asia, Africa, and the Americas.
 This was the single most important cultural change in the history of humanity, and it
made possible the transition from hunter-gatherer societies to permanent settlements.

Concept 30.1 The reduced gametophytes of seed plants are protected in ovules and
pollen grains
 A number of terrestrial adaptations contributed to the success of seed plants.
 These adaptations include the seed, the reduction of the gametophyte generation,
heterospory, ovules, and pollen.
 Bryophyte life cycles are dominated by the gametophyte generation, while seedless
vascular plants have sporophyte-dominated life cycles.
 The trend to gametophyte reduction continued in the lineage of vascular plants that led to
seed plants.
 Seedless vascular plants have tiny gametophytes that are visible to the naked eye.
 The gametophytes of seed plants are microscopically small and develop from spores
retained within the moist sporangia of the parental sporophyte.
 In seed plants, the delicate female gametophyte and the young sporophyte embryo are
protected from many environmental stresses, including drought and UV radiation.
 The gametophytes of seed plants obtain nutrients from their parents, while the free-
living gametophytes of seedless vascular plants must fend for themselves.
Heterospory is the rule among seed plants.
 Nearly all seedless plants are homosporous, producing a single kind of spore that forms a
hermaphroditic gametophyte.
 Seed plants likely had homosporous ancestors.
 All seed plants are heterosporous, producing two different types of sporangia that produce
two types of spores.
 Megasporangia produce megaspores, which give rise to female (egg-containing)
gametophytes.
 Microsporangia produce microspores, which give rise to male (sperm-containing)
gametophytes.
Biology Chapter Notes
 Seed plants produce ovules.
 In contrast to the few species of heterosporous seedless vascular plants, seed plants are
unique in retaining their megaspores within the parent sporophyte.
 Layers of sporophyte tissue, integuments, envelop and protect the megasporangium.
 Gymnosperm megaspores are surrounded by one integument.
 Angiosperm megaspores are surrounded by two integuments.
 An ovule consists of the megasporangium, megaspores, and integuments.
 A female gametophyte develops from a megaspore and produces one or more egg cells.
Pollen eliminated the liquid-water requirement for fertilization.
 The microspores develop into pollen grains that are released from the microsporangium.
 Pollen grains are covered with a tough coat containing sporopollenin.
 They are carried by wind or animals.
 The transfer of pollen to the vicinity of the ovule is called pollination.
 The pollen grain germinates and grows as a pollen tube into the ovule, where it delivers
one or two sperm into the female gametophyte.
 Bryophytes and seedless vascular plants have flagellated sperm cells that swim a few
centimeters through a film of water to reach the egg cells within the archegonium.
 In seed plants, the female gametophyte is retained within the sporophyte ovule.
 Male gametophytes travel long distances as pollen grains.
 The sperm of seed plants lack flagella and do not require a film of water, as they rely
on the pollen tube to reach the egg cell of the female gametophyte within the ovule.
 The sperm of some gymnosperm species retain the ancestral flagellated condition,
providing evidence of this evolutionary transition.
 The evolution of pollen contributed to the success and diversity of seed plants.
Seeds became an important means of dispersing offspring.
 What is a seed?
 When a sperm fertilizes an egg of a seed plant, the zygote forms and develops into a
sporophyte embryo.
 The ovule develops into a seed, consisting of the embryo and its food supply within a
protective coat derived from the integuments.
 The evolution of the seed enabled plants to resist harsh environments and disperse
offspring more widely.
 For bryophytes and seedless vascular plants, single-celled spores are the only protective
stage in the life cycle.
 Moss spores can survive even if the local environment is too cold, too hot, or too dry
for the moss plants themselves to survive.
 Because of their tiny size, the spores themselves can be dispersed in a dormant state to
a new area.
 Spores were the main way that plants spread over Earth for the first 100 million years
of life on land.
 The seed represents a different solution to resisting harsh environments and dispersing
offspring.

Biology Chapter Notes

  In contrast to a single-celled spore, a multicellular seed is a much more complex,
resistant structure.
 After being released from the parent plant, a seed may remain dormant for days or
years.
 Under favorable conditions, it germinates and the sporophyte embryo emerges as a
seedling.

Concept 30.2 Gymnosperms bear “naked” seeds, typically on cones

 The ovules and seeds of gymnosperms (“naked seeds”) develop on the surfaces of
modified leaves that usually form cones (strobili).
 In contrast, ovules and seeds of angiosperms develop in enclosed chambers called
ovaries.
 The most familiar gymnosperms are the conifers, cone-bearing trees such as pine, fir, and
redwood.
The four phyla of extant gymnosperms are Cycadophyta, Ginkgophyta, Gnetophyta, and
Coniferophyta.
 There are four plant phyla grouped as gymnosperms.
 Phylum Ginkgophyta consists of only a single extant species, Ginkgo biloba.
 This popular ornamental species has fanlike leaves that turn gold before they fall off in
the autumn.
 Landscapers usually plant only male trees because the coats of seeds produced by
female plants produce a repulsive odor as they decay.
 Cycads (phylum Cycadophyta) have large cones and palmlike leaves.
 130 species of cycads survive today.
 Cycads flourished in the Mesozoic era, which was known as the “Age of Cycads.”
 Phylum Gnetophyta consists of three very different genera.
 Weltwitschia plants, from deserts in southwestern Africa, have straplike leaves that are
among the largest known leaves.
 Gentum species are tropical trees or vines.
 Ephedra (Mormon tea) is a shrub of the American deserts.
 The conifers belong to the largest gymnosperm phylum, the phylum Coniferophyta.
 The term conifer comes from the reproductive structure, the cone, which is a cluster of
scalelike sporophylls.
 Although there are only about 600 species of conifers, a few species dominate vast
forested regions in the Northern Hemisphere where the growing season is short.
 Conifers include pines, firs, spruces, larches, yews, junipers, cedars, cypresses, and
redwoods.
 Most conifers are evergreen, retaining their leaves and photosynthesizing throughout the
year.
 Some conifers, like the dawn redwood and tamarack, are deciduous, dropping their
leaves in autumn.
 The needle-shaped leaves of some conifers, such as pines and firs, are adapted for dry
conditions.
Biology Chapter Notes
  A thick cuticle covering the leaf and the placement of stomata in pits further reduce
water loss.
 Much of our lumber and paper comes from the wood (actually xylem tissue) of conifers.
 This tissue gives the tree structural support.
 Coniferous trees are amongst the largest and oldest organisms of Earth.
 Redwoods from northern California can grow to heights of over 100 m.
 One bristlecone pine, also from California, is more than 4,600 years old, and may be
the world’s oldest living organism.
The Mesozoic era was the age of gymnosperms.
 The gymnosperms probably descended from progymnosperms, a group of Devonian
plants that were heterosporous but lacked seeds.
 The first seed plants to appear in the fossil record were gymnosperms dating from around
360 million years ago.
 Angiosperms arose more than 200 million years later.
 The two surviving clades of seed plants are gymnosperms and angiosperms.
 Early gymnosperms lived in Carboniferous ecosystems dominated by seedless vascular
plants.
 The flora and fauna of Earth changed dramatically during the formation of the
supercontinent Pangaea in the Permian.
 Climatic conditions became warmer and drier, favoring the spread of gymnosperms.
 Many groups of organisms disappeared while others emerged.
 Amphibians decreased in diversity and were replaced by reptiles, which were better
adapted to dry conditions.
 The lycophytes, horsetails, and ferns that had dominated in Carboniferous swamps were
largely replaced by gymnosperms.
 The change in organisms was so dramatic that geologists use the end of the Permian, 251
million years ago, as the boundary between the Paleozoic (“old life”) and Mesozoic (“new
life”) eras.
 The terrestrial animals of the Mesozoic, including dinosaurs, were supported by a
vegetation consisting mostly of conifers and cycads, both gymnosperms.
 The dinosaurs did not survive the mass extinction at the end of the Mesozoic, but many
gymnosperms persisted and are still an important part of Earth’s flora.
The life cycle of a pine demonstrates the key reproductive adaptations of seed plants.
 The life cycle of a pine illustrates the three key adaptations to terrestrial life in seed
plants:
o Increasing dominance of the sporophyte.
o The advent of the seed as a resistant, dispersal stage in the life cycle.
o The evolution of pollen as an airborne agent bringing gametes together.
 The pine tree is the sporophyte.
 It produces its sporangia on scalelike sporophylls that are packed densely on cones.
 Conifers, like all seed plants, are heterosporous.
 Male and female gametophytes develop from different types of spores produced by
separate cones: small pollen cones and large ovulate cones.
Biology Chapter Notes
  Most pine species produce both types of cones.
 A pollen cone contains hundreds of microsporangia held on small sporophylls.
 Each cone produces microspore mother cells that undergo meiosis to produce haploid
microspores.
 Each microspore develops into a pollen grain containing a male gametophyte.
 A larger ovulate cone consists of many scales, each with two ovules.
 Each ovule includes a megasporangium.
 Ovulate cones produce megaspore mother cells that undergo meiosis to produce four
haploid cells, one of which will develop into a megaspore.
 Surviving megaspores develop into female gametophytes, which are retained within
the sporangia.
 Two or three archegonia, each with an egg, develop within the gametophyte.
 During pollination, windblown pollen falls on the ovulate cone and grows into the ovule
through the micropyle.
 Fertilization of egg and sperm follows.
 The pine embryo, the new sporophyte, has a rudimentary root and several embryonic
leaves.
 The female gametophyte surrounds and nourishes the embryo.
 The ovule develops into a pine seed, which consists of an embryo (new sporophyte),
its food supply (derived from gametophyte tissue), and a seed coat derived from the
integuments of the parent tree (parent sporophyte).
 It takes three years from the appearance of young cones on a pine tree to the formation of
mature seeds.
 The scales of ovulate cone separate and the seeds are typically dispersed by the wind.
 A seed that lands in a habitable place germinates, and its embryo emerges as a pine
seedling.

Concept 30.3 The reproductive adaptations of angiosperms include flowers and fruits
 Angiosperms, commonly known as flowering plants, are vascular seed plants that produce
flowers and fruits.
 They are the most diverse and geographically widespread of all plants, including more
than 90% of plant species.
 There are about 250,000 known species of angiosperms.
 All angiosperms are placed in a single phylum, the phylum Anthophyta.
The flower is the defining reproductive adaptation of angiosperms.
 The flower is an angiosperm structure specialized for sexual reproduction.
 In many species of angiosperms, insects and other animals transfer pollen from one
flower to female sex organs of another.
 Some species that occur in dense populations, like grasses, are wind pollinated.
 A flower is a specialized shoot with up to four circles of modified leaves: sepals, petals,
stamens, and carpals.
 The sepals at the base of the flower are modified leaves that are usually green and enclose
the flower before it opens.
Biology Chapter Notes
 The petals lie inside the ring of sepals.
 These are often brightly colored in plant species that are pollinated by animals.
 They typically lack bright coloration in wind-pollinated plant species.
 Sepals and petals are sterile floral parts, not directly involved in reproduction.
 Stamens, the male reproductive organs, are sporophylls that produce microspores that
will give rise to pollen grains containing male gametophytes.
 A stamen consists of a stalk (the filament) and a terminal sac (the anther) where
pollen is produced.
 Carpals are female sporophylls that produce megaspores and their products, female
gametophytes.
 At the tip of the carpal is a sticky stigma that receives pollen.
 A style leads to the ovary at the base of the carpal.
 Ovules are protected within the ovary.
Fruits help disperse the seeds of angiosperms.
 A fruit usually consists of a mature ovary.
 As seeds develop from ovules after fertilization, the wall of the ovary thickens to form
the fruit.
 Fruits protect dormant seeds and aid in their dispersal.
 The fruit develops after pollination triggers hormonal changes that cause ovarian growth.
 The wall of the ovary becomes the pericarp, the thickened wall of the fruit.
 The other parts of the flower wither away in many plants.
 If a flower has not been pollinated, the fruit usually does not develop, and the entire
flower withers and falls away.
 Mature fruits can be fleshy or dry.
 Oranges and grapes are fleshy fruits, in which one or more pericarp layers soften
during ripening.
 Dry fruits include beans and grains.
 The dry, wind-dispersed fruits of grasses are major food staples for humans.
 The cereal grains of wheat, rice, and maize are fruits with a dry pericarp that adheres to
the seed coat of the seed.
 Fruits are classified according to whether they develop from a single ovary, from multiple
ovaries, or from more than one flower.
 By selectively breeding plants, humans have capitalized on the production of edible fruits.
 Fruits are adapted to disperse seeds.
 Winged seeds may function as kites or propellers to assist wind dispersal.
 Coconuts are specialized for water dispersal.
 Some fruits are modified as burrs that cling to animal fur.
 Many fruits are edible, nutritious, sweet tasting, and colorful.
 These fruits rely on animals to eat the fruit and deposit the seeds, along with a
supply of fertilizer, some distance from the parent plant.
The life cycle of an angiosperm is a highly refined version of the alternation of
generations common to all plants.

Biology Chapter Notes

 All angiosperms are heterosporous, producing microspores that form male gametophytes
and megaspores that form female gametophytes.
 The immature male gametophytes are contained within pollen grains, which develop
within the anthers of stamens.
 Each pollen grain has two haploid cells: a generative cell that divides to form two
sperm and a tube cell that produces a pollen tube.
 The ovule, which develops in the ovary, contains the female gametophyte, the embryo
sac.
 The embryo sac consists of only a few cells, one of which is the egg.
 The life cycle of an angiosperm begins with the formation of a mature flower on a
sporophyte plant and culminates in a germinating seed.
o Anthers contain microsporangia, containing microspore mother cells that produce
microspores by meiosis.
o Microspores form pollen grains, which are immature male gametophytes.
o In the ovule, the megaspore mother cell produces four megaspores by meiosis.
 One megaspore survives and forms a female gametophyte, or embryo sac.
o The pollen is released from the anther and carried to the sticky stigma of the carpel.
 Most flowers have mechanisms to ensure cross-pollination.
o The pollen grain germinates and is now a mature male gametophyte.
 The pollen tube grows down within the style.
 After reaching the ovary, the pollen tube penetrates the micropyle, a pore in the
integuments of the ovule.
 Two sperm are discharged into the female gametophyte.
 One fertilizes the egg to form a diploid zygote.
 The other fuses with two polar nuclei in the large central cell of the embryo sac to
form the triploid endosperm nucleus.
 Double fertilization is unique to angiosperms.
o The zygote develops into an embryo that is packaged with food into the seed.
 The embryo has a rudimentary root and one or two seed leaves, or cotyledons.
o When a seed germinates, the embryo develops into a mature sporophyte.
 Monocots store most of the food for the developing embryo as endosperm, which
develops as a triploid tissue in the center of the embryo sac.
 Beans and many dicots transfer most of the nutrients from the endosperm to the
developing cotyledons.
 One hypothesis for the function of double fertilization is that it synchronizes the
development of food storage in the seed with development of the embryo.
 Double fertilization may prevent flowers from squandering nutrients on infertile
ovules.
 Another type of double fertilization, in which two embryos are formed, has evolved
independently in gymnosperms of the phylum Gnetophyta.
 The seed consists of the embryo, endosperm, remnants of the sporangium, and a seed coat
derived from the integuments.
 As the ovules develop into seeds, the ovary develops into a fruit.
 After dispersal by wind or animals, a seed germinates if environmental conditions are
favorable.
Biology Chapter Notes
  During germination, the seed coat ruptures and the embryo emerges as a seedling.
 It initially uses the food stored in the endosperm and cotyledons to support
development.
The origin and evolution of angiosperms is complex.
 Earth’s landscape changed dramatically with the origin and radiation of flowering plants.
 The oldest angiosperm fossils are about 140 million years old.
 By the end of the Cretaceous period, 65 million years ago, angiosperms had become the
dominant plants on Earth.
 In the late 1990s, scientists in China discovered fossils of 125-million-year-old
angiosperms named Archaefructus liaoningensis and Archaefructus sinensis.
 These fossils display both derived and primitive traits.
 A. sinensis has anthers and seeds inside closed carpels but lacks petals and sepals.
 This species may be a “proto-angiosperm,” suggesting that the ancestors of flowering
plants were herbaceous rather than woody.
 It was found along with fish fossils and may be aquatic.
 Some paleobotanists suggest that angiosperms originated as aquatic plants.
 Others dispute this, pointing out that aquatic angiosperms tend to evolve simpler
flowers such as the “primitive” flowers of Archaefructus.
 An “evo-devo” approach, synthesizing evolutionary and developmental biology, has lead
to a hypothesis about the evolution of bisexual flowers.
 The “mostly male” hypothesis proposes that the ancestor of angiosperms had separate
male and female structures, and that, as a result of a mutation, ovules developed on
some microsporophylls, which evolved into carpels.
 Flower-development genes are usually related to gymnosperm pollen-producing genes.
 Certain mutations cause angiosperms to grow ovules on sepals and petals,
demonstrating that the position of ovules can change.
Angiosperms are very diverse.
 Angiosperms have diversified into more than 250,000 species that dominate most
terrestrial ecosystems.
 Until the late 1990s, flowering plants were divided into monocots and dicots on the basis
of number of cotyledons or seed leaves.
 Current research supports the view that monocots form a clade but reveals that dicots are
not monophyletic.
 The majority of plants traditionally called “dicots” form a clade now known as
“eudicots.”
 The remaining plants are divided into several small lineages.
 Three of these lineages are called basal angiosperms, because they include the oldest
known lineages of flowering plants.
 Amborella is a basal angiosperm that lacks vessels that are found in more derived
angiosperms.
 Another lineage is the magnoliids.
 Magnoliids include 8,000 species, including magnolias.
 These angiosperms share primitive traits such as spiral arrangement of floral parts with
the basal angiosperms.
Biology Chapter Notes
 One quarter of angiosperms are monocots.
 Monocot traits include single cotyledons, parallel venation, scattered vascular bundles,
fibrous root systems, pollen grains with a single opening, and floral parts in multiples
of three.
 More than two-thirds of angiosperms—170,000 species—are eudicots.
 Eudicot traits include two cotyledons, netlike venation, vascular bundles arranged as a
ring, a taproot, pollen grains with three openings, and floral parts in multiples of four
or five.
Animals and angiosperms share evolutionary links.
 Ever since they colonized the land, animals have influenced the evolution of terrestrial
plants and vice versa.
 Plants and animals have been important selective agents on one another.
 Natural selection favored plants that kept their spores and gametophytes above the
ground, rather than dropping them within the reach of hungry ground animals.
 This may, in turn, have been a selective factor in the evolution of flying insects.
 Some herbivores were beneficial to plants by dispersing their pollen and seeds.
 The animals received a benefit in turn, as they ate the nectar, seeds, and fruits of
plants.
 Natural selection reinforced these interactions when they improved the reproductive
success of both partners.
 Pollinator-plant relationships are partly responsible for increased diversity of angiosperms
and animals.
 In many cases, a plant species may be pollinated by a group of pollinators, such as
many species of bees or hummingbirds, and have evolved flower color, fragrance, and
structures to facilitate this.
 Conversely, a single species, such as a honeybee species, may pollinate many plant
species.
 Some individual species of flower can only be pollinated by a single animal species.
 In Madagascar, one species of orchid has an 11-inch long nectary and can only be
pollinated by a moth species with an 11-inch proboscis.
 Such linked adaptations, involving reciprocal genetic modifications in two species,
are coevolution.
 The expansion of grasslands over the past 65 million years has increased the diversity of
grazing animals such as horses.
 Grasses are C4 photosynthesizers that spread as declining atmospheric CO 2 levels gave
them a selective advantage.
 The shift from forests to grasslands in Africa between 10 and 2 million year ago was
crucial to hominid evolution.

Concept 30.4 Human welfare depends greatly on seed plants

 The absolute dependence of humans on Earth’s flora is a specific and highly refined case
of the more general connection between animals and plants.
 Like other organisms, we depend on photosynthetic organisms for food production and
oxygen release.
Biology Chapter Notes
  However, we use technology to manipulate or select plants that maximize the harvest
of plant products for human use.
 We rely on seed plants for food, fuel, wood, and medicine.
Agriculture is based almost entirely on angiosperms.
 Flowering plants provide nearly all our food.
 Just six crops—wheat, rice, maize, potatoes, cassava, and sweet potatoes—yield 80% of
all calories consumed by humans.
 Modern crops are the products of a relatively recent burst of genetic change, resulting
from artificial selection after the domestication of plants 13,000 years ago.
 In maize, key changes such as increased cob size and removal of the hard coating of
the kernels may have been initiated by as few as five gene mutations.
 How did wild plants change so dramatically so quickly?
 The answer is likely a combination of deliberate and unconscious selection for plants
with desirable traits, such as large fruits and lack of toxins.
 Angiosperms also provide important nonstable foods such as coffee, chocolate, and
spices.
 Gymnosperms and angiosperms are sources of wood, which is absent in all living seedless
plants and consists of an accumulation of tough-walled xylem cells.
 Wood is the primary source of fuel for much of the world.
 It is used to make paper, and is the world’s most widely used construction material.
 Humans depend on seed plants for medicines.
 Most cultures have a tradition of herbal medicine.
 Scientific research has identified the relevant secondary compounds in many of these
plants, leading to the synthesis of many modern medicines.
Plant diversity is a nonrenewable resource.
 Although plants are a renewal resource, plant diversity is not.
 The demand for space and natural resources resulting from the exploding human
population is extinguishing plant species at an unprecedented rate.
 This is especially acute in the tropics, where more than half the human population lives
and where population growth rates are highest.
 Due primarily to the slash-and-burn clearing of forests for agriculture, tropical forests
may be completely eliminated within 25 years.
 As the forests disappear, thousand of plant species and the animals that depend on these
plants also go extinct.
 The destruction of these areas is an irrevocable loss of these nonrenewable resources.
 The rate of loss is faster than in any other period, even during the Permian and
Cambrian extinctions.
 While the loss of species is greatest in the tropics, the threat is global.
 In addition to the ethical concerns that many people have concerning the extinction of
living forms, there are also practical reasons to be concerned about the loss of plant
diversity.
 We depend on plants for food, building materials, and medicines.

Biology Chapter Notes

  We have explored the potential uses for only a tiny fraction of the 290,000 known
plant species.
 Almost all of our food is based on cultivation of only about two dozen species.
 Researchers have investigated fewer than 5,000 plant species as potential sources of
medicines.
 Pharmaceutical companies were led to most of these species by local people who used
the plants in preparing their traditional medicines.
 The tropical rain forests and other plant communities may be a medicine chest of
healing plants that could be extinct before we even know they exist.
 We need to view rain forests and other ecosystems as living treasures that we can harvest
only at sustainable rates.

Biology Chapter Notes

 Chapter 31 Fungi
Chapter Notes

Overview: Mighty Mushrooms

 The honey mushroom Armillaria ostoyae in Malheur National Park in eastern Oregon is
enormous.
 Its subterranean mycelium covers 890 hectares, weighs hundreds of tons, and has been
growing for 2,600 years.
 Ten thousand species of fungi have been described, but it is estimated that there are
actually up to 1.5 million species of fungi.
 Fungal spores have been found 160 km above the ground.
 Fungi play an important role in ecosystems, decomposing dead organisms, fallen leaves,
feces, and other organic materials.
 This decomposition recycles vital chemical elements back to the environment in forms
other organisms can assimilate.
 Most plants depend on mutualistic fungi to help their roots absorb minerals and water
from the soil.
 Humans have cultivated fungi for centuries for food, to produce antibiotics and other
drugs, to make bread rise, and to ferment beer and wine.

Concept 31.1 Fungi are heterotrophs that feed by absorption

Absorptive nutrition enables fungi to live as decomposers and symbionts.
 Fungi are heterotrophs that acquire their nutrients by absorption.
 They absorb small organic molecules from the surrounding medium.
 Exoenzymes, powerful hydrolytic enzymes secreted by the fungus, break down food
outside its body into simpler compounds that the fungus can absorb and use.
 The absorptive mode of nutrition is associated with the ecological roles of fungi as
decomposers (saprobes), parasites, and mutualistic symbionts.
 Saprobic fungi absorb nutrients from nonliving organisms.
 Parasitic fungi absorb nutrients from the cells of living hosts.
 Some parasitic fungi, including some that infect humans and plants, are pathogenic.
 Fungi cause 80% of plant diseases.
 Mutualistic fungi also absorb nutrients from a host organism, but they reciprocate with
functions that benefit their partner in some way.
Extensive surface area and rapid growth adapt fungi for absorptive nutrition.
 Yeasts are single-celled fungi. Most other species of fungi are multicellular.
 The vegetative bodies of most fungi are constructed of tiny filaments called hyphae that
form an interwoven mat called a mycelium.
 Fungal mycelia can be huge, but they usually escape notice because they are
subterranean.
Biology Chapter Notes
 Fungal hyphae have cell walls.
 These are built mainly of chitin, a strong but flexible nitrogen-containing
polysaccharide identical to that found in arthropods.
 Most fungi are multicellular with hyphae divided into cells by cross walls, or septa.
 These generally have pores large enough for ribosomes, mitochondria, and even nuclei
to flow from cell to cell.
 Fungi that lack septa, coenocytic fungi, consist of a continuous cytoplasmic mass with
hundreds or thousands of nuclei.
 This results from repeated nuclear division without cytoplasmic division.
 Parasitic fungi usually have some hyphae modified as haustoria, nutrient-absorbing
hyphal tips that penetrate the tissues of their host.
 Some fungi even have hyphae adapted for preying on animals.
 The filamentous structure of the mycelium provides an extensive surface area that suits
the absorptive nutrition of fungi.
 One cubic centimeter of rich organic soil may contain 1 km of fungal hyphae with a
surface area of more than 300 cm2.
 A fungal mycelium grows rapidly.
 Proteins and other materials synthesized by the entire mycelium are channeled by
cytoplasmic streaming to the tips of the extending hyphae.
 The fungus concentrates its energy and resources on adding hyphal length and absorptive
surface area.
 While fungal mycelia are nonmotile, by swiftly extending the tips of its hyphae it can
extend into new territory.

Concept 31.2 Fungi produce spores through sexual or asexual life cycles
 Fungi reproduce by producing vast numbers of spores, either sexually or asexually.
 The output of spores from one reproductive structure can be enormous.
 Puffballs may release trillions of spores.
 Dispersed widely by wind or water, spores germinate to produce mycelia if they land in a
moist place where there is food.
Many fungi have a heterokaryotic stage.
 The nuclei of fungal hyphae and spores of most species are haploid, except for transient
diploid stages that form during sexual life cycles.
 Sexual reproduction in fungi begins when hyphae from two genetically distinct mycelia
release sexual signaling molecules called pheromones.
 Pheromones from each partner bind to receptors on the surface of the other.
 The union of the cytoplasm of the two parent mycelia is known as plasmogamy.
 In many fungi, the haploid nuclei do not fuse right away.
 In some species, heterokaryotic mycelia become mosaics, with different nuclei
remaining in separate parts of the same mycelium or mingling and even exchanging
chromosomes and genes.
 In some fungi, the haploid nuclei pair off two to a cell, one from each parent.
 Such a mycelium is called dikaryotic, meaning “two nuclei.”
Biology Chapter Notes
 In many fungi with sexual life cycles, karyogamy, fusion of haploid nuclei contributed by
two parents, occurs well after plasmogamy, cytoplasmic fusion of cells from the two
parents.
 The delay may be hours, days, or even centuries.
 During karyogamy, the haploid nuclei contributed by the two parents fuse, producing
diploid cells.
 In most fungi, the zygotes of transient structures formed by karyogamy are the only
diploid stage in the life cycle.
 These undergo meiosis to produce haploid cells that develop as spores in specialized
reproductive structures.
 These spores disperse to form new haploid mycelia.
 The sexual processes of karyogamy and meiosis generate genetic variation.
 The heterokaryotic condition also offers some of the advantages of diploidy, in that one
haploid genome may be able to compensate for harmful mutations in the other.
Many fungi reproduce asexually.
 The processes of asexual reproduction in fungi vary widely.
 Some species reproduce only asexually.
 Some fungi that can reproduce asexually grow as mold.
 Molds grow rapidly as mycelia and produce spores.
 Yeasts live in liquid or moist habitats.
 Instead of producing spores, yeasts reproduce asexually by simple cell division or by
budding of small cells.
 Most molds and yeasts have no known sexual stage.
 Such fungi are called deuteromycetes, or imperfect fungi.
 Whenever a sexual stage of a deuteromycete is discovered, the species is classified in a
particular phylum depending on its sexual structures.
 Fungi can be identified from their sexual stages and by new genetic techniques.

Concept 31.3 Fungi descended from an aquatic, single-celled, flagellated protist

 Data from paleontology and molecular systematics offer insights into the early evolution
of fungi.
 Systematists recognize Fungi and Animalia as sister kingdoms.
 Fungi and animals are more closely related to each other than they are to plants or
other eukaryotes.
Phylum Chytridiomycota: Chytrids may provide clues about fungal origins.
 Phylogenetic systematics suggests that fungi evolved from a unicellular, flagellated
protist.
 The lineages of fungi that diverged earliest (the chytrids) have flagella.
 Members of the clade Opisthokonta, including animals, fungi, and closely related
protists, possess flagella.
 This name refers to the posterior (opistho) location of the flagellum.

Biology Chapter Notes

 Scientists estimate that the ancestors of animals and fungi diverged into separate lineages
1.5 billion years ago.
 However, the oldest undisputed fungal structures are only 460 million years old.
 It is likely that the first fungi were unicellular and did not fossilize.
 Fungi underwent an adaptive radiation when life began to colonize land.
 Fossils of the first vascular plants from the Silurian period contain evidence of
mycorrhizae, symbiotic relationships between plants and subterranean fungi.

Concept 31.4 Fungi have radiated into a diverse set of lineages

 Fungi classified in the phylum Chytridiomycota, called the chytrids, are ubiquitous in
lakes, ponds, and soil.
 Some are saprobes, while others parasitize protists, plants, and animals.
 However, recent molecular evidence supports the hypothesis that chytrids diverged
earliest in fungal evolution.
 Like other fungi, chytrids use an absorptive mode of nutrition, have chitinous cell walls,
and have similar key enzymes and metabolic pathways.
 While there are a few unicellular chytrids, most form coenocytic hyphae.
 Chytrids are unique among fungi in having flagellated spores, called zoospores.
 Until recently, systematists thought that fungi lost flagella only once in their history, after
chytrids had diverged from other lineages.
 However, molecular data now indicates that some flagellated fungi are more closely
related to another fungal group, the zygomycetes.
 If this is true, flagella were lost on more than one occasion during fungal evolution.
Phylum Zygomycota: Zygote fungi form resistant structures during sexual reproduction.
 The 1,000 zygomycetes exhibit a considerable diversity of life history.
 The phylum includes fast-growing molds, parasites, and commensal symbionts.
 The life cycle and biology of Rhizopus stolonifer, black bread mold, is typical of
zygomycetes.
 The hyphae are coenocytic, with septa found only where reproductive cells are formed.
 Horizontal hyphae spread out over food, penetrate it, and digest nutrients.
 In the asexual phase, hundreds of haploid spores develop in sporangia at the tips of
upright hyphae.
 Some zygomycetes, such as Pilobolus, can actually aim their sporangia toward
conditions that would be favorable for their spores.
 If environmental conditions deteriorate, Rhizopus may reproduce sexually.
 Plasmogamy of opposite mating types produces a zygosporangium.
 Inside this multinucleate structure, the heterokaryotic nuclei fuse to form diploid nuclei
that undergo meiosis.
 The zygosporangia are resistant to freezing and drying.
 When conditions improve, the zygosporangia undergo meiosis and release haploid spores
that colonize new substrates.
Biology Chapter Notes
 Microsporidia are unicellular parasites.
 Microsporidia are unicellular parasites of animals and protists.
 They are often used in biological control of insect pests.
 Microsporidia lack conventional mitochondria, and represent something of a taxonomic
mystery.
 Some researchers suggest that they are an ancient, deep-branching eukaryotic lineage.
 Recent evidence suggests that they are highly derived parasites that may be related to
zygomycete fungi.
Glomeromycetes form mycorrhizae.
 Only 160 species of glomeromycetes have been identified.
 Nonetheless, they are an economically significant group.
 All glomeromycetes form symbiotic mycorrhizae with plant roots.
 Mycorrhizal fungi can deliver phosphate ions and other minerals to plants.
 In exchange, the plants supply the fungi with organic nutrients.
 There are several different types of mycorrhizal fungi.
 Ectomycorrhizal fungi form sheaths of hyphae over the surface of the plant root and
grow into the extracellular spaces of the root cortex.
 Endomycorrhizal fungi extend their hyphae through the root cell wall and into tubes
formed by invagination of the root cell membrane.
 Glomeromycetes all form a distinct type of endomycorrhizae called arbuscular
mycorrhizae.
 The tips of the hyphae that push into plant root cells branch into tiny treelike structures
known as arbuscles.
 Such symbiotic partnerships with glomeromycetes are present in 90% of all plants.
Phylum Ascomycota: Sac fungi produce sexual spores in saclike asci.
 Mycologists have described more than 32,000 species of ascomycetes, or sac fungi, from
a variety of marine, freshwater, and terrestrial habitats.
 Ascomycetes produce sexual spores in saclike asci and are called sac fungi.
 Most ascomycetes bear their sexual stages in fruiting bodies called ascocarps.
 They range in size and complexity from unicellular yeasts to elaborate cup fungi and
morels.
 Some are devastating plant pathogens.
 Many are important saprobes, particularly of plant material.
 About 40% of ascomycete species live with green algae or cyanobacteria in mutualistic
associations called lichens.
 Some ascomycetes form mycorrhizae with plants or live between mesophyll cells in
leaves where they may help protect the plant tissue from insects by releasing toxins.
 Ascomycetes reproduce asexually by producing enormous numbers of asexual spores,
which are usually dispersed by the wind.
 These naked spores, or conidia, develop in long chains or clusters at the tips of
specialized hyphae called conidiophores.

Biology Chapter Notes

 Ascomycetes are characterized by an extensive heterokaryotic stage during the formation
of ascocarps.
 Plasmogamy between two parental hyphae produces a heterokaryotic bulge called an
ascogonium.
 The coenocytic ascogonium extends hyphae that are partitioned by septa into dikaryotic
cells, each with two haploid nuclei representing two parents.
 The cells at the tip of these dikaryotic hyphae develop into asci.
 Within an ascus, karyogamy combines the two parental genomes, and meiosis forms four
genetically different nuclei forming eight ascospores.
 In many asci, the eight ascospores are lined up in a row in the order in which they
formed from a single zygote nucleus.
 One of the best-studied ascomycetes is Neurospora crassa, a bread mold.
 This ascomycete serves as a model organism.
 In 2003, its entire genome was published.
 With 10,000 genes, the genome of this tiny fungus is three-fourths the size of the
Drosophila genome and one-third the size of the human genome.
 The Neurospora genome is compact, with few stretches of noncoding DNA.
 Neurospora may have a genomic defense system to prevent “junk DNA” from
accumulating in its genome.
Phylum Basidiomycota: Club fungi have long-lived dikaryotic mycelia.
 Approximately 30,000 fungi, including mushrooms and shelf fungi, are called
basidiomycetes and are classified in the phylum Basidiomycota.
 The name of the phylum is derived from the basidium, a transient diploid stage.
 The clublike shape of the basidium is responsible for the common name club fungus.
 Basidiomycetes are important decomposers of wood and other plant materials.
 Of all fungi, the saprobic basidiomycetes are best at decomposing the complex
polymer lignin, abundant in wood.
 The life cycle of a club fungus usually includes a long-lived dikaryotic mycelium.
 Environmental cues, such as rain or temperature change, induce the dikaryotic mycelium
to reproduce sexually by producing elaborate fruiting bodies called basidiocarps.
 A mushroom is a familiar basidiocarp that can pop up overnight as it absorbs water and
as cytoplasm steams in from the dikaryotic mycelium.
 The dikaryotic mycelia are long-lived, generally producing a new crop of basidiocarps
each year.
 The cap of a mushroom supports and protects a large surface area of basidia on the gills.
 The basidia form sexual spores called basidiospores.
 A common white mushroom has a gill surface of about 200 cm2 and may release a
billion basidiospores, which drop from the cap and blow away.
 Asexual reproduction is much less common in basidiomycetes than in ascomycetes.

Concept 31.5 Fungi have a powerful impact on ecosystems and human welfare
Ecosystems depend on fungi as decomposers and symbionts.
Biology Chapter Notes
 Fungi are important decomposers of organic material, including cellulose and lignin of
plant cell walls.
 Fungi and bacteria are essential for providing ecosystems with the inorganic nutrients
responsible for plant growth.
 Without decomposers, carbon, nitrogen, and other elements would become tied up in
organic matter.
 Fungi form symbiotic relationships with plants, algae, and animals.
 Mycorrhizae are extremely important in natural ecosystems and agriculture.
 Almost all vascular plants have mycorrhizae and rely on their fungal partners for
essential nutrients.
 Some fungi break down plant material in the guts of cows and other grazers.
 Many species of ants and termites raise fungi in “farms” and feed them leaves.
 The fungi break the leaves down into a substance that the insects can digest.
 Some mutualistic associations between “farmer” insects and “farmed” fungi have been
established for more than 50 million years.
 In many cases, the fungi can no longer survive without the insects.
 Lichens are a symbiotic association of millions of photosynthetic microorganisms held in
a mesh of fungal hyphae.
 The fungal component is commonly an ascomycete, but several basidiomycete lichens are
known.
 The photosynthetic partners are usually unicellular or filamentous green algae or
cyanobacteria.
 The fungal hyphae provide most of the lichen’s mass and give it an overall shape and
structure.
 The algae or cyanobacteria usually occupy an inner layer below the lichen surface.
 The merger of fungus and algae is so complete that they are actually given genus and
species names, as though they were single organisms.
 More than 13,500 species of lichen have been described—a fifth of all known fungi.
 In most lichens, each partner provides things the other could not obtain on its own.
 For example, the alga provides the fungus with food by “leaking” carbohydrate from
their cells.
 The cyanobacteria provide organic nitrogen through nitrogen fixation.
 The fungus provides a suitable physical environment for growth, retaining water and
minerals, allowing for gas exchange, shading the algae or cyanobacteria from intense
sunlight with pigments, and deterring consumers with toxic compounds.
 The fungus also secretes acids, which aids in the uptake of minerals.
 The fungi of many lichens reproduce sexually by forming ascocarps or basidiocarps.
 Lichen algae reproduce independently by asexual cell division.
 Asexual reproduction of symbiotic units occurs either by fragmentation of the parental
lichen or by the formation of structures called soredia, small clusters of hyphae with
embedded algae.
 Phylogenetic studies of lichen DNA have helped illuminate the evolution of this
symbiosis.

Biology Chapter Notes

 Molecular studies published in 2001 support the hypothesis that all living lichens can be
traced to three original associations involving a fungus and a photosynthetic symbiont.
 The same studies also suggest that many free-living fungi, including Penicillium,
descended from lichen-forming ancestors.
 Lichens are important pioneers on newly cleared rock and soil surfaces, such as burned
forests and volcanic flows.
 The lichen acids penetrate the outer crystals of rocks and help break down the rock.
 This allows soil-trapping lichens to establish and starts the process of succession.
 Nitrogen-fixing lichens also add organic nitrogen to some ecosystems.
 Some lichens can survive severe cold or desiccation.
 In the arctic tundra, herds of caribou and reindeer graze on carpets of reindeer lichens
under the snow in winter.
 In dry habitats, lichens may absorb water quickly from fog or rain, gaining more than
ten times their mass in water.
 Lichens are particularly sensitive to air pollution, and their deaths can serve as an early
warning of deteriorating air quality.
Some fungi are pathogens.
 About 30% of the 100,000 known species of fungi are parasites, mostly on or in plants.
 Invasive ascomycetes have had drastic effects on forest trees such as American elms
and American chestnuts in the northeastern United States.
 Other fungi, such as rusts and ergots, infect grain crops, causing tremendous economic
losses each year.
 Fungi are also serious agricultural pests.
 Between 10% and 50% of the world’s fruit harvest is lost each year to fungal attack.
 Some fungi that attack food crops produce compounds that are harmful to humans.
 For example, the mold Aspergillus can contaminate improperly stored grains and
peanuts with aflatoxins, which are carcinogenic.
 Poisons produced by ergots of the ascomycete Claviceps purpurea can cause gangrene,
nervous spasms, burning sensations, hallucinations, and temporary insanity when
infected rye is milled into flour and consumed.
 One of the compounds to have been isolated from ergots is lysergic acid, the raw
material from which the hallucinogen LSD is made.
 Animals are much less susceptible to parasitic fungi than are plants.
 Only about 50 fungal species are known to parasitize humans and other animals, but
their damage can be disproportionate to their taxonomic diversity.
 The general term for a fungal infection is mycosis.
 Infections of ascomycetes produce the disease ringworm, known as athlete’s foot when
they grow on the feet.
 Systemic mycoses spread through the body and cause very serious illnesses.
 They are typically caused by inhaled spores.
 Coccidiodomycosis is a systemic mycosis that produces tuberculosis-like symptoms in
the lungs.
 It is so deadly that it is now considered a potential biological weapon.
 Some mycoses are opportunistic, occurring only when a change in the body’s
microbiology, chemistry, or immunology allows the fungi to grow unchecked.
Biology Chapter Notes
  Candida albicans is a normal inhabitant of moist epithelia such as human vaginal
lining, but it can become an opportunistic pathogen.
 Other opportunistic mycoses have become more common due to AIDS, which
weakens the immune system.
Fungi are commercially important.
 In addition to the benefits that we receive from fungi in their roles as decomposers and
recyclers of organic matter, we use fungi in a number of ways.
 Most people have eaten mushrooms, the fruiting bodies (basidiocarps) of subterranean
fungi.
 The fruiting bodies of certain mycorrhizal ascomycetes, truffles, are prized by
gourmets for their complex flavors.
 The distinctive flavors of certain cheeses come from the fungi used to ripen them.
 The ascomycete mold Aspergillus is used to produce citric acid for colas.
 Yeasts are even more important in food production.
 Yeasts are used in baking, brewing, and winemaking.
 The yeast Saccharomyces cerevisiae is the most important of all cultured fungi, and is
available in many strains as baker’s and brewer’s yeast.
 Contributing to medicine, some fungi produce antibiotics used to treat bacterial diseases.
 In fact, the first antibiotic discovered was penicillin, made by the common mold
Penicillium.
 A compound extracted from ergots is used to reduce high blood pressure and stop
maternal bleeding after childbirth.
 Fungi play an important role in molecular biology and biotechnology.
 Researchers use Saccharomyces to study the molecular genetics of eukaryotes.
 Scientists have learned about the genes involved in Parkinson’s and Huntington’s
diseases by examining the homologous genes in Saccharomyces.
 Genetically modified fungi are used to produce human glycoproteins.

Biology Chapter Notes

 Chapter 32 An Introduction to Animal Diversity
Chapter Notes

Overview: Welcome to Your Kingdom

 Biologists have identified 1.3 million living species of animals.

 Estimates of the total number of animal species run far higher, from 10 to 20 million to as
many as 100 to 200 million.

Concept 32.1 Animals are multicellular, heterotrophic eukaryotes with tissues that
develop from embryonic layers
 There are exceptions to nearly every criterion for distinguishing an animal from other life
forms.
 However, five criteria, taken together, comprise a reasonable definition.
o Animals are multicellular, ingestive heterotrophs.
 Animals take in preformed organic molecules through ingestion, eating other
organisms or organic material that is decomposing.
o Animal cells lack cell walls that provide structural support for plants and fungi.
 The multicellular bodies of animals are held together by extracellular structural
proteins, especially collagen.
 Animals have other unique types of intercellular junctions, including tight junctions,
desmosomes, and gap junctions, which hold tissues together.
 These junctions are also composed of structural proteins.
o Animals have two unique types of cells: nerve cells for impulse conduction and muscle
cells for movement.
o Most animals reproduce sexually, with the diploid stage usually dominating the life
cycle.
 In most species, a small flagellated sperm fertilizes a larger, nonmotile egg.
 The zygote undergoes cleavage, a succession of mitotic cell divisions, leading to the
formation of a multicellular, hollow ball of cells called the blastula.
 During gastrulation, part of the embryo folds inward, forming layers of embryonic
tissues that will develop into adult body parts.
 The resulting development stage is called a gastrula.
 Some animals develop directly through transient stages into adults, but others have a
distinct larval stage or stages.
 A larva is a sexually immature stage that is morphologically distinct from the adult,
usually eats different foods, and may live in a different habitat from the adult.
 Animal larvae eventually undergo metamorphosis, transforming the animal into an
adult.
o Animals share a unique homeobox-containing family of genes known as Hox genes.
 All eukaryotes have genes that regulate the expression of other genes.
 Many of these regulatory genes contain common modules of DNA sequences called
homeoboxes.
Biology Chapter Notes
  All animals share the unique family of Hox genes, suggesting that this gene family
arose in the eukaryotic lineage that gave rise to animals.
 Hox genes play important roles in the development of animal embryos, regulating the
expression of dozens or hundreds of other genes.
 Hox genes control cell division and differentiation, producing different
morphological features of animals.
 Hox genes in sponges regulate the formation of channels, the primary feature of
sponge morphology.
 In more complex animals, the Hox gene family underwent further duplication.
 In bilaterians, Hox genes regulate patterning of the anterior-posterior axis.
 The same conserved genetic network governs the development of a large range of
animals.

Concept 32.2 The history of animals may span more than a billion years
 Various studies suggest that animals began to diversify more than a billion years ago.
 Some calculations based on molecular clocks estimate that the ancestors of animals
diverged from the ancestors of fungi as much as 1.5 billion years ago.
 Similar studies suggest that the common ancestor of living animals lived 1.2 billion to 800
million years ago.
 The common ancestor was probably a colonial flagellated protist and may have resembled
modern choanoflagellates.
Neoproterozoic Era (1 billion–542 million years ago)
 Although molecular data indicates a much earlier origin of animals, the oldest generally
accepted animal fossils are only 575 million years old.
 These fossils are known as the Ediacara fauna, named for the Ediacara Hills of
Australia.
 Ediacara fauna consist primarily of cnidarians, but soft-bodied mollusks were also
present, and numerous fossilized burrows and tracks indicate the presence of worms.
Paleozoic Era (542–251 million years ago)
 Animals underwent considerable diversification between 542–525 million years ago,
during the Cambrian period of the Paleozoic Era.
 During this period, known as the Cambrian explosion, about half of extant animal
phyla arose.
 Fossils of Cambrian animals include the first animals with hard, mineralized skeletons.
 There are several hypotheses regarding the cause of the Cambrian explosion.
o The new predator-prey relationships that emerged in the Cambrian may have generated
diversity through natural selection.
 Predators acquired adaptations that helped them catch prey.
 Prey acquired adaptations that helped them resist predation.
o A rise of atmospheric oxygen preceded the Cambrian explosion.
 More oxygen may have provided opportunities for animals with higher metabolic rates
and larger body sizes.
o The evolution of the Hox complex provided the developmental flexibility that resulted
in variations in morphology.
Biology Chapter Notes
  These hypotheses are not mutually exclusive; all may have played a role.
 In the Silurian and Devonian periods, animal diversity continued to increase, punctuated
by episodes of mass extinction.
 Vertebrates (fishes) became the top predators of marine food webs.
 By 460 million years ago, arthropods began to adapt to terrestrial habitats.
 Vertebrates moved to land about 360 million years ago and diversified into many
lineages.
 Two of these survive today: amphibians and amniotes.
Mesozoic Era (251–65.5 million years ago)
 Few new animal body plans emerged among animals during the Mesozoic era.
 Animal phyla began to spread into new ecological niches.
 In the oceans, the first coral reefs formed.
 On land, birds, pterosaurs, dinosaurs, and tiny nocturnal insect-eating mammals arose.
Cenozoic Era (65.5 million years ago to the present)
 Insects and flowering plants both underwent a dramatic diversification during the
Cenozoic era.
 This era began with mass extinctions of terrestrial and marine animals.
 Among the groups of species that disappeared were large, nonflying dinosaurs and the
marine reptiles.
 Large mammalian herbivores and carnivores diversified as mammals exploited vacated
ecological niches.
 Some primate species in Africa adapted to open woodlands and savannas as global
climates cooled.
 Our ancestors were among these grassland apes.

Concept 32.3 Animals can be characterized by “body plans”

 Zoologists may categorize the diversity of animals by general features of morphology and
development.
 A group of animal species that share the same level of organizational complexity is called
a grade.
 Certain body-plan features shared by a group of animals define a grade.
o Animals can be categorized according to the symmetry of their bodies.
 Sponges lack symmetry.
 Some animals, such as sea anemones, have radial symmetry.
 Many animals have bilateral symmetry.
 A bilateral animal has a dorsal (top) side and a ventral (bottom side), a left and
right side, and an anterior (head) end and a posterior (tail) end.
 Linked with bilateral symmetry is cephalization, an evolutionary trend toward the
concentration of sensory equipment on the anterior end.
 Cephalization also includes the development of a central nervous system
concentrated in the head and extending toward the tail as a longitudinal nerve cord.
 The symmetry of an animal generally fits its lifestyle.
Biology Chapter Notes
  Many radial animals are sessile or planktonic and need to meet the environment
equally well from all sides.
 Animals that move actively are generally bilateral.
 Their central nervous system allows them to coordinate complex movements
involved in crawling, burrowing, flying, and swimming.
o The animal body plans also vary according to the organization of the animal’s tissues.
 True tissues are collections of specialized cells isolated from other tissues.
 Sponges lack true tissues.
 In all other animals, the embryo becomes layered through the process of
gastrulation.
 As development progresses, germ layers, concentric layers of embryonic tissue, form
various tissues and organs.
 Ectoderm, covering the surface of the embryo, gives rise to the outer covering and,
in some phyla, to the central nervous system.
 Endoderm, the innermost layer, lines the developing digestive tube, or
archenteron, and gives rise to the lining of the digestive tract and the organs
derived from it, such as the liver and lungs of vertebrates.
 Animals with only two germ layers, such as cnidarians, are diploblastic.
 Other animals are triploblastic and have three germ layers.
 In these animals, a third germ layer, the mesoderm, lies between the endoderm and
ectoderm.
 The mesoderm develops into the muscles and most other organs between the
digestive tube and the outer covering of the animal.
o The Bilateria can be divided by the presence or absence of a body cavity (a fluid-filled
space separating the digestive tract from the outer body wall) known as a coelom and
by the structure of the body cavity.
 A true coelom forms from tissue derived from mesoderm.
 The inner and outer layers of tissue that surround the coelom connect dorsally and
ventrally and form mesenteries that suspend the internal organs.
 Animals that possess a true coelom are known as coelomates.
 Some triploblastic animals have a cavity formed from blastocoel, rather than
mesoderm. Such a cavity is a “pseudocoel” and animals that have one are called
pseudocoelomates.
 Some animals lack a coelom. These animals are known as acoelomates, and have a
solid body without a body cavity.
 A body cavity has many functions.
 Its fluid cushions the internal organs, helping to prevent internal injury.
 The noncompressible fluid of the body cavity can function as a hydrostatic skeleton
against which muscles can work.
 The presence of a cavity enables the internal organs to grow and move
independently of the outer body wall.
 Current research suggests that true coeloms and pseudocoels have evolved many
times in the course of animal evolution.
 Thus, the terms coelomate and pseudocoelomate refer to grades, not clades.
o Most animals can be categorized as having one of two developmental modes:
protostome development or deuterostome development.
 The differences between these modes of development center on cleavage pattern,
coelom formation, and blastopore fate.
Biology Chapter Notes
  Many protostomes undergo spiral cleavage, in which planes of cell division are
diagonal to the vertical axis of the embryo.
 Some protostomes also show determinate cleavage, where the fate of each
embryonic cell is determined early in development.
 Many deuterostomes undergo radial cleavage in which the cleavage planes are parallel
or perpendicular to the vertical egg axis.
 Most deuterostomes show indeterminate cleavage, whereby each cell in the early
embryo retains the capacity to develop into a complete embryo.
 In gastrulation, the developing digestive tube of an embryo initially forms as a blind
pouch, the archenteron.
 As the archenteron forms in a protostome, solid masses of mesoderm split to form the
coelomic cavities, in a pattern called schizocoelous development.
 In deuterostomes, mesoderm buds off from the wall of the archenteron and hollows to
become the coelomic cavities, in a pattern called enterocoelous development.
 The third difference centers on the fate of the blastopore, the opening of the archenteron.
 In many protostomes, the blastopore develops into the mouth, and a second opening at
the opposite end of the gastrula develops into the anus.
 In deuterostomes, the blastopore usually develops into the anus, and the mouth is
derived from the secondary opening.

Concept 32.4 Leading hypotheses agree on major features of the animal phylogenetic
tree
 Zoologists currently recognize about 35 animal phyla.
 The relationships between these phyla continue to be debated.
 Traditionally, zoologists have tested hypotheses about animal phylogeny through
morphological studies.
 Currently, zoologists also study the molecular systematics of animals.
 New studies of lesser-known phyla and fossil analyses help distinguish between ancestral
and derived traits in various animal groups.
 Modern phylogenetic systematics is based on the identification of clades, monophyletic
sets of taxa defined by shared derived features unique to those taxa and their common
ancestor.
 This creates a phylogenetic tree that is a hierarchy of clades nested within larger
clades.
 Defining the shared derived characteristics is key to a particular hypothesis.
 Whether the data are “traditional” morphological characters, “new” molecular
sequences, or some combination of the two, the assumptions and inferences inherent in
the tree are the same.
 Two current phylogenetic hypotheses can be compared: one based on systematic analyses
of morphological characters and the other based on recent molecular studies.
 The hypotheses agree on the following major features of animal phylogeny.
o All animals share a common ancestor.

Biology Chapter Notes

  Both trees indicate that the animal kingdom is monophyletic, representing a clade
called Metazoa.
o Sponges are basal animals.
 Sponges branch from the base of both animal trees.
 They exhibit a parazoan grade of organization, without tissues.
 Recent molecular analyses suggest that sponges are paraphyletic.
o Eumetazoa is a clade of animals with true tissues.
 All animals except sponges belong to a clade of eumetazoans.
 The common ancestor of living eumetazoans acquired true tissues.
o Most animal phyla belong to the clade Bilateria.
 Bilateral symmetry is a shared derived character that helps to define a clade called the
bilaterians.
o Vertebrates and some other phyla belong to the clade Deuterostomia.
 The name deuterostome refers to an animal development grade and also to a clade that
includes vertebrates.
 The hypotheses also disagree on some significant points, including the relationships
among the bilaterians.
 The morphology-based tree divides the bilaterians into two clades: deuterostomes and
protostomes.
 This assumes that these two modes of development reflect a phylogenetic pattern.
 The molecular evidence assigns two sister taxa to the protostomes: the ecdysozoans and
the lophotrochozoans.
 The name Ecdysozoa (nematodes, arthropods, and other phyla) refers to animals that
secrete external skeletons (exoskeleton).
 As the animal grows, it molts the old exoskeleton and secretes a new, larger one, a
process called ecdysis.
 While named for this process, the clade is actually defined mainly by molecular
evidence.
 The name Lophotrochozoa refers to two characteristic features of animals in this clade.
 Some animals, such as ectoprocts, develop a lophophore, a horseshoe-shaped crown
of ciliated tentacles used for feeding.
 Other phyla, including annelids and mollusks, have a distinctive larval stage called a
trochophore larva.
 Animal systematics continues to evolve.
 Systematists are now conducting large-scale analyses of multiple genes across a wide
range of animal phyla, in an effort to gain a clearer picture of how the diversity of animal
body plans arose.

Biology Chapter Notes

 Chapter 33 Invertebrates
Chapter Notes

Overview: Life Without a Backbone

 Invertebrates—animals without a backbone—account for 95% of known animal species

and all but one of the roughly 35 animal phyla that have been described.
 More than a million extant species of animals are known, and at least as many more
will probably be identified by future biologists.
 Invertebrates inhabit nearly all environments on Earth, from the scalding water of deep-
sea hydrothermal vents to the rocky, frozen ground of Antarctica.

Concept 33.1 Sponges are sessile and have a porous body and choanocytes
 Sponges (phylum Porifera) are so sedentary that they were mistaken for plants by the
early Greeks.
 Living in freshwater and marine environments, sponges are suspension feeders.
 The body of a simple sponge resembles a sac perforated with holes.
 Water is drawn through the pores into a central cavity, the spongocoel, and flows out
through a larger opening, the osculum.
 More complex sponges have folded body walls, and many contain branched water
canals and several oscula.
 Sponges range in height from about a few mm to 2 m and most are marine.
 About 100 species live in fresh water.
 Unlike eumetazoa, sponges lack true issues, groups of similar cells that form a functional
unit.
 The germ layers of sponges are loose federations of cells, which are not really tissues
because the cells are relatively unspecialized.
 The sponge body does contain different cell types.
 Sponges collect food particles from water passing through food-trapping equipment.
 Flagellated choanocytes, or collar cells, lining the spongocoel (internal water
chambers) create a flow of water through the sponge with their flagella and trap food
with their collars.
 Based on both molecular evidence and the morphology of their choanocytes, sponges
evolved from a colonial choanoflagellate ancestor.
 The body of a sponge consists of two cell layers separated by a gelatinous region, the
mesohyl.
 Wandering though the mesohyl are amoebocytes.
 They take up food from water and from choanocytes, digest it, and carry nutrients to
other cells.
 They also secrete tough skeletal fibers within the mesohyl.
 In some groups of sponges, these fibers are sharp spicules of calcium carbonate or
silica.
Biology Chapter Notes
  Other sponges produce more flexible fibers from a collagen protein called spongin.
 We use these pliant, honeycombed skeletons as bath sponges.

 Most sponges are sequential hermaphrodites, with each individual producing both sperm
and eggs in sequence.
 Gametes arise from choanocytes or amoebocytes.
 The eggs are retained, but sperm are carried out the osculum by the water current.
 Sperm are drawn into neighboring individuals and fertilize eggs in the mesohyl.
 The zygotes develop into flagellated, swimming larvae that disperse from the parent.
 When a larva finds a suitable substratum, it develops into a sessile adult.
 Sponges produce a variety of antibiotics and other defensive compounds.
 Researchers are now isolating these compounds, which may be useful in fighting
human disease.

Concept 33.2 Cnidarians have radial symmetry, a gastrovascular cavity, and cnidocytes
 All animals except sponges belong to the Eumetazoa, the animals with true tissues.
 The cnidarians (hydras, jellies, sea anemones, and coral animals) have a relatively simple
body construction.
 They are a diverse group with more than 10,000 living species, most of which are
marine.
 They exhibit a relatively simple, diploblastic body plan that arose 570 million years
ago.
 The basic cnidarian body plan is a sac with a central digestive compartment, the
gastrovascular cavity.
 A single opening to this cavity functions as both mouth and anus.
 This basic body plan has two variations: the sessile polyp and the floating medusa.
 The cylindrical polyps, such as hydras and sea anemones, adhere to the substratum by the
aboral end and extend their tentacles, waiting for prey.
 Medusas (also called jellies) are flattened, mouth-down versions of polyps that move by
drifting passively and by contracting their bell-shaped bodies.
 The tentacles of a jelly dangle from the oral surface.
 Some cnidarians exist only as polyps.
 Others exist only as medusas.
 Still others pass sequentially through both a medusa stage and a polyp stage in their
life cycle.
 Cnidarians are carnivores that use tentacles arranged in a ring around the mouth to capture
prey and push the food into the gastrovascular chamber for digestion.
 Batteries of cnidocytes on the tentacles defend the animal or capture prey.
 Organelles called cnidae evert a thread that can inject poison into the prey, or stick
to or entangle the target.
 Cnidae called nematocysts are stinging capsules.
 Muscles and nerves exist in their simplest forms in cnidarians.
 Cells of the epidermis and gastrodermis have bundles of microfilaments arranged into
contractile fibers.
Biology Chapter Notes
  True muscle tissue appears first in triploblastic animals.
 When the animal closes its mouth, the gastrovascular cavity acts as a hydrostatic
skeleton against which the contractile cells can work.
 Movements are controlled by a noncentralized nerve net associated with simple sensory
receptors that are distributed radially around the body.
 The phylum Cnidaria is divided into four major classes: Hydrozoa, Scyphozoa, Cubozoa,
and Anthozoa.
 The four cnidarian classes show variations on the same body theme of polyp and medusa.
 Most hydrozoans alternate polyp and medusa forms, as in the life cycle of Obelia.
 The polyp stage, often a colony of interconnected polyps, is more conspicuous than the
medusa.
 Hydras, among the few freshwater cnidarians, are unusual members of the class Hydrozoa
in that they exist only in the polyp form.
 When environmental conditions are favorable, a hydra reproduces asexually by
budding, the formation of outgrowths that pinch off from the parent to live
independently.
 When environmental conditions deteriorate, hydras form resistant zygotes that remain
dormant until conditions improve.
 The medusa generally prevails in the life cycle of class Scyphozoa.
 The medusae of most species live among the plankton as jellies.
 Most coastal scyphozoans go through small polyp stages during their life cycle.
 Jellies that live in the open ocean generally lack the sessile polyp.
 Cubozoans have a box-shaped medusa stage.
 They can be distinguished from scyphozoans in other significant ways, such as having
complex eyes in the fringe of the medusae.
 Cubozoans, which generally live in tropical oceans, are often equipped with highly toxic
cnidocytes.
 Sea anemones and corals belong to the class Anthozoa.
 They occur only as polyps.
 Coral animals live as solitary or colonial forms and secrete a hard external skeleton of
calcium carbonate.
 Each polyp generation builds on the skeletal remains of earlier generations to form
skeletons that we call coral.
 In tropical seas, coral reefs provide habitat for a great diversity of invertebrates and fishes.
 Coral reefs in many parts of the world are currently being destroyed by human activity.
 Pollution, overfishing, and global warming are contributing to their demise.

Concept 33.3 Most animals have bilateral symmetry

 The vast majority of animal species belong to the clade Bilateria, which consists of
animals with bilateral symmetry and triploblastic development.
 Most bilaterians are also coelomates.
 The most recent common ancestor of living bilaterians probably lived in the later
Proterozoic.
Biology Chapter Notes
 During the Cambrian explosion, most major groups of bilaterians emerged.
Phylum Platyhelminthes: Flatworms are acoelomates with gastrovascular cavities.
 Flatworms live in marine, freshwater, and damp terrestrial habitats.
 They also include many parasitic species, such as the flukes and tapeworms.
 Flatworms have thin bodies, ranging in size from nearly microscopic to tapeworms more
than 20 m long.
 Flatworms and other bilaterians are triploblastic, with a middle embryonic tissue layer, a
mesoderm, which contributes to more complex organs and organ systems and to true
muscle tissue.
 While flatworms are structurally more complex than cnidarians, they are simpler than
other bilaterians.
 Like cnidarians, flatworms have a gastrovascular cavity with only one opening (and
tapeworms lack a digestive system entirely and absorb nutrients across their body
surface).
 Unlike other bilaterians, flatworms lack a coelom.
 The flat shape of a flatworm places all cells close to the surrounding water, enabling gas
exchange and the elimination of nitrogenous wastes (ammonia) by diffusion across the
body surface.
 Flatworms have no specialized organs for gas exchange and circulation, and their
relatively simple excretory apparatus functions mainly to maintain osmotic balance.
 This apparatus consists of ciliated cells called flame bulbs that waft fluid through
branched ducts that open to the outside.
 Flatworms are divided into four classes: Turbellaria, Monogenia, Trematoda, and
Cestoidea.
 Turbellarians are nearly all free-living (nonparasitic) and most are marine.
 Planarians, members of the genus Dugesia, are carnivores or scavengers in unpolluted
ponds and streams.
 Planarians move using cilia on the ventral epidermis, gliding along a film of mucus they
secrete.
 Some turbellarians use muscles for undulatory swimming.
 A planarian has a head with a pair of eyespots to detect light, and lateral flaps that
function mainly for smell.
 The planarian nervous system is more complex and centralized than the nerve net of
cnidarians.
 Planarians can learn to modify their responses to stimuli.
 Planarians reproduce asexually through regeneration.
 The parent constricts in the middle, and each half regenerates the missing end.
 Planarians can also reproduce sexually.
 These hermaphrodites cross-fertilize.
 The monogeneans (class Monogenea) and the trematodes (class Trematoda) live as
parasites in or on other animals.
 Many have suckers for attachment to their host.
 A tough covering protects the parasites.
 Reproductive organs nearly fill the interior of these worms.
Biology Chapter Notes
 Trematodes parasitize a wide range of hosts, and most species have complex life cycles
with alternation of sexual and asexual stages.
 Many require an intermediate host in which the larvae develop before infecting the
final hosts (usually a vertebrate) where the adult worm lives.
 The blood fluke Schistosoma infects 200 million people, leading to body pains and
dysentery.
 The intermediate host for Schistosoma is a snail.
 Living within different hosts puts demands on trematodes that free-living animals do not
face.
 A blood fluke must evade the immune systems of two very different hosts.
 By mimicking their host’s surface proteins, blood flukes create a partial
immunological camouflage.
 They also release molecules that manipulate the host’s immune system.
 These defenses are so effective that individual flukes can survive in a human host for
more than 40 years.
 Most monogeneans are external parasites of fishes.
 Their life cycles are simple, with a ciliated, free-living larva that starts an infection on
a host.
 While traditionally aligned with trematodes, some structural and chemical evidence
suggests that they are more closely related to tapeworms.
 Tapeworms (class Cestoidea) are also parasitic.
 The adults live mostly in vertebrates, including humans.
 Suckers and hooks on the head, or scolex, anchor the worm in the digestive tract of the
host.
 Tapeworms lack a gastrovascular cavity and absorb food particles from their hosts.
 A long series of proglottids, sacs of sex organs, lie posterior to the scolex.
 Mature proglottids, loaded with thousands of eggs, are released from the posterior end
of the tapeworm and leave with the host’s feces.
 In one type of cycle, tapeworm eggs in contaminated food or water are ingested by
intermediary hosts, such as pigs or cattle.
 The eggs develop into larvae that encyst in the muscles of their host.
 Humans acquire the larvae by eating undercooked meat contaminated with cysts.
 The larvae develop into mature adults within the human.
Phylum Rotifera: Rotifers are pseudocoelomates with jaws, crowns of cilia, and complete
digestive tracts.
 Rotifers are tiny animals (5 µm to 2 mm), most of which live in freshwater.
 Some live in the sea or in damp soil.
 Rotifers are smaller than many protists but are truly multicellular, with specialized organ
systems.
 Rotifers have an alimentary canal, a digestive tract with a separate mouth and anus.
 Internal organs lie in the pseudocoelom, a body cavity that is not completely lined with
mesoderm.
 The fluid in the pseudocoelom serves as a hydrostatic skeleton.
 Through the movements of nutrients and wastes dissolved in the coelomic fluid, the
pseudocoelom also functions as a circulatory system.
Biology Chapter Notes
 The word rotifer, “wheel-bearer,” refers to the crown of cilia that draws a vortex of water
into the mouth.
 Food particles drawn in by the cilia are captured by the jaws (trophi) in the pharynx
and ground up.
 Some rotifers exist only as females that produce more females from unfertilized eggs, a
type of parthenogenesis.
 Other species produce two types of eggs that develop by parthenogenesis.
 One type forms females, and the other forms degenerate males that survive just long
enough to fertilize eggs.
 The zygote forms a resistant stage that can withstand environmental extremes until
conditions improve.
 The zygote then begins a new female generation that reproduces by parthenogenesis
until conditions become unfavorable again.
 It is puzzling that so many rotifers survive without males.
 The vast majority of animals and plants reproduce sexually at least some of the time,
and sexual reproduction has certain advantages over asexual reproduction.
 For example, species that reproduce asexually tend to accumulate harmful mutations in
their genomes faster than sexually reproducing species.
 As a result, asexual species experience higher rates of extinction and lower rates of
speciation.
 A class of asexual rotifers called Bdelloidea consists of 360 species that all reproduce by
parthenogenesis without males.
 Thirty-five-million-year-old bdelloid rotifers have been found preserved in amber.
 The morphology of these fossils resembles the female form.
 DNA comparisons of bdelloids with their closest sexually reproducing rotifer relatives
suggest that bdelloids have been asexual for far more than 35 million years.
 Bdelloid rotifers raise interesting questions about the evolution of sex.
The lophophorate phyla: ectoprocts, phoronids, and brachiopods are coelomates with
ciliated tentacles around their mouths.
 Bilaterians in three phyla—Ectoprocta, Phoronida, and Brachiopoda—are traditionally
called lophophorate animals because they all have a lophophore.
 The lophophore is a horseshoe-shaped or circular fold of the body wall bearing ciliated
tentacles that surround and draw water toward the mouth.
 The tentacles trap suspended food particles.
 In addition to the lophophore, these three phyla share a U-shaped digestive tract and the
absence of a head.
 These may be adaptations to a sessile existence.
 In contrast to flatworms, which lack a body cavity, and rotifers, which have a
pseudocoelom, lophophorates have true coeloms completely lined with mesoderm.
 Ectoprocts are colonial animals that superficially resemble plants.
 In most species, the colony is encased in a hard exoskeleton.
 The lophophores extend through pores in the exoskeleton.
 Most ectoprocts are marine, where they are widespread and numerous sessile animals,
with several species that can be important reef builders.
 Ectoprocts also live in lakes and rivers.
Biology Chapter Notes
 Phoronids are tube-dwelling marine worms ranging from 1 mm to 50 cm in length.
 Some live buried in the sand within chitinous tubes.
 They extend the lophophore from the tube when feeding and pull it back in when
threatened.
 Brachiopods, or lampshells, superficially resemble clams and other bivalve molluscs.
 However, the two halves of the brachiopod are dorsal and ventral to the animal, rather
than lateral as in clams.
 All brachiopods are marine.
 Most live attached to the substratum by a stalk, opening their shell slightly to allow
water to flow over the lophophore.
 The living brachiopods are remnants of a richer past.
 Thirty thousand species of brachiopod fossils have been described from the Paleozoic
and Mesozoic eras.
Phylum Nemertea: Proboscis worms are named for their prey-capturing apparatus.
 The members of the Phylum Nemertea, proboscis worms or ribbon worms, have bodies
much like those of flatworms.
 However, they have a small fluid-filled sac that may be a reduced version of a true
coelom.
 The sac and fluid hydraulics operate an extensible proboscis, which the worm uses to
capture prey.
 Nemerteans range in length from less than 1 mm to several meters.
 Nearly all nemerteans are marine, but a few species inhabit fresh water or damp soil.
 Some are active swimmers, and others burrow into the sand.
 Nemerteans and flatworms have similar excretory, sensory, and nervous systems.
 However, nemerteans have an alimentary canal and a closed circulatory system in which
the blood is contained in vessels.
 Nemerteans have no heart, and the blood is propelled by muscles squeezing the
vessels.

Concept 33.4 Molluscs have a muscular foot, a visceral mass, and a mantle
 The phylum Mollusca includes many diverse forms, including snails and slugs, oysters
and clams, and octopuses and squids.
 Most molluscs are marine, though some inhabit fresh water, and some snails and slugs
live on land.
 Molluscs are soft-bodied animals, but most are protected by a hard shell of calcium
carbonate.
 Slugs, squids, and octopuses have reduced or lost their shells completely during their
evolution.
 Despite their apparent differences, all molluscs have a similar body plan with a muscular
foot (typically for locomotion), a visceral mass with most of the internal organs, and a
mantle.
 The mantle, which secretes the shell, drapes over the visceral mass and creates a water-
filled chamber, the mantle cavity, with gills, anus, and excretory pores.
Biology Chapter Notes
  Many molluscs feed by using a straplike rasping organ, a radula, to scrape up food.
 Most molluscs have separate sexes, with gonads located in the visceral mass.
 However, many snails are hermaphrodites.
 The life cycle of many marine molluscs includes a ciliated larva, the trochophore.
 This larva is also found in marine annelids (segmented worms) and some other
lophotrochozoans.
 The basic molluscan body plan has evolved in various ways in the eight classes of the
phylum.
 The four most prominent are the Polyplacophora (chitons), Gastropoda (snails and
slugs), Bivalvia (clams, oysters, and other bivalves), and Cephalopoda (squids,
octopuses, cuttlefish, and chambered nautiluses).
 Chitons are marine animals with oval shapes and shells divided into eight dorsal plates.
 The chiton body is unsegmented.
 Chitons use their muscular foot to grip the rocky substrate tightly and to creep slowly over
the rock surface.
 Chitons are grazers that use their radulas to scrape and ingest algae.
 Almost three-quarters of all living species of molluscs are gastropods.
 Most gastropods are marine, but there are also many freshwater species.
 Garden snails and slugs have adapted to land.
 During embryonic development, gastropods undergo torsion in which the visceral mass is
rotated up to 180 degrees, so the anus and mantle cavity are above the head in adults.
 After torsion, some of the organs that were bilateral are reduced or lost on one side of
the body.
 Most gastropods are protected by single, spiral shells into which the animals can retreat if
threatened.
 Torsion and formation of the coiled shell are independent developmental processes.
 While gastropod shells are typically conical, those of abalones and limpets are somewhat
flattened.
 Many gastropods have distinct heads with eyes at the tips of tentacles.
 They move by a rippling motion of their foot or by means of cilia.
 Most gastropods use their radula to graze on algae or plant material.
 Some species are predators.
 In these species, the radula is modified to bore holes in the shells of other organisms or
to tear apart tough animal tissues.
 In the tropical marine cone snails, teeth on the radula form separate poison darts,
which penetrate and stun their prey, including fishes.
 In place of the gills found in most aquatic gastropods, the lining of the mantle cavity of
terrestrial snails functions as a lung.
 The class Bivalvia includes clams, oysters, mussels, and scallops.
 Bivalves have shells divided into two halves.
 The two parts are hinged at the mid-dorsal line, and powerful adductor muscles close
the shell tightly to protect the animal.
 Bivalves have no distinct head, and the radula has been lost.
Biology Chapter Notes
  Some bivalves have eyes and sensory tentacles along the outer edge of the mantle.
 The mantle cavity of a bivalve contains gills that are used for feeding and gas exchange.
 Most bivalves are suspension feeders, trapping fine particles in mucus that coats the gills.
 Cilia convey the particles to the mouth.
 Water flows into the mantle cavity via the incurrent siphon, passes over the gills, and
exits via the excurrent siphon.
 Most bivalves live rather sedentary lives, a characteristic suited to suspension feeding.
 Sessile mussels secrete strong threads that tether them to rocks, docks, boats, and the
shells of other animals.
 Clams can pull themselves into the sand or mud, using the muscular foot as an anchor.
 Scallops can swim in short bursts to avoid predators by flapping their shells and jetting
water out their mantle cavity.
 Cephalopods are active predators that use rapid movements to dart toward their prey,
which they capture with several long tentacles.
 Squids and octopuses use beak-like jaws to bite their prey and then inject poison to
immobilize the victim.
 A mantle covers the visceral mass, but the shell is reduced and internal in squids, missing
in many octopuses, and exists externally only in chambered nautiluses.
 Fast movements by a squid occur when it contracts its mantle cavity and fires a stream of
water through the excurrent siphon.
 By pointing the siphon in different directions, the squid can rapidly move in different
directions.
 The foot of a cephalopod has been modified into the muscular siphon and parts of the
tentacles and head.
 Cephalopods are the only molluscs with a closed circulatory system.
 They also have well-developed sense organs and a complex brain.
 The ancestors of octopuses and squid were probably shelled molluscs that took up a
predatory lifestyle.
 Shelled cephalopods called ammonites were the dominant invertebrate predators of the
seas for hundreds of millions of years until their disappearance in the mass extinctions at
the end of the Cretaceous period.
 Most squid are less than 75 cm long.
 In 2003, a squid with a mantle 2.5 meters long was captured near Antarctica.
 The specimen was possibly a juvenile, only half the size of an adult.
 Large squid are thought to feed on large fish in the deep ocean, where sperm whales
are their only natural predators.

Concept 33.5 Annelids are segmented worms

 All annelids (“little rings”) have segmented bodies.
 They range in length from less than 1 mm to 3 m for the giant Australian earthworm.
 Annelids live in the sea, most freshwater habitats, and damp soil.
 The phylum Annelida is divided into three classes: Oligochaeta (earthworms), Polychaeta
(polychaetes), and Hirudinea (leeches).
Biology Chapter Notes
 Oligochaetes are named for their relatively sparse chaetae, or bristles made of chitin.
 This class of segmented worms includes the earthworms and a variety of aquatic species.
 Earthworms eat their way through soil, extracting nutrients as the soil passes through the
alimentary canal.
 Undigested material is egested as castings.
 Earthworms till the soil, enriching it with their castings.
 Earthworms are cross-fertilizing hermaphrodites.
 Two earthworms exchange sperm and then separate.
 The received sperm are stored while a special organ, the clitellum, secretes a mucous
cocoon.
 As the cocoon slides along the body, it picks up eggs and stored sperm and slides off
the body into the soil.
 Some earthworms can also reproduce asexually by fragmentation followed by
regeneration.
 Each segment of a polychaete (“many setae”) has a pair of paddlelike or ridgelike
parapodia (“almost feet”) that function in locomotion.
 Each parapodium has several chitinous setae.
 In many polychaetes, the rich blood vessels in the parapodia function as gills.
 Most polychaetes are marine.
 Many crawl on or burrow in the seafloor, while a few drift and swim in the plankton.
 Some live in tubes that the worms make by mixing mucus with sand and broken shells.
Others construct tubes from their own secretions.
 The majority of leeches inhabit fresh water, but land leeches move through moist
vegetation.
 Leeches range in size from about 1 to 30 cm.
 Many leeches feed on other invertebrates, but some blood-sucking parasites feed by
attaching temporarily to other animals, including humans.
 Some parasitic species use blade-like jaws to slit the host’s skin, while others secrete
enzymes that digest a hole through the skin.
 The host is usually unaware of the attack because the leech secretes an anesthetic.
 The leech also secretes hirudin, an anticoagulant, into the wound, allowing the leech to
suck as much blood as it can hold.
 Until the 20th century, leeches were frequently used by physicians for bloodletting.
 Leeches are still used to drain blood that accumulates in tissues following injury or
surgery.
 Researchers are also investigating the potential use of hirudin to dissolve unwanted
blood clots from surgery or heart disease.
 A recombinant form of hirudin has been developed and is in clinical trials.

Concept 33.6 Nematodes are nonsegmented pseudocoelomates covered by a tough

cuticle
 Roundworms are found in most aquatic habitats, wet soil, moist tissues of plants, and the
body fluids and tissues of animals.

Biology Chapter Notes

 They range in size from less than 1 mm to more than a meter.
 The cylindrical bodies of roundworms are covered with a tough exoskeleton, the cuticle.
 As the worm grows, it periodically sheds its old cuticle and secretes a new, larger one.
 They have an alimentary tract and use the fluid in their pseudocoelom to transport
nutrients since they lack a circulatory system.
 Their thrashing motion is due to contraction of longitudinal muscles.
 Nematodes usually reproduce sexually.
 The sexes are separate in most species, and fertilization is internal.
 Females may lay 100,000 or more fertilized eggs per day.
 The zygotes of most nematodes are resistant cells that can survive harsh conditions.
 Abundant, free-living nematodes live in moist soil and in decomposing organic matter on
the bottom of lakes and oceans.
 There are 25,000 described species, and perhaps ten times that number actually exist.
 If nothing but nematodes remained, it has been said, they would still preserve the
outline of the planet and many of its features.
 They play a major role in decomposition and nutrient recycling.
 The soil nematode, Caenorhabditis elegans, has become a model organism in
developmental biology.
 The nematodes include many species that are important agricultural pests that attack plant
roots.
 Other species parasitize animals.
 More than 50 nematode species, including various pinworms and hookworms,
parasitize humans.
 Trichinella spiralis causes trichinosis when the nematode worms encyst in a variety of
human organs, including skeletal muscle.
 They are acquired by eating undercooked meat that has juvenile worms encysted in the
muscle tissue.
 Parasitic nematodes are able to hijack some of the cellular functions of their hosts.
 Plant-parasitic nematodes produce molecules that induce the development of root cells
that provide nutrients to the parasites.
 Trichenella in human muscle cells controls the expression of muscle cell genes that
code for proteins that make the cell elastic enough to house the nematode.
 The muscle cell also releases signals to attract blood vessels, supplying the
nematode with nutrients.

Concept 33.7 Arthropods are segmented coelomates that have an exoskeleton and
jointed appendages
 The world arthropod population has been estimated at a billion billion (10 18) individuals.
 Nearly a million arthropod species have been described.
 Two out of every three known species are arthropods.
 This phylum is represented in nearly all habitats in the biosphere.
 On the criteria of species diversity, distribution, and sheer numbers, arthropods must be
regarded as the most successful animal phylum.
Biology Chapter Notes
 The diversity and success of arthropods are largely due to three features: body
segmentation, a hard exoskeleton, and jointed appendages.
 Early arthropods such as the trilobites had pronounced segmentation, but little
variation in their appendages.
 Groups of segments and their appendages have become specialized for a variety of
functions, permitting efficient division of labor among regions.
 The body of an arthropod is completely covered by the cuticle, an exoskeleton
constructed from layers of protein and chitin.
 The exoskeleton protects the animal and provides points of attachment for the muscles
that move appendages.
 It is thick and inflexible in some regions, such as crab claws, and thin and flexible in
others, such as joints.
 The exoskeleton of arthropods is strong and relatively impermeable to water.
 In order to grow, an arthropod must molt its old exoskeleton and secrete a larger one, a
process called ecdysis that leaves the animal temporarily vulnerable to predators and
other dangers.
 The exoskeleton’s relative impermeability to water helped prevent desiccation and
provided support on land.
 Arthropods moved to land after the colonization of land by plants and fungi.
 In 2004, an amateur fossil hunter found a 428-million-year-old fossil of a millipede.
Fossilized arthropod tracks date from 450 million years ago.
 Arthropods have well-developed sense organs, including eyes for vision, olfactory
receptors for smell, and antennae for touch and smell.
 Most sense organs are located at the anterior end of the animal, which shows extensive
cephalization.
 Arthropods have an open circulatory system in which hemolymph fluid is propelled by a
heart through short arteries into sinuses (the hemocoel) surrounding tissues and organs.
 Hemolymph returns to the heart through valved pores.
 The hemocoel is not a coelom; the true coelom is much reduced in most arthropods.
 Open circulatory systems evolved convergently in arthropods and molluscs.
 Arthropods have evolved a variety of specialized organs for gas exchange.
 Most aquatic species have gills with thin, feathery extensions that have an extensive
surface area in contact with water.
 Terrestrial arthropods generally have internal surfaces specialized for gas exchange.
 For example, insects have tracheal systems, branched air ducts leading into the
interior from pores in the cuticle.
 Molecular systematics is suggesting new hypotheses about arthropod relationships.
 Evidence shows that arthropods diverged early in their history into four main
evolutionary lineages: cheliceriformes (sea spiders, horseshoe crabs, scorpions, ticks,
spiders), myriapods (centipedes and millipedes), hexapods (insects and their
wingless, six-legged relatives), and crustaceans (crabs, lobsters, shrimps, barnacles,
and many others).
 Cheliceriformes are named for their clawlike feeding appendages, chelicerae, which serve
as pincers or fangs.
 Cheliceriformes have an anterior cephalothorax and a posterior abdomen.
 They lack sensory antennae, and most have simple eyes (eyes with a single lens).
Biology Chapter Notes
  The earliest cheliceriformes were eurypterids, or water scorpions, marine and
freshwater predators that grew up to 3 m long.
 Modern marine cheliceriformes include the sea spiders (pycnogonids) and the
horseshoe crabs.
 The majority of living cheliceriformes are arachnids, a group that includes scorpions,
spiders, ticks, and mites.
 Nearly all ticks are blood-sucking parasites on the body surfaces of reptiles or mammals.
 Parasitic mites live on or in a wide variety of vertebrates, invertebrates, and plants.
 The arachnid cephalothorax has six pairs of appendages.
 There are four pairs of walking legs.
 A pair of pedipalps function in sensing or feeding.
 The chelicerae usually function in feeding.
 Spiders inject poison from glands on the chelicerae to immobilize their prey and while
chewing their prey, spill digestive juices into the tissues and suck up the liquid meal.
 In most spiders, gas exchange is carried out by book lungs.
 These are stacked plates contained in an internal chamber.
 The plates present an extensive surface area, enhancing exchange of gases between the
hemolymph and air.
 A unique adaptation of many spiders is the ability to catch flying insects in webs of silk.
 The silk protein is produced as a liquid by abdominal glands and spun by spinnerets
into fibers that solidify.
 Web designs are characteristic of each species.
 Silk fibers have other functions as egg covers, drop lines for a rapid escape, and “gift
wrapping” for nuptial gifts.
 Millipedes and centipedes belong to the subphylum Myriapoda, the myriapods.
 All living myriapods are terrestrial.
 Millipedes (class Diplopoda) have two pairs of walking legs on each of their many
trunk segments, formed by two fused segments.
 They eat decaying leaves and plant matter.
 They may have been among the earliest land animals.
 Centipedes (class Chilopoda) are terrestrial carnivores.
 The head has a pair of antennae and three pairs of appendages modified as mouth
parts, including the jawlike mandibles.
 Each segment in the trunk region has one pair of walking legs.
 Centipedes have poison claws on the anteriormost trunk segment that paralyze prey
and aid in defense.
 Insects and their relatives (subphylum Hexapoda) are more species-rich than all other
forms of life combined.
 They live in almost every terrestrial habitat and in fresh water, and flying insects fill the
air.
 They are rare, but not absent, from the sea, where crustaceans dominate.
 The oldest insect fossils date back to the Devonian period, about 416 million years ago.
 When insect flight evolved in the Carboniferous and Permian periods, it sparked an
explosion in insect varieties.
Biology Chapter Notes
  Diversification of mouthparts for feeding on gymnosperms and other Carboniferous
plants also contributed to the adaptive radiation of insects.
 In one widely held hypothesis, the radiation of flowering plants triggered the greatest
diversification of insects in the Cretaceous and early Tertiary periods.
 However, new research suggests that insects diversified first and, as pollinators and
herbivores, may have caused the angiosperm radiation.
 Flight is one key to the great success of insects.
 Flying animals can escape many predators, find food and mates, and disperse to new
habitats faster than organisms that must crawl on the ground.
 Many insects have one or two pairs of wings that emerge from the dorsal side of the
thorax.
 Wings are extensions of the cuticle and are not true appendages.
 Several hypotheses have been proposed for the evolution of wings.
 In one hypothesis, wings first evolved as extensions of the cuticle that helped the insect
absorb heat and were later modified for flight.
 A second hypothesis argues that wings allowed animals to glide from vegetation to the
ground.
 Alternatively, wings may have served as gills in aquatic insects.
 Still another hypothesis proposes that insect wings functioned for swimming before
they functioned for flight.
 Insect wings are also very diverse.
 Dragonflies, among the first insects to fly, have two similar pairs of wings.
 The wings of bees and wasps are hooked together and move as a single pair.
 Butterfly wings operate similarly because the anterior wings overlap the posterior
wings.
 In beetles, the posterior wings function in flight, while the anterior wings act as covers
that protect the flight wings when the beetle is on the ground or burrowing.
 The internal anatomy of an insect includes several complex organ systems.
 In the complete digestive system, there are regionally specialized organs with discrete
functions.
 Metabolic wastes are removed from the hemolymph by Malpighian tubules,
outpockets of the digestive tract.
 Respiration is accomplished by a branched, chitin-lined tracheal system that carries
O2 from the spiracles directly to the cells.
 The insect nervous system consists of a pair of ventral nerve cords with several segmental
ganglia.
 The two cords meet in the head, where the ganglia from several anterior segments are
fused into a cerebral ganglion (brain).
 This structure is close to the antennae, eyes, and other sense organs concentrated on
the head.
 Metamorphosis is central to insect development.
 In incomplete metamorphosis (seen in grasshoppers and some other orders), the
young resemble adults but are smaller and have different body proportions.
 Through a series of molts, the young look more and more like adults until they
reach full size.

Biology Chapter Notes

  In complete metamorphosis, larval stages specialized for eating and growing change
morphology completely during the pupal stage and emerge as adults.
 Reproduction in insects is usually sexual, with separate male and female individuals.
 Coloration, sound, or odor bring together opposite sexes at the appropriate time.
 In most species, sperm cells are deposited directly into the female’s vagina at the time
of copulation.
 In a few species, females pick up a sperm packet deposited by a male.
 The females store sperm in the spermatheca, in some cases holding enough sperm from
a single mating to last a lifetime.
 After mating, females lay their eggs on a food source appropriate for the next
generation.
 Insects affect the lives of all other terrestrial organisms.
 Insects are important natural and agricultural pollinators.
 On the other hand, insects are carriers for many diseases, including malaria and
African sleeping sickness.
 Insects compete with humans for food, consuming crops intended to feed and clothe
human populations.
 Billions of dollars each year are spent by farmers on pesticides to minimize losses
to insects.
 In parts of Africa, insects claim about 75% of the crops.
 While arachnids and insects thrive on land, most crustaceans remain in marine and
freshwater environments.
 Crustaceans typically have biramous (branched) appendages that are extensively
specialized.
 Lobsters and crayfish have 19 pairs of appendages, adapted to a variety of tasks.
 In addition to two pairs of antennae, crustaceans have three or more pairs of
mouthparts, including hard mandibles.
 Walking legs are present on the thorax and other appendages for swimming or
reproduction are found on the abdomen.
 Crustaceans can regenerate lost appendages during molting.
 Small crustaceans exchange gases across thin areas of the cuticle, but larger species have
gills.
 The circulatory system is open, with a heart pumping hemolymph into short arteries and
then into sinuses that bathe the organs.
 Nitrogenous wastes are excreted by diffusion through thin areas of the cuticle, but glands
regulate the salt balance of the hemolymph.
 Most crustaceans have separate sexes.
 In lobsters and crayfish, males use a specialized pair of appendages to transfer sperm
to the female’s reproductive pore.
 Most aquatic species have several larval stages.
 The isopods, with about 10,000 species, are one of the largest groups of crustaceans.
 Most are small marine species, and some are abundant at the bottom of deep oceans.
 Isopods also include the land-dwelling pill bugs, or wood lice, that live underneath
moist logs and leaves.

Biology Chapter Notes

 Decapods, including lobsters, crayfish, crabs, and shrimp, are among the largest
crustaceans.
 The cuticle is hardened with calcium carbonate.
 The exoskeleton over the cephalothorax forms a shield called the carapace.
 While most decapods are marine, crayfish live in fresh water and some tropical crabs
are terrestrial as adults.
 Many small crustaceans are important members of marine and freshwater plankton
communities.
 Planktonic crustaceans include many species of copepods, which are among the most
numerous of all animals.
 Krill are shrimplike planktonic organisms that reach about 3 cm long.
 A major food source for baleen whales and other ocean predators, they are now
harvested extensively by humans for food and agricultural fertilizer.
 Barnacles are primarily sessile crustaceans with parts of their cuticle hardened by calcium
carbonate.
 They anchor themselves to rocks, boat hulls, and pilings and strain food from the water
by extending their appendages.
 Their adhesive is as strong as any synthetic glue.

Concept 33.8 Echinoderms and chordates are deuterostomes

 At first glance, sea stars and other echinoderms would seem to have little in common with
the phylum Chordata, which includes the vertebrates.
 However, these animals share the deuterostome characteristics of radial cleavage, type of
development of the coelom from the archenteron, and formation of the anus from the
blastopore.
 Molecular systematics has reinforced the Deuterostomia as a clade of bilaterian animals.
Phylum Echinodermata: Echinoderms have a water vascular system and secondary radial
symmetry.
 Sea stars and most other echinoderms are sessile or slow-moving marine animals.
 A thin skin covers an endoskeleton of hard calcareous plates.
 Most echinoderms are prickly from skeletal bumps and spines that have various
functions.
 Unique to echinoderms is the water vascular system, a network of hydraulic canals
branching into extensions called tube feet.
 These function in locomotion, feeding, and gas exchange.
 Sexual reproduction in echinoderms usually involves the release of gametes by separate
males and females into the seawater.
 The internal and external parts of the animal radiate from the center, often as five spokes.
 However, the radial anatomy of adult echinoderms is a secondary adaptation, as
echinoderm larvae have bilateral symmetry.
 The symmetry of adult echinoderms is not perfectly radial.

Biology Chapter Notes

 Living echinoderms are divided into six classes: Asteroidea (sea stars), Ophiuroidea
(brittle stars), Echinoidea (sea urchins and sand dollars), Crinoidea (sea lilies and feather
stars), Holothuroidea (sea cucumbers), and Concentricycloidea (sea daisies).
 Sea stars have multiple arms radiating from a central disk.
 The undersides of the arms have rows of tube feet.
 Each can act like a suction disk that is controlled by hydraulic and muscular action.
 Sea stars use the tube feet to grasp the substrate, to creep slowly over the surface, or to
capture prey.
 When feeding on closed bivalves, the sea star grasps the bivalve tightly and everts its
stomach through its mouth and into the narrow opening between the shells of the
bivalve.
 Enzymes from the sea star’s digestive organs then begin to digest the soft body of the
bivalve inside its own shell.
 Sea stars and some other echinoderms can regenerate lost arms and, in a few cases, even
regrow an entire body from a single arm.
 Brittle stars have a distinct central disk and long, flexible arms.
 Their tube feet lack suckers.
 They move by a serpentine lashing of their arms.
 Some species are suspension feeders, and others are scavengers or predators.
 Sea urchins and sand dollars have no arms, but they do have five rows of tube feet that are
used for locomotion.
 Sea urchins can also move by pivoting their long spines.
 The mouth of an urchin is ringed by complex jawlike structures adapted for eating
seaweed and other foods.
 Sea urchins are roughly spherical, while sand dollars are flattened and disk-shaped.
 Sea lilies are attached to the substratum by stalks, and feather stars crawl using their long,
flexible arms.
 Both use their arms for suspension feeding.
 The arms circle the mouth, which is directed upward, away from the substrate.
 Crinoids are an ancient class with very conservative evolution.
 Fossilized sea lilies from 500 million years ago could pass for modern members of the
class.
 Sea cucumbers do not look much like other echinoderms.
 They lack spines, the endoskeleton is much reduced, and the oral-aboral axis is
elongated.
 However, they do have five rows of tube feet, like other echinoderms, and other shared
features.
 Some tube feet around the mouth function as feeding tentacles for suspension feeding
or deposit feeding
 Sea daisies were discovered in 1986, and only two species are known.
 Their armless bodies are disk-shaped with five-fold symmetry.
 They are less than a centimeter in diameter.
 Sea daisies absorb nutrients through the membrane surrounding their body.
 Some taxonomists consider sea daisies to be highly derived sea stars.

Biology Chapter Notes

 Phylum Chordata: The chordates include two invertebrate subphyla and all vertebrates.
 The phylum to which we belong consists of two subphyla of invertebrate animals plus the
hagfishes and vertebrates.
 Both groups of deuterostomes, the echinoderms and chordates, have existed as distinct
phyla for at least half a billion years.

Biology Chapter Notes

 Chapter 34 Vertebrates
Chapter Notes

Overview: Half a Billion Years of Backbones

 Vertebrates are named for vertebrae, the series of bones that make up the vertebral
column or backbone.
 There are about 52,000 species of vertebrates, far fewer than the 1 million insect species
on Earth.
 Plant-eating dinosaurs, at 40,000 kg, were the heaviest animals to walk on land.
 The biggest animal that ever existed is the blue whale, at 100,000 kg.
 Humans and our closest relatives are vertebrates.
 This group includes other mammals, birds, lizards, snakes, turtles, amphibians, and the
various classes of fishes.

Concept 34.1 Chordates have a notochord and a dorsal, hollow nerve cord
 The vertebrates belong to one of the two major phyla in the Deuterostomia, the
chordates.
 Chordates are bilaterian animals, belonging to the Deuterostomia.
 The phylum Chordata includes three subphyla, the vertebrates and two phyla of
invertebrates—the urochordates and the cephalochordates.
Four derived characters define the phylum Chordata.
 Although chordates vary widely in appearance, all share the presence of four anatomical
structures at some point in their lifetime.
 These chordate characteristics are a notochord; a dorsal, hollow nerve cord; pharyngeal
slits; and a muscular, post-anal tail.
o The notochord, present in all chordate embryos, is a longitudinal, flexible rod located
between the digestive tube and the nerve cord.
 It is composed of large, fluid-filled cells encased in fairly stiff, fibrous tissue.
 It provides skeletal support throughout most of the length of the animal.
 While the notochord persists in the adult stage of some invertebrate chordates and
primitive vertebrates, it remains only as a remnant in vertebrates with a more complex,
jointed skeleton.
 For example, it is the gelatinous material of the disks between vertebrae in humans.
o The dorsal, hollow nerve cord of a chordate embryo develops from a plate of ectoderm
that rolls into a tube dorsal to the notochord.
 Other animal phyla have solid nerve cords, usually located ventrally.
 The nerve cord of the chordate embryo develops into the central nervous system: the
brain and spinal cord.
o The digestive tube of chordates extends from the mouth to the anus.
 The region posterior to the mouth is the pharynx.

Biology Chapter Notes

  In all chordate embryos, a series of pouches separated by grooves forms along the
sides of the pharynx.
 In most chordates, these grooves (known as pharyngeal clefts) develop into
pharyngeal gill slits that allow water that enters the mouth to exit without continuing
through the entire digestive tract.
 In many invertebrate chordates, the pharyngeal gill slits function as suspension-feeding
devices.
 The slits and the structures that support them have become modified for gas exchange
(in aquatic vertebrates), jaw support, hearing, and other functions during vertebrate
evolution.
o Most chordates have a muscular tail extending posterior to the anus.
 In contrast, nonchordates have a digestive tract that extends nearly the whole length of
the body.
 The chordate tail contains skeletal elements and muscles.
 It provides much of the propulsive force in many aquatic species.
Invertebrate chordates provide clues to the origin of vertebrates.
 Members of the subphylum Urochordata, commonly called tunicates, belong to the
deepest-branching lineage of chordates.
 They most resemble chordates during their larval stage, which may be brief.
 The tunicate larva uses its tail muscles and notochord to swim through the water in search
of a suitable substrate on which it can settle, guided by cues from light- and gravity-
sensitive cells.
 Tunicates undergo a radical metamorphosis to form a sessile adult with few chordate
characteristics.
 Its tail and notochord are resorbed, its nervous system degenerates, and its organs
rotate 90 degrees.
 Tunicates are suspension feeders.
 Seawater passes inside the animal via an incurrent siphon, through the pharyngeal gill
slits, and into a ciliated chamber, the atrium.
 Food filtered from the water is trapped by a mucous net that is passed by cilia into the
intestine.
 Filtered water and feces exit through an anus that empties into an excurrent siphon.
 Lancelets (members of the subphylum Cephalochordata) are blade-like in shape.
 The notochord; dorsal, hollow nerve cord; numerous gill slits; and post-anal tail all
persist in the adult stage.
 Lancelets are up to 5 cm long.
 They live with their posterior end buried in the sand and the anterior end exposed for
feeding.
 Adult lancelets retain key chordate characteristics.
 Lancelets are suspension feeders, feeding by trapping tiny particles on mucous nets
secreted across the pharyngeal slits.
 Ciliary pumping creates a flow of water with suspended food particles into the mouth
and out the gill slits.
 In lancelets, the pharynx and gill slits are feeding structures and play only a minor role
in respiration, which primarily occurs across the external body surface.
 A lancelet frequently leaves its burrow to swim to a new location.
Biology Chapter Notes
 Though feeble swimmers, their swimming mechanism resembles that of fishes through
the coordinated contraction of serial muscle blocks.
 Contraction of chevron-shaped muscles flexes the notochord and produces lateral
undulations that thrust the body forward.
 The muscle segments develop from blocks of mesoderm, called somites, arranged
serially along each side of the notochord of the embryo.
 Tunicates and lancelets may provide clues about the evolutionary origin of the vertebrate
body plan.
 Tunicates display a number of chordate characteristics only as larvae, while lancelets
retain those characters as adults.
 Thus, an adult lancelet looks more like a larval tunicate than like an adult tunicate.
 In the 1920s, biologist William Garstang suggested that tunicates represent an early stage
in chordate evolution.
 This stage may have occurred through paedogenesis, the precocious development of
sexual maturity in a larva.
 Garstang proposed that ancestral chordates became sexually mature while still in the
larval stage.
 The paedogenetic hypothesis is deduced from comparing modern forms, but the weight of
evidence is against it.
 The degenerate adult stage of tunicates appears to be a derived trait that evolved only after
the tunicate lineage branched off from other chordates.
 Even the tunicate larva appears to be highly derived.
 Studies of Hox gene expression suggest that the tunicate larva does not develop the
posterior part of its body axis.
 Rather, the anterior region is elongated and contains a heart and digestive system.
 Research on lancelets has revealed important clues about the evolution of the chordate
brain.
 Rather than a full-fledged brain, lancelets have only a slightly swollen tip on the
anterior end of the dorsal nerve cord.
 The same genes that organize major regions of the forebrain, midbrain, and hindbrain
of vertebrates express themselves in a corresponding pattern in this small cluster of
cells in the lancelet’s nerve cord.
 The vertebrate brain apparently is an elaboration of an ancestral structure similar to the
lancelet’s simple nerve cord tip.

Concept 34.2 Craniates are chordates that have a head

 After the evolution of the basic chordate body plan, the next major transition was the
appearance of a head.
 Chordates with a head are known as craniates.
 The origin of a head—with a brain at the anterior end of the dorsal nerve cord, eyes and
other sensory organs, and a skull—opened up a new way of feeding for chordates: active
predation.
Living craniates have a set of derived characters.

Biology Chapter Notes

 Living craniates share a set of derived characters that distinguishes them from other
chordates.
 On the genetic level, they possess two clusters of Hox genes, while lancelets and
chordates have only one.
 Other important families of genes that produce signaling molecules and transcription
factors are also duplicated in craniates.
 This additional genetic complexity made a more complex morphology possible.
 In craniates, a group of embryonic cells called the neural crest forms near the dorsal
margins of the closing neural tube.
 Neural crest cells disperse through the body and contribute to the formation of various
structures, such as teeth, some of the bones and cartilages of the skull, the dermis of
the face, several types of neurons, and the sensory capsules of the eyes and other sense
organs.
 The vertebrate cranium and brain (the enlarged anterior end of the dorsal, hollow nerve
cord) and the anterior sensory organs are evidence of a high degree of cephalization,
the concentration of sensory and neural equipment in the head.
 In craniates, the pharyngeal clefts evolved into gill slits.
 Unlike the pharyngeal slits of lancelets, which are used primarily for suspension
feeding, gill slits are associated with muscles and nerves that allow water to be pumped
through the slits.
 This pumping sucks in food and facilitates gas exchange.
Cambrian fossils provide clues to craniate origins.
 Several recent fossil finds in China of early chordates have provided information about
the origin of craniates.
 They appear to be “missing links” that straddle the transition to craniates.
 The most primitive of these fossils is a 3-cm-long animal called Haikouella.
 This animal resembles a lancelet and was probably a suspension feeder.
 Haikouella also had a small but well-formed brain, eyes, and muscular segments.
 It also had hardened structures (“denticles”) in the pharynx that may have
functioned somewhat like teeth.
 However, Haikouella did not have a skull.
 In other Cambrian rocks, paleontologists have found fossils of more advanced
chordates, such as Haikouichthys.
 Haikouichthys had a skull composed of cartilage and is the oldest known true
craniate.
 These fossils push craniate origins back to the Cambrian explosion.

Class Myxini: Hagfishes are the least derived craniate lineage.

 Hagfishes have a skull of cartilage but lack jaws and vertebrae.
 They swim in a snakelike fashion by using their segmental muscles to exert force
against their notochord, which they retain in adulthood as a strong, flexible rod of
cartilage.
 Hagfishes have a small brain, eyes, ears, and a nasal opening that connects with the
pharynx.
 They have toothlike formations made of keratin.
Biology Chapter Notes
 All of the 30 or so species of hagfishes are marine scavengers, feeding on worms and sick
or dead fish.
 Rows of slime glands along a hagfish’s body produce small amounts of slime perhaps
to repulse other scavengers or larger amounts to deter a potential predator.
 Vertebrate systematists do not consider hagfishes to be fish.
 The taxonomic term fish refers only to a specific clade of vertebrates, the
actinopterygians.

Concept 34.3 Vertebrates are craniates that have a backbone

 During the Cambrian period, a lineage of craniates evolved into vertebrates.
 With a more complex nervous system and a more elaborate skeleton, vertebrates became
active predators.
 After vertebrates branched off from other craniates, they underwent another genetic
duplication, this one involving a group of transcription factor genes called the Dlx family.
 This additional genetic complexity was associated with innovations in vertebrate nervous
systems and skeletons, including a more extensive skull and a backbone composed of
vertebrae.
 In the majority of vertebrates, the vertebrae enclose the spinal cord and have taken over
the biomechanical roles of the notochord.
 Aquatic vertebrates also have a number of adaptations associated with faster swimming,
including fins stiffened by fin rays and a more efficient gas exchange system in the gills.
Class Cephalaspidomorphi: Lampreys are the oldest living lineage of vertebrates.
 Like hagfishes, lampreys offer clues to early chordate evolution but also have acquired
unique characters.
 There are about 35 species of lampreys inhabiting both marine and freshwater
environments.
 Most lampreys are parasites that feed by clamping a round, jawless mouth onto a fish.
 They use their rasping tongues to penetrate the skin of their fish prey and to ingest the
prey’s blood.
 Lampreys live as suspension-feeding larvae in streams for years before migrating to the
sea or lakes as adults.
 These larvae resemble lancelets and live partially buried in sediment.
 Some species of lampreys feed only as larvae.
 After metamorphosis, these lampreys attain sexual maturity, reproduce, and die within
a few days.
 The skeletons of lampreys are made of cartilage.
 Unlike most vertebrate cartilage, lamprey cartilage contains no collagen. Instead, it is a
stiff protein matrix.
 The notochord persists as the main axial skeleton in adult lampreys.
 Lampreys also have a cartilaginous pipe surrounding the rodlike notochord.
 Pairs of cartilaginous projections extend dorsally, partially enclosing the nerve cord
with what might be a vestige of an early-stage vertebral column.

Biology Chapter Notes

 Many vertebrate lineages emerged early.
 Conodonts were slender, soft-bodied vertebrates with prominent eyes.
 At the anterior end of their mouth, they had a set of barbed hooks made of mineralized
dental tissue.
 Conodonts ranged in length from 3 to 30 cm.
 They probably hunted with their large eyes and impaled their prey on hooks.
 The food then passed to the pharynx, where a different set of dental elements crushed
and sliced it.
 Conodonts were very abundant for more than 300 million years.
 Other vertebrates emerged during the Ordovician and Silurian periods.
 These vertebrates had paired fins and an inner ear with two semicircular canals that
provided a sense of balance.
 Although they lacked jaws, they had a muscular pharynx that may have sucked in detritus
or bottom-dwelling organisms.
 They were armored with mineralized bone that offered protection from predators.
 The vertebrate skeleton evolved initially as a structure of unmineralized cartilage.
 Its mineralization began only after lampreys diverged from other vertebrates.
 What initiated the process of mineralization in vertebrates?
 Mineralization may have been associated with the transition to new feeding
mechanisms.
 The earliest known mineralized structures in vertebrates were conodont dental elements.
 The armor seen in later jawless vertebrates was derived from dental mineralization.
 Only in more derived vertebrates did the endoskeleton begin to mineralize, starting
with the skull.

Concept 34.4 Gnathostomes are vertebrates that have jaws

 The gnathostomes have true jaws, hinged structures that enable vertebrates to grasp food
firmly.
 According to one hypothesis, gnathostome jaws evolved by modification of the
skeletal rods that had previously supported the anterior pharyngeal gill slits.
 The remaining gill slits were no longer required for suspension feeding and remained
as the major sites of respiratory gas exchange.
Gnathostomes have a number of shared, derived characters.
 Gnathostomes share other derived characters besides jaws.
 The common ancestors of all gnathostomes underwent an additional duplication of the
Hox genes, so that the single cluster present in early chordates became four.
 Other gene clusters also duplicated, allowing further complexity in the development of
gnathostome embryos.
 The gnathostome forebrain is enlarged, in association with enhanced senses of vision and
smell.
 The lateral line system evolved as a row of microscopic organs sensitive to vibrations in
the surrounding water.
Biology Chapter Notes
 The common ancestor of living gnathostomes had a mineralized axial skeleton, shoulder
girdle, and two sets of paired appendages.
 Gnathostomes appeared in the fossil record in the mid-Ordovician period, about 470
million years ago, and steadily diversified.
 Gnathostome jaws and paired fins were major evolutionary breakthroughs.
 Jaws, with the help of teeth, enable the animal to grip food items firmly and slice them
up.
 Paired fins, along with the tail, enable fishes to maneuver accurately while swimming.
 With these adaptations, many fish species were active predators, allowing for the
diversification of both lifestyles and nutrient sources.
 The earliest gnathostomes in the fossil record are an extinct lineage of armored vertebrates
called placoderms.
 Most placoderms were less than a meter long, although some giants were more than 10
m long.
 Another group of jawed vertebrates called acanthodians radiated in the Devonian.
 Acanthodians were closely related to the ancestors of osteichthyans (ray-finned and lobe-
finned fishes).
 Both placoderms and acanthodians disappeared by the beginning of the Carboniferous
period, 360 million years ago.
Class Chondrichthyes: Sharks and rays have cartilaginous skeletons.
 The class Chondrichthyes, sharks and their relatives, includes some of the biggest and
most successful vertebrate predators in the oceans.
 Chondrichthyes have relatively flexible endoskeletons of cartilage rather than bone.
 In most species, parts of the skeleton are impregnated by calcium.
 Conodonts and armored, jawless fishes show that mineralization of the vertebrate skeleton
had begun before the chondrichthyan lineage branched off from other vertebrates.
 Traces of bone can be found in living chondrichthyes, in their scales, at the base of
their teeth and (in some sharks) in a thin layer on the surface of their vertebrae.
 The loss of bone in chondrichthyes is a derived condition, which emerged after they
diverged from other gnathostomes.
 There are about 750 extant species, almost all in the subclass of sharks and rays, with a
few dozen species in a second subclass of chimaeras or ratfishes.
 All have well-developed jaws and paired fins.
 The streamlined bodies of most sharks enable them to be swift, but not maneuverable,
swimmers.
 Powerful axial muscles power undulations of the body and caudal fin to drive the fish
forward.
 The dorsal fins provide stabilization.
 While some buoyancy is provided by low-density oils in the large liver, the flow of
water over the pectoral and pelvic fins also provides lift to keep the animal suspended
in the water column.
 Continual swimming also ensures that water flows into the mouth and out through the
gills.
 Some sharks and many skates and rays spend much time resting on the seafloor, using
the muscles of their jaws and pharynx to pump water over the gills.
Biology Chapter Notes
 Most sharks are carnivores that swallow their prey whole or use their powerful jaws and
sharp teeth to tear flesh from animals too large to swallow.
 In contrast, the largest sharks and rays are suspension feeders that consume plankton.
 Sharks have several rows of teeth that gradually move to the front of the mouth as old
teeth are lost.
 Within the intestine of a shark is a spiral valve, a corkscrew-shaped ridge that
increases surface area and prolongs the passage of food along the short digestive tract.
 Acute senses are adaptations that go along with the active, carnivorous lifestyle of sharks.
 Sharks have sharp vision but cannot distinguish colors.
 Their acute olfactory sense (smelling) occurs in a pair of nostrils that do not function in
breathing.
 Sharks can detect electrical fields, including those generated by the muscle
contractions of nearby prey, through patches of specialized skin pores.
 The lateral line system, a row of microscopic organs sensitive to pressure changes, can
detect low-frequency vibrations.
 In sharks, the whole body transmits sound to the hearing organs of the inner ear.
 Shark eggs are fertilized internally.
 Males transfer sperm via claspers on their pelvic fins to the reproductive tract of the
female.
 Oviparous sharks encase their eggs in protective cases and lay them outside the
mother’s body.
 These hatch months later as juveniles.
 Ovoviviparous sharks retain fertilized eggs in the oviduct.
 The embryo completes development in the uterus, nourished by the egg yolk.
 A few sharks are viviparous, providing nutrients through a placenta to the developing
offspring.
 Rays are closely related to sharks, but they have adopted a very different lifestyle.
 Most rays are flattened bottom dwellers that crush molluscs and crustaceans in their
jaws.
 The enlarged pectoral fins of rays are used like wings to propel the animal through the
water.
 The tail of many rays is whiplike and may bear venomous barbs for defense against
threats.
 Chondrichthyans have changed little in more than 300 million years.
 They are severely threatened by overfishing.
 In 2003, researchers reported that shark stocks in the northwest Atlantic declined 75%
in 15 years.
Osteichthyes: The extant classes of bony fishes are the ray-finned fishes, the lobe-finned
fishes, and the lungfishes.
 The vast majority of bony fishes belong to a clade of gnathostomes called the
Osteichthyes (meaning “bony fish”).
 Systematists today include tetrapods with bony fish in Osteichthyes, which otherwise
would be paraphyletic.
 Nearly all bony fishes have an ossified endoskeleton with a hard matrix of calcium
phosphate.
Biology Chapter Notes
  It is not clear when the shift to a bony skeleton took place during gnathostome
evolution.
 Bony fishes breathe by drawing water over four or five pairs of gills located in chambers
covered by a protective flap, the operculum.
 Water is drawn into the mouth, through the pharynx, and out between the gills by
movements of the operculum and muscles surrounding the gill chambers.
 Most fishes have an internal, air-filled sac, the swim bladder.
 The positive buoyancy provided by air counters the negative buoyancy of the tissues,
enabling many fishes to be neutrally buoyant and remain suspended in the water.
 The swim bladder evolved from balloonlike lungs that may have been used to breathe
air when dissolved oxygen levels were low in stagnant shallow waters.
 The skin of bony fishes is often covered with thin, flattened bony scales that differ in
structure from the toothlike scales of sharks.
 Glands in the skin secrete mucus that reduces drag in swimming.
 Like sharks, aquatic osteichthyes have a lateral line system, which is evident as a row of
tiny pits in the skin on either side of the body.
 The reproduction of aquatic osteichthyes varies.
 Most species are oviparous, reproducing by external fertilization after the female sheds
large numbers of small eggs.
 Internal fertilization and birthing characterize other species.
 The most familiar families of fishes belong to the ray-finned fishes, members of class
Actinopterygii.
 This class includes bass, trout, perch, tuna, and herring.
 In this group, the fins are supported by long, flexible rays.
 The fins may be modified for maneuvering, defense, and other functions.
 Bony fishes, including the ray-finned fishes, probably evolved in fresh water and then
spread to the seas during their long history.
 Many species of ray-finned fishes returned to fresh water at some point in their
evolution.
 Some ray-finned fishes, such as salmon, make a round-trip from fresh water to
seawater and back to fresh water during their life cycle.
 Ray-finned fishes evolved during the Devonian period, along with the lobe-finned fishes
(Sarcopterygii).
 The key derived character in lobe-fins is the presence of muscular pectoral and pelvic fins
supported by extensions of the bony skeleton.
 Many Devonian lobe-fins were large, bottom dwellers that may have used their paired,
muscular fins to “walk” along the bottom.
 By the end of the Devonian period, lobe-fin diversity was dwindling.
 Today, only three lineages survive.
 One lineage, the coelacanths (class Actinistia) probably originated as freshwater
animals with lungs, but others shifted to the ocean, including the only living genus,
Latimeria.
 The second lineage of living lobe-fins is represented by three genera of lungfishes
(class Dipnoi), which live today in the Southern Hemisphere.
 They generally inhabit stagnant ponds and swamps.
Biology Chapter Notes
  They can gulp air into lungs connected to the pharynx of the digestive tract to
provide oxygen for metabolism.
 Lungfishes also have gills, which are the main organs for gas exchange in
Australian lungfishes.
 When ponds shrink during the dry season, some lungfishes can burrow into the mud
and estivate.
 The third lineage of lobe-fins that survives today is far more diverse than coelacanths
or lungfishes.
 During the mid-Devonian, the tetrapods adapted to life on land and gave rise to terrestrial
vertebrates, including humans.

Concept 34.5 Tetrapods are gnathostomes that have limbs and feet
 One of the most significant events in vertebrate history took place 360 million years ago,
when the fins of some lobe-fins evolved into tetrapod limbs and feet.
 The most significant character of tetrapods is the four limbs, which allow them to support
their weight on land.
 The feet of tetrapods have digits that allow them to transmit muscle-generated forces to
the ground when they walk.
 With the move to land, the bones of the pelvic girdle (to which the hind legs are attached)
became fused to the backbone, permitting forces generated by the hind legs against the
ground to be transferred to the rest of the body.
 Living tetrapods do not have pharyngeal gill slits.
 The ears are adapted to the detection of airborne sounds.
 The Devonian coastal wetlands were home to a wide range of lobe-fins. Those that
entered shallow, oxygen-poor water could use their lungs to breathe air.
 Some species likely used their stout fins to move across the muddy bottom.
 At the water’s edge, leglike appendages were probably better equipment than fins for
paddling and crawling through the dense vegetation in shallow water.
 The tetrapod body plan was thus a modification of a preexisting body plan.
 In one lineage of lobe-fins, the fins became progressively more limb-like, while the rest of
the body retained adaptations for aquatic life.
 For example, fossils of Acanthostega from 365 million years ago had bony gill
supports and rays in its tail to support propulsion in water, but it also had fully formed
legs, ankles, and digits.
 Acanthostega is representative of a period of vertebrate evolution when adaptations for
shallow water allowed certain fishes to make a gradual transition to the terrestrial side
of the water’s edge.
 A great diversity of tetrapods emerged during the Carboniferous period.
 Judging from the morphology and location of the fossils, most of these early tetrapods
remained tied to water.
Class Amphibia: Salamanders, frogs, and caecilians are the three extant amphibian
orders.

Biology Chapter Notes

 Today the amphibians (class Amphibia) are represented by about 4,800 species of
salamanders (order Urodela, “tailed ones”), frogs (order Anura, “tail-less ones”), and
caecilians (order Apoda, “legless ones”).
 Some of the 500 species of urodeles are entirely aquatic, but others live on land as adults
or throughout life.
 On land, most salamanders walk with a side-to-side bending of the body that may
resemble the swagger of the early terrestrial tetrapods.
 The 4,200 species of anurans are more specialized than urodeles for moving on land.
 Adult frogs use powerful legs to hop along the terrain.
 Frogs nab insects by flicking out their sticky tongues, which are attached to the front of
the mouth.
 Anurans may be camouflaged or secrete a distasteful, even poisonous, mucus from skin
glands.
 Many poisonous species are brightly colored, perhaps to warn predators who associate
the coloration with danger.
 Apodans, the caecilians (about 150 species), are legless and nearly blind.
 The reduction of legs evolved secondarily from a legged ancestor.
 Superficially resembling earthworms, most species burrow in moist forest soil in the
tropics.
 A few South American species live in freshwater ponds and streams.
 Amphibian means “two lives,” a reference to the metamorphosis of many frogs from an
aquatic stage, the tadpole, to the terrestrial adult.
 Tadpoles are usually aquatic herbivores with gills and a lateral line system, and they
swim by undulating their tails.
 During metamorphosis, the tadpole develops legs, the lateral line disappears, and lungs
replace gills.
 Adult frogs are carnivorous hunters.
 Many amphibians do not live a dualistic—aquatic and terrestrial—life.
 There are some strictly aquatic, and some strictly terrestrial frogs, salamanders, and
caecilians.
 The larvae of salamanders and caecilians look like adults and are also carnivorous.
 Paedomorphosis, the retention of some larval features in a sexually mature adult, is
common among some groups of salamanders.
 For example, the mudpuppy (Necturus) retains gills and other larval features when
sexually mature.
 Most amphibians retain close ties with water and are most abundant in damp habitats.
 Those adapted to drier habitats spend much of their time in burrows or under moist
leaves where the humidity is higher.
 Most amphibians rely heavily on their moist skin to carry out gas exchange with the
environment.
 Some terrestrial species lack lungs entirely and breathe exclusively through their
skin and oral cavity.
 Amphibian eggs lack a shell and dehydrate quickly in dry air.
 Most species have external fertilization, with eggs shed in ponds or swamps or at least
in moist environments.
Biology Chapter Notes
  Some species lay vast numbers of eggs in temporary pools where mortality is high.
 Others display various types of parental care and lay relatively few eggs.
 In some species, males or females may house eggs on the back, in the mouth, or
even in the stomach.
 Some species are ovoviviparous or viviparous, retaining the developing eggs in the
female reproductive tract until released as juveniles.
 Many amphibians display complex and diverse social behavior, especially during the
breeding season.
 Then many male frogs fill the air with their mating calls as they defend breeding
territories or attract females.
 In some terrestrial species, migrations to specific breeding sites may involve vocal
communication, celestial navigation, or chemical signaling.
 For the past 25 years, zoologists have been documenting a rapid and alarming decline in
amphibian populations throughout the world.
 Several causes that have been proposed include habitat degradation, the spread of a
pathogen (a chytrid fungus), and acid precipitation.
 Acid precipitation is damaging to amphibians because of their dependence on wet
places for completion of their life cycles.

Concept 34.6 Amniotes are tetrapods that have a terrestrially adapted egg
 The amniote clade consists of the mammals and reptiles (including birds).
 The evolution of amniotes from an amphibian ancestor involved many adaptations for
terrestrial living.
 The amniotic egg is the major derived character of the clade.
 Inside the shell of the amniotic egg are several extraembryonic membranes that function
in gas exchange, waste storage, and the transfer of stored nutrients to the embryo.
 The amniotic egg is named for one of these membranes, the amnion, which encloses a
fluid-filled “private pond” that bathes the embryo and acts as a hydraulic shock
absorber.
 The amniotic eggs enabled terrestrial vertebrates to complete their life cycles entirely on
land.
 In contrast to the shell-less eggs of amphibians, the amniotic eggs of most amniotes
have a shell that retains water and can be laid in a dry place.
 The calcareous shells of bird eggs are inflexible, while the leathery eggs of many
reptiles are flexible.
 Most mammals have dispensed with the shell.
 The embryo implants in the wall of the uterus and obtains its nutrition from the
mother.
 Amniotes acquired other adaptations to terrestrial life, including less-permeable skin and
the increasing use of the rib cage to ventilate the lungs.
 Amniotes adopt a more elevated stance than earlier tetrapods and living amphibians.
 The most recent common ancestor of living amphibians and amniotes lived about 340
million years ago, in the early Carboniferous period.
 No fossils of amniotic eggs have been found from that time.
Biology Chapter Notes
 Early amniotes lived in drier environments than did earlier tetrapods.
 Some were herbivores, with grinding teeth. Others were large and predatory.
The reptile clade includes birds.
 The reptile clade includes tuatara, lizards, snakes, turtles, crocodilians, and birds, as well
as extinct groups such as dinosaurs.
 Reptiles have several adaptations for terrestrial life not generally found in amphibians.
 Scales containing the protein keratin waterproof the skin, preventing dehydration in
dry air.
 Crocodiles, which are adapted to water, have evolved more permeable scales called
scutes.
 Reptiles obtain all their oxygen with lungs, not through their dry skin.
 As an exception, many turtles can use the moist surfaces of their cloaca for gas
exchange.
 Most reptiles lay shelled amniotic eggs on land.
 Fertilization occurs internally, before the shell is secreted as the egg passes through the
female’s reproductive tract.
 Some species of lizards and snakes are viviparous, with their extraembryonic
membranes forming a placenta that enables the embryo to obtain nutrients from its
mother.
 Nonbird reptiles are sometimes labeled “cold-blooded” because they do not use their
metabolism extensively to control body temperature.
 However, many nonbird reptiles regulate their body temperature behaviorally by
basking in the sun when cool and seeking shade when hot.
 Because they absorb external heat rather than generating much of their own, nonbird
reptiles are more appropriately called ectotherms.
 One advantage of this strategy is that an ectothermic reptile can survive on less than
10% of the calories required by a mammal of equivalent size.
 The reptile clade is not entirely ectothermic.
 Birds are endothermic, capable of keeping the body warm through metabolism.
 The oldest reptilian fossils date back to the Carboniferous period, about 300 million years
ago.
 The first major group of reptiles to emerge was the parareptiles, large, stocky,
quadrupedal herbivores.
 Some parareptiles had dermal plates on their skin, which may have provided defense
against predators.
 Parareptiles died out 200 million years ago, at the end of the Triassic period.
 As parareptiles were dwindling, an equally ancient clade of reptiles, the diapsids, was
diversifying.
 The most obvious derived character of diapsids is a pair of holes on each side of the
skull, behind the eye socket.
 The diapsids are composed of two main lineages.
 One, the lepidosaurs, includes lizards, snakes, and tuataras.
 This lineage also produced a number of marine reptiles including plesiosaurs and
ichthyosaurs.
Biology Chapter Notes
  The archosaurs include crocodilians, and the extinct pterosaurs and dinosaurs.
 Pterosaurs, which originated in the late Triassic, were the first flying tetrapods.
 The pterosaur wing is formed from a bristle-covered membrane of skin that stretched
between the hind leg and the tip of an elongated finger.
 Well-preserved fossils show the presence of muscles, blood vessels, and nerves in the
wing membrane, suggesting that pterosaurs could dynamically adjust their membranes
to assist their flight.
 Dinosaurs were an extremely diverse group varying in body shape, size, and habitat.
 There were two main dinosaur lineages: the ornithischians, which were mostly
herbivorous, and the saurischians, which included both long-necked giant herbivores
and bipedal carnivorous theropods.
 Theropods included the famous Tyrannosaurus rex as well as the ancestors of birds.
 There is increasing evidence that many dinosaurs were agile; fast moving; and, in some
species, social.
 Paleontologists have discovered signs of parental care among dinosaurs.
 There is continuing debate about whether dinosaurs were endothermic, capable of
keeping their body warm through metabolism.
 Some experts are skeptical.
 In the warm, consistent Mesozoic climate, behavioral adaptations may have been
sufficient for maintaining a suitable body temperature for terrestrial dinosaurs.
 Also, the low surface-to-volume ratios would have reduced the effects of daily
fluctuations in air temperature on the animal’s internal temperature.
 Some anatomical evidence supports the hypothesis that at least some dinosaurs were
endotherms.
 Paleontologists have found fossils of dinosaurs in both Antarctica and the Arctic,
although the climate in those areas was milder during the Mesozoic than today.
 The dinosaur that gave rise to birds was certainly endothermic, as are all birds.
 By the end of the Cretaceous, all dinosaurs (except birds) became extinct.
 It is uncertain whether dinosaurs were declining before they were finished off by an
asteroid or comet impact.
 Lepidosaurs are represented by two living lineages.
 One lineage includes the tuatara, two species of lizard-like reptiles found only on 30
islands off the coast of New Zealand.
 Tuatara relatives lived at least 220 million years ago, when they thrived on every
continent well into the Cretaceous period.
 The other major living lineage of lepidosaurs are the squamates (lizards and snakes).
 Lizards are the most numerous and diverse reptiles alive today.
 Most are relatively small, but they range in length from 16 mm to 3 m.
 Snakes are legless lepidosaurs that evolved from lizards closely related to the Komodo
dragon.
 It was once thought that snakes were descendents of lizards that adapted to a burrowing
lifestyle through the loss of limbs.
 However, recently discovered fossils of aquatic snakes with complete hind legs
suggest that snakes likely evolved in water and then recolonized land.

Biology Chapter Notes

  Some species of snakes retain vestigial pelvic and limb bones, providing evidence of
their ancestry.
 Snakes are carnivorous, and a number of adaptations aid them in hunting and eating prey.
 Snakes have acute chemical sensors and are sensitive to ground vibrations.
 The flicking tongue fans odors toward olfactory organs on the roof of the mouth.
 Heat-detecting organs of pit vipers, including rattlesnakes, enable these night hunters
to locate warm animals.
 Some poisonous snakes inject their venom through a pair of sharp, hollow or grooved
teeth.
 Loosely articulated jaws enable most snakes to swallow prey larger than the diameter
of the snake itself.
 Turtles are the most distinctive group of reptiles alive today.
 All turtles have a boxlike shell made up of upper and lower shields that are fused to the
vertebrae, clavicles, and ribs.
 The earliest fossils of turtles are 220 million years old, with fully developed shells.
 The origin of the turtle shell remains a puzzle.
 Some paleontologists suggest that turtle shells evolved from the dermal shells of
parareptiles.
 Other studies link turtles to archosaurs or lepidosaurs.
 There are two separate branches of turtles that have independently evolved
mechanisms to retract their heads.
 Turtles live in a variety of environments, from deserts to ponds to the sea.
 Crocodiles and alligators (crocodilians) are among the largest living reptiles.
 They spend most of their time in water, breathing air through upturned nostrils.
 Crocodilians are confined to the tropics and subtropics.
Birds evolved as feathered dinosaurs.
 Like crocodilians, birds are archosaurs, but highly specialized for flight.
 In addition to amniotic eggs and scales, modern birds have feathers and other
distinctive flight equipment.
 Almost every part of a typical bird’s anatomy is modified in some way to reduce weight
and enhance flight.
 One adaptation to reduce weight is the absence of some organs.
 For instance, females have only one ovary.
 Modern birds are toothless and grind their food in a muscular gizzard near the
stomach.
 The skeletons of birds have several adaptations that make them light and flexible, but
strong.
 The bones are air-filled and honeycombed to reduce weight without sacrificing much
strength.
 A bird’s feathers have a hollow, air-filled shaft that is light and strong.
 Feathers are made of beta-keratin, a protein similar to the keratin of reptile scales.
 The shape and arrangement of feathers forms wings into airfoils.
 Power for flapping the wings comes from contractions of the pectoral muscles, anchored
to a keel on the sternum.
Biology Chapter Notes
 The evolution of flight required radical alteration in body form but provides many
benefits.
 Flight enhances hunting and scavenging.
 It enables many birds to exploit flying insects, an abundant, highly nutritious food
resource.
 Flight provides a ready escape from earthbound predators.
 It enables many birds to migrate great distances to exploit different food resources and
seasonal breeding areas.
 Flying requires a great expenditure of energy with an active metabolism.
 Birds are endothermic, using their own metabolic heat to maintain a constant body
temperature.
 Feathers and, in some species, a layer of fat provide insulation.
 Efficient respiratory and circulatory systems with a four-chambered heart keep tissues
well supplied with oxygen and nutrients.
 The lungs have tiny tubes leading to and from elastic air sacs that help dissipate
heat and reduce body density.
 Birds have excellent vision and coordination, supported by well-developed areas of the
brain.
 The large brains of birds (proportionately larger than those of reptiles or
amphibians) support very complex behavior.
 During the breeding season, birds engage in elaborate courtship rituals.
 This culminates in copulation, contact between the mates’ vents, the openings to
their cloacae.
 After eggs are laid, the avian embryo is kept warm through brooding by the mother,
father, or both, depending on the species.
 Cladistic analyses of fossilized skeletons support the hypothesis that the closest reptilian
ancestors of birds were theropods.
 In the late 1990s, Chinese paleontologists unearthed a treasure trove of feathered
theropods that are shedding light on bird origins.
 These fossils suggest that feathers evolved long before feathered flight, possibly for
insulation or courtship.
 Theropods may have evolved powered flight by one of two possible routes.
o Small ground-running dinosaurs chasing prey or evading predation may have used
feathers to gain extra lift as they jumped into the air.
o Dinosaurs could have glided from trees, aided by feathers.
 The most famous Mesozoic bird is Archaeopteryx, known from fossils from a German
limestone quarry.
 This ancient bird lived about 150 million years ago, during the late Jurassic period.
 Archaeopteryx had clawed forelimbs, teeth, and a long tail containing vertebrae.
 Without its feathers, Archaeopteryx would probably be classified as a theropod
dinosaur.
 Its skeletal anatomy indicates that it was a weak flyer, perhaps a tree-dwelling
glider.
 Neornithes, the clade that includes 28 orders of living birds, arose after the Cretaceous-
Tertiary boundary, 65 million years ago.

Biology Chapter Notes

 Most birds can fly, but Neornithes includes a few flightless birds, the ratites, which lack
both a breastbone and large pectoral muscles.
 The ratites include the ostrich, kiwi, and emu.
 The penguins make up the flightless order Sphenisciformes.
 They have powerful pectoral muscles, which they use in swimming.
 The demands of flight have rendered the general form of all flying birds similar to one
another.
 The beak of birds is very adaptable, taking on a great variety of shapes for different
diets.

Concept 34.7 Mammals are amniotes that have hair and produce milk
Mammals diversified extensively in the wake of the Cretaceous extinctions.
 Mammals have a number of derived traits.
 All mammalian mothers use mammary glands to nourish their babies with milk, a
balanced diet rich in fats, sugars, proteins, minerals, and vitamins.
 All mammals also have hair, made of keratin.
 Hair and a layer of fat under the skin retain metabolic heat, contributing to
endothermy in mammals.
 Endothermy is supported by an active metabolism, made possible by efficient
respiration and circulation.
 Adaptations include a muscular diaphragm and a four-chambered heart.
 Mammals generally have larger brains than other vertebrates of equivalent size.
 Many species are capable of learning.
 The relatively long period of parental care extends the time for offspring to learn
important survival skills by observing their parents.
 Feeding adaptations of the jaws and teeth are other important mammalian traits.
 Unlike the uniform conical teeth of most reptiles, the teeth of mammals come in a
variety of shapes and sizes adapted for processing many kinds of foods.
 During the evolution of mammals from reptiles, two bones formerly in the jaw joint
were incorporated into the mammalian ear and the jaw joint was remodeled.
 Mammals belong to a group of amniotes known as synapsids.
 Synapsids have a temporal fenestra behind the eye socket on each side of the skull.
 Synapsids evolved into large herbivores and carnivores during the Permian period.
 Mammal-like synapsids emerged by the end of the Triassic, 200 million years ago.
 These animals were not mammals, but they were small and likely hairy, fed on insects
at night, and had a higher metabolism that other synapsids.
 They likely laid eggs.
 The first true mammals arose in the Jurassic periods.
 Early mammals diversified into a number of lineages, all about the size of a shrew.
 During the Mesozoic, mammals coexisted with dinosaurs and underwent a great adaptive
radiation in the Cenozoic in the wake of the Cretaceous extinctions.
 Modern mammals are split into three groups: monotremes (egg-laying mammals),
marsupials (mammals with pouches), and eutherian (placental) mammals.

Biology Chapter Notes

 Monotremes—the platypuses and the echidnas—are the only living mammals that lay
eggs.
 The reptile-like egg contains enough yolk to nourish the developing embryo.
 Monotremes have hair, and females produce milk in specialized glands.
 After hatching, the baby sucks milk from the mother’s fur because she lacks nipples.
 Marsupials include opossums, kangaroos, bandicoots, and koalas.
 In contrast to monotremes, marsupials have a higher metabolic rate, have nipples that
produce milk, and give birth to live young.
 A marsupial is born very early in development and, in most species, completes its
embryonic development while nursing within a maternal pouch, the marsupium.
 In most species, the tiny offspring climbs from the exit of the female’s reproductive
tract to the mother’s pouch.
 Marsupials existed worldwide throughout the Mesozoic area but now are restricted to
Australia and the Americas.
 In Australia, marsupials have radiated and filled niches occupied by eutherian
mammals in other parts of the world.
 Through convergent evolution, these diverse marsupials resemble eutherian
mammals that occupy similar ecological roles.
 While marsupial mammals diversified throughout the Tertiary in South America and
Australia, the placental mammals began an adaptive radiation on the northern continents.
 Australia’s isolation facilitated the diversification and survival of its marsupial fauna.
 Invasions of placental mammals from North America impacted the marsupial fauna of
South America about 12 million years ago and then again about 3 million years ago
when the continents were connected by the Isthmus of Panama.
 This mammalian biogeography is an example of the interplay between biological
and geological evolution.
 Compared to marsupials, eutherian mammals (placentals) have a longer period of
pregnancy.
 Young eutherians complete their embryonic development within the uterus, joined to
the mother by the placenta.
 Eutherians are commonly called placental mammals because their placentas are more
complex than those of marsupials and provide a more intimate and long-lasting
association between mother and young.

Concept 34.8 Humans are bipedal hominoids with a large brain

Primate evolution provides a context for understanding human origins.
 Primates include lemurs, monkeys, and apes.
 Primates have large brains and short jaws.
 Their eyes are forward-looking.
 Most primates have hands and feet adapted for grasping.
 Relative to other mammals, they have large brains and short jaws.
 They have flat nails on their digits, rather than narrow claws.

Biology Chapter Notes

 Primates also have relatively well-developed parental care and relatively complex social
behavior.
 The earliest primates were probably tree dwellers, shaped by natural selection for arboreal
life.
 The grasping hands and feet of primates are adaptations for hanging on to tree
branches.
 All modern primates, except Homo, have a big toe that is widely separated from the
other toes.
 The thumb is relatively mobile and separate from the fingers in all primates, but a
fully opposable thumb is found only in anthropoid primates.
 The unique dexterity of humans, aided by distinctive bone structure at the thumb
base, represents descent with modification from ancestral hands adapted for life in
the trees.
 Other primate features also originated as adaptations for tree dwelling.
 The overlapping fields of vision of the two eyes enhance depth perception, an obvious
advantage when brachiating.
 Excellent hand-eye coordination is also important for arboreal maneuvering.
 Primates are divided into two subgroups.
 The Prosimii (prosimians) probably resemble early arboreal primates and include the
lemurs of Madagascar and the lorises, pottos, and tarsiers of tropical Africa and
southern Asia.
 The Anthropoidea (anthropoids) include monkeys, apes, and humans.
 The oldest known anthropoid fossils, from about 45 million years ago, support the
hypothesis that tarsiers are the prosimians most closely related to anthropoids.
 By the Oligocene, monkeys were established in Africa, Asia, and South America.
 The Old World and New World monkeys underwent separate adaptive radiations.
 All New World monkeys are arboreal, but Old World monkeys include arboreal and
ground-dwelling species.
 Most monkeys in both groups are diurnal, and usually live in bands held together by
social behavior.
 In addition to monkeys, the anthropoid suborder also includes four genera of apes:
Hylobates (gibbons), Pongo (orangutans), Gorilla (gorillas), and Pan (chimpanzees and
bonobos).
 Modern apes are confined exclusively to the tropical regions of the Old World.
 They evolved from Old World monkeys about 20–25 million years ago.
 With the exception of gibbons, modern apes are larger than monkeys, with relatively long
arms and short legs and no tails.
 Only gibbons and orangutans are primarily arboreal.
 Social organization varies among the genera, with gorillas and chimpanzees being highly
social.
 Apes have relatively larger brains than monkeys, and their behavior is more flexible.
Humans are bipedal hominoids.
 In the continuity of life spanning more than 3.5 billion years, humans and apes have
shared ancestry for all but the past few million years.
 Human evolution is marked by the evolution of several major features.
Biology Chapter Notes
  Humans stand upright and walk on two legs.
 Humans have a much larger brain than other hominoids and are capable of language,
symbolic thought, and tool use.
 Humans have reduced jawbones and muscles and a shorter digestive tract.
 Human and chimpanzee genomes are 99% identical.
 Scientists are comparing the genomes of humans and chimpanzees to investigate
the 1% difference.
 Paleoanthropology is the study of human origins and evolution.
 Paleoanthropologists have found fossils of 20 species of extinct hominoids that are more
closely related to humans than to chimpanzees.
 These species are known as hominids.
 The oldest hominid is Sahelanthropus tchandensis, which lived 7 million years ago.
 Sahelanthropus and other early hominids shared some of the derived characters of
humans.
 They had reduced canine teeth and relatively flat faces.
 They were more upright and bipedal than other hominoids.
 While early hominids were becoming bipedal, their brains remained small—about 400 to
450 cm3 in volume.
 Early hominids were small in stature, with relatively large teeth and a protruding lower
jaw.
 Avoid three common sources of confusion:
o First, our ancestors were not chimpanzees or any other modern apes.
 Chimpanzees and humans represent two divergent branches of the hominoid tree
that evolved from a common ancestor that was neither a chimpanzee nor a human.
o Second, human evolution did not occur as a ladder with a series of steps leading
directly from an ancestral hominoid to Homo sapiens.
 If human evolution is a parade, then many splinter groups traveled down dead ends,
and several different human species coexisted.
 Human phylogeny is more like a multibranched bush with our species as the tip of the
only surviving twig.
o Third, the various human characteristics, such as upright posture and an enlarged brain,
did not evolve in unison.
 Different features evolved at different rates, called mosaic evolution.
 Our pedigree includes ancestors who walked upright but had brains much less
developed than ours.
 After dismissing some of the folklore on human evolution, we must admit that many
questions about our own ancestry remain.
 Hominid diversity increased dramatically between 4 and 2 million years ago.
 The various pre-Homo hominids are classified in the genus Australopithecus (“southern
ape”) and are known as australopiths.
 The first australopith, A. africanus, was discovered in 1924 by Raymond Dart in a
quarry in South Africa.
 From this and other skeletons, it became clear that A. africanus probably walked
fully erect and had humanlike hands and teeth.
 However, the brain was only about one-third the size of a modern human’s brain.
 In 1974, a new fossil, about 40% complete, was discovered in the Afar region of Ethiopia.
Biology Chapter Notes
  This fossil, nicknamed “Lucy,” was described as a new species, A. afarensis.
 Based on this fossil and other discoveries, this species had a brain the size of a
chimpanzee, a prognathous jaw, longer arms (for some level of arboreal locomotion), and
sexual dimorphism more apelike than human.
 However, the pelvis and skull bones and fossil tracks showed that A. afarensis walked
bipedally.
 Two lineages appeared after A. afarensis: the “robust” australopithecines with sturdy
skulls and powerful jaws and teeth for grinding and chewing hard, tough foods; and the
“gracile” australopithecines with lighter feeding equipment adapted for softer foods.
 Combining evidence from the earliest hominids with the fossil record of australopiths
makes it possible to consider hypotheses about trends in hominid evolution.
 Why did hominids become bipedal?
 Our anthropoid ancestors of 30–35 million years ago were tree dwelling.
 Twenty million years ago, the forests contracted as the climate became drier.
 The result was an increased savanna with few trees.
 For decades, paleontologists thought that bipedalism was an adaptation to life on
the savanna.
 All early hominids show indications of bipedalism, but they lived in forests and open
woodlands, not savanna.
 An alternate hypothesis is that bipedalism allowed hominids to reach low-hanging
fruits.
 About 1.9 million years ago, hominids living in arid environments walked long
distances on two legs.
 The manufacture and use of complex tools is a derived human character.
 When and why did tool use arise in the human lineage?
 Other hominoids are capable of sophisticated tool use.
 Orangutans can fashion probes from sticks for retrieving insects from their nests.
 Chimps use rocks to smash open food and put leaves on their feet to walk over
thorns.
 The oldest generally accepted evidence of tool use is 2.5-million-year-old cut marks on
animal bones found in Ethiopia.
 The australopith fossils near the site had relatively small brains.
 Perhaps tool use originated before large hominid brains evolved.
 The earliest fossils that anthropologists place in our genus, Homo, are classified as Homo
habilis.
 These fossils range in age from 2.4 to 1.6 million years old.
 This species had less prognathic jaws and larger brains (about 600–750 cm3) than
australopiths.
 In some cases, anthropologists have found sharp stone tools with these fossils,
indicating that some hominids had started to use their brains and hands to fashion
tools.
 Fossils from 1.9 to 1.6 million years ago are recognized as a distinct species, Homo
ergaster.
 H. ergaster had a larger brain than Homo habilis, as well as long slender legs well
adapted for long-distance walking.

Biology Chapter Notes

  This species lived in more-arid environments and was associated with more-
sophisticated tool use.
 Its reduced teeth suggest that it might have been able to cook or mash its food before
eating it.
 Specimens of early Homo show reduced sexual dimorphism, a trend that continued with
our species.
 Sexual dimorphism is reduced in pair-bonding species.
 Male and female Homo ergaster may have engaged in more pair-bonding than earlier
hominids, perhaps in order to provide long-term biparental care of babies.
 Some paleontologists still think that Homo ergaster were merely early specimens of
Homo erectus.
 Homo erectus was the first hominid species to migrate out of Africa, colonizing Asia and
Europe.
 They lived from about 1.8 million to 500,000 years ago.
 Fossils from Asia are known by such names as “Beijing man” and “Java Man.”
 In Europe, Neanderthals arose from an earlier species, Homo heidelbergensis,
which arose in Africa about 600,000 years ago and spread to Europe.
 The term Neanderthal is now used for humans who lived throughout Europe from about
200,000 to 30,000 years ago.
 Fossilized skulls indicate that Neanderthals had brains as large as ours, though
somewhat different in shape.
 They made hunting tools from stone and wood.
 Neanderthals were generally more heavily built than modern humans.
 Neanderthals apparently went extinct about 30,000 years ago, contributing little to the
gene pool of modern humans.
 Evidence of the extinction of Neanderthal can be found in their DNA.
 Scientists have extracted DNA from four fossil Neanderthals living at different times
and places in Europe.
 All Neanderthals formed a clade, while modern Europeans were more closely
related to modern Africans and Asians.
 In 2003, researchers in Ethiopia found 160,000-year-old fossils of Homo sapiens, the
oldest members of our species.
 These early humans were slender and lacked brow ridges.
 Evidence suggests that all living humans are more closely related to each other than to
Neanderthals.
 Europeans and Asians share a relatively recent common ancestor and many African
lineages branched off from more ancient positions on the human family tree.
 This is supported by analysis of mDNA and Y chromosomes of various populations.
 These findings strongly suggest that all living humans arose from Africa and migrated
from there 50,000 years ago.
 Our ancestors emerged in one or more waves, spreading into Asia, then Europe, and
Australia.
 The rapid expansion of our species may have been spurred by the evolution of human
cognition.

Biology Chapter Notes

  Neanderthals produced sophisticated tools, but had little creativity or capacity for
symbolic thought.
 In 2002, researchers found 77,000-year-old from South Africa.
 By 36,000, humans were producing spectacular cave paintings.
 Symbolic thought may have emerged along with full-blown human language, raising the
reproductive fitness of humans by allowing them to construct new tools and teach others
how to build them.
 Population pressure may have driven humans to migrate into Asia and then Europe.
 In 2002, geneticists found that FOXP2, a gene essential for human language, experienced
intense natural selection after the ancestors of humans and chimps diverged.
 Comparisons of flanking regions of the gene suggest that most changes took place
within the past 200,000 years.
 The evolutionary change in FOXP2 may be the first genetic clue about how our own
species came to be.

Biology Chapter Notes

Chapter 35 Plant Structure, Growth, and Development
Chapter Notes

Overview: No Two Plants Are Alike

 The fanwort, an aquatic weed, demonstrates the great developmental plasticity that is
characteristic of plants. The fanwort has feathery underwater leaves and large, flat,
floating surface leaves. Both leaf types have genetically identical cells, but the dissimilar
environments in which they develop cause different genes involved in leaf formation to be
turned on or off.
 The form of any plant is controlled by environmental and genetic factors. As a result, no
two plants are identical.
 In addition to plastic structural responses of individual plants to specific environments,
plant species have adaptive features that benefit them in their specific environments.
 For example, cacti have leaves that are reduced as spines and a stem that serves as the
primary site of photosynthesis. These adaptations reduce water loss in desert
environments.
 Angiosperms comprise 90% of plant species and are at the base of the food web of nearly
every terrestrial ecosystem.
 Most land animals, including humans, depend on angiosperms directly or indirectly for
sustenance.

Concept 35.1 The plant body has a hierarchy of organs, tissues, and cells
 Plants, like multicellular animals, have organs that are composed of different tissues, and
tissues are composed of different cell types.
 A tissue is a group of cells with a common structure and function.
 An organ consists of several types of tissues that work together to carry out particular
functions.
Vascular plants have three basic organs: roots, stems, and leaves.
 The basic morphology of vascular plants reflects their evolutionary history as terrestrial
organisms that inhabit and draw resources from two very different environments.
 Plants obtain water and minerals from the soil.
 They obtain CO2 and light above ground.
 To obtain the resources they need, vascular plants have evolved two systems: a
subterranean root system and an aerial shoot system of stems and leaves.
 Each system depends on the other.
 Lacking chloroplasts and living in the dark, roots would starve without the sugar and
other organic nutrients imported from the photosynthetic tissues of the shoot system.
 Conversely, the shoot system (and its reproductive tissues, flowers) depends on water
and minerals absorbed from the soil by the roots.
 A root is an organ that anchors a vascular plant in the soil, absorbs minerals and water,
and stores food.

Biology Chapter Notes

  Most eudicots and gymnosperms have a taproot system, consisting of one large
vertical root (the taproot) that produces many small lateral, or branch, roots.
 In angiosperms, taproots often store food that supports flowering and fruit
production later.
 Seedless vascular plants and most monocots, including grasses, have fibrous root
systems consisting of a mat of thin roots that spread out below the soil surface.
 A fibrous root system is usually shallower than a taproot system.
 Grass roots are concentrated in the upper few centimeters of soil. As a result,
grasses make excellent ground cover for preventing erosion.
 Sturdy, horizontal, underground stems called rhizomes anchor large monocots such
as palms and bamboo.
 The root system helps anchor a plant.
 In both taproot and fibrous root systems, absorption of water and minerals occurs near
the root tips, where vast numbers of tiny root hairs enormously increase the surface
area.
 Root hairs are extensions of individual epidermal cells on the root surface.
 Absorption of water and minerals is also increased by mutualistic relationships
between plant roots and bacteria and fungi.
 Some plants have modified roots. Some arise from roots while adventitious roots arise
aboveground from stems or even from leaves.
 Some modified roots provide additional support and anchorage. Others store water
and nutrients or absorb oxygen or water from the air.
 A stem is an organ consisting of alternating nodes, the points at which leaves are
attached, and internodes, the stem segments between nodes.
 At the angle formed by each leaf and the stem is an axillary bud with the potential to
form a lateral shoot or branch.
 Growth of a young shoot is usually concentrated at its apex, where there is a terminal
bud with developing leaves and a compact series of nodes and internodes.
 The presence of a terminal bud is partly responsible for inhibiting the growth of axillary
buds, a phenomenon called apical dominance.
 By concentrating resources on growing taller, apical dominance is an evolutionary
adaptation that increases the plant’s exposure to light.
 In the absence of a terminal bud, the axillary buds break dominance and give rise to a
vegetative branch complete with its own terminal bud, leaves, and axillary buds.
 Modified shoots with diverse functions have evolved in many plants.
 These shoots, which include stolons, rhizomes, tubers, and bulbs, are often mistaken
for roots.
 Stolons, such as the “runners” of strawberry plants, are horizontal stems that grow
on the surface and enable a plant to colonize large areas asexually as plantlets form
at nodes along each runner.
 Rhizomes, like those of ginger, are horizontal stems that grow underground.
 Tubers, including potatoes, are the swollen ends of rhizomes specialized for food
storage.
 Bulbs, such as onions, are vertical, underground shoots consisting mostly of the
swollen bases of leaves that store food.
 Leaves are the main photosynthetic organs of most plants, although green stems are also
photosynthetic.
Biology Chapter Notes
  While leaves vary extensively in form, they generally consist of a flattened blade and a
stalk, the petiole, which joins the leaf to a stem node.
 Grasses and other monocots lack petioles. In these plants, the base of the leaf forms a
sheath that envelops the stem.
 Most monocots have parallel major veins that run the length of the blade, while eudicot
leaves have a multibranched network of major veins.
 Plant taxonomists use floral morphology, leaf shape, spatial arrangement of leaves, and
the pattern of veins to help identify and classify plants.
 For example, simple leaves have a single, undivided blade, while compound leaves
have several leaflets attached to the petiole.
 The leaflet of a compound leaf has no axillary bud at its base.
 In a doubly compound leaf, each leaflet is divided into smaller leaflets.
 Most leaves are specialized for photosynthesis.
 Some plants have leaves that have become adapted for other functions.
 These include tendrils that cling to supports, spines of cacti for defense, leaves
modified for water storage, and brightly colored leaves that attract pollinators.
Plant organs are composed of three tissue systems: dermal, vascular, and ground.
 Each organ of a plant has three tissue systems: dermal, vascular, and ground.
 Each system is continuous throughout the plant body.
 The dermal tissue is the outer covering.
 In nonwoody plants, it is a single layer of tightly packed cells, or epidermis, that covers
and protects all young parts of the plant.
 The epidermis has other specialized characteristics consistent with the function of the
organ it covers.
 For example, the root hairs are extensions of epidermal cells near the tips of the roots.
 The epidermis of leaves and most stems secretes a waxy coating, the cuticle, which
helps the aerial parts of the plant retain water.
 In woody plants, protective tissues called periderm replace the epidermis in older regions
of stems and roots.
 Vascular tissue, continuous throughout the plant, is involved in the transport of materials
between roots and shoots.
 Xylem conveys water and dissolved minerals upward from roots into the shoots.
 Phloem transports food made in mature leaves to the roots; to nonphotosynthetic parts
of the shoot system; and to sites of growth, such as developing leaves and fruits.
 The vascular tissue of a root or stem is called the stele.
 In angiosperms, the vascular tissue of the root forms a solid central vascular
cylinder, while stems and leaves have vascular bundles, strands consisting of
xylem and phloem.
 Ground tissue is tissue that is neither dermal tissue nor vascular tissue.
 In eudicot stems, ground tissue is divided into pith, internal to vascular tissue, and
cortex, external to the vascular tissue.
 The functions of ground tissue include photosynthesis, storage, and support.
 For example, the cortex of a eudicot stem typically consists of both fleshy storage cells
and thick-walled support cells.

Biology Chapter Notes

 Plant tissues are composed of three basic cell types: parenchyma, collenchyma, and
sclerenchyma.
 Plant cells are differentiated, with each type of plant cell possessing structural adaptations
that make specific functions possible.
 Cell differentiation may be evident within the protoplast, the cell contents exclusive
of the cell wall.
 Modifications of cell walls also play a role in plant cell differentiation.
 We will consider the major types of differentiated plant cells: parenchyma, collenchyma,
sclerenchyma, water-conducting cells of the xylem and sugar-conducting cells of the
phloem.
 Mature parenchyma cells have primary walls that are relatively thin and flexible, and
most lack secondary walls.
 The protoplast of a parenchyma cell usually has a large central vacuole.
 Parenchyma cells are often depicted as “typical” plant cells because they generally are
the least specialized, but there are exceptions.
 For example, the highly specialized sieve-tube members of the phloem are parenchyma
cells.
 Parenchyma cells perform most of the metabolic functions of the plant, synthesizing and
storing various organic products.
 For example, photosynthesis occurs within the chloroplasts of parenchyma cells in the
leaf.
 Some parenchyma cells in the stems and roots have colorless plastids that store starch.
 The fleshy tissue of most fruit is composed of parenchyma cells.
 Most parenchyma cells retain the ability to divide and differentiate into other cell types
under special conditions, such as the repair and replacement of organs after injury to
the plant.
 In the laboratory, it is possible to regenerate an entire plant from a single parenchyma
cell.
 Collenchyma cells have thicker primary walls than parenchyma cells, though the walls
are unevenly thickened.
 Grouped into strands or cylinders, collenchyma cells help support young parts of the
plant shoot.
 Young stems and petioles often have strands of collenchyma just below the epidermis,
providing support without restraining growth.
 Mature collenchyma cells are living and flexible and elongate with the stems and
leaves they support.
 Sclerenchyma cells have thick secondary walls usually strengthened by lignin and
function as supporting elements of the plant.
 They are much more rigid than collenchyma cells.
 Unlike parenchyma cells, they cannot elongate.
 Sclerenchyma cells occur in plant regions that have stopped lengthening.
 Many sclerenchyma cells are dead at functional maturity, but they produce rigid
secondary cells walls before the protoplast dies.
 In parts of the plant that are still elongating, secondary walls are deposited in a spiral
or ring pattern, enabling the cell wall to stretch like a spring as the cell grows.

Biology Chapter Notes

 Two types of sclerenchyma cells, fibers and sclereids, are specialized entirely for
support.
 Fibers are long, slender, and tapered, and usually occur in groups.
 Those from hemp fibers are used for making rope, and those from flax are woven
into linen.
 Sclereids are irregular in shape and are shorter than fibers.
 They have very thick, lignified secondary walls.
 Sclereids impart hardness to nutshells and seed coats and the gritty texture to pear
fruits.
 The water-conducting elements of xylem, the tracheids and vessel elements, are
elongated cells that are dead at functional maturity.
 The thickened cell walls remain as a nonliving conduit through which water can flow.
 Both tracheids and vessels have secondary walls interrupted by pits, thinner regions
where only primary walls are present.
 Tracheids are long, thin cells with tapered ends.
 Water moves from cell to cell mainly through pits.
 Because their secondary walls are hardened with lignin, tracheids function in support
as well as transport.
 Vessel elements are generally wider, shorter, thinner walled, and less tapered than
tracheids.
 Vessel elements are aligned end to end, forming long micropipes or xylem vessels.
 The ends are perforated, enabling water to flow freely.
 In the phloem, sucrose, other organic compounds, and some mineral ions move through
tubes formed by chains of cells called sieve-tube members.
 These are alive at functional maturity, although a sieve-tube member lacks a nucleus,
ribosomes, and a distinct vacuole.
 The end walls, the sieve plates, have pores that facilitate the flow of fluid between
cells.
 Each sieve-tube member has a nonconducting nucleated companion cell, which is
connected to the sieve-tube member by numerous plasmodesmata.
 The nucleus and ribosomes of the companion cell serve both that cell and the adjacent
sieve-tube member.
 In some plants, companion cells in leaves help load sugar into the sieve-tube members,
which transport the sugars to other parts of the plant.

Concept 35.2 Meristems generate cells for new organs

 A major difference between plants and most animals is that plant growth is not limited to
an embryonic period.
 Most plants demonstrate indeterminate growth, growing as long as the plant lives.
 In contrast, most animals and certain plant organs, such as flowers and leaves, undergo
determinate growth, ceasing to grow after they reach a certain size.
 Indeterminate growth does not mean immortality.
 Annual plants complete their life cycle—from germination through flowering and seed
production to death—in a single year or less.
Biology Chapter Notes
  Many wildflowers and important food crops, such as cereals and legumes, are annuals.
 The life of a biennial plant spans two years.
 Often, there is an intervening cold period between the vegetative growth season and
the flowering season.
 Plants such as trees, shrubs, and some grasses that live many years are perennials.
 Perennials do not usually die from old age, but from an infection or some
environmental trauma.
 A plant is capable of indeterminate growth because it has perpetually embryonic tissues
called meristems in its regions of growth.
 These cells divide to generate additional cells, some of which remain in the
meristematic region, while others become specialized and are incorporated into the
tissues and organs of the growing plant.
 Cells that remain as wellsprings of new cells in the meristem are called initials.
 Those that are displaced from the meristem, derivatives, continue to divide for some
time until the cells they produce differentiate within developing tissues.
 The pattern of plant growth depends on the location of meristems.
 Apical meristems, located at the tips of roots and in the buds of shoots, supply cells for
the plant to grow in length.
 This elongation, primary growth, enables roots to extend through the soil and shoots
to increase their exposure to light and carbon dioxide.
 In herbaceous plants, primary growth produces almost all of the plant body.
 Woody plants also show secondary growth, progressive thickening of roots and
shoots where primary growth has ceased.
 Secondary growth is produced by lateral meristems, cylinders of dividing cells
that extend along the length of roots and shoots.
 The vascular cambium adds layers of vascular tissue called secondary xylem and
phloem.
 The cork cambium replaces the epidermis with thicker, tougher periderm.
 In woody plants, primary growth produces young extensions of roots and shoots each
growing season, while secondary growth thickens and strengthens the older parts of the
plant.
 At the tip of a winter twig of a deciduous tree is the dormant terminal bud, enclosed by
bud scales that protect its apical meristem.
 In the spring, the bud will shed its scales and begin a new spurt of primary growth.
 Along each growth segment, nodes are marked by scars left when leaves fell in
autumn.
 Above each leaf scar is either an axillary bud or a branch twig.
 Farther down the twig are whorls of scars left by the scales that enclosed the terminal bud
during the previous winter.
 Each spring and summer, as the primary growth extends the shoot, secondary growth
thickens the parts of the shoot that formed in previous years.

Concept 35.3 Primary growth lengthens roots and shoots

 Primary growth produces the primary plant body, the parts of the root and shoot systems
produced by apical meristems.
Biology Chapter Notes
 An herbaceous plant and the youngest parts of a woody plant represent the primary plant
body.
 Apical meristems lengthen both roots and shoots. However, there are important
differences in the primary growth of these two systems.
 The root tip is covered by a thimblelike root cap, which protects the meristem as the root
pushes through the abrasive soil during primary growth.
 The cap also secretes a polysaccharide slime that lubricates the soil around the growing
root tip.
 Growth in length is concentrated just behind the root tip, where three zones of cells at
successive stages of primary growth are located.
 These zones—the zone of cell division, the zone of elongation, and the zone of
maturation—grade together.
 The zone of cell division includes the root apical meristem and its derivatives.
 New root cells are produced in this region, including the cells of the root cap.
 The zone of cell division blends into the zone of elongation where cells elongate,
sometimes to more than ten times their original length.
 It is this elongation of cells that is mainly responsible for pushing the root tip,
including the meristem, ahead.
 The meristem sustains growth by continuously adding cells to the youngest end of the
zone of elongation.
 In the zone of maturation, cells become differentiated and become functionally
mature.
 The primary growth of roots consists of the epidermis, ground tissue, and vascular tissue.
 Water and minerals absorbed from the soil must enter through the epidermis, a single
layer of cells covering the root.
 Root hairs greatly increase the surface area of epidermal cells.
 Most roots have a solid core of xylem and phloem. The xylem radiates from the center
in two or more spokes, with phloem developing in the wedges between the spokes.
 In monocot roots, the vascular tissue consists of a central core of parenchyma
surrounded by alternating patterns of xylem and phloem.
 The ground tissue of roots consists of parenchyma cells that fill the cortex, the region
between the vascular cylinder and the epidermis.
 Cells within the ground tissue store food and are active in the uptake of minerals that
enter the root with the soil solution.
 The innermost layer of the cortex, the endodermis, is a cylinder one cell thick that forms
a selective barrier between the cortex and the vascular cylinder.
 An established root may sprout lateral roots from the outermost layer of the vascular
cylinder, the pericycle.
 The vascular tissue of the lateral root maintains its connection to the vascular tissue of
the primary root.
 The apical meristem of a shoot is a dome-shaped mass of dividing cells at the terminal
bud.
 Leaves arise as leaf primordia on the flanks of the apical meristem.
 Axillary buds develop from islands of meristematic cells left by apical meristems at the
bases of the leaf primordia.

Biology Chapter Notes

 Within a bud, leaf primordia are crowded close together because internodes are very short.
 Most of the elongation of the shoot occurs by growth in length of slightly older
internodes below the shoot apex.
 This growth is due to cell division and cell elongation within the internode.
 In some plants, including grasses, internodes continue to elongate all along the length
of the shoot over a prolonged period.
 These plants have meristematic regions called intercalary meristems at the base of
each leaf.
 This explains why grass continues to grow after being mowed.
 Unlike their central position in a root, vascular tissue runs the length of a stem in strands
called vascular bundles.
 Because the vascular system of the stem is near the surface, branches can develop with
connections to the vascular tissue without having to originate from deep within the
main shoot.
 In gymnosperms and most eudicots, the vascular bundles are arranged in a ring, with pith
inside and cortex outside the ring.
 The vascular bundles have xylem facing the pith and phloem facing the cortex.
 In the stems of most monocots, the vascular bundles are scattered throughout the ground
tissue rather than arranged in a ring.
 In both monocots and eudicots, the stem’s ground tissue is mostly parenchyma.
 Many stems are strengthened by collenchyma just beneath the epidermis.
 Sclerenchyma fiber cells within vascular bundles also help support stems.
 The leaf epidermis is composed of cells tightly locked together like pieces of a puzzle.
 The leaf epidermis is the first line of defense against physical damage and pathogenic
organisms, and its waxy cuticle is a barrier to water loss from the plant.
 The epidermal barrier is interrupted only by the stomata, tiny pores flanked by
specialized epidermal cells called guard cells.
 Each stoma is an opening between a pair of guard cells that regulate the opening and
closing of the pore.
 The stomata regulate CO2 exchange between the surrounding air and the
photosynthetic cells inside the leaf.
 They are also the major avenues of evaporative water loss from the plant—a process
called transpiration.
 The ground tissue of the leaf, the mesophyll, is sandwiched between the upper and lower
epidermis.
 It consists mainly of parenchyma cells with many chloroplasts and specialized for
photosynthesis.
 In many eudicots, a layer or more of columnar palisade mesophyll lies over spongy
mesophyll.
 Carbon dioxide and oxygen circulate through the labyrinth of air spaces around the
irregularly spaced cells of the spongy mesophyll.
 The air spaces are particularly large near stomata, where gas exchange with the
outside air occurs.
 The vascular tissue of a leaf is continuous with the xylem and phloem of the stem.
 Leaf traces, branches of vascular bundles in the stem, pass through petioles and into
leaves.
Biology Chapter Notes
  Vascular bundles in the leaves are called veins. Each vein is enclosed in a protective
bundle sheath consisting of one or more layers of parenchyma.
 Within a leaf, veins subdivide repeatedly and branch throughout the mesophyll.
 The xylem brings water and minerals to the photosynthetic tissues and the phloem
carries sugars and other organic products to other parts of the plant.
 The vascular infrastructure also functions to support and reinforce the shape of the
leaf.

Concept 35.4 Secondary growth adds girth to stems and roots in woody plants
 The stems and roots of most eudicots increase in girth by secondary growth.
 The secondary plant body consists of the tissues produced during this secondary
growth in diameter.
 Primary and secondary growth occur simultaneously but in different regions.
 While elongation of the stem (primary growth) occurs at the apical meristem, increases
in diameter (secondary growth) occur farther down the stem.
 The vascular cambium is a cylinder of meristematic cells that forms secondary vascular
tissue.
 It forms successive layers of secondary xylem to its interior and secondary phloem to
its exterior.
 The accumulation of this tissue over the years accounts for most of the increase in
diameter of a woody plant.
 The vascular cambium develops from parenchyma cells that retain the capacity to
divide.
 This meristem forms in a layer between the primary xylem and primary phloem of
each vascular bundle and in the ground tissue between the bundles.
 The meristematic bands unite to form a continuous cylinder of dividing cells.
 This ring of vascular cambium consists of regions of ray initials and fusiform initials.
 The tapered, elongated cells of the fusiform initials form secondary xylem to the
inside of the vascular cambium and secondary phloem to the outside.
 Ray initials produce vascular rays that transfer water and nutrients laterally within the
woody stem and also store starch and other reserves.
 As secondary growth continues over the years, layer upon layer of secondary xylem
accumulates, producing the tissue we call wood.
 Wood consists mainly of tracheids, vessel elements (in angiosperms), and fibers.
 These cells, dead at functional maturity, have thick, lignified walls that give wood its
hardness and strength.
 In temperate regions, secondary growth in perennial plants ceases during the winter.
 The first tracheid and vessel cells formed in the spring (early wood) have larger
diameters and thinner walls than cells produced later in the summer (late wood).
 The structure of the early wood maximizes delivery of water to new, expanding leaves.
 The thick-walled cells of later wood provide more physical support.
 This pattern of growth—cambium dormancy, early wood production, and late wood
production—produces annual growth rings.
 As a tree or woody shrub ages, the older layers of secondary xylem, known as
heartwood, no longer transport water and minerals.
Biology Chapter Notes
 The outer layers, known as sapwood, continue to transport xylem sap.
 Only the youngest secondary phloem, closest to the vascular cambium, functions in sugar
transport.
 The older secondary phloem dies and is sloughed off as part of the bark.
 The cork cambium acts as a meristem for a tough, thick covering for stems and roots that
replaces the epidermis.
 Early in secondary growth, the epidermis produced by primary growth splits, dries, and
falls off the stem or root.
 It is replaced by two tissues produced by the first cork cambium, which arises in the
outer cortex of stems and in the outer layer of the pericycle of roots.
 The first tissue, phelloderm, is a thin layer of parenchyma cells that forms to the
interior of the cork cambium.
 Cork cambium also produces cork cells, which accumulate at the cambium’s
exterior.
 Waxy material called suberin deposited in the cell walls of cork cells before they
die acts as a barrier against water loss, physical damage, and pathogens.
 The cork plus the cork cambium form the periderm, a protective layer that replaces the
epidermis.
 In areas called lenticels, spaces develop between the cork cells of the periderm.
 These areas within the trunk facilitate gas exchange with the outside air.
 Unlike the vascular cambium, cells of the cork cambium do not divide.
 The thickening of a stem or root splits the first cork cambium, which loses its
meristematic activity and differentiates into cork cells.
 A new cork cambium forms to the inside, resulting in a new layer of periderm.
 As this process continues, older layers of periderm are sloughed off.
 This produces the cracked, peeling bark of many tree trunks.
 Bark refers to all tissues external to the vascular cambium, including secondary phloem,
cork cambium, and cork.

Concept 35.5 Growth, morphogenesis, and differentiation produce the plant body
 During plant development, a single cell, the zygote, gives rise to a multicellular plant of
particular form with functionally integrated cells, tissues, and organs.
 An increase in mass, or growth, results from cell division and cell expansion.
 The development of body form and organization is called morphogenesis.
 The specialization of cells with the same set of genetic instructions to produce a
diversity of cell types is called differentiation.
 Plants have tremendous developmental plasticity.
 Plant form, including height, branching patterns, and reproductive output, is greatly
influenced by environmental factors.
 A broad range of morphologies can result from the same genotype as three
developmental processes—growth, morphogenesis, and differentiation—transform a
zygote into an adult plant.
Molecular biology is revolutionizing the study of plants.
Biology Chapter Notes
 Modern molecular techniques allow plant biologists to investigate how growth,
morphogenesis, and cellular differentiation give rise to a plant.
 Much of this research has focused on Arabidopsis thaliana, a small weed in the
mustard family.
 Thousands of these small plants can be cultivated in a few square meters of lab space.
 With a generation time of about six weeks, it is an excellent model for genetic studies.
 The genome of Arabidopsis is among the tiniest of all known plants.
 Arabidopsis was the first plant to have its genome sequenced, in a six-year multinational
project.
 Arabidopsis has a total of about 26,000 genes, with fewer than 15,000 different types of
genes.
 Now that the DNA sequence of Arabidopsis is known, plant biologists are working to
identify the functions of every one of the plant’s genes by the year 2010.
 To aid in this effort, biologists are attempting to create mutants for every gene in the
plant’s genome.
 Study of the function of these genes has already expanded our understanding of plant
development.
 By identifying each gene’s function, researchers aim to establish a blueprint for how
plants are built.
 One day it may be possible to create a computer-generated “virtual plant” that will
enable researchers to visualize which plant genes are activated in different parts of the
plant during the entire course of development.
Growth involves both cell division and cell expansion.
 Cell division in meristems increases cell number, increasing the potential for growth.
 However, it is cell expansion that accounts for the actual increase in plant mass.
 The plane (direction) and symmetry of cell division are important determinants of plant
form.
 If the planes of division by a single cell and its descendents are parallel to the plane of
the first cell division, a single file of cells will be produced.
 If the planes of cell division of the descendent cells vary at random, an unorganized
clump of cells will result.
 While mitosis results in symmetrical redistribution of chromosomes between daughter
cells, cytokinesis may be asymmetrical.
 Asymmetrical cell division, in which one cell receives more cytoplasm than the other,
is common in plant cells and usually signals a key developmental event.
 For example, guard cells form from an unspecialized epidermal cell through an
asymmetrical cell division and a change in the plane of cell division.
 The plane in which a cell will divide is determined during late interphase.
 Microtubules in the outer cytoplasm become concentrated into a ring, the preprophase
band.
 While this disappears before metaphase, its “imprint” consists of an ordered array of
actin microfilaments that remains after the microtubules disperse and signals the future
plane of cell division.
 Cell expansion in animal cells is quite different from cell expansion in plant cells.
 Animal cells grow by synthesizing a protein-rich cytoplasm, a metabolically expensive
process.
Biology Chapter Notes
  While growing plant cells add some organic material to their cytoplasm, water uptake
by the large central vacuole accounts for 90% of a plant cell’s expansion.
 This enables plants to grow economically and rapidly.
 Bamboo shoots can elongate more than 2 m per week.
 Rapid expansion of shoots and roots increases their exposure to light and soil, an
important evolutionary adaptation to the immobile lifestyle of plants.
 The greatest expansion of a plant cell is usually oriented along the plant’s main axis.
 The orientations of cellulose microfibrils in the innermost layers of the cell wall cause
this differential growth, as the cell expands mainly perpendicular to the “grain” of the
microfibrils.
 Studies of Arabidopsis mutants have confirmed the importance of cortical microtubules in
both cell division and expansion.
 For example, fass mutants have unusually squat cells, which follow seemingly random
planes of cell division.
 Their roots and stems lack the ordered cell files and layers.
 Fass mutants develop into tiny adult plants with all their organs compressed
longitudinally.
 The cortical microtubular organization of fass mutants is abnormal.
 Although the microtubules involved in chromosome movement and in cell plate
deposition are normal, preprophase bands do not form prior to mitosis.
 In interphase cells, the cortical microtubules are randomly positioned.
 Therefore, the cellulose microfibrils deposited in the cell wall cannot be arranged to
determine the direction of the cell’s elongation.
 Cells with a fass mutation expand in all directions equally and divide in a
haphazard arrangement, leading to stout stature and disorganized tissues.
Morphogenesis depends on pattern formation.
 Morphogenesis organizes dividing and expanding cells into multicellular tissues and
organs.
 The development of specific structures in specific locations is called pattern
formation.
 Pattern formation depends to a large extent on positional information, signals that
continuously indicate each cell’s location within an embryonic structure.
 Within a developing organ, each cell responds to positional information by
differentiating into a particular cell type.
 Developmental biologists are accumulating evidence that gradients of specific molecules,
generally proteins or mRNAs, provide positional information.
 For example, a substance diffusing from a shoot’s apical meristem may “inform” the
cells below of their distance from the shoot tip.
 A second chemical signal produced by the outermost cells may enable a cell to gauge
their position relative to the radial axis of the developing organ.
 Developmental biologists are testing the hypothesis that diffusible chemical signals
provide plant cells with positional information.
 One type of positional information is polarity, the identification of the root end and shoot
end along a well-developed axis.
 This polarity results in morphological and physiological differences, and it impacts the
emergence of adventitious roots and shoots from the appropriate ends of plant cuttings.
Biology Chapter Notes
  The first division of the zygote is asymmetrical and may initiate the polarization of the
plant body into root and shoot ends.
 Once the polarity has been induced, it is very difficult to reverse experimentally.
 The establishment of axial polarity is a critical step in plant morphogenesis.
 In the gnom mutant of Arabidopsis, the first division is symmetrical, and the resulting
ball-shaped plant lacks roots and leaves.
 Other genes that regulate pattern formation and morphogenesis include the homeotic
genes, which mediate many developmental events, such as organ initiation.
 For example, the protein product of the KNOTTED-1 homeotic gene is important for
the development of leaf morphology, including production of compound leaves.
 Overexpression of this gene causes the compound leaves of a tomato plant to become
“supercompound.”
Cellular differentiation depends on the control of gene expression.
 The diverse cell types of a plant, including guard cells, sieve-tube members, and xylem
vessel elements, all descend from a common cell, the zygote, and share the same DNA.
 The cloning of whole plants from single somatic cells demonstrates that the genome of a
differentiated cell remains intact and can “dedifferentiate” to give rise to the diverse cell
types of a plant.
 Cellular differentiation depends, to a large extent, on control of gene expression.
 Cells with the same genomes follow different developmental pathways because they
selectively express certain genes at specific times during differentiation.
 For example, two distinct cell types in Arabidopsis, root hair cells and hairless epidermal
cells, develop from immature epidermal cells.
 Cells in contact with one underlying cortical cell differentiate into mature, hairless
cells, while those in contact with two underlying cortical cells differentiate into root
hair cells.
 The homeotic gene GLABRA-2 is normally expressed only in hairless cells. If it is
rendered dysfunctional, every root epidermal cell develops a root hair.
Clonal analysis of the shoot apex emphasizes the importance of a cell’s location in its
developmental fate.
 In the process of shaping a rudimentary organ, patterns of cell division and cell expansion
affect the differentiation of cells by placing them in specific locations relative to other
cells.
 Thus, positional information underlies all the processes of development: growth,
morphogenesis, and differentiation.
 One approach to studying the relationship among these processes is clonal analysis,
mapping the cell lineages (clones) derived from each cell in an apical meristem as organs
develop.
 Researchers induce some change in a cell that tags it in some way such that it (and its
descendents) can be distinguished from its neighbors.
 For example, a somatic mutation in an apical cell that prevents chlorophyll production
will produce an “albino” cell.
 This cell and all its descendants will appear as a linear file of colorless cells running
down the long axis of the green shoot.
 To some extent, the developmental fates of cells in the shoot apex are predictable.

Biology Chapter Notes

  For example, clonal mapping has shown that almost all the cells derived from division
of the outermost meristematic cells become part of the dermal tissue of leaves and
stems.
 However, it is not possible to pinpoint precisely which cells of the meristem will give rise
to specific tissues and organs because random changes in rates and planes of cell division
can reorganize the meristem.
 For example, the outermost cells usually divide in a plane parallel to the surface of the
shoot apex.
 Occasionally, an outer cell divides in a plane perpendicular to this layer, placing one
daughter cell beneath the surface, among cells derived from different lineages.
 In plants, a cell’s developmental fate is determined not by its membership in a particular
lineage but by its final position in an emerging organ.
Phase changes mark major shifts in development.
 In plants, developmental changes can occur within the shoot apical meristem, leading to a
phase change in the organs produced.
 One example of a phase change is the gradual transition from a juvenile phase to an
adult phase.
 In some plants, the result of the phase change is a change in the morphology of the
leaves.
 The leaves of juvenile versus mature shoot regions differ in shape and other features.
 Once the meristem has laid down the juvenile nodes and internodes, they retain that
status even as the shoot continues to elongate and the meristem changes to the mature
phase.
 If axillary buds give rise to branches, those shoots reflect the developmental phase of the
main shoot region from which they arise.
 Though the main shoot apex may have made the transition to the mature phase, the
older region of the shoot continues to give rise to branches bearing juvenile leaves if
that shoot region was laid down when the main apex was still in the juvenile phase.
 A branch with juvenile leaves may actually be older than a branch with mature leaves.
 The juvenile-to-mature phase transition points to another difference in the development of
plants versus animals.
 In an animal, this transition occurs at the level of the entire organism, as a larva
develops into an adult animal.
 In plants, phase changes during the history of apical meristems can result in juvenile
and mature regions coexisting along the axis of each shoot.
Genes controlling transcription play key roles in a meristem’s change from a vegetative to
a floral phase.
 Another striking phase change in plant development is the transition from a vegetative
shoot tip to a floral meristem.
 This transition is triggered by a combination of environmental cues, such as day
length, and internal signals, such as hormones.
 Unlike vegetative growth, which is indeterminate, the production of a flower by an apical
meristem terminates primary growth of that shoot tip as the apical meristem develops into
the flower’s organs.
 This transition is associated with the switching on of floral meristem identity genes.

Biology Chapter Notes

  The protein products of these genes are transcription factors that help activate the
genes required for the development of the floral meristem.
 Once a shoot meristem is induced to flower, positional information commits each
primordium arising from the flanks of the shoot tip to develop into a specific flower
organ.
 Organ identity genes regulate positional information and function in the development
of the floral pattern.
 Mutations in these genes may lead to the substitution of one type of floral organ for
the expected one.
 Organ identity genes code for transcription factors.
 Positional information determines which organ identity genes are expressed in which
particular floral-organ primordium.
 In Arabidopsis, three classes of organ identity genes interact to produce the spatial
pattern of floral organs.
 The ABC model of flower formation identifies how these genes direct the formation of
four types of floral organs.
 The model proposes that each class of organ identity genes is switched on in two
specific whorls of the floral meristem.
 A genes are switched on in the two outer whorls (sepals and petals), B genes are
switched on in the two middle whorls (petals and stamens), and C genes are
switched on in the two inner whorls (stamens and carpels).
 Sepals arise in those parts of the floral meristems in which only A genes are
active.
 Petals arise in those parts of the floral meristems in which A and B genes are
active.
 Stamens arise in those parts of the floral meristems in which B and C genes are
active.
 Carpels arise in those parts of the floral meristems in which only C genes are
active.
 The ABC model can account for the phenotypes of mutants lacking A, B, or C gene
activity.

Biology Chapter Notes

 Chapter 36 Transport in Vascular Plants
Chapter Notes

Overview: Pathways for Survival

 The algal ancestors of plants obtained water, minerals and CO 2 from the water in which
they were completely immersed.
 For vascular plants, the evolutionary journey onto land involved the differentiation of the
plant body into roots, which absorb water and minerals from the soil, and shoots, which
absorb light and atmospheric CO2 for photosynthesis.
 This morphological solution created a new problem: the need to transport materials
between roots and shoots.
 Xylem transports water and minerals from the roots to the shoots.
 Phloem transports sugars from the site of production to the regions that need them for
growth and metabolism.

Concept 36.1 Physical forces drive the transport of materials in plants over a range of
distances
 Transport in plants occurs on three levels:
o The uptake and loss of water and solutes by individual cells, such as root hairs.
o Short-distance transport of substances from cell to cell at the level of tissues or organs,
such as the loading of sugar from photosynthetic leaf cells into the sieve tubes of
phloem.
o Long-distance transport of sap within xylem and phloem at the level of the whole
plant.
Transport at the cellular level depends on the selective permeability of membranes.
 The selective permeability of a plant cell’s plasma membrane controls the movement of
solutes between the cell and the extracellular solution.
 Molecules tend to move down their concentration gradient. Diffusion across a
membrane is called passive transport and occurs without the direct expenditure of
metabolic energy by the cell.
 Active transport is the pumping of solutes across membranes against their
electrochemical gradients, and requires expenditure of energy by the cell.
 The cell must expend metabolic energy, usually in the form of ATP, to transport
solutes “uphill.”
 Transport proteins embedded in the membrane can speed movement across the
membrane.
 Some transport proteins bind selectively to a solute on one side of the membrane and
release it on the opposite side.
 Others act as selective channels, providing a selective passageway across the
membrane.
 For example, the membranes of most plant cells have potassium channels that allow
potassium ions (K+) to pass, but not similar ions, such as sodium (Na+).

Biology Chapter Notes

 Some channels are gated, opening or closing in response to certain environmental or
biochemical stimuli.
Proton pumps play a central role in transport across plant membranes.
 The most important active transport protein in the plasma membrane of plant cells is the
proton pump.
 It hydrolyzes ATP and uses the released energy to pump hydrogen ions (H+) out of the
cell.
 This creates a proton gradient because the H+ concentration is higher outside the cell
than inside.
 It also creates a membrane potential or voltage, a separation of opposite charges
across a membrane.
 Both the concentration gradient and the membrane potential are forms of potential
(stored) energy that can be harnessed to perform cellular work.
 This potential energy is used to drive the transport of many different solutes.
 For example, the membrane+ potential generated by proton pumps contributes to the
uptake of potassium ions (K ) by root cells.
 The proton gradient also functions in cotransport, in which the downhill passage of one
solute (H+) is coupled with the uphill passage of another, such as NO3− or sucrose.
 The role of proton pumps in transport is a specific application of the general mechanism
called chemiosmosis, a unifying process in cellular energetics.
 In chemiosmosis, a transmembrane proton gradient links energy-releasing processes to
energy-consuming processes.
 The ATP synthases that couple H+ diffusion to ATP synthesis during cellular
respiration and photosynthesis function somewhat like proton pumps.
 However, proton pumps normally run in reverse, using ATP energy to pump H +
against its gradient.
Differences in water potential drive water transport in plant cells.
 The survival of plant cells depends on their ability to balance water uptake and loss.
 The net uptake or loss of water by a cell occurs by osmosis, the passive transport of water
across a membrane.
 In the case of a plant cell, the direction of water movement depends on solute
concentration and physical pressure.
 The combined effects of solute concentration and pressure are called water potential,
represented by the Greek letter “psi.”
 Water will move across a membrane from the solution with the higher water potential
to the solution with the lower water potential.
 For example, if a plant cell is immersed in a solution with a higher water potential than
the cell, osmotic uptake of water will cause the cell to swell.
 By moving, water can perform work, such as expanding the cell.
 Therefore the potential in water potential refers to the potential energy that can be
released to do work when water moves from a region with higher psi to lower psi.
 Plant biologists measure psi in units called megapascals (MPa), where one MPa is equal
to about 10 atmospheres of pressure.
 An atmosphere is the pressure exerted at sea level by an imaginary column of air—
about 1 kg of pressure per square centimeter.

Biology Chapter Notes

  A car tire is usually inflated to a pressure of about 0.2 MPa; water pressure in home
plumbing is about 0.25 MPa.
 In contrast, plant cells exist at approximately 1 MPa.
 Both pressure and solute concentration affect water potential.
 The combined effects of pressure and solute concentrations on water potential are
incorporated into the following equation, where psi p is the pressure potential and psis is
the solute potential (or osmotic potential).
 psi = psip + psis
 Pressure potential is the physical pressure on a solution and can be positive or
negative.
 The water in the dead vessel element cells of xylem may be under negative pressure
of less than −2 MPa.
 Water in living cells is usually under positive pressure. The cell contents press the
plasma membrane against the cell wall, producing turgor pressure.
 The solute potential (or osmotic potential) of a solution is proportional to the number
of dissolved solute molecules.
 By definition, the solute potential of pure water is 0.
 The addition of solutes lowers the water potential because the solutes bind water
molecules, which have less freedom to move than they do in pure water.
 Any solution at atmospheric pressure has a negative water potential.
 For instance, a 0.1-molar (M) solution of any solute has a water potential of
−0.23 MPa.
 If a 0.1 M solution is separated from pure water by a selectively permeable
membrane, water will move by osmosis into the solution.
 Water will move from the region of higher psi (0 MPa) to the region of lower psi
(−0.23 MPa).
 Water potential affects the uptake and loss of water in plant cells.
 In a flaccid cell, psip = 0 and the cell is limp.
 If this cell is placed in a solution with a higher solute concentration (and, therefore, a
lower psi), water will leave the cell by osmosis.
 Eventually, the cell will plasmolyze by shrinking and pulling away from its wall.
 If a flaccid cell is placed in pure water (psi = 0), the cell will have lower water potential
than pure water due to the presence of solutes, and water will enter the cell by osmosis.
 As the cell begins to swell, it will push against the cell wall, producing turgor pressure.
 The partially elastic wall will push back until this pressure is great enough to offset the
tendency for water to enter the cell because of solutes.
 When psip and psis are equal in magnitude (but opposite in sign), psi = 0, and the cell has
reached a dynamic equilibrium with the environment, with no further net movement of
water in or out.
 A walled cell with a greater solute concentration than its surroundings will be turgid, or
firm.
 Healthy plants are turgid most of the time, and their turgor contributes to support in
nonwoody parts of the plant.
 You can see the effects of turgor loss in wilting, the drooping of leaves and stems as
plant cells become flaccid.

Biology Chapter Notes

 Aquaporins affect the rate of water transport across membranes.
 Both plant and animal membranes have specific transport proteins, aquaporins, which
facilitate the passive movement of water across a membrane.
 Aquaporins do not affect the water potential gradient or the direction of water flow, but
rather increase the rate at which water diffuses down its water potential gradient.
 Evidence is accumulating that the rate of water movement through aquaporins is
regulated by changes in second messengers such as calcium ions (Ca 2+).
 This raises the possibility that the cell can regulate its rate of water uptake or loss when
its water potential is different from that of its environment.
Vacuolated plant cells have three major compartments.
 While the thick cell wall helps maintain cell shape, it is the cell membrane, not the cell
wall, which regulates the traffic of material into and out of the protoplast.
 This membrane is a barrier between two major compartments: the cell wall and the
cytosol.
 Most mature plants have a third major compartment, the vacuole, a large organelle that
can occupy as much as 90% of the protoplast’s volume.
 The membrane that bounds the vacuole, the tonoplast, regulates molecular traffic
between the cytosol and the contents of the vacuole, called the cell sap.
 Proton pumps in the tonoplast expel H+ from the cytosol into the vacuole.
 The resulting pH gradient is used to move other ions across the tonoplast by
chemiosmosis.
 In most plant tissues, two of the three cellular compartments are continuous from cell to
cell.
 Plasmodesmata connect the cytosolic compartments of neighboring cells.
 This cytoplasmic continuum, the symplast, forms a continuous pathway for transport
of certain molecules between cells.
 The walls of adjacent plant cells are also in contact, forming a second continuous
compartment, the apoplast.
 The vacuole is not shared with neighboring cells.
Both the symplast and the apoplast function in transport within tissues and organs.
 Short-distance transport in plants, the movement of water and solutes from one location to
another within plant tissues and organs, is called lateral transport because its usual
direction is along the radial axis of plant organs, rather than up or down the length of the
plant.
 Three routes are available for lateral transport.
 In one route, substances move out of one cell, across the cell wall, and into the
neighboring cell, which may then pass the substances along to the next cell by the same
mechanism.
 This transmembrane route requires repeated crossings of plasma membranes.
 The second route, via the symplast, requires only one crossing of a plasma membrane.
 After entering one cell, solutes and water move from cell to cell via plasmodesmata.
 The third route is along the apoplast, the extracellular pathway consisting of cell wall and
extracellular spaces.
 Water and solutes can move from one location to another within a root or other organ
through the continuum of cell walls without ever entering a cell.
Biology Chapter Notes
 Bulk flow functions in long-distance transport.
 Diffusion in a solution is fairly efficient for transport over distances of cellular dimensions
(less than 100 microns).
 However, diffusion is much too slow for long-distance transport within a plant, such as
the movement of water and minerals from roots to leaves.
 Water and solutes move through xylem vessels and sieve tubes by bulk flow, the
movement of a fluid driven by pressure.
 In phloem, hydrostatic pressure generated at one end of a sieve tube forces sap to the
opposite end of the tube.
 In xylem, it is actually tension (negative pressure) that drives long-distance transport.
 Transpiration, the evaporation of water from a leaf, reduces pressure in the leaf
xylem.
 This creates a tension that pulls xylem sap upward from the roots.
 Rate of flow through a pipe depends on a pipe’s internal diameter.
 To maximize bulk flow, the sieve-tube members are almost entirely devoid of internal
organelles.
 Vessel elements and tracheids are dead at maturity.
 The porous plates that connect contiguous sieve-tube members and the perforated end
walls of xylem vessel elements also enhance bulk flow.

Concept 36.2 Roots absorb water and minerals from the soil
 Water and mineral salts from soil enter the plant through the epidermis of roots, cross the
root cortex, pass into the vascular cylinder, and then flow up xylem vessels to the shoot
system.
o The uptake of soil solution by the hydrophilic epidermal walls of root hairs provides
access to the apoplast, and water and minerals can soak into the cortex along this route.
o Minerals and water that cross the plasma membranes of root hairs enter the symplast.
o Some water and minerals are transported into cells of the epidermis and cortex and
then move inward via the symplast.
o Materials flowing along the apoplastic route are blocked by the waxy Casparian strip at
the endodermis. Some minerals detour around the Casparian strip by crossing the
plasma membrane of an endodermal cell to pass into the vascular cylinder.
o Endodermal and parenchyma cells within the vascular cylinder discharge water and
minerals into their walls (apoplast). The water and minerals enter the dead cells of
xylem vessels and are transported upward into the shoots.
Root hairs, mycorrhizae, and a large surface area of cortical cells enhance water and
mineral absorption.
 Much of the absorption of water and minerals occurs near root tips, where the epidermis is
permeable to water and where root hairs are located.
 Root hairs, extensions of epidermal cells, account for much of the surface area of roots.
 The soil solution flows into the hydrophilic walls of epidermal cells and passes freely
along the apoplast into the root cortex, exposing all the parenchyma cells to soil
solution and increasing membrane surface area.
 As the soil solution moves along the apoplast into the roots, cells of the epidermis and
cortex take up water and certain solutes into the symplast.
Biology Chapter Notes
  Selective transport proteins of the plasma membrane and tonoplast enable root cells to
extract essential minerals from the dilute soil solution and concentrate them hundreds
of times higher than in the soil solution.
 This selective process
+
enables the cell to extract K +, an essential mineral nutrient, and
exclude most Na .
 Most plants form partnerships with symbiotic fungi to absorb water and minerals from
soil.
 “Infected” roots form mycorrhizae, symbiotic structures consisting of the plant’s roots
united with the fungal hyphae.
 Hyphae absorb water and selected minerals, transferring much of these to the host plants.
 The mycorrhizae create an enormous surface area for absorption and enable older regions
of the roots to supply water and minerals to the plant.
The endodermis functions as a selective sentry between the root cortex and vascular
tissue.
 Water and minerals in the root cortex cannot be transported to the rest of the plant until
they enter the xylem of the vascular cylinder.
 The endodermis, the innermost layer of cells in the root cortex, surrounds the vascular
cylinder and functions as a final checkpoint for the selective passage of minerals from
the cortex into the vascular tissue.
 Minerals already in the symplast continue through the plasmodesmata of the
endodermal cells and pass into the vascular cylinder.
 These minerals were already screened by the selective membrane they crossed to enter
the symplast.
 Those minerals that reach the endodermis via the apoplast are blocked by the Casparian
strip in the walls of each endodermal cell.
 This strip is a belt of suberin, a waxy material that is impervious to water and dissolved
minerals.
 To enter the vascular cylinder, minerals must cross the plasma membrane of the
endodermal cell and enter the vascular cylinder via the symplast.
 The endodermis, with its Casparian strip, ensures that no minerals reach the vascular
tissue of the root without crossing a selectively permeable plasma membrane.
 The endodermis acts as a sentry on the cortex-vascular cylinder border.
 The last segment in the soil-to-xylem pathway is the passage of water and minerals into
the tracheids and vessel elements of the xylem.
 Because these cells lack protoplast, the lumen and the cell walls are part of the
apoplast.
 Endodermal cells and parenchyma cells within the vascular cylinder discharge
minerals into their walls.
 Both diffusion and active transport are involved in the transfer of solutes from the
symplast to apoplast, finally entering the tracheids and xylem vessels.

Concept 36.3 Water and minerals ascend from roots to shoots through the xylem
 Xylem sap flows upward to veins that branch throughout each leaf, providing each with
water.

Biology Chapter Notes

 Plants lose an astonishing amount of water by transpiration, the loss of water vapor from
leaves and other aerial parts of the plant.
 A single corn plant transpires 125 L of water during its growing season.
 The flow of water transported up from the xylem replaces the water lost in transpiration
and also carries minerals to the shoot system.
The ascent of xylem sap depends mainly on transpiration and the physical properties of
water.
 Xylem sap rises against gravity to reach heights of more than 100 m in the tallest trees.
 At night, when transpiration is very low or zero, the root cells continue to expend energy
while pumping mineral ions into the xylem.
 The accumulation of minerals in the vascular cylinder lowers water potential there,
generating a positive pressure, called root pressure, which forces fluid up the xylem.
 Root pressure causes guttation, the exudation of water droplets that can be seen in the
morning on the tips of grass blades or the leaf margins of some small, herbaceous dicots.
 In most plants, root pressure is not the major mechanism driving the ascent of xylem sap.
 At most, root pressure can force water upward only a few meters, and many plants
generate no root pressure at all.
 For the most part, xylem sap is not pushed from below by root pressure but is pulled
upward by the leaves themselves.
 Transpiration provides the pull, and the cohesion and adhesion of water due to
hydrogen bonding transmits the upward pull along the entire length of the xylem to the
roots.
 The mechanism of transpiration depends on the generation of negative pressure (tension)
in the leaf due to the unique physical properties of water.
 As water transpires from the leaf, water coating the mesophyll cells replaces water lost
from the air spaces.
 As water evaporates, the remaining film of liquid water retreats into the pores of the
cell walls, attracted by adhesion to the hydrophilic walls.
 Cohesive forces in water resist an increase in the surface area of the film.
 Adhesion to the wall and surface tension cause the surface of the water film to form a
meniscus, “pulling on” the water by adhesive and cohesive forces.
 The water film at the surface of leaf cells has a negative pressure, a pressure less than
atmospheric pressure.
 The more concave the meniscus, the more negative the pressure of the water film.
 This tension is the pulling force that draws water out of the leaf xylem, through the
mesophyll, and toward the cells and surface film bordering the air spaces.
 The tension generated by adhesion and surface tension lowers the water potential, drawing
water from an area of high water potential to an area of lower water potential.
 Mesophyll cells lose water to the surface film lining the air spaces, which in turn loses
water by transpiration.
 The water lost via the stomata is replaced by water pulled out of the leaf xylem.
 The transpirational pull on xylem sap is transmitted all the way from the leaves to the root
tips and even into the soil solution.
 Cohesion of water due to hydrogen bonding makes it possible to pull a column of sap
from above without the water molecules separating.
Biology Chapter Notes
  Helping to fight gravity is the strong adhesion of water molecules to the hydrophilic
walls of the xylem cells.
 The very small diameter of the tracheids and vessel elements exposes a large
proportion of the water to the hydrophilic walls.
 The upward pull on the cohesive sap creates tension within the xylem.
 This tension can actually cause a measurable decrease in the diameter of a tree on a
warm day.
 Transpiration puts the xylem under tension all the way down to the root tips, lowering
the water potential in the root xylem and pulling water from the soil.
 Transpirational pull extends down to the roots only through an unbroken chain of water
molecules.
 Cavitation, the formation of water vapor pockets in the xylem vessel, breaks the chain.
 This occurs when xylem sap freezes in water.
 Small plants use root pressure to refill xylem vessels in spring.
 Root pressure cannot push water to the top of a tree. In trees, a xylem vessel with a
water vapor pocket can never function as a water pipe again.
 The transpirational stream can detour around the water vapor pocket, and secondary
growth adds a new layer of xylem vessels each year.
 Only the youngest, outermost secondary xylem vessels in trees transport water. The
older xylem vessels no longer function in water transport but do provide support for
the tree.
Xylem sap ascends by solar-powered bulk flow: a review.
 Long-distance transport of water from roots to leaves occurs by bulk flow.
 The movement of fluid is driven by a water potential difference at opposite ends of a
conduit, the xylem vessels or chains of tracheids.
 The water potential difference is generated at the leaf end by transpirational pull,
which lowers water potential (increases tension) at the “upstream” end of the xylem.
 On a smaller scale, gradients of water potential drive the osmotic movement of water
from cell to cell within root and leaf tissue.
 Differences in both solute concentration and turgor pressure contribute to this
microscopic transport.
 In contrast, bulk flow, the mechanism for long-distance transport up xylem vessels,
depends only on pressure.
 In contrast to osmosis, bulk flow moves the whole solution, water plus minerals and
any other solutes dissolved in the water.
 The plant expends none of its own metabolic energy to lift xylem sap up to the leaves by
bulk flow.
 The absorption of sunlight drives transpiration by causing water to evaporate from the
moist walls of mesophyll cells and by lowering the water potential in the air spaces within
a leaf.
 Thus, the ascent of xylem sap is ultimately solar powered.

Concept 36.4 Stomata help regulate the rate of transpiration

Most leaves have broad surface areas and high ratios of surface area to volume.
Biology Chapter Notes
  These features are morphological adaptations to enhance the absorption of light for
photosynthesis.
 They also increase water loss through stomata.
 To make food, a plant must spread its leaves to the sun and obtain CO2 from air.
 Carbon dioxide diffuses into and oxygen diffuses out of the leaf via the stomata.
 Within the leaf, CO2 enters a honeycomb of air spaces formed by the irregularly
shaped parenchyma cells.
 This internal surface may be 10 to 30 times greater than the external leaf surface.
 This structural feature increases exposure to CO2 but also increases the surface area
for evaporation.
 A leaf may transpire more than its weight in water each day.
 Water flows in xylem vessels may reach 75 cm/min.
 Transpiration also results in evaporative cooling, which can lower the temperature of a
leaf by as much as 10–15°C relative to the surrounding air.
 About 90% of the water that a plant loses escapes through stomata, though these pores
account for only 1–2% of the external leaf surface.
 The amount of water lost by a leaf depends on the number of stomata and the average size
of their apertures.
 The stomatal density of a leaf is under both genetic and environmental control.
 Desert plants have lower stomatal densities than do marsh plants.
 High light intensities and low carbon dioxide levels during plant development tend to
increase stomatal density in many plant species.
 A recent British survey found that stomatal density of many woodland species has
decreased since 1927. This is consistent with the dramatic increases in CO2 levels due
to burning of fossil fuels.
 This prevents the leaf from reaching temperatures that could denature enzymes.
Guard cells mediate the photosynthesis-transpiration compromise.
 Each stoma is flanked by a pair of guard cells that are suspended by other epidermal cells
over an air chamber, leading to the internal air space.
 Guard cells control the diameter of the stoma by changing shape, thereby widening or
narrowing the gap between the two cells.
 When guard cells take in water by osmosis, they become more turgid, and because of
the orientation of cellulose microfibrils, the guard cells buckle outward.
 This increases the gap between cells.
 When guard cells lose water and become flaccid, they become less bowed, and the
space between them closes.
 Changes in turgor pressure that open and close stomata result primarily from the
reversible uptake and loss of potassium ions (K+) by guard cells.
 Stomata open when guard cells actively accumulate K+ into the vacuole.
 This decreases water potential in guard cells, leading to an inflow of water by osmosis
and increasing cell turgor.
 Stomatal closing results from an exodus of K+ from guard cells, leading to osmotic loss
of water.
 Regulation of aquaporins may also be involved in the swelling and shrinking of guard
cells by varying the permeability of the membranes to water.
Biology Chapter Notes
 The K+ fluxes across the guard cell membranes are coupled to the generation of
membrane potentials by proton pumps.
 Stomatal opening correlates with active transport of H+ out of guard cells.
 The resulting voltage (membrane potential) drives K + into the cell through specific
membrane channels.
 In general, stomata are open during the day and closed at night to minimize water loss
when it is too dark for photosynthesis.
 At least three cues contribute to stomatal opening at dawn.
 First, blue-light receptors in the guard cells stimulate the activity of ATP-powered
proton pumps in the plasma membrane, promoting the uptake of K+.
 A second stimulus is depletion of CO2 within air spaces of the leaf as photosynthesis
begins.
 A third cue in stomatal opening is an internal “clock” located in the guard cells.
 Even in the dark, stomata will continue their daily rhythm of opening and closing due
to the presence of internal clocks that regulate cyclic processes.
 The opening and closing cycle of the stomata is an example of a circadian rhythm,
cycles that have intervals of approximately 24 hours.
 Various environmental stresses can cause stomata to close during the day.
 When the plant is suffering a water deficiency, guard cells may lose turgor and close
stomata.
 Abscisic acid, a hormone produced by the mesophyll cells in response to water
deficiency, signals guard cells to close stomata.
 While reducing further wilting, this also slows photosynthesis.
Xerophytes have evolutionary adaptations that reduce transpiration.
 Plants adapted to arid climates, called xerophytes, have various leaf modifications that
reduce the rate of transpiration.
 Many xerophytes have small, thick leaves, reducing leaf surface area relative to leaf
volume.
 A thick cuticle gives some of these leaves a leathery consistency.
 During the driest months, some desert plants shed their leaves, while others (such as
cacti) subsist on water stored in fleshy stems during the rainy season.
 In most plants, the stomata are concentrated on the lower (shady) leaf surface.
 In xerophytes, they are often located in depressions (“crypts”) that shelter the pores
from the dry wind.
 Trichomes (“hairs”) also help minimize transpiration by breaking up the flow of air,
keeping humidity higher in the crypt than in the surrounding atmosphere.
 An elegant adaptation to arid habitats is found in ice plants, in succulent species of the
family Crassulaceae, and in representatives of many other families.
 These assimilate CO2 by an alternative photosynthetic pathway, crassulacean acid
metabolism (CAM).
 Mesophyll cells in CAM plants store CO2 in organic acids during the night and release
the CO2 from these organic acids during the day.
 This CO2 is used to synthesize sugars by the conventional (C3) photosynthetic
pathway, allowing the stomata to remain closed during the day when transpiration
is greatest.

Biology Chapter Notes

Concept 36.5 Organic nutrients are translocated through the phloem
 The phloem transports the organic products of photosynthesis throughout the plant via a
process called translocation.
 In angiosperms, the specialized cells of the phloem that function in translocation are
the sieve-tube members.
 These are arranged end to end to form long sieve tubes with porous cross-walls
between cells along the tube.
 Phloem sap is an aqueous solution in which sugar, primarily the disaccharide sucrose, is
the most common solute.
 Sucrose concentration in sap can be as high as 30% by weight.
 Sap may also contain minerals, amino acids, and hormones.
Phloem translocates its sap from sugar sources to sugar sinks.
 In contrast to the unidirectional flow of xylem sap from roots to leaves, the direction that
phloem sap travels can vary.
 Sieve tubes always carry food from a sugar source to a sugar sink.
 A sugar source is a plant organ (especially mature leaves) in which sugar is being
produced by either photosynthesis or the breakdown of starch.
 A sugar sink is an organ (such as growing roots, shoots, or fruit) that is a net
consumer or store of sugar.
 Mature leaves are the primary sugar sources.
 Growing roots, buds, stems, and fruits are sugar sinks.
 A storage organ, such as a tuber or a bulb, may be either a source or a sink, depending on
the season.
 When the storage organ is stockpiling carbohydrates during the summer, it is a sugar
sink.
 After breaking dormancy in the early spring, the storage organ becomes a source as its
starch is broken down to sugar, which is carried away in the phloem to the growing
buds of the shoot system.
 Other solutes, such as minerals, are also transported to sinks along with sugar.
 A sugar sink usually receives its sugar from the sources nearest to it.
 The upper leaves on a branch may send sugar to the growing shoot tip, whereas the
lower leaves of the same branch export sugar to roots.
 One sieve tube in a vascular bundle may carry phloem sap in one direction while sap in a
different tube in the same bundle may flow in the opposite direction.
 The direction of transport in each sieve tube depends only on the locations of the
source and sink connected by that tube.
 Sugar from mesophyll cells or other sources must be loaded into sieve-tube members
before it can be exported to sugar sinks.
 In some species, sugar moves from mesophyll cells to sieve-tube members via the
symplast.
 In other species, sucrose reaches sieve-tube members by a combination of symplastic
and apoplastic pathways.

Biology Chapter Notes

 For example, in corn leaves, sucrose diffuses through the symplast from mesophyll cells
into small veins.
 Much of this sugar moves out of the cells into the apoplast in the vicinity of sieve-tube
members and companion cells.
 Companion cells pass the sugar they accumulate into the sieve-tube members via
plasmodesmata.
 In some plants, companion cells (transfer cells) have numerous ingrowths in their walls
to increase the cell’s surface area and enhance the transfer of solutes between apoplast and
symplast.
 In corn and many other plants, sieve-tube members accumulate sucrose at concentrations
two to three times higher than those in mesophyll cells.
 This requires active transport to load the phloem.
 Proton pumps generate an H+ gradient, which drives sucrose across the +membrane via
a cotransport protein that couples sucrose transport to the diffusion of H back into the
cell.
 Downstream, at the sink end of the sieve tube, phloem unloads its sucrose.
 The mechanism of phloem unloading is highly variable and depends on plant species
and type of organ.
 Regardless of mechanism, because the concentration of free sugar in the sink is lower
than in the phloem, sugar molecules diffuse from the phloem into the sink tissues.
 Water follows by osmosis.
Pressure flow is the mechanism of translocation in angiosperms.
 Phloem sap flows from source to sink at rates as great as 1 m/hr, faster than can be
accounted for by either diffusion or cytoplasmic streaming.
 Phloem sap moves by bulk flow driven by positive pressure.
 Higher levels of sugar at the source lowers the water potential and causes water to flow
into the tube.
 Removal of sugar at the sink increases the water potential and causes water to flow out
of the tube.
 The difference in hydrostatic pressure drives phloem sap from the source to the sink.
 Pressure flow in a sieve tube drives the bulk flow of phloem sap.
o Loading of sugar into the sieve tube at the source reduces the water potential inside the
sieve-tube members and causes the uptake of water.
o This absorption of water generates hydrostatic pressure that forces the sap to flow
along the tube.
o The pressure is relieved by unloading of sugar and loss of water from the tube at the
sink.
o For leaf-to-root translocation, xylem recycles water from sink to source
 The pressure flow model explains why phloem sap always flows from source to sink.
 Researchers have devised several experiments to test this model, including an innovative
experiment that exploits natural phloem probes: aphids that feed on phloem sap.
 The closer the aphid’s stylet is to a sugar source, the faster the sap will flow and the
greater its sugar concentration.
 In our study of how sugar moves in plants, we have seen examples of plant transport on
three levels.
Biology Chapter Notes
 o At the cellular level across membranes, sucrose accumulates in phloem cells by active
transport.
o At the short-distance level within organs, sucrose migrates from mesophyll to phloem
via the symplast and apoplast.
o At the long-distance level between organs, bulk flow within sieve tubes transports
phloem sap from sugar sources to sugar sinks.
 Interestingly, the transport of sugar from the leaf, not photosynthesis, limits plant yields.
 Genetic engineering of higher-yielding crop plants may depend on a better understanding
of factors that limit bulk flow of sugars.


Biology Chapter Notes

 Chapter 37 Plant Nutrition
Chapter Notes

Outline: A Nutritional Network

 Every organism is an open system linked to its environment by a continuous exchange of

energy and materials.
 In ecosystems, plants and other photosynthetic autotrophs perform the crucial step of
transforming inorganic compounds into organic ones.
 Plants need sunlight as the energy source for photosynthesis.
 They also need inorganic raw materials such as water, CO2, and inorganic ions to
synthesize organic molecules.
 Plants obtain CO2 from the air. Most vascular plants obtain water and minerals from
the soil through their roots.
 The branching root and shoot systems of vascular plants allow them to draw from soil
and air reservoirs of inorganic nutrients.
 Roots, through fungal mycorrhizae and root hairs, absorb water and minerals from
the soil.
 CO2 diffuses into leaves from the surrounding air through stomata.

Concept 37.1 Plants require certain chemical elements to complete their life cycle
 Early ideas about plant nutrition were not entirely correct and included:
 Aristotle’s hypothesis that soil provided the substance for plant growth.
 van Helmont’s conclusion from his experiments that plants grow mainly from water.
 Hale’s postulate that plants are nourished mostly by air.
 In fact, soil, water, and air all contribute to plant growth.
 Plants extract mineral nutrients from the soil. Mineral nutrients are essential chemical
elements absorbed from soil in the form of inorganic ions.
 For example, many plants acquire nitrogen in the form of nitrate ions (NO 3−).
 However, as van Helmont’s data suggested, mineral nutrients from the soil contribute
little to the overall mass of a plant.
 About 80–90% of a plant is water. Because water contributes most of the hydrogen ions
and some of the oxygen atoms that are incorporated into organic atoms, one can consider
water a nutrient.
 However, only a small fraction of the water entering a plant contributes to organic
molecules.
 More than 90% of the water absorbed by a field of corn is lost by transpiration.
 Most of the water retained by a plant functions as a solvent, provides most of the mass
for cell elongation, and helps maintain the form of soft tissues by keeping cells turgid.
 By weight, the bulk of the organic material of a plant is derived not from water or soil
minerals, but from the CO2 assimilated from the atmosphere.

Biology Chapter Notes

 The dry weight of an organism can be determined by drying it to remove all water. About
95% of the dry weight of a plant consists of organic molecules. The remaining 5%
consists of inorganic molecules.
 Most of the organic material is carbohydrate, including cellulose in cell walls.
 Carbon, hydrogen, and oxygen are the most abundant elements in the dry weight of
a plant.
 Because some organic molecules contain nitrogen, sulfur, and phosphorus, these
elements are also relatively abundant in plants.
 More than 50 chemical elements have been identified among the inorganic substances
present in plants.
 However, not all of these 50 are essential elements, required for the plant to complete
its life cycle and reproduce.
 Roots are able to absorb minerals somewhat selectively, enabling the plant to accumulate
essential elements that may be present in low concentrations in the soil.
 However, the minerals in a plant also reflect the composition of the soil in which the
plant is growing.
 Some elements are taken up by plant roots even though they do not have any function
in the plant.
Plants require nine macronutrients and at least eight micronutrients.
 Plants can be grown in hydroponic culture to determine which mineral elements are
actually essential nutrients.
 Plants are grown in solutions of various minerals in known concentrations.
 If the absence of a particular mineral, such as potassium, causes a plant to become
abnormal in appearance when compared to controls grown in a complete mineral
medium, then that element is essential.
 Such studies have identified 17 elements that are essential nutrients in all plants and a
few other elements that are essential to certain groups of plants.
 Elements required by plants in relatively large quantities are macronutrients.
 There are nine macronutrients in all, including the six major ingredients in organic
compounds: carbon, oxygen, hydrogen, nitrogen, sulfur, and phosphorus.
 The other three macronutrients are potassium, calcium, and magnesium.
 Elements that plants need in very small amounts are micronutrients.
 The eight micronutrients are iron, chlorine, copper, zinc, manganese, molybdenum,
boron, and nickel.
 Most of these function as cofactors, nonprotein helpers in enzymatic reactions.
 For example, iron is a metallic component in cytochromes, proteins that function in the
electron transfer chains of chloroplasts and mitochondria.
 While the requirement for these micronutrients is modest (e.g., only one atom of
molybdenum for every 60 million hydrogen atoms in dry plant material), a deficiency
of a micronutrient can weaken or kill a plant.
The symptoms of a mineral deficiency depend on the function and mobility of the element.
 The symptoms of a mineral deficiency depend in part on the function of that nutrient in
the plant.
 For example, a deficiency in magnesium, an ingredient of chlorophyll, causes
yellowing of the leaves, or chlorosis.
 The relationship between a mineral deficiency and its symptoms can be less direct.
Biology Chapter Notes
  For example, chlorosis can also be caused by iron deficiency because iron is a required
cofactor in chlorophyll synthesis.
 Mineral deficiency symptoms also depend on the mobility of the nutrient within the plant.
 If a nutrient can move freely from one part of a plant to another, then symptoms of the
deficiency will appear first in older organs.
 Young, growing tissues have more “drawing power” than old tissues for nutrients
in short supply.
 For example, a shortage of magnesium will initially lead to chlorosis in older
leaves.
 If a nutrient is relatively immobile, then a deficiency will affect young parts of the
plant first.
 Older tissue may have adequate supplies, which they can retain during periods of
shortage.
 For example, iron does not move freely within a plant. Chlorosis due to iron
deficiency appears first in young leaves.
 The symptoms of a mineral deficiency are often distinctive enough for a plant
physiologist or farmer to make a preliminary diagnosis of the problem.
 This can be confirmed by analyzing the mineral content of the plant and the soil.
 Deficiencies of nitrogen, potassium, and phosphorus are the most common problems.
 Shortages of micronutrients are less common and tend to be geographically localized
due to differences in soil composition.
 The amount of micronutrient needed to correct a deficiency is usually quite small.
Care must be taken, because a nutrient overdose can be toxic to plants.
 One way to ensure optimal mineral nutrition is to grow plants hydroponically on nutrient
solutions that can be precisely regulated.
 This technique is practiced commercially, but the requirements for labor and
equipment make it relatively expensive compared with growing crops in soil.
 Mineral deficiencies are not limited to terrestrial ecosystems or to plants.
 Photosynthetic protists and bacteria can also suffer from mineral deficiencies.
 For example, populations of planktonic algae in the southern oceans are limited by iron
deficiency.
 In a trial in relatively unproductive seas between Tasmania and Antarctica,
researchers demonstrated that dispersing small amounts of iron produced large algal
blooms that pulled carbon dioxide out of the air.
 Seeding the oceans with iron may help slow the increase in carbon dioxide levels in
the atmosphere, but it may cause unanticipated environmental effects.

Concept 37.2 Soil quality is a major determinant of plant distribution and growth
Soil texture and composition are key environmental factors in terrestrial ecosystems.
 The texture and chemical composition of soil are major factors determining what kinds of
plants can grow well in a particular location.
 Texture is the general structure of soil, including the relative amounts of various sizes
of soil particles.
 Composition is the soil’s organic and inorganic components.

Biology Chapter Notes

 Plants that grow naturally in a certain type of soil are adapted to its texture and
composition and are able to absorb water and extract essential nutrients from that soil.
 Plants, in turn, affect the soil.
 The soil-plant interface is a critical component of the chemical cycles that sustain
terrestrial ecosystems.
 Soil has its origin in the weathering of solid rock.
 Water that seeps into crevices and freezes in winter fractures rock. Acids dissolved in
soil water also help break down rock chemically.
 Organisms, including lichens, fungi, bacteria, mosses, and the roots of vascular plants,
accelerate the breakdown by the secretion of acids and the expansion of roots in
fissures.
 This activity eventually results in topsoil, a mixture of particles from rock; living
organisms; and humus, a residue of partially decayed organic material.
 Topsoil and other distinct soil layers, called horizons, are often visible in a vertical profile
through soil.
 Topsoil, or the A horizon, is richest in organic material and is thus the most important
horizon for plant growth.
 The texture of topsoil depends on the size of its particles, which are classified from coarse
sand to microscopic clay particles.
 The most fertile soils are loams, made up of roughly equal amounts of sand, silt
(particles of intermediate size), and clay.
 Loamy soils have enough fine particles to provide a large surface area for retaining
minerals and water, which adhere to the particles.
 Loams also have enough course particles to provide air spaces that supply oxygen to
the root for cellular respiration.
 Inadequate drainage can dramatically impact survival of many plants.
 Plants can suffocate if air spaces are replaced by water.
 Roots can also be attacked by molds that flourish in soaked soil.
 Topsoil is home to an astonishing number and variety of organisms.
 A teaspoon of soil has about 5 billion bacteria that cohabit with various fungi, algae
and other protists, insects, earthworms, nematodes, and the roots of plants.
 The activities of these organisms affect the physical and chemical properties of soil.
 For example, earthworms aerate soil by burrowing and add mucus that holds fine
particles together.
 Bacterial metabolism alters the mineral composition of soil.
 Plant roots extract water and minerals. They also affect soil pH by releasing organic
acids and reinforce the soil against erosion.
 Humus is the decomposing organic material formed by the action of bacteria and fungi on
dead organisms, feces, fallen leaves, and other organic refuse.
 Humus prevents clay from packing together and builds a crumbly soil that retains
water but is still porous enough for the adequate aeration of roots.
 Humus is also a reservoir of mineral nutrients that are returned to the soil by
decomposition.
 After a heavy rainfall, water drains away from the larger spaces of the soil, but smaller
spaces retain water because of water’s attraction for the electrically charged surfaces of
soil particles.
Biology Chapter Notes
  Some water adheres so tightly to hydrophilic particles that plants cannot extract it,
while water that is bound less tightly to the particles can be taken up by roots.
 Many 2+
minerals, especially those
2+
with a positive charge, such as potassium (K +), calcium
(Ca ), and magnesium (Mg ), adhere by electrical attraction to the negatively charged
surfaces of clay particles.
 Clay in soil prevents the leaching of mineral nutrients during heavy rain or irrigation
because of its large surface area for binding minerals.
 Minerals that2−are negatively charged, such as nitrate (NO 3−), phosphate (H2PO4−), and
sulfate (SO4 ), are less tightly bound to soil particles and tend to leach away more
quickly.
 Positively charged mineral ions are made available to the plant when hydrogen ions in the
soil displace the mineral ions from the clay particles.
 This process, called cation exchange, is stimulated by the roots, which secrete H+ and
compounds that form acids in the soil solution.
Soil conservation is one step toward sustainable agriculture.
 It can take centuries for soil to become fertile through the breakdown of soil and the
accumulation of organic material.
 However, human mismanagement can destroy soil fertility within just a few years.
 Soil mismanagement has been a recurring problem in human history.
 For example, the Dust Bowl was an ecological and human disaster that occurred in the
southwestern Great Plains of the United States in the 1930s.
 Before the arrival of farmers, the region was covered with hardy grasses that held the
soil in place in spite of long recurrent droughts and torrential rains.
 In the 30 years before World War I, homesteaders planted wheat and raised cattle,
which left the soil exposed to wind erosion.
 Several years of drought resulted in the loss of centimeters of topsoil that were blown
away by the winds.
 Millions of hectares of farmland became useless, and hundreds of thousands of people
were forced to abandon their homes and land.
 To understand soil conservation, we must begin with the premise that agriculture is not
natural and can only be sustained by human intervention.
 In natural ecosystems, mineral nutrients are recycled by the decomposition of dead
organic material.
 In contrast, when we harvest a crop, we remove essential elements.
 In general, agriculture depletes minerals in the soil.
 To grow 1,000 kg of wheat, the soil gives up 20 kg of nitrogen, 4 kg of phosphorus,
and 4.5 kg of potassium.
 The fertility of the soil diminishes unless minerals are replaced by fertilizers.
 Most crops require far more water than the natural vegetation for that area, making
irrigation necessary.
 The goals of soil conservation include prudent fertilization, thoughtful irrigation, and
prevention of erosion.
 Complementing soil conservation is soil reclamation, the return of agricultural
productivity to damaged soil.
 A third of the world’s farmland suffers from low productivity due to poor soil conditions.
Biology Chapter Notes
 Farmers have been using fertilizers to improve crop yields since prehistory.
 Historically, these have included animal manure and fish carcasses.
 In developed nations today, most farmers use commercial fertilizers containing
minerals that are either mined or prepared by industrial processes.
 These are usually enriched in nitrogen, phosphorus, and potassium, the macronutrients
most often deficient in farm and garden soils.
 Fertilizers are labeled with their N-P-K ratio. A fertilizer marked “10-12-8” is 10%
nitrogen (as ammonium or nitrate), 12% phosphorus (as phosphoric acid), and 8%
potassium (as the mineral potash).
 Manure, fishmeal, and compost are “organic” fertilizers because they are of biological
origin and contain material in the process of decomposing.
 The organic material must be decomposed to inorganic nutrients before it can be
absorbed by roots.
 However, the minerals that a plant extracts from the soil are in the same form whether
they came from organic fertilizer or from a chemical factory.
 Compost releases nutrients gradually, while minerals in commercial fertilizers are
available immediately.
 Excess minerals are often leached from fertilized soil by rainwater or irrigation and
may pollute groundwater, streams, and lakes.
 Genetically engineered “smart plants” have been produced. These plants produce a blue
pigment in their leaves to warn the farmer of impending nutrient deficiency.
 To fertilize judiciously, a farmer must maintain an appropriate soil pH. pH affects cation
exchange and influences the chemical form of all minerals.
 Even if an essential element is abundant in the soil, plants may starve for that element
if it is bound too tightly to clay or is in a chemical form that the plant cannot absorb.
 Adjustments to soil pH of soil may make one mineral more available but another
mineral less available.
 The pH of the soil must be matched to the specific mineral needs of the crop.
 Sulfate lowers pH, while liming (addition of calcium carbonate or calcium hydroxide)
increases pH.
 A major problem with acidic soils, particularly in tropical areas, is that aluminum
dissolves in the soil at low pH and becomes toxic to roots.
 Some plants cope with high aluminum levels in the soil by secreting organic ions that
bind the aluminum and render it harmless.
 Water is the most common factor limiting plant growth.
 Irrigation can transform a desert into a garden, but farming in arid regions is a huge
drain on water resources.
 Irrigation in an arid region can gradually make the soil so salty that it becomes
completely infertile. Salts in the irrigation water accumulate in the soil as the water
evaporates.
 Eventually, the water potential of the soil solution becomes lower than that of root
cells, which lose water to the soil instead of absorbing it.
 Valuable topsoil is lost to wind and water erosion each year.
 This can be reduced by planting rows of trees between fields as a windbreak and
terracing a hillside to prevent topsoil from washing away.
 Some crops such as alfalfa and wheat provide good ground cover and protect soil
better than corn and other crops that are usually planted in widely spaced rows.
Biology Chapter Notes
 Soil is a renewable resource in which farmers can grow food for generations to come.
 The goal is sustainable agriculture, a commitment embracing a variety of farming
methods that are conservation-minded, environmentally safe, and profitable.
 Some areas have become unfit for agriculture or wildlife as the result of human activities
that contaminate the soil or groundwater with toxic heavy metals or organic pollutants.
 In place of costly and disruptive remediation technologies such as removal and storage
of contaminated soils, phytoremediation takes advantage of the remarkable abilities
of some plant species to extract heavy metals and other pollutants from the soil.
 These pollutants are concentrated in plant tissues that can be harvested.
 For example, alpine pennycress (Thlaspi caerulescens) can accumulate zinc in its
shoots at concentrations that are 300 times the level most plants can tolerate.
 Phytoremediation is part of a more general technology of bioremediation, which
includes the use of prokaryotes and protists to detoxify polluted sites.

Concept 37.3 Nitrogen is often the mineral that has the greatest effect on plant growth
The metabolism of soil bacteria makes nitrogen available to plants.
 Of all mineral nutrients, nitrogen has the greatest effect on plant growth and crop yields.
 It is ironic that plants sometimes suffer nitrogen deficiencies, for the atmosphere is nearly
80% nitrogen as N2.
 Plants cannot use nitrogen in the form of N2.
 It must first be converted to ammonium (NH4+) or nitrate (NO3−).
 The main source of ammonium and nitrate is the decomposition of humus by
microbes, including ammonifying bacteria.
 Nitrogen is lost from this local cycle when soil microbes called denitrifying bacteria
convert NO3− to N2, which diffuses into the atmosphere.
 Other bacteria, nitrogen-fixing bacteria, restock nitrogenous minerals in the soil by
converting N2 to NH3 (ammonia) by the metabolic process of nitrogen fixation.
 All life on Earth depends on nitrogen fixation, a process performed only by certain
bacterial species.
 In soil, these include several species of free-living bacteria and several others that live
in symbiotic relationships with plants.
 The reduction of N2 to NH3 is a complicated, multistep process, catalyzed by one
enzyme complex, nitrogenase, and simplified as:
 N2 + 8e− + 8H+ + 16ATP -> 2NH3 + H2 + 16ADP + 16Pi
 Nitrogen fixation is a very costly process, costing the bacterium 8 ATP for every
ammonia molecule synthesized.
 Nitrogen-fixing bacteria are most abundant in soils rich in organic materials, which
provide fuels for cellular respiration to support this expensive metabolic process.
 In the soil solution, ammonia picks up another hydrogen ion to form ammonium (NH 4+),
which plants can absorb.
 Nitrifying bacteria in the soil oxidize ammonium to nitrate (NO 3−), the required form of
nitrogen for most plants.
 After nitrate is absorbed by roots, plant enzymes reduce nitrate back to ammonium,
which other enzymes then incorporate into amino acids and other organic compounds.
Biology Chapter Notes
  Most plant species export nitrogen from roots to shoots via the xylem, in the form of
nitrate or organic compounds that have been synthesized in the roots.
Improving the protein yield of crops is a major goal of agricultural research.
 The ability of plants to incorporate fixed nitrogen into proteins and other organic
substances has a major impact on human welfare.
 Protein deficiency is the most common form of malnutrition.
 Either by choice or economic necessity, the majority of the world’s people have a
predominately vegetarian diet.
 Unfortunately, plants are a poor source of protein and may be deficient in one or more
of the amino acids that humans need from their diet.
 Plant breeding has resulted in new varieties of corn, wheat, and rice that are enriched in
protein.
 However, many of these “super” varieties have an extraordinary demand for nitrogen,
which is usually supplied by commercial fertilizer produced by energy-costly
industrial production.
 Generally, the countries that most need high-protein crops are the ones least able to
afford to pay for the fossil fuels to power the factories that make fertilizers.
 Agricultural scientists are pursuing a variety of strategies to overcome this protein
deficiency.
 For example, the use of new nitrogenase-based catalysts to fix nitrogen may make
commercial production of nitrogen fertilizers cheaper.
 Alternatively, improvements in the productivity of symbiotic nitrogen fixation may
increase protein yields of crops.

Concept 37.4 Plant nutritional adaptations often involve relationships with other
organisms
 The roots of plants belong to subterranean communities that interact with a diversity of
other organisms.
 Among these are certain species of bacteria and fungi that have coevolved with
specific plants, forming symbiotic relationships with roots that enhance the nutrition of
both partners.
 The two most important examples of mutualistic interactions are nitrogen fixation
(symbiosis of plant roots and bacteria) and the formation of mycorrhizae (symbiosis of
plant roots and fungi).
Symbiotic nitrogen fixation results from intricate interactions between roots and bacteria.
 Some plant species form symbiotic relationships with nitrogen-fixing bacteria.
 This provides their roots with a built-in source of fixed nitrogen for assimilation into
organic compounds.
 Much of the research on this symbiosis has focused on the agriculturally important
members of the legume family, including peas, beans, soybeans, peanuts, alfalfa, and
clover.
 A legume’s roots have swellings called nodules, composed of plant cells that contain
nitrogen-fixing bacteria of the genus Rhizobium.
 Inside the nodule, Rhizobium bacteria assume a form called bacteriods, which are
contained within vesicles formed by the root cell.
Biology Chapter Notes
  Legume-Rhizobium symbioses produce more usable nitrogen for plants than all
industrial fertilizers, at no cost to farmers. Subsequent crops can also benefit from the
usable nitrogen left in the soil by a legume crop.
 Nitrogen fixation requires an anaerobic environment.
 Lignified external layers of the nodule limit gas exchange.
 Nodules produce leghemoglobin, an iron-containing protein that binds reversibly to
oxygen. Leghemoglobin provides oxygen for Rhizobium’s intense respiration, while
protecting nitrogenase from free oxygen.
 The development of root nodules begins after bacteria enter the root through an infection
thread.
o Chemical signals from the root attract the Rhizobium bacteria, and chemical signals
from the bacteria lead to the production of an infection thread.
o The bacteria penetrate the root cortex within the infection thread.
o Growth in cortex and pericycle cells which are “infected” with bacteria in vesicles
continues until the two masses of dividing cells fuse, forming the nodule.
o As the nodule continues to grow, vascular tissue connects the nodule to the xylem and
phloem of the stele, providing nutrients to the nodule and carrying nitrogenous
compounds to the rest of the plant.
 The symbiotic relationship between a legume and nitrogen-fixing bacteria is mutualistic,
with both partners benefiting.
 The bacteria supply the legume with fixed nitrogen.
 Most of the ammonium produced by symbiotic nitrogen fixation is used by the
nodules to make amino acids, which are then transported to the shoot and leaves via
the xylem.
 The plant provides the bacteria with carbohydrates and other organic compounds and
protects the nitrogenase from free oxygen.
 The common agricultural practice of crop rotation exploits symbiotic nitrogen fixation.
 One year, a nonlegume crop such as corn is planted. The following year, alfalfa or
another legume is planted to restore the concentration of fixed soil nitrogen.
 Often, the legume crop is not harvested but is plowed under to decompose as “green
manure.”
 To ensure the formation of nodules, the legume seeds may be soaked in a culture of the
correct Rhizobium bacteria or dusted with bacterial spores before sowing.
 Species from many other plant families also benefit from symbiotic nitrogen fixation.
 For example, alder trees and certain tropical grasses host nitrogen-fixing bacteria of the
actinomycetes group.
 Rice benefits indirectly from symbiotic nitrogen fixation because it is often cultivated
in paddies with the water fern Azolla, which has symbiotic nitrogen-fixing
cyanobacteria.
 This increases the fertility of the rice paddy through the activity of the
cyanobacteria.
 The growing rice eventually shades and kills the Azolla.
 The decomposition of water fern adds more nitrogenous compounds to the paddy.
The molecular biology of root nodule formation is increasingly well understood.
 The specific recognition between legume and bacteria and the development of the nodule
is the result of a chemical dialogue between the bacteria and the root.
Biology Chapter Notes
  Each partner responds to the chemical signals of the other by expressing certain genes
whose products contribute to nodule formation.
 The plant initiates the communication when its roots secrete molecules called
flavonoids, which enter Rhizobium cells living in the vicinity of the roots.
 Each particular legume species secretes a type of flavonoid that only a certain
Rhizobium species can detect and absorb.
o A specific flavonoid signal travels from the root to the plant’s Rhizobium partner.
o The flavonoid activates a gene-regulating protein in the bacterium, which switches on
a cluster of bacterial genes called nod (for nodulation genes).
o The nod genes produce enzymes that catalyze production of species-specific molecules
called Nod factors.
o Nod factors signal the root to initiate the infection process, enabling Rhizobium to
enter the root and begin forming the root nodule.
o The plant’s responses 2+ require activation of early nodulin genes by a signal transduction
pathway involving Ca as second messengers.
 It may be possible in the future to induce Rhizobium uptake and nodule formation in
crop plants that do not normally form such nitrogen-fixing symbioses.
 In the short term, research is focused on improving the efficiency of nitrogen fixation
and protein production.
Mycorrhizae are symbiotic associations of roots and fungi that enhance plant nutrition.
 Mycorrhizae (“fungus roots”) are modified roots, consisting of mutualistic associations
of fungi and roots.
 The fungus benefits from a hospitable environment and a steady supply of sugar
donated by the host plant.
 The fungus provides several potential benefits to the host plant.
 First, the fungi increase the surface area for water uptake and selectively absorb
phosphate and other minerals in the soil and supply them to the plant.
 The fungi also secrete growth factors that stimulate roots to grow and branch.
 The fungi produce antibiotics that may help protect the plant from pathogenic bacteria
and fungi in the soil.
 Almost all plant species produce mycorrhizae.
 This plant-fungus symbiosis may have been one of the evolutionary adaptations that
made it possible for plants to colonize land in the first place.
 Fossilized roots from some of the earliest land plants include mycorrhizae.
 Mycorrhizal fungi are more efficient at absorbing minerals than roots, which may have
helped nourish pioneering plants, especially in the nutrient-poor soils present when
terrestrial ecosystems were young.
 Today, the first plants to become established on nutrient-poor soils are usually well
endowed with mycorrhizae.
 Mycorrhizae take two major forms: ectomycorrhizae and endomycorrhizae.
 In ectomycorrhizae, the mycelium forms a dense sheath over the surface of the root.
 Some hyphae grow into the cortex in extracellular spaces between root cells. Hyphae
do not penetrate root cells but form a network in the extracellular spaces to facilitate
nutrient exchange.
 The mycelium of ectomycorrhizae extends from the mantle surrounding the root into
the soil, greatly increasing the surface area for water and mineral absorption.

Biology Chapter Notes

  Compared with “uninfected” roots, ectomycorrhizae are generally thicker, shorter,
more branched, and lack root hairs.
 Ten percent of plant families have species that form ectomycorrhizae.
Ectomycorrhizae are especially common in woody plants, including trees of the pine,
spruce, oak, walnut, birch, willow, and eucalyptus families.
 Endomycorrhizae have fine fungal hyphae that extend from the root into the soil.
 Hyphae also extend inward by digesting small patches of the root cell walls, forming
tubes by invagination of the root cell’s membrane.
 Some fungal hyphae within these invaginations may form dense knotlike structures
called arbuscles that are important sites of nutrient transfer.
 Roots with endomycorrhizae look like “normal” roots with root hairs, but the
microscopic symbiotic connections are very important.
 Endomycorrhizae are found in more than 85% of plant species, including important
crop plants such as corn, wheat, and legumes.
 Roots can be transformed into mycorrhizae only if they are exposed to the appropriate
fungal species.
 In most natural systems, these fungi are present in the soil, and seedlings develop
mycorrhizae.
 However, seeds planted in foreign soil may develop into plants that show signs of
malnutrition because of the absence of the plant’s mycorrhizal partners.
 Researchers observe similar results in experiments in which soil fungi are poisoned.
 Farmers and foresters are already applying the lessons learned from this research by
inoculating plants with the spores from the appropriate fungal partner to ensure
development of mycorrhizae.
Epiphytes nourish themselves but grow on other plants.
 An epiphyte is an autotrophic plant that nourishes itself but grows on the surface of
another plant, usually on the branches or trunks of trees.
 Epiphytes absorb water and minerals from rain, mostly through their leaves.
 Examples of epiphytes are staghorn ferns, some mosses, Spanish moss, and many
species of bromeliads and orchids.
Parasitic plants extract nutrients from other plants.
 A variety of plants parasitize other plants to extract nutrients to supplement or even
replace the production of organic molecules by photosynthesis by the parasitic plant.
 Many species have roots that function as haustoria, nutrient-absorbing roots that enter the
host plant.
 Mistletoe supplements its photosynthesis by using projections called haustoria to siphon
xylem sap from the vascular tissue of the host tree.
 Both dodder and Indian pipe are parasitic plants that do not perform photosynthesis at all.
 The haustoria (modified roots) of dodder tap into the host’s vascular tissue for water
and nutrients.
 Indian pipe obtains its nutrition indirectly via its association with fungal hyphae of the
host tree’s mycorrhizae.
Carnivorous plants supplement their mineral nutrition by digesting animals.
 Carnivorous plants are photosynthetic but obtain some nitrogen and minerals by killing
and digesting insects and other small animals.
Biology Chapter Notes
 Such plants live in acid bogs and other habitats where soil conditions are poor in nitrogen
and other minerals.
 Various types of insect traps have evolved by the modification of leaves.
 The traps are usually equipped with glands that secrete digestive juices.
 Examples are the Venus flytrap, pitcher plant, and sundew.

Biology Chapter Notes

 Chapter 38 Angiosperm Reproduction and
Biotechnology
Chapter Notes

Overview: To Seed or Not to Seed

 Sexual reproduction is not the sole means by which flowering plants reproduce.
 Many species can also reproduce asexually, creating offspring that are genetically identical to them.
 The propagation of flowering plants by sexual and asexual reproduction forms the basis of agriculture.
 For 10,000 years, plant breeders have altered the traits of a few hundred angiosperm species by artificial selection,
transforming them into today’s crops.

Concept 38.1 Pollination enables gametes to come together within a flower

Sporophyte and gametophyte generations alternate in the life cycles of plants.
 The life cycles of angiosperms and other plants are characterized by an alternation of generations, in which
haploid (n) and diploid (2n) generations take turns producing each other.
 The diploid plant, the sporophyte, produces haploid spores by meiosis.
 These spores divide by mitosis, giving rise to multicellular male and female haploid plants—the
gametophytes.
 The gametophytes produce gametes—sperm and eggs.
 Fertilization results in diploid zygotes, which divide by mitosis to form new sporophytes.
 In angiosperms, the sporophyte is the dominant generation, the conspicuous plant we see.
 Over the course of seed plant evolution, gametophytes became reduced in size and dependent on their
sporophyte parents.
 Angiosperm gametophytes are the most reduced of all plants, consisting of only a few cells.
 In angiosperms, the sporophyte produces a unique reproductive structure, the flower.
 Male and female gametophytes develop within the anthers and ovules, respectively, of a sporophyte flower.
 Pollination by wind, water, or animals brings a male gametophyte (pollen grain) to a female gametophyte
contained in an ovule embedded in the ovary of a flower.
Union of gametes (fertilization) takes place within the ovary.
Ovules develop into seeds, while the ovary itself develops into the fruit around the seed.
Flowers are specialized shoots bearing the reproductive organs of the angiosperm sporophyte.
 Flowers, the reproductive shoots of the angiosperm sporophyte, are typically composed of four whorls of highly
modified leaves called floral organs, which are separated by very short internodes.
 Unlike the indeterminate growth of vegetative shoots, flowers are determinate shoots in that they cease
growing once the flower and fruit are formed.
 The four kinds of floral organs are the sepals, petals, stamens, and carpels.
 Their site of attachment to the stem is the receptacle.
 Sepals and petals are sterile.

Biology Chapter Notes

  Sepals, which enclose and protect the floral bud before it opens, are usually green and more leaflike in
appearance than the other floral organs.
 In many angiosperms, the petals are brightly colored and advertise the flower to insects and other pollinators.
 Stamens and carpels are the male and female reproductive organs, respectively.
 A stamen consists of a stalk (the filament) and a terminal anther containing chambers called pollen sacs.
 The pollen sacs produce pollen.
 A carpel has an ovary at the base and a slender neck, the style.
 At the top of the style is a sticky structure called the stigma that serves as a landing platform for pollen.
 Within the ovary are one or more ovules.
 Some flowers have a single carpel.
 In others, several carpels are fused into a single structure, producing an ovary with two or more chambers,
each containing one or more ovules.
 The anthers and the ovules bear sporangia, where spores are produced by meiosis and where gametophytes later
develop.
 The male gametophytes are sperm-producing structures called pollen grains, which form within the pollen
sacs of anthers.
 The female gametophytes are egg-producing structures called embryo sacs, which form within the ovules in
ovaries.
 Pollination is the transfer of pollen from an anther to a stigma.
 It begins the process by which the male and female gametophytes are brought together so their gametes can
unite.
 Pollination occurs when pollen released from anthers is carried by wind, water, or animals to land on a stigma.
 Each pollen grain produces a pollen tube, which grows down into the ovary via the style and discharges sperm
into the embryo sac, fertilizing the egg.
 The zygote gives rise to an embryo.
 The ovule develops into a seed, and the entire ovary develops into a fruit containing one or more seeds.
 Fruits carried by wind, water, or animals disperse seeds away from the source plant where the seed germinates.
 Numerous floral variations have evolved during the 130 million years of angiosperm history.
 Plant biologists distinguish between complete flowers, those having all four organs, and incomplete flowers,
those lacking one or more of the four floral parts.
 A bisexual flower is equipped with both stamens and carpels.
 All complete and many incomplete flowers are bisexual.
 A unisexual flower is missing either stamens (therefore, a carpellate flower) or carpels (therefore, a staminate
flower).
 A monoecious plant has staminate and carpellate flowers at separate locations on the same individual plant.
 For example, maize and other corn varieties have ears derived from clusters of carpellate flowers, while the
tassels consist of staminate flowers.
 A dioecious species has staminate flowers and carpellate flowers on separate plants.
 For example, date palms have carpellate individuals that produce dates and staminate individuals that produce
pollen.
 In addition to these differences based on the presence of floral organs, flowers vary in size, shape, and color.
 Much of this diversity represents adaptations of flowers to different animal pollinators.
 The presence of animals in the environment has been a key factor in angiosperm evolution.
Male and female gametophytes develop within anthers and ovaries, respectively; pollination brings them together.
Biology Chapter Notes
 The male gametophyte begins its development within the sporangia (pollen sacs) of the anther.
 Within the sporangia are microsporocytes, each of which will form four haploid microspores through meiosis.
 Each microspore can give rise to a haploid male gametophyte.
 A microspore divides once by mitosis and produces a generative cell and a tube cell.
 The generative cell will eventually form sperm.
 During maturation of the male gametophyte, the generative cell passes into the tube cell.
 The tube cell, enclosing the generative cell, produces the pollen tube, which delivers sperm to the egg.
 This is a pollen grain, an immature male gametophyte.
 This two-celled structure is encased in a thick, ornate, distinctive, and resistant wall.
 A pollen grain becomes a mature gametophyte when the generative cell divides by mitosis to form two sperm
cells.
 In most species, this occurs after the pollen grain lands on the stigma of the carpel and the pollen tube begins
to form.
 The pollen tube grows through the long style of the carpel and into the ovary, where it releases the sperm cells in
the vicinity of the embryo sac.
 Ovules, each containing a single sporangium, form within the chambers of the ovary.
 One cell in the sporangium of each ovule, the megasporocyte, grows and then goes through meiosis, producing
four haploid megaspores.
 In many angiosperms, only one megaspore survives.
 This megaspore divides by mitosis three times without cytokinesis, forming in one cell with eight haploid nuclei.
 Membranes partition this mass into a multicellular female gametophyte—the embryo sac.
 Three cells sit at one end of the embryo sac: two synergid cells flanking the egg cell.
 The synergids function in the attraction and guidance of the pollen tube.
 At the other end of the egg sac are three antipodal cells of unknown function.
 The other two nuclei, the polar nuclei, share the cytoplasm of the large central cell of the embryo sac.
 The ovule now consists of the embryo sac and the surrounding integuments, layers of protective tissue from the
sporophyte that will eventually develop into the seed coat.
 Pollination, which brings male and female gametophytes together, is the first step in the chain of events that leads
to fertilization.
 Some plants, such as grasses and many trees, release large quantities of pollen on the wind to compensate for
the randomness of this dispersal mechanism.
 At certain times of the year, the air is loaded with pollen, as anyone plagued by pollen allergies can attest.
 Some aquatic plants rely on water to disperse pollen.
 Most angiosperms interact with insects or other animals that transfer pollen directly between flowers.
Plants have various mechanisms that prevent self-fertilization.
 Some flowers self-fertilize or “self,” but most angiosperms have mechanisms that make this difficult or
impossible.
 The various barriers that prevent self-fertilization contribute to genetic variety by ensuring that sperm and eggs
come from different parents.
 Dioecious plants cannot self-fertilize because they are unisexual.
 In plants with bisexual flowers, a variety of mechanisms may prevent self-fertilization.
 For example, in some species stamens and carpels mature at different times.

Biology Chapter Notes

  Alternatively, they may be arranged in such a way that it is mechanically unlikely that an animal pollinator
could transfer pollen from the anthers to the stigma of the same flower.
 The most common anti-selfing mechanism is self-incompatibility, the ability of a plant to reject its own
pollen and that of closely related individuals.
 If a pollen grain from an anther happens to land on a stigma of a flower on the same plant, a biochemical block
prevents the pollen from completing its development and fertilizing an egg.
 The self-incompatibility systems in plant are analogous to the immune response of animals.
 Both are based on the ability of organisms to distinguish “self” from “nonself.”
 The key difference is that the animal immune system rejects nonself, but self-incompatibility in plants is a
rejection of self.
 Recognition of “self” pollen is based on genes for self-incompatibility, called S-genes, with dozens of different
alleles in a population.
 If a pollen grain and the carpel’s stigma have matching alleles at the S-locus, then the pollen grain fails to
initiate or complete the formation of a pollen tube.
 Because the pollen grain is haploid, it will be recognized as “self” if its one S-allele matches either of the two
S-alleles of the diploid stigma.
 Although self-incompatibility genes are all referred to as S-loci, such genes have evolved independently in various
plant families.
 As a consequence, self-recognition blocks pollen tube growth by different molecular mechanisms.
 In some cases, the block occurs in the pollen grain itself, called gametophytic self-incompatibility.
 In some species, self-recognition leads to enzymatic destruction of RNA within the rudimentary pollen tube.
 RNases are present in the style of the carpel, and they can enter the pollen tube and attack its RNA only if the
pollen is of a “self” type.
 In other cases, the block is a response by the cells of the carpel’s stigma, called sporophytic self-incompatibility.
 In some species, self-recognition activates a signal transduction pathway in epidermal cells that prevents
germination of the pollen grain.
 Germination may be prevented when cells of the stigma take up additional water, preventing the stigma from
hydrating the relatively dry pollen.
 Basic research on self-incompatibility may lead to agricultural applications.
 Many agricultural plants are self-compatible.
 Plant breeders sometimes hybridize different varieties of a crop plant to combine the best traits of the varieties
and counter the loss of vigor that can result from excessive inbreeding.
 To maximize hybrid seed production, breeders currently prevent self-fertilization by laboriously removing
anthers from the parent plants that provide the seeds or by developing male sterile plants.
 Eventually, it may be possible to impose self-incompatibility on species that are normally self-compatible.

Concept 38.2 After fertilization, ovules develop into seeds and ovaries into fruits
Double fertilization gives rise to the zygote and endosperm.
 After landing on a receptive stigma, the pollen grain absorbs moisture and germinates, producing a pollen tube that
extends down the style toward the ovary.
 The nucleus of the generative cell divides by mitosis to produce two sperm, the male gametes.
 The germinated pollen grain contains the mature male gametophyte.
 Directed by a chemical attractant, possibly calcium, the tip of the pollen tube enters the ovary, probes through
the micropyle (a gap in the integuments of the ovule), and discharges two sperm within the embryo sac.
 Both sperm fuse with nuclei in the embryo sac.
Biology Chapter Notes
  One sperm fertilizes the egg to form the zygote.
 The other sperm combines with the two polar nuclei to form a triploid nucleus in the central cell.
 This large cell will give rise to the endosperm, a food-storing tissue of the seed.
 The union of two sperm cells with different nuclei of the embryo sac is termed double fertilization.
 Double fertilization ensures that the endosperm will develop only in ovules where the egg has been fertilized.
 This prevents angiosperms from squandering nutrients.
 Normally nonreproductive tissues surrounding the embryo have prevented researchers from visualizing
fertilization in plants, but recently, scientists have been able to isolate sperm cells and eggs and observe
fertilization in vitro.
 The first cellular event after gamete fusion is an increase in cytoplasmic Ca2+ levels, which also occurs during
animal gamete fusion.
 In another similarity to animals, plants establish a block to polyspermy, the fertilization of an egg by more than
one sperm cell.
 In plants, this may be through deposition of cell wall material that mechanically impedes sperm.
 In maize, this barrier is established within 45 seconds after the initial sperm fusion with the egg.
The ovule develops into a seed containing an embryo and a supply of nutrients.
 After double fertilization, the ovule develops into a seed, and the ovary develops into a fruit enclosing the seed(s).
 As the embryo develops, the seed stockpiles proteins, oils, and starch.
 Initially, these nutrients are stored in the endosperm.
 Later in seed development in many species, the storage function is taken over by the swelling storage leaves
(cotyledons) of the embryo itself.
 Endosperm development usually precedes embryo development.
 After double fertilization, the triploid nucleus of the ovule’s central cell divides, forming a multinucleate
“supercell” having a milky consistency.
 It becomes multicellular when cytokinesis partitions the cytoplasm between nuclei.
 Cell walls form, and the endosperm becomes solid.
 Coconut “milk” is an example of liquid endosperm and coconut “meat” is an example of solid endosperm.
 The endosperm is rich in nutrients, which it provides to the developing embryo.
 In most monocots and some dicots, the endosperm also stores nutrients that can be used by the seedling after
germination.
 In many dicots, the food reserves of the endosperm are completely exported to the cotyledons before the seed
completes its development, and consequently the mature seed lacks endosperm.
 The first mitotic division of the zygote is transverse, splitting the fertilized egg into a basal cell and a terminal cell.
 The terminal cell gives rise to most of the embryo.
 The basal cell continues to divide transversely, producing a thread of cells, the suspensor, which anchors the
embryo to its parent.
 The suspensor functions in the transfer of nutrients to the embryo from the parent.
 The terminal cell divides several times and forms a spherical proembryo attached to the suspensor.
 Cotyledons begin to form as bumps on the proembryo.
 A eudicot, with its two cotyledons, is heart-shaped at this stage.
 Only one cotyledon develops in monocots.
 After the cotyledons appear, the embryo elongates.
 Cradled between cotyledons is the embryonic shoot apex with the apical meristem of the embryonic shoot.
 At the opposite end of the embryo axis is the apex of the embryonic root, also with a meristem.
Biology Chapter Notes
 After the seed germinates, the apical meristems at the tips of the shoot and root sustain primary growth as long as
the plant lives.
 During the last stages of maturation, a seed dehydrates until its water content is only about 5–15% of its weight.
 The embryo stops growing and becomes dormant until the seed germinates.
 The embryo and its food supply are enclosed by a protective seed coat formed by the integuments of the
ovule.
 In the seed of a common bean, the embryo consists of an elongate structure, the embryonic axis, attached to fleshy
cotyledons.
 Below the point at which the fleshy cotyledons are attached, the embryonic axis is called the hypocotyl; above
it is the epicotyl.
 At the tip of the epicotyl is the plumule, consisting of the shoot tip with a pair of miniature leaves.
 The hypocotyl terminates in the radicle, or embryonic root.
 While the cotyledons of the common bean supply food to the developing embryo, the seeds of some dicots, such as
castor beans, retain their food supply in the endosperm and have cotyledons that are very thin.
 The cotyledons will absorb nutrients from the endosperm and transfer them to the embryo when the seed
germinates.
 The embryo of a monocot has a single cotyledon.
 Members of the grass family, including maize and wheat, have a specialized cotyledon called a scutellum.
 The scutellum is very thin, with a large surface area pressed against the endosperm, from which the scutellum
absorbs nutrients during germination.
 The embryo of a grass seed is enclosed by two sheathes, a coleorhiza, which covers the young root, and a
coleoptile, which covers the young shoot.
The ovary develops into a fruit adapted for seed dispersal.
 As the seeds are developing from ovules, the ovary of the flower is developing into a fruit, which protects the
enclosed seeds and aids in their dispersal by wind or animals.
 Fertilization triggers hormonal changes that cause the ovary to begin its transformation into a fruit.
 If a flower has not been pollinated, fruit usually does not develop, and the entire flower withers and falls away.
 The wall of the ovary becomes the pericarp, the thickened wall of the fruit, while other parts of the flower wither
and are shed.
 In some angiosperms, other floral parts contribute to the fruit.
 In apples, the fleshy part of the fruit is derived mainly from the swollen receptacle, while the core of the apple
fruit develops from the ovary.
 Fruits are classified into several types, depending on their developmental origin.
 A typical fruit is derived from a single carpel or several fused carpels and is called a simple fruit.
 Some simpler fruits are fleshy, like a peach, while others are dry, like a pea pod.
 An aggregate fruit results from a single flower that has more than one carpel, each forming a small fruit.
 The fruitlets are clustered together on a single receptacle, like a raspberry.
 A multiple fruit develops from an inflorescence, a group of flowers tightly clustered together.
 When the walls of the ovaries thicken, they fuse together and form one fruit, as in a pineapple.
 The fruit usually ripens about the same time as its seeds are completing their development.
 For a dry fruit such as a soybean pod, ripening is a little more than senescence of the fruit tissues, which
allows the fruit to open and release the seeds.
 The ripening of fleshy fruits is more elaborate, its steps controlled by the complex interactions of hormones.
 Ripening results in an edible fruit that serves as an enticement to the animals that help spread the seeds.
Biology Chapter Notes
  The “pulp” of the fruit becomes softer as a result of enzymes digesting components of the cell walls.
 Color changes from green to red, orange, or yellow.
 The fruit becomes sweeter as organic acids or starch molecules are converted to sugar.
Evolutionary adaptations of seed germination contribute to seedling survival.
 As a seed matures, it dehydrates and enters a dormancy phase, a condition of extremely low metabolic rate and a
suspension of growth and development.
 Conditions required to break dormancy and resume growth and development vary between species.
 Some seeds germinate as soon as they are in a suitable environment.
 Others remain dormant until some specific environmental cue causes them to break dormancy.
 Seed dormancy increases the chances that germination will occur at a time and place most advantageous to the
seedling.
 For example, seeds of many desert plants germinate only after a substantial rainfall, ensuring enough water to
complete development.
 Where natural fires are common, many seeds require intense heat to break dormancy, allowing them to take
advantage of new opportunities and open space.
 Where winters are harsh, seeds may require extended exposure to cold.
 Small seeds such as lettuce require light for germination and break dormancy only if they are buried near the
surface.
 Other seeds require a chemical attack or physical abrasion as they pass through an animal’s digestive tract
before they can germinate.
 The length of time that a dormant seed remains viable and capable of germinating varies from a few days to
decades or longer.
 It depends on the species and on environmental conditions.
 Most seeds are durable enough to last for a year or two until conditions are favorable for germination.
 Thus, the soil has a pool of nongerminated seeds that may have accumulated for several years.
 This is one reason vegetation reappears so rapidly after a fire, drought, flood, or some other environmental
disruption.
 Germination of seeds depends on imbibition, the uptake of water due to the low water potential of the dry seed.
 This causes the expanding seed to rupture its seed coat and triggers metabolic changes in the embryo that
enable it to resume growth.
 Enzymes begin digesting the storage materials of endosperm or cotyledons, and the nutrients are transferred to
the growing regions of the embryo.
 The first organ to emerge from the germinating seed is the radicle, the embryonic root.
 Next, the shoot tip must break through the soil surface.
 In garden beans and many other dicots, a hook forms in the hypocotyl, and growth pushes it aboveground.
 Stimulated by light, the hypocotyl straightens, raising the cotyledons and epicotyl.
 As it rises into the air, the epicotyl spreads its first foliage leaves (true leaves).
 These foliage leaves expand, become green, and begin making food by photosynthesis.
 After the cotyledons have transferred all their nutrients to the developing plant, they shrivel and fall off the
seedling.
 Corn and other grasses, which are monocots, use a different method for breaking ground when they germinate.
 The coleoptile, the sheath enclosing and protecting the embryonic shoot, pushes upward through the soil and
into the air.
 The shoot tip then grows straight up through the tunnel provided by the tubular coleoptile.

Biology Chapter Notes

 The tough seed gives rise to a fragile seedling that will be exposed to predators, parasites, wind, and other hazards.
 Because only a small fraction of seedlings endure long enough to become parents, plants must produce
enormous numbers of seeds to compensate for low individual survival.
 This provides ample genetic variation for natural selection to screen.
 However, flowering and fruiting in sexual reproduction is an expensive way of plant propagation in terms of
the resources consumed.

Concept 38.3 Many flowering plants clone themselves by asexual reproduction

 Many plants clone themselves by asexual reproduction.
 Many plants are capable of both sexual and asexual reproduction, and each offers advantages in certain situations.
 When reproducing asexually, a plant passes on all of its genes to its offspring.
 When reproducing sexually, it passes on only half of its genes.
 If a plant is superbly suited to a stable environment, asexual reproduction has advantages.
 A plant can clone many copies of itself rapidly.
 If the environmental conditions remain stable, the clones will be well suited to the environment.
 The offspring are not as frail as the seedlings produced by sexual reproduction in seed plants.
 They are usually mature vegetative fragments of the parent plant.
 In unstable environments, where evolving pathogens and other variables affect survival and reproductive success,
sexual reproduction can be advantageous because it generates variation in offspring.
 In contrast, the genotypic uniformity of asexually produced plants puts them at great risk of local extinction if
there is a catastrophic environmental change, such as a new strain of disease.
 Seeds produced by sexual reproduction can disperse to new locations and wait for favorable growing
conditions.
 Seed dormancy allows growth to be suspended until hostile environmental conditions are reversed.
 Asexual reproduction is an extension of the capacity of plants for indeterminate growth.
 Meristematic tissues with dividing undifferentiated cells can sustain or renew growth indefinitely.
 Parenchyma cells throughout the plant can divide and differentiate into various types of specialized cells.
 Detached fragments of some plants can develop into whole offspring.
 In fragmentation, a parent plant separates into parts that re-form into whole plants.
 A variation of this occurs in some dicots, in which the root system of a single parent gives rise to many
adventitious shoots that become separate root systems, forming a clone.
 A ring of creosote bushes in the Mojave Desert of California is believed to be at least 12,000 years old.
 A different method of asexual reproduction, called apomixis, is found in dandelions and some other plants.
 These produce seed without their flowers being fertilized.
 A diploid cell in the ovule gives rise to the embryo, and the ovules mature into seeds.
 These seeds are dispersed by the wind.
 This combines asexual reproduction and seed dispersal.
Vegetative propagation of plants is common in agriculture.
 Various methods have been developed for the asexual propagation of crop plants, orchards, and ornamental plants.
 These can be reproduced asexually from plant fragments called cuttings.
 These are typically pieces of shoots or stems.

Biology Chapter Notes

 At the cut end, a mass of dividing, undifferentiated cells called the callus forms, and then adventitious roots
develop from the callus.
 If the shoot fragment includes a node, then adventitious roots form without a callus stage.
 Some plants, including African violets, can be propagated from single leaves.
 In others, specialized storage stems can be cut into several pieces and develop into clones.
 For example, a piece of a potato including a vegetative bud or “eye” can regenerate a whole plant.
 A twig or bud from one plant can be grafted onto a plant of a closely related species or a different variety of the
same species.
 This makes it possible to combine the best properties of different species or varieties into a single plant.
 The plant that provides the root system is called the stock, and the twig grafted onto the stock is the scion.
 For example, scions of French vines, which produce superior grapes, are grafted onto roots of American
varieties, which are more resistant to certain soil pathogens.
 The quality of the fruit is not influenced by the genetic makeup of the stock.
 In some cases of grafting, however, the stock can alter the characteristic of the shoot system that develops from the
scion.
 For example, dwarf fruit trees are made by grafting normal twigs onto dwarf stock varieties that retard the
vegetative growth of the shoot system.
 Because the seeds are produced by the scion part of the plant, they give rise to plants of the scion species if
planted.
 Plant biotechnologists have adopted in vitro methods to create and clone novel plant varieties.
 Whole plants are cultured from small explants (small tissue pieces) or even single parenchyma cells on an
artificial medium containing nutrients and hormones.
 The cultured cells divide and form an undifferentiated callus.
 Through manipulations of the hormonal balance, the callus that forms can be induced to develop shoots and
roots with fully differentiated cells.
 Once roots and shoots have developed, the test-tube plantlets can be transferred to soil, where they continue their
growth.
 This test-tube cloning can be used to clone a single plant into thousands of copies by subdividing calluses as
they grow.
 This technique is used to propagate orchids and to clone pine trees that deposit wood at an unusually fast rate.
 Plant tissue culture facilitates genetic engineering of plants.
 Most techniques for the introduction of foreign genes into plants start with small pieces of plant material or
single plant cells.
 Transgenic plants are genetically modified (GM) plants that have been genetically engineered to express a
gene from another species.
 Test-tube culture makes it possible to regenerate a GM plant from a single cell into which foreign DNA has
been incorporated.
 Another approach combines protoplast fusion with tissue culture methods to invent new plant varieties that can
be cloned.
 Protoplasts are plant cells that have had their cell walls removed enzymatically by cellulases and pectinases.
 It is possible in some cases to fuse two protoplasts from different plant species that would otherwise be
incompatible.
 The hybrids can regenerate the cell wall, be cultured, and produce a hybrid plantlet.
 One success of this technique has been the development of a hybrid between a potato and a wild relative called
black nightshade.

Biology Chapter Notes

  The nightshade is resistant to an herbicide that is commonly used to kill weeds.
 The hybrids are also resistant, enabling a farmer to “weed” a potato field with an herbicide without killing the
potato plants.

Concept 38.4 Plant biotechnology is transforming agriculture

 Plant biotechnology has two meanings.
 One is innovation in the use of plants, or of substances obtained from plants, to make products of use to
humans.
 This began in prehistory.
 In a more specific sense, biotechnology refers to the use of genetically modified (GM) organisms in
agriculture and industry.
 Over the past two decades, the terms genetic engineering and biotechnology have become synonymous in the
media.
Neolithic humans created new plant varieties by artificial selection.
 Humans have intervened in the reproduction and genetic makeup of plants for thousands of years.
 Neolithic (late Stone Age) humans domesticated virtually all of our crop species over a relatively short period
about 10,000 years ago.
 Even for these plants, genetic modifications began long before humans started altering crops by artificial
selection.
 For example, the wheat groups that we harvest are the result of natural hybridizations between different
species of grasses.
 Selective breeding by humans has created plants that could not survive or reproduce in the wild.
 For example, maize cannot spread its seeds naturally.
 Humans selected for a larger central axis (“the cob”), permanent attachment of the maize kernels to the cob,
and a permanent protection by tough, overlapping leaf sheathes (“the husk”).
 Maize is a staple in many developing countries.
 However, because most varieties are a relatively poor source of protein, a diet of maize must be supplemented
with other protein sources such as beans.
 Forty years ago, a mutant maize known as opaque-2 was discovered with increased levels of tryptophan and
lysine, two essential amino acids.
 This maize is more nutritious, and swine fed with opaque-2 maize gain weight three times faster than those fed
with normal maize.
 However, the beneficial trait was closely associated with several undesirable ones.
 It took nearly 20 years for plant breeders, using conventional breeding methods of hybridization and artificial
selection, to create maize varieties that had higher nutritional value without the undesirable traits.
 If modern methods of genetic engineering had been available, the desirable varieties could have been
developed in only a few years.
 Unlike traditional plant breeders, modern plant biotechnologists, using the techniques of genetic engineering, are
not limited to transferring genes between closely related species or varieties of the same species.
 Genes can be transferred between distantly related plant species to create transgenic plants.
 Whatever the social and demographic causes of human starvation around the world, increasing food production
seems like a humane objective.
 Because land and water are the most limiting resources for food production, the best option is to increase
yields on available land.

Biology Chapter Notes

  Based on conservative estimates of population growth, the world’s farmers will have to produce 40% more
grain per hectare to feed the human population in 2020.
 Plant biotechnology can help make these plant yields possible.
 The commercial adoption by farmers of transgenic crops has been one of the most rapid cases of technology
transfer in the history of agriculture.
 These crops include cotton, maize, and potatoes that contain genes from a bacterium Bacillus thuringiensis.
 These “transgenes” encode for a protein (Bt toxin) that effectively controls several insect pests.
 This has reduced the need for application of chemical insecticides.
 Bt toxin is produced in the plant as a harmless protoxin that becomes toxic when activated by alkaline
conditions in the guts of insects.
 In the acid guts of vertebrates, the protoxin is destroyed without becoming active.
 Considerable progress has been made in the development of transgenic plants of cotton, maize, soybeans, sugar
beat, and wheat that are tolerant of a number of herbicides.
 Researchers have also engineered transgenic plants with enhanced resistance to disease.
 Transgenic papaya resistant to ringspot virus was introduced to Hawaii, thereby saving the papaya industry.
 “Golden rice,” a transgenic variety with a few daffodil genes that increase quantities of vitamin A, is under
development.
 It is hoped that this rice will prevent blindness in those whose diet is chronically deficient in vitamin A.
Plant biotechnology has incited much public debate.
 Many people, including some scientists, are concerned about the unknown risks associated with the release of GM
organisms into the environment.
 Much of the animosity regarding GM organisms is political, economic, or ethical in nature, but there are also
biological concerns about GM crops.
 The most fundamental debate centers on the extent to which GM organisms are an unknown risk that could
potentially cause harm to human health or to the environment.
 One specific concern is that genetic engineering could potentially transfer allergens, molecules to which some
humans are allergic, from a gene source to a plant used for food.
 Biotechnologists are engaged in removing genes that code allergenic proteins from soybeans and other crops.
 So far there is no credible evidence that any GM plants specifically designed for human consumption have had
any adverse effect on human health.
 Some GM foods are potentially healthier than non-GM foods.
 Bt maize contains 90% less of a carcinogen produced by a fungus that infects insect-damaged maize.
 Since Bt maize suffers less insect damage, it contains less of the fungal carcinogen.
 GM-organism opponents lobby for clear labeling of all foods made wholly or in part from products of GM
organisms and for strict regulations against mixing GM foods with non-GM foods at any stage of food
preparation.
 Biotechnology advocates argue that similar demands were not raised when “transgenic” crops were produced
by traditional plant-breeding techniques.
 There are concerns that growing GM crops might have unforeseen effects on nontarget organisms.
 One study suggested that the caterpillars of monarch butterflies responded adversely and even died after
consuming milkweed leaves heavily dusted with pollen from transgenic maize that produced Bt toxin.
 Bt toxin is normally toxic to pests closely related to monarch butterflies.
 This study has since been discredited.
 When the original researchers shook the male maize inflorescences onto the milkweed leaves in the laboratory,
other floral parts rained onto the leaves.
Biology Chapter Notes
  It was those floral parts, not the pollen, that contained Bt toxin in high concentrations.
 These floral parts would not be blown by wind to neighboring milkweed plants under normal field conditions.
 The alternative to transgenic maize, spraying chemical insecticides, is more harmful to monarch populations.
 Probably the most serious concern that some scientists raise is the possibility that introduced genes may escape
from a transgenic crop into related weeds through crop-to-weed hybridization.
 This spontaneous hybridization may lead to a “superweed,” which may have a selective advantage and be
difficult to control.
 Some crops do hybridize with weedy relatives, and crop-to-weed transgene escape is a possibility.
 Its likelihood depends on the ability of the crop and weed to hybridize and on how the transgenes affect the
overall fitness of the hybrids.
 Strategies to minimize risk include planting a border of unrelated plants with which the transgenic plants could
not hybridize.
 Another possibility is breeding male sterility in transgenic plants.
 Alternatively, the transgenes can be engineered into chloroplasts, which are inherited maternally only.
 “Terminator technology” may offer another approach to the problem of transgene escape.
 Plants that are genetically modified to undergo the terminator process grow normally until the last stages of
seed maturation.
 At this point, a gene expressing a “terminator” protein toxic to plants but harmless to animals is activated in
the new seeds.
 The seeds are inviable.
 Terminator proteins are only produced if the original seeds are pretreated with a specific chemical.
 There is the potential for seed companies to control supplies of viable seeds.
 Seeds sold to farmers would be pretreated with the chemical that activates the terminator process.
 Some argue that poor farmers in developing countries will not be able to produce their own seed, because the
plants they grow would produce inviable seeds.
 The continuing debate about GM organisms in agriculture exemplifies the relationship of science and technology
to society.
 Technological advances almost always involve some risk that unintended outcomes could occur.
 In the case of plant biotechnology, zero risk is unrealistic and probably unattainable.
 Scientists and the public need to assess the possible benefits of transgenic products versus the risks that society
is willing to take on a case-by-case basis.
 These discussions and decisions should be based on sound scientific information and testing rather than on
reflexive fear or blind optimism.

Biology Chapter Notes

 Chapter 39 Plant Responses to Internal and External
Signals
Chapter Notes

Overview: Stimuli and a Stationary Life

 At every stage in the life of a plant, sensitivity to the environment and coordination of
responses are evident.
 One part of a plant can send signals to other parts.
 Plants can sense gravity and the direction of light.
 A plant’s morphology and physiology are constantly tuned to its variable surroundings
by complex interactions between environmental stimuli and internal signals.
 At the organismal level, plants and animals respond to environmental stimuli by very
different means.
 Animals, being mobile, respond mainly by behavioral mechanisms, moving toward
positive stimuli and away from negative stimuli.
 Rooted in one location for life, a plant generally responds to environmental cues by
adjusting its pattern of growth and development.
 As a result, plants of the same species vary in body form much more than do
animals of the same species.
 At the cellular level, plants and all other eukaryotes are surprisingly similar in their
signaling mechanisms.

Concept 39.1 Signal transduction pathways link signal reception to response

 All organisms, including plants, have the ability to receive specific environmental and
internal signals and respond to them in ways that enhance survival and reproductive
success.
 Like animals, plants have cellular receptors that they use to detect important changes
in their environment.
 These changes may be an increase in the concentration of a growth hormone, an
injury from a caterpillar munching on leaves, or a decrease in day length as winter
approaches.
 In order for an internal or external stimulus to elicit a physiological response, certain cells
in the organism must possess an appropriate receptor, a molecule that is sensitive to and
affected by the specific stimulus.
 Upon receiving a stimulus, a receptor initiates a specific series of biochemical steps, a
signal transduction pathway.
 This couples reception of the stimulus to the response of the organism.
 Plants are sensitive to a wide range of internal and external stimuli, and each of these
initiates a specific signal transduction pathway.
 Plant growth patterns vary dramatically in the presence versus the absence of light.
 For example, a potato (a modified underground stem) can sprout shoots from its “eyes”
(axillary buds).
Biology Chapter Notes
  These shoots are ghostly pale and have long, thin stems; unexpanded leaves; and
reduced roots.
 These morphological adaptations, called etiolation, are seen also in seedlings germinated
in the dark and make sense for plants sprouting underground.
 The shoot is supported by the surrounding soil and does not need a thick stem.
 Expanded leaves would hinder soil penetration and be damaged as the shoot pushes
upward.
 Because little water is lost in transpiration, an extensive root system is not required.
 The production of chlorophyll is unnecessary in the absence of light.
 A plant growing in the dark allocates as much energy as possible to the elongation of
stems to break ground before the nutrient reserves in the tuber are exhausted.
 Once a shoot reaches the sunlight, its morphology and biochemistry undergo profound
changes, collectively called de-etiolation, or greening.
 The elongation rate of the stems slows.
 The leaves expand, and the roots start to elongate.
 The entire shoot begins to produce chlorophyll.
 The de-etiolation response is an example of how a plant receives a signal—in this case,
light—and how this reception is transduced into a response (de-etiolation).
 Studies of mutants have provided valuable insights into the roles played by various
molecules in the three stages of cell-signal processing: reception, transduction, and
response.
 Signals, whether internal or external, are first detected by receptors, proteins that change
shape in response to a specific stimulus.
 The receptor for de-etiolation in plants is called a phytochrome, which consists of a
light-absorbing pigment attached to a specific protein.
 Unlike many receptors, which are in the plasma membrane, this phytochrome is in
the cytoplasm.
 The importance of this phytochrome was confirmed through investigations of a tomato
mutant, called aurea, which greens less when exposed to light.
 Injecting additional phytochrome into aurea leaf cells and exposing them to light
produced a normal de-etiolation response.
 Receptors such as phytochrome are sensitive to very weak environmental and chemical
signals.
 For example, just a few seconds of moonlight slow stem elongation in dark-grown oak
seedlings.
 These weak signals are amplified by second messengers—small, internally produced
chemicals that transfer and amplify the signal from the receptor to proteins that cause
the specific response.
 In the de-etiolation response, each activated phytochrome may give rise to hundreds of
molecules of a second messenger, each of which may lead to the activation of
hundreds of molecules of a specific enzyme.
 Light causes phytochrome to undergo a conformational change that leads to increases in
levels of the second messengers’ cyclic GMP (cGMP) and Ca2+.
 Changes in cGMP levels can lead to ionic changes within the cell by influencing
properties of ion channels.
 Cyclic GMP also activates specific protein kinases, enzymes that phosphorylate and
activate other proteins.
Biology Chapter Notes
  The microinjection of cyclic GMP into aurea tomato cells induces a partial de-
etiolation response, even without the addition of phytochrome.
 Changes in cytosolic Ca2+ levels also play an important role in phytochrome signal
transduction.
 The concentration of Ca2+ is generally very low in the cytoplasm.
 Phytochrome activation 2+can open Ca2+ channels and lead to transient 100-fold
increases in cytosolic Ca .
 Ultimately, a signal transduction pathway leads to the regulation of one or more cellular
activities.
 In most cases, these responses to stimulation involve the increased activity of certain
enzymes.
 This occurs through two mechanisms: by stimulating transcription of mRNA for the
enzyme or by activating existing enzyme molecules (post-translational modification).
 In transcriptional regulation, transcription factors bind directly to specific regions of DNA
and control the transcription of specific genes.
 In the case of phytochrome-induced de-etiolation, several transcription factors are
activated by phosphorylation, some through the cyclic GMP pathway, while activation
of others requires Ca2+.
 The mechanism by which a signal promotes a new developmental course may depend
on the activation of positive transcription factors (proteins that increase transcription
of specific genes) or negative transcription factors (proteins that decrease
transcription).
 During post-translational modifications of proteins, the activities of existing proteins are
modified.
 In most cases, these modifications involve phosphorylation, the addition of a
phosphate group onto the protein by a protein kinase.
 Many second messengers, such as cyclic GMP, and some receptors, including some
phytochromes, activate protein kinases directly.
 One protein kinase can phosphorylate other protein kinases, creating a kinase cascade,
finally leading to phosphorylation of transcription factors and impacting gene
expression.
 Thus, they regulate the synthesis of new proteins, usually by turning specific genes
on and off.
 Signal pathways must also have a means for turning off once the initial signal is no longer
present.
 Protein phosphatases, enzymes that dephosphorylate specific proteins, are involved in
these “switch off” processes.
 At any given moment, the activities of a cell depend on the balance of activity of many
types of protein kinases and protein phosphatases.
 During the de-etiolation response, a variety of proteins are either synthesized or activated.
 These include enzymes that function in photosynthesis directly or that supply the
chemical precursors for chlorophyll production.
 Others affect the levels of plant hormones that regulate growth.
 For example, the levels of two hormones (auxin and brassinosteroids) that enhance
stem elongation will decrease following phytochrome activation—hence, the
reduction in stem elongation that accompanies de-etiolation.

Biology Chapter Notes

Concept 39.2 Plant hormones help coordinate growth, development, and responses to
stimuli
 The word hormone is derived from a Greek verb meaning “to excite.”
 Found in all multicellular organisms, hormones are chemical signals that are produced in
one part of the body, transported to other parts, bind to specific receptors, and trigger
responses in target cells and tissues.
 Only minute quantities of hormones are necessary to induce substantial change in an
organism.
 Hormone concentration or rate of transport can change in response to environmental
stimuli.
 Often the response of a plant is governed by the interaction of two or more hormones.
Research on how plants grow toward light led to the discovery of plant hormones.
 The concept of chemical messengers in plants emerged from a series of classic
experiments on how stems respond to light.
 Plants grow toward light, and if you rotate a plant, it will reorient its growth until its
leaves again face the light.
 Any growth response that results in curvature of whole plant organs toward or away
from stimuli is called a tropism.
 The growth of a shoot toward light is called positive phototropism; growth away from
light is negative phototropism.
 Much of what is known about phototropism has been learned from studies of grass
seedlings, particularly oats.
 The shoot of a grass seedling is enclosed in a sheath called the coleoptile, which grows
straight upward if kept in the dark or illuminated uniformly from all sides.
 If it is illuminated from one side, it will curve toward the light as a result of differential
growth of cells on opposite sides of the coleoptile.
 The cells on the darker side elongate faster than the cells on the brighter side.
 In the late 19th century, Charles Darwin and his son Francis observed that a grass seedling
bent toward light only if the tip of the coleoptile was present.
 This response stopped if the tip was removed or covered with an opaque cap (but not a
transparent cap).
 While the tip was responsible for sensing light, the actual growth response occurred
some distance below the tip, leading the Darwins to postulate that some signal was
transmitted from the tip downward.
 Later, Peter Boysen-Jensen demonstrated that the signal was a mobile chemical substance.
 He separated the tip from the remainder of the coleoptile by a block of gelatin,
preventing cellular contact, but allowing chemicals to pass.
 These seedlings were phototropic.
 However, if the tip was segregated from the lower coleoptile by an impermeable
barrier, no phototropic response occurred.
 In 1926, Frits Went extracted the chemical messenger for phototropism, naming it auxin.

Biology Chapter Notes

 Modifying the Boysen-Jensen experiment, he placed excised tips on agar blocks,
collecting the hormone.
 If an agar block with this substance was centered on a coleoptile without a tip, the
plant grew straight upward.
 If the block was placed on one side, the plant began to bend away from the agar block.
 The classical hypothesis for what causes grass coleoptiles to grow toward light, based on
the previous research, is that an asymmetrical distribution of auxin moving down from the
coleoptile tip causes cells on the dark side to elongate faster than cells on the brighter side.
 However, studies of phototropism by organs other than grass coleoptiles provide less
support for this idea.
 There is, however, an asymmetrical distribution of certain substances that may act as
growth inhibitors, with these substances more concentrated on the lighted side of a
stem.
Plant hormones help coordinate growth, development, and responses to environmental
stimuli.
 In general, plant hormones control plant growth and development by affecting the
division, elongation, and differentiation of cells.
 Some hormones also mediate shorter-term physiological responses of plants to
environmental stimuli.
 Each hormone has multiple effects, depending on its site of action, its concentration,
and the developmental stage of the plant.
 Some of the major classes of plant hormones include auxin, cytokinins, gibberellins,
brassinosteroids, abscisic acid, and ethylene.
 Many molecules that function in plant defenses against pathogens are probably plant
hormones as well.
 Plant hormones tend to be relatively small molecules that are transported from cell to
cell across cell walls, a pathway that blocks the movement of large molecules.
 Plant hormones are produced at very low concentrations.
 Signal transduction pathways amplify the hormonal signal many-fold and connect it to
a cell’s specific responses.
 These include altering the expression of genes, affecting the activity of existing
enzymes, or changing the properties of membranes.
 Response to a hormone usually depends not so much on its absolute concentration as on
its relative concentration compared to other hormones.
 It is hormonal balance, rather than hormones acting in isolation, that control growth
and development of the plants.
 The term auxin is used for any chemical substance that promotes the elongation of
coleoptiles, although auxins actually have multiple functions in both monocots and dicots.
 The natural auxin occurring in plants is indoleacetic acid, or IAA.
 In growing shoots, auxin is transported unidirectionally, from the shoot apex down to the
base.
 The speed at which auxin is transported down the stem from the shoot apex is about 10
mm/hr, a rate that is too fast for diffusion, but slower than translocation in the phloem.
 Auxin seems to be transported directly through parenchyma tissue, from one cell to the
next.
 This unidirectional transport of auxin is called polar transport, and has nothing to do
with gravity.
Biology Chapter Notes
  Auxin travels upward if a stem or coleoptile is placed upside down.
 The polarity of auxin transport is due to the polar distribution of auxin transport
protein in the cells.
 Concentrated at the basal end of the cells, auxin transporters move the hormone out of
the cell and into the apical end of the neighboring cell.
 Although auxin affects several aspects of plant development, one of its chief functions is
to stimulate the elongation of cells in young shoots.
 The apical meristem of a shoot is a major site of auxin synthesis.
 As auxin moves from the apex down to the region of cell elongation, the hormone
stimulates cell growth, binding to a receptor in the plasma membrane.
 Auxin−4 stimulates cell growth only over a certain concentration range, from about 10 −8
to 10 M.
 At higher concentrations, auxins may inhibit cell elongation, probably by inducing
production of ethylene, a hormone that generally acts as an inhibitor of elongation.
 According to the acid growth hypothesis, in a shoot’s region of elongation, auxin
stimulates plasma membrane proton pumps, increasing the voltage across the membrane
and lowering the pH in the cell wall.
 Lowering the pH activates expansin enzymes that break the cross-links between
cellulose microfibrils and other cell wall constituents, loosening the wall.
 Increasing the membrane potential enhances ion uptake into the cell, which causes the
osmotic uptake of water.
 Uptake of water increases turgor and elongates the loose-walled cell.
 Auxin also alters gene expression rapidly, causing cells in the region of elongation to
produce new proteins within minutes.
 Some of these proteins are short-lived transcription factors that repress or activate the
expression of other genes.
 Auxin stimulates a sustained growth response of making the additional cytoplasm and
wall material required by elongation.
 Auxins are used commercially in the vegetative propagation of plants by cuttings.
 Treating a detached leaf or stem with rooting powder containing auxin often causes
adventitious roots to form near the cut surface.
 Auxin is also involved in the branching of roots.
 One Arabidopsis mutant that exhibits extreme proliferation of lateral roots has an
auxin concentration 17-fold higher than normal.
 Synthetic auxins, such as 2,4-dinitrophenol (2,4-D), are widely used as selective
herbicides.
 Monocots, such as maize or turfgrass, can rapidly inactivate these synthetic auxins.
 However, dicots cannot and die from a hormonal overdose.
 Spraying cereal fields or turf with 2,4-D eliminates dicot (broadleaf) weeds such as
dandelions.
 Auxin also affects secondary growth by inducing cell division in the vascular cambium
and by influencing the growth of secondary xylem.
 Developing seeds synthesize auxin, which promotes the growth of fruit.
 Synthetic auxins sprayed on tomato vines induce development of seedless tomatoes
because the synthetic auxins substitute for the auxin normally synthesized by the
developing seeds.
Biology Chapter Notes
 Cytokinins stimulate cytokinesis, or cell division.
 They were originally discovered in the 1940s by Johannes van Overbeek, who found
that he could stimulate the growth of plant embryos by adding coconut milk to his
culture medium.
 A decade later, Folke Skoog and Carlos O. Miller induced cultured tobacco cells to
divide by adding degraded samples of DNA.
 The active ingredients in both were modified forms of adenine, one of the components
of nucleic acids.
 These growth regulators were named cytokinins because they stimulate cytokinesis.
 The most common naturally occurring cytokinin is zeatin, named from the maize (Zea
mays) in which it was found.
 Much remains to be learned about cytokinin synthesis and signal transduction.
 Cytokinins are produced in actively growing tissues, particularly in roots, embryos, and
fruits.
 Cytokinins produced in the root reach their target tissues by moving up the plant in the
xylem sap.
 Cytokinins interact with auxins to stimulate cell division and differentiation.
 In the absence of cytokinins, a piece of parenchyma tissue grows large, but the cells do
not divide.
 In the presence of cytokinins and auxins, the cells divide, while cytokinins alone have
no effect.
 If the ratio of cytokinins and auxins is at a specific level, then the mass of growing
cells, called a callus, remains undifferentiated.
 If cytokinin levels are raised, shoot buds form from the callus.
 If auxin levels are raised, roots form.
 Cytokinins, auxins, and other factors interact in the control of apical dominance, the
ability of the terminal bud to suppress the development of axillary buds.
 Until recently, the leading hypothesis for the role of hormones in apical dominance—
the direct inhibition hypothesis—proposed that auxin and cytokinin act
antagonistically in regulating axillary bud growth.
 Auxin levels would inhibit axillary bud growth, while cytokinins would stimulate
growth.
 Many observations are consistent with the direct inhibition hypothesis.
 If the terminal bud, the primary source of auxin, is removed, the inhibition of axillary
buds is removed and the plant becomes bushier.
 This can be inhibited by adding auxins to the cut surface.
 The direct inhibition hypothesis predicts that removing the primary source of auxin should
lead to a decrease in auxin levels in the axillary buds.
 However, experimental removal of the terminal shoot (decapitation) has not demonstrated
this.
 In fact, auxin levels actually increase in the axillary buds of decapitated plants.
 Further research is necessary to uncover all pieces of this puzzle.
 Cytokinins retard the aging of some plant organs.
 They inhibit protein breakdown by stimulating RNA and protein synthesis and by
mobilizing nutrients from surrounding tissues.

Biology Chapter Notes

  Leaves removed from a plant and dipped in a cytokinin solution stay green much
longer than otherwise.
 Cytokinins also slow deterioration of leaves on intact plants.
 Florists use cytokinin sprays to keep cut flowers fresh.
 A century ago, farmers in Asia noticed that some rice seedlings grew so tall and spindly
that they toppled over before they could mature and flower.
 In 1926, E. Kurosawa discovered that a fungus in the genus Gibberella causes this
“foolish seedling disease.”
 The fungus induced hyperelongation of rice stems by secreting a chemical, given the
name gibberellin.
 In the 1950s, researchers discovered that plants also make gibberellins. Researchers have
identified more than 100 different natural gibberellins.
 Typically each plant produces a much smaller number.
 Foolish rice seedlings, it seems, suffer from an overdose of growth regulators normally
found in lower concentrations.
 Roots and leaves are major sites of gibberellin production.
 Gibberellins stimulate growth in both leaves and stems but have little effect on root
growth.
 In stems, gibberellins stimulate cell elongation and cell division.
 One hypothesis proposes that gibberellins stimulate cell wall–loosening enzymes that
facilitate the penetration of expansin proteins into the cell well.
 Thus, in a growing stem, auxin, by acidifying the cell wall and activating expansins,
and gibberellins, by facilitating the penetration of expansins, act in concert to promote
elongation.
 The effects of gibberellins in enhancing stem elongation are evident when certain dwarf
varieties of plants are treated with gibberellins.
 After treatment with gibberellins, dwarf pea plants grow to normal height.
 However, if gibberellins are applied to normal plants, there is often no response,
perhaps because these plants are already producing the optimal dose of the hormone.
 The most dramatic example of gibberellin-induced stem elongation is bolting, the rapid
formation of the floral stalk.
 In their vegetative state, some plants develop in a rosette form with a body low to the
ground with short internodes.
 As the plant switches to reproductive growth, a surge of gibberellins induces
internodes to elongate rapidly, which elevates the floral buds that develop at the tips of
the stems.
 In many plants, both auxin and gibberellins must be present for fruit to set.
 Spraying of gibberellin during fruit development is used to make the individual grapes
grow larger and to make the internodes of the grape bunch elongate.
 This enhances air circulation between the grapes and makes it harder for yeast and
other microorganisms to infect the fruits.
 The embryo of a seed is a rich source of gibberellins.
 After hydration of the seed, the release of gibberellins from the embryo signals the
seed to break dormancy and germinate.
 Some seeds that require special environmental conditions to germinate, such as
exposure to light or cold temperatures, will break dormancy if they are treated with
gibberellins.
Biology Chapter Notes
  Gibberellins support the growth of cereal seedlings by stimulating the synthesis of
digestive enzymes that mobilize stored nutrients.
 First isolated from Brassica pollen in 1979, brassinosteroids are steroids chemically
similar to cholesterol and the sex hormones of animals.
 Brassinosteroids induce cell−12 elongation and division in stem segments and seedlings at
concentrations as low as 10 M.
 They also retard leaf abscission and promote xylem differentiation.
 Their effects are so qualitatively similar to those of auxin that it took several years for
plant physiologists to accept brassinosteroids as nonauxin hormones.
 Joann Chory and her colleagues provided evidence from molecular biology that
brassinosteroids were plant hormones.
 An Arabidopsis mutant that has morphological features similar to light-grown plants
even when grown in the dark lacks brassinosteroids.
 This mutation affects a gene that normally codes for an enzyme similar to one involved
in steroid synthesis in mammalian cells.
 Abscisic acid (ABA) was discovered independently in the 1960s by one research group
studying bud dormancy and another investigating leaf abscission (the dropping of autumn
leaves).
 Ironically, ABA is no longer thought to play a primary role in either bud dormancy or
leaf abscission, but it is an important plant hormone with a variety of functions.
 ABA generally slows down growth.
 Often ABA antagonizes the actions of the growth hormones—auxins, cytokinins, and
gibberellins.
 It is the ratio of ABA to one or more growth hormones that determines the final
physiological outcome.
 One major affect of ABA on plants is seed dormancy.
 The levels of ABA may increase 100-fold during seed maturation, leading to inhibition
of germination and the production of special proteins that help seeds withstand the
extreme dehydration that accompanies maturation.
 Seed dormancy has great survival value because it ensures that the seed will germinate
only when there are optimal conditions of light, temperature, and moisture.
 Many types of dormant seeds will germinate when ABA is removed or inactivated.
 For example, the seeds of some desert plants break dormancy only when heavy rains
wash ABA out of the seed.
 Other seeds require light or prolonged exposure to cold to trigger the inactivation of
ABA.
 A maize mutant that has seeds that germinate while still on the cob lacks a functional
transcription factor required for ABA to induce expression of certain genes.
 ABA is the primary internal signal that enables plants to withstand drought.
 When a plant begins to wilt, ABA accumulates in leaves and causes stomata to close
rapidly, reducing transpiration and preventing further water loss.
 ABA causes an increase in the opening of outwardly directed potassium channels in
the plasma membrane of guard cells, leading to a massive loss of potassium.
 The accompanying osmotic loss of water leads to a reduction in guard cell turgor, and
the stomata close.
 In some cases, water shortages in the root system can lead to the transport of ABA
from roots to leaves, functioning as an “early warning system.”
Biology Chapter Notes
  Mutants that are prone to wilting are often deficient in ABA production.
 In 1901, Dimitry Neljubow demonstrated that the gas ethylene was the active factor that
caused leaves to drop from trees that were near leaking gas mains.
 Plants produce ethylene in response to stresses such as drought, flooding, mechanical
pressure, injury, and infection.
 Ethylene production also occurs during fruit ripening and during programmed cell
death.
 Ethylene is also produced in response to high concentrations of externally applied
auxins.
 Ethylene instigates a seedling to perform a growth maneuver called the triple response
that enables a seedling to circumvent an obstacle as it grows through soil.
 Ethylene production is induced by mechanical stress on the stem tip.
 In the triple response, stem elongation slows, the stem thickens, and curvature causes the
stem to start growing horizontally.
 As the stem continues to grow horizontally, its tip touches upward intermittently.
 If the probes continue to detect a solid object above, then another pulse of ethylene is
generated, and the stem continues its horizontal progress.
 If upward probes detect no solid object, then ethylene production decreases, and the
stem resumes its normal upward growth.
 It is ethylene, not the physical obstruction per se, that induces the stem to grow
horizontally.
 Normal seedlings growing free of all physical impediments will undergo the triple
response if ethylene is applied.
 Arabidopsis mutants with abnormal triple responses have been used to investigate the
signal transduction pathways leading to this response.
 Ethylene-insensitive (ein) mutants fail to undergo the triple response after exposure to
ethylene.
 Some lack a functional ethylene receptor.
 Other mutants undergo the triple response in the absence of physical obstacles.
 Some mutants (eto) produce ethylene at 20 times the normal rate.
 Other mutants, called constitutive triple-response (ctr) mutants, undergo the triple
response in air but do not respond to inhibitors of ethylene synthesis.
 Ethylene signal transduction is permanently turned on even though there is no
ethylene present.
 The various ethylene signal-transduction mutants can be distinguished by their different
responses to experimental treatments.
 The affected gene in ctr mutants codes for a protein kinase.
 Because this mutation activates the ethylene response, this suggests that the normal
kinase product of the wild-type allele is a negative regulator of ethylene signal
transduction.
 One hypothesis proposes that binding of the hormone ethylene to a receptor leads to
inactivation of the kinase and inactivation of this negative regulator allows synthesis of
the proteins required for the triple response.
 The cells, organs, and plants that are genetically programmed to die on a particular
schedule do not simply shut down their cellular machinery and await death.

Biology Chapter Notes

  Rather, during programmed cell death, called apoptosis, there is active expression of
new genes, which produce enzymes that break down many chemical components,
including chlorophyll, DNA, RNA, proteins, and membrane lipids.
 A burst of ethylene productions is associated with apoptosis whether it occurs during
the shedding of leaves in autumn, the death of an annual plant after flowering, or as the
final step in the differentiation of a xylem vessel element.
 The loss of leaves each autumn is an adaptation that keeps deciduous trees from
desiccating during winter when roots cannot absorb water from the frozen ground.
 Before leaves abscise, many essential elements are salvaged from the dying leaves and
stored in stem parenchyma cells.
 These nutrients are recycled back to developing leaves the following spring.
 When an autumn leaf falls, the breaking point is an abscission layer near the base of the
petiole.
 The parenchyma cells here have very thin walls, and there are no fiber cells around the
vascular tissue.
 The abscission layer is further weakened when enzymes hydrolyze polysaccharides in
the cell walls.
 The weight of the leaf, with the help of the wind, causes a separation within the
abscission layer.
 A change in the balance of ethylene and auxin controls abscission.
 An aged leaf produces less and less auxin, and this makes the cells of the abscission
layer more sensitive to ethylene.
 As the influence of ethylene prevails, the cells in the abscission layer produce enzymes
that digest the cellulose and other components of cell walls.
 The consumption of ripe fruits by animals helps disperse the seeds of flowering plants.
 Immature fruits are tart, hard, and green but become edible at the time of seed
maturation, triggered by a burst of ethylene production.
 Enzymatic breakdown of cell wall components softens the fruit, and conversion of
starches and acids to sugars makes the fruit sweet.
 The production of new scents and colors helps advertise fruits’ ripeness to animals,
which eat the fruits and disperse the seeds.
 A chain reaction occurs during ripening: ethylene triggers ripening and ripening, in turn,
triggers even more ethylene production—a rare example of positive feedback on
physiology.
 Because ethylene is a gas, the signal to ripen even spreads from fruit to fruit.
 Fruits can be ripened quickly by storing the fruit in a plastic bag, accumulating
ethylene gas, or by enhancing ethylene levels in commercial production.
 Alternatively, to prevent premature ripening, apples are stored in bins flushed with
carbon dioxide, which prevents ethylene from accumulating and inhibits the synthesis
of new ethylene.
 Genetic engineering of ethylene signal transduction pathways has potentially important
commercial applications after harvest.
 For example, molecular biologists have blocked the transcription of one of the genes
required for ethylene synthesis in tomato plants.
 These tomato fruits are picked while green and are induced to ripen on demand when
ethylene gas is added.

Biology Chapter Notes

 Plant responses often involve interactions of many hormones and their signal transduction
pathways.
 The study of hormone interactions can be a complex problem.
 For example, flooding of deepwater rice leads to a 50-fold increase in internal ethylene
and a rapid increase in stem elongation.
 Flooding also leads to an increase in sensitivity to GA that is mediated by a
decrease in ABA levels.
 Thus, stem elongation is the result of interaction among three hormones and their
signal transduction chains.
 Imagine that you are a molecular biologist assigned the task of genetically engineering
a rice plant that will grow faster when submerged.
 What is the best molecular target for genetic manipulation? Is it an enzyme that
inactivates ABA, an ethylene receptor, or an enzyme that produces more GA?
 Many plant biologists are promoting a systems-based approach.
 Using genomic techniques, biologists can identify all the genes in a plant.
 Two plants are already sequenced: Arabidopsis and the rice plant Oryza sativa.
 Using microassay and proteomic techniques, scientists can determine which genes
are inactivated or activated in response to an environmental change.
 New hypotheses and approaches will emerge from analysis of these comprehensive
data sets.

Concept 39.3 Responses to light are critical for plant success

 Light is an especially important factor in the lives of plants.
 In addition to being required for photosynthesis, light also cues many key events in
plant growth and development.
 These effects of light on plant morphology are what plant biologists call
photomorphogenesis.
 Light reception is also important in allowing plants to measure the passage of days and
seasons.
 Plants detect the presence, direction, intensity, and wavelength of light.
 For example, the measure of the action spectrum of photosynthesis has two peaks,
one in the red and one in the blue.
 These match the absorption peaks of chlorophyll.
 Action spectra can be useful in the study of any process that depends on light.
 A close correspondence between an action spectrum of a plant response and the
absorption spectrum of a purified pigment suggests that the pigment may be the
photoreceptor involved in mediating the response.
 Action spectra reveal that red and blue light are the most important colors regulating a
plant’s photomorphogenesis.
 These observations led researchers to two major classes of light receptors: a
heterogeneous group of blue-light photoreceptors and a family of photoreceptors
called phytochromes that absorb mostly red light.
Blue-light photoreceptors are a heterogeneous group of pigments.
 The action spectra of many plant processes demonstrate that blue light is effective in
initiating diverse responses.
Biology Chapter Notes
 The biochemical identity of the blue-light photoreceptor was so elusive that they were
called cryptochromes.
 In the 1990s, molecular biologists analyzing Arabidopsis mutants found three
completely different types of pigments that detect blue light.
 These are cryptochromes (for the inhibition of hypocotyl elongation), phototropin
(for phototropism), and a carotenoid-based photoreceptor called zeaxanthin (for
stomatal opening).
Phytochromes function as photoreceptors in many plant responses to light.
 Phytochromes were discovered from studies of seed germination.
 Because of their limited food resources, successful sprouting of many types of small
seeds, such as lettuce, requires that they germinate only when conditions, especially
light conditions, are near optimal.
 Such seeds often remain dormant for many years until light conditions change.
 For example, the death of a shading tree or the plowing of a field may create a
favorable light environment.
 In the 1930s, scientists at the U.S. Department of Agriculture determined the action
spectrum for light-induced germination of lettuce seeds.
 They exposed water-swollen seeds to a few minutes of monochromatic light of various
wavelengths and stored them in the dark for two days and recorded the number of
seeds that had germinated under each light regimen.
 While red light (660 nm) increased germination, far-red light (730 nm) inhibited it and
the response depended on the last flash of light.
 The photoreceptor responsible for these opposing effects of red and far-red light is a
phytochrome.
 It consists of a protein covalently bonded to a nonprotein part that functions as a
chromophore, the light-absorbing part of the molecule.
 The chromophore is photoreversible and reverts back and forth between two isomeric
forms with one (Pr) absorbing red light and becoming (P fr), and the other (Pfr)
absorbing far-red light and becoming (Pr).
 This interconversion between isomers acts as a switching mechanism that controls various
light-induced events in the life of the plant.
 The Pfr form triggers many of the plant’s developmental responses to light.
 Exposure to far-red light inhibits the germination response.
 Plants synthesize phytochrome as Pr, and if seeds are kept in the dark, the pigment
remains almost entirely in the Pr form.
 If the seeds are illuminated with sunlight, the phytochrome is exposed to red light
(along with other wavelengths), and much of the P r is converted to Pfr, triggering
germination.
 The phytochrome system also provides plants with information about the quality of light.
 During the day, with the mix of both red and far-red radiation, the Pr <=>Pfr
photoreversion reaches a dynamic equilibrium.
 Plants can use the ratio of these two forms to monitor and adapt to changes in light
conditions.
 For example, changes in this equilibrium might be used by a tree that requires high light
intensity as a way to assess appropriate growth strategies.
 If other trees shade this tree, its phytochrome ratio will shift in favor of P r because the
canopy screens out more red light than far-red light.
Biology Chapter Notes
  The tree could use this information to indicate that it should allocate resources to
growing taller.
 If the target tree is in direct sunlight, then the proportion of Pfr will increase, which
stimulates branching and inhibits vertical growth.
Biological clocks control circadian rhythms in plants and other eukaryotes.
 Many plant processes, such as transpiration and synthesis of certain enzymes, oscillate
during the day.
 This is often in response to changes in light levels, temperature, and relative humidity
that accompany the 24-hour cycle of day and night.
 Even under constant conditions in a growth chamber, many physiological processes in
plants, such as opening and closing of stomata and the production of photosynthetic
enzymes, continue to oscillate with a frequency of about 24 hours.
 For example, many legumes lower their leaves in the evening and raise them in the
morning.
 These movements continue even if plants are kept in constant light or constant
darkness.
 Such physiological cycles with a frequency of about 24 hours that are not directly
paced by any known environmental variable are called circadian rhythms.
 These rhythms are ubiquitous features of eukaryotic life.
 Because organisms continue their rhythms even when placed in the deepest mine shafts or
when orbited in satellites, they do not appear to be triggered by some subtle but pervasive
environmental signal.
 All research thus far indicates that the oscillator for circadian rhythms is endogenous
(internal).
 This internal clock, however, is entrained (set) to a period of precisely 24 hours by
daily signals from the environment.
 If an organism is kept in a constant environment, its circadian rhythms deviate from a 24-
hour period to free-running periods ranging from 21 to 27 hours.
 Deviations of the free-running period from 24 hours does not mean that the biological
clocks drift erratically, but that they are not synchronized with the outside world.
 In considering biological clocks, we need to distinguish between the oscillator (clock) and
the rhythmic processes it controls.
 For example, if we were to restrain the leaves of a bean plant so they cannot move,
they will rush to the appropriate position for that time of day when we release them.
 We can interfere with a biological rhythm, but the clockwork goes right on ticking off
the time.
 A leading hypothesis for the molecular mechanisms underlying biological timekeeping is
that it depends on synthesis of a protein that regulates its own production through
feedback control.
 This protein may be a transcription factor that inhibits transcription of the gene that
encodes for the transcription factor itself.
 The concentration of this transcription factor may accumulate during the first half of
the circadian cycle and decline during the second half due to self-inhibition of its own
production.
 Researchers have recently used a novel technique to identify clock mutants in
Arabidopsis.

Biology Chapter Notes

  Molecular biologists spliced the gene for luciferase to the promoter of certain
photosynthesis-related genes that show circadian rhythms in transcription.
 Luciferase is the enzyme responsible for bioluminescence in fireflies.
 When the biological clock turned on the promoter of the photosynthesis genes in
Arabidopsis, it also stimulated production of luciferase, and the plant glowed.
 This enabled researchers to screen plants for clock mutations, several of which are
defects in proteins that normally bind photoreceptors.
 The altered genes in some of these mutants affect proteins that normally bind
photoreceptors.
Light entrains the biological clock.
 Because the free running period of many circadian rhythms is greater than or less than the
24-hour daily cycle, they eventually become desynchronized with the natural environment
when denied environmental cues.
 Humans experience this type of desynchronization when we cross several times zones
in an airplane, leading to the phenomenon we call jet lag.
 Eventually, our circadian rhythms become resynchronized with the external
environment.
 Plants are also capable of reestablishing (entraining) their circadian synchronization.
 Both phytochrome and blue-light photoreceptors can entrain circadian rhythms of plants.
 The phytochrome system involves turning cellular responses off and on by means of
the Pr <=> Pfr switch.
 In darkness, the phytochrome ratio shifts gradually in favor of the P r form, in part from
synthesis of new Pr molecules and, in some species, by slow biochemical conversion of
Pfr to Pr.
 When the sun rises, the Pfr level suddenly increases by rapid photoconversion of P r.
 This sudden increase in Pfr each day at dawn resets the biological clock.
Photoperiodism synchronizes many plant responses to changes of season.
 The appropriate appearance of seasonal events is of critical importance in the life cycles
of most plants.
 These seasonal events include seed germination, flowering, and the onset and breaking
of bud dormancy.
 The environmental stimulus that plants use most often to detect the time of year is the
photoperiod, the relative lengths of night and day.
 A physiological response to photoperiod, such as flowering, is called photoperiodism.
 One of the earliest clues to how plants detect the progress of the seasons came from a
mutant variety of tobacco studied by W. W. Garner and H. A. Allard in 1920.
 This variety, Maryland Mammoth, does not flower in summer as normal tobacco
plants do, but in winter.
 In light-regulated chambers, they discovered that this variety would flower only if the
day length was 14 hours or shorter, which explained why it would not flower during
the longer days of the summer.
 Garner and Allard termed the Maryland Mammoth a short-day plant, because it required
a light period shorter than a critical length to flower.
 Other examples include chrysanthemums, poinsettias, and some soybean varieties.
 Long-day plants will only flower when the light period is longer than a critical number
of hours.
Biology Chapter Notes
  Examples include spinach, iris, and many cereals.
 Day-neutral plants will flower when they reach a certain stage of maturity, regardless of
day length.
 Examples include tomatoes, rice, and dandelions.
 In the 1940s, researchers discovered that it is actually night length, not day length, that
controls flowering and other responses to photoperiod.
 Research demonstrated that the cocklebur, a short-day plant, would flower if the
daytime period was broken by brief exposures to darkness, but not if the nighttime
period was broken by a few minutes of dim light.
 Short-day plants are actually long-night plants, requiring a minimum length of
uninterrupted darkness.
 Cocklebur is actually unresponsive to day length, but it requires at least 8 hours of
continuous darkness to flower.
 Similarly, long-day plans are actually short-night plants.
 A long-day plant grown on photoperiods of long nights that would not normally induce
flowering will flower if the period of continuous darkness is interrupted by a few
minutes of light.
 Long-day and short-day plants are distinguished not by an absolute night length but by
whether the critical night lengths sets a maximum (long-day plants) or minimum (short-
day plants) number of hours of darkness required for flowering.
 In both cases, the actual number of hours in the critical night length is specific to each
species of plant.
 While the critical factor is night length, the terms “long-day” and “short-day” are
embedded firmly in the jargon of plant physiology.
 Red light is the most effective color in interrupting the nighttime portion of the
photoperiod.
 Action spectra and photoreversibility experiments show that phytochrome is the active
pigment.
 If a flash of red light during the dark period is followed immediately by a flash of far-red
light, then the plant detects no interruption of night length, demonstrating red/far-red
photoreversibility.
 Plants measure night length very accurately.
 Some short-day plants will not flower if night is even one minute shorter than the
critical length.
 Some plants species always flower on the same day each year.
 Humans can exploit the photoperiodic control of flowering to produce flowers “out of
season.”
 By punctuating each long night with a flash of light, the floriculture industry can
induce chrysanthemums, normally a short-day plant that blooms in fall, to delay their
blooming until Mother’s Day in May.
 The plants interpret this as not one long night, but two short nights.
 While some plants require only a single exposure to the appropriate photoperiod to begin
flowering, others require several successive days of the appropriate photoperiod.
 Other plants respond to photoperiod only if pretreated by another environmental stimulus.

Biology Chapter Notes

  For example, winter wheato will not flower unless it has been exposed to several weeks
of temperatures below 10 C (called vernalization) before exposure to the appropriate
photoperiod.
 While buds produce flowers, it is leaves that detect photoperiod and trigger flowering.
 If even a single leaf receives the appropriate photoperiod, all buds on a plant can be
induced to flower, even if they have not experienced this signal.
 Plants lacking leaves will not flower, even if exposed to the appropriate photoperiod.
 The flowering signal, not yet chemically identified, is called florigen, and it may be a
hormone or some change in the relative concentrations of two or more hormones.
 Whatever combination of environmental cues (such as photoperiod or vernalization) and
internal signals (such as hormones) is necessary for flowering to occur, the outcome is the
transition of a bud’s meristem from a vegetative state to a flowering state.
 This requires that meristem-identity genes that induce the bud to form a flower must be
switched on.
 Then organ-identity genes that specify the spatial organization of floral organs—
sepals, petals, stamens, and carpels—are activated in the appropriate regions of the
meristem.
 Identification of the signal transduction pathways that link external cues to the gene
changes required for flowering are active areas of research.

Concept 39.4 Plants respond to a wide variety of stimuli other than light
 Because of their immobility, plants must adjust to a wide range of environmental
circumstances through developmental and physiological mechanisms.
 While light is one important environmental cue, other environmental stimuli also
influence plant development and physiology.
Plants respond to environmental stimuli through a combination of developmental and
physiological mechanisms.
 Both the roots and shoots of plants respond to gravity, or gravitropism, although in
diametrically different ways.
 Roots demonstrate positive gravitropism, and shoots exhibit negative gravitropism.
 Gravitropism ensures that the root grows in the soil and that the shoot reaches sunlight
regardless of how a seed happens to be oriented when it lands.
 Auxin plays a major role in gravitropic responses.
 Plants may tell up from down by the settling of statoliths, specialized plastids containing
dense starch grains, to the lower portions of cells.
 In one hypothesis, the aggregation of statoliths at low points in cells of the root cap
triggers the redistribution of calcium, which in turn causes lateral transport of auxin
within the root.
 The high concentrations of auxin on the lower side of the zone of elongation inhibits
cell elongation, slowing growth on that side and curving the root downward.
 Experiments with Arabidopsis and tobacco mutants have demonstrated the importance of
“falling statoliths” in root gravitropism, but these have also indicated that other factors or
organelles may be involved.
 Mutants lacking statoliths have a slower response than wild-type plants.

Biology Chapter Notes

  One possibility is that the entire cell helps the root sense gravity by mechanically
pulling on proteins that tether the protoplast to the cell wall, stretching proteins on the
“up” side and compressing proteins on the “down side.”
 Other dense organelles may also contribute to gravitropism by distorting the
cytoskeleton.
 Plants can change form in response to mechanical perturbations.
 Such thigmomorphogenesis may be seen when comparing a short, stocky tree
growing on a windy mountain ridge with a taller, more slender member of the same
species growing in a more sheltered location.
 Because plants are very sensitive to mechanical stress, researchers have found that
even measuring the length of a leaf with a ruler alters its subsequent growth.
 Rubbing the stems of young plants a few times results in plants that are shorter than
controls.
 Mechanical stimulation activates a signal transduction pathway that increases
cytoplasmic calcium, which mediates the activity of specific genes, including some
that encode for proteins that affect cell wall properties.
 Some plant species have become, over the course of their evolution, “touch specialists.”
 For example, most vines and other climbing plants have tendrils that grow straight
until they touch something.
 Contact stimulates a coiling response, thigmotropism, caused by differential growth
of cells on opposite sides of the tendril.
 This allows a vine to take advantage of whatever mechanical support it comes across
as it climbs upward toward a forest canopy.
 Some touch specialists undergo rapid leaf movements in response to mechanical
stimulation.
 For example, when the compound leaf of a Mimosa plant is touched, it collapses and
leaflets fold together.
 This occurs when pulvini, motor organs at the joints of leaves, become flaccid from a
loss of potassium and subsequent loss of water by osmosis.
 It takes about ten minutes for the cells to regain their turgor and restore the
“unstimulated” form of the leaf.
 The folding of Mimosa leaves may reduce surface area in response to strong winds,
thus reducing water loss. Collapse of the leaves exposes thorns on the stem, which may
serve to deter herbivory.
 One remarkable feature of rapid leaf movement is that signals are transmitted from leaflet
to leaflet via action potentials.
 Traveling at about a centimeter per second through the leaf, these electrical impulses
resemble nervous-system messages in animals, although the action potentials of plants
are thousands of times slower.
 Action potentials, which have been discovered in many species of algae and plants,
may be widely used as a form of internal communication.
 In the carnivorous Venus flytrap, stimulation of sensory hairs in the trap results in an
action potential that travels to the cells that close the trap.
 Occasionally, factors in the environment change severely enough to have an adverse
effect on a plant’s survival, growth, and reproduction.
 These environmental stresses can devastate crop yields.
 In natural ecosystems, plants that cannot tolerate environmental stress will either
succumb or be outcompeted by other plants, and they will become locally extinct.
Biology Chapter Notes
 Thus, environmental stresses, both biotic and abiotic, are important in determining the
geographic range of plants.
 On a bright, warm, dry day, a plant may be stressed by a water deficit because it is losing
water by transpiration faster than water can be restored by uptake from the soil.
 Prolonged drought can stress or even kill crops and plants in natural ecosystems.
 Plants have control systems that enable them to cope with less extreme water deficits.
 Much of the plant’s response to a water deficit helps the plant conserve water by reducing
transpiration.
 As the water deficit in a leaf rises, guard cells lose turgor and the stomata close.
 A water deficit also stimulates increased synthesis and release of abscisic acid in a leaf,
which also signals guard cells to close stomata.
 Because cell expansion is a turgor-dependent process, a water deficit will inhibit the
growth of young leaves.
 As plants wilt, their leaves may roll into a shape that reduces transpiration by exposing
less leaf surface to dry air and wind.
 These responses also reduce photosynthesis.
 Root growth also responds to water deficit.
 During a drought, the soil usually dries from the surface down.
 This inhibits the growth of shallow roots, partly because cells cannot maintain the
turgor required for elongation.
 Deeper roots surrounded by soil that is still moist continue to grow, and the root
system proliferates in a way that maximizes exposure to soil water.
 Plants in flooded soils (or overwatered houseplants) can suffocate because the soil lacks
the air spaces that provide oxygen for cellular respiration in the roots.
 Some plants are adapted to very wet habitats.
 Mangroves, inhabitants of coastal marshes, produce aerial roots that provide access to
oxygen.
 Less specialized plants in waterlogged soils may produce ethylene in the roots, causing
some cortical cells to undergo apoptosis, which creates air tubes that function as
“snorkels.”
 An excess of sodium chloride or other salts in the soil threaten plants for two reasons.
 First, by lowering the water potential of the soil, plants can lose water to the
environment rather than absorb it.
 Second, sodium and certain other ions are toxic to plants when their concentrations are
relatively high.
 The selectively permeable membranes of root cells impede the uptake of most harmful
ions, but this aggravates the problem of acquiring water.
 Some plants produce compatible solutes, organic compounds that keep the water potential
of the cell more negative than that of the soil, without the toxic quantities of salt.
 Still, most plants cannot survive salt stress for long.
 The exceptions are halophytes, salt-tolerant plants with adaptations such as salt glands
that pump salts out across the leaf epidermis.
 Excessive heat can harm and eventually kill a plant by denaturing its enzymes and
damaging its metabolism.
 Transpiration helps dissipate excess heat through evaporative cooling, but at the cost of
possibly causing a water deficit in many plants.
Biology Chapter Notes
  Closing stomata to preserve water sacrifices evaporative cooling.
 Most plants have a backup response that enables them to survive heat stress.
 Above a certain temperature—about 40°C for most plants in temperate regions—plant
cells begin to synthesize relatively large quantities of heat-shock proteins.
 Some heat-shock proteins are identical to chaperone proteins, which function in
unstressed cells as temporary scaffolds that help other proteins fold into their
functional shapes.
 Similarly, heat-shock proteins may embrace enzymes and other proteins and help
prevent denaturation.
 One problem that plants face when the temperature of the environment falls is a change in
the fluidity of cell membranes.
 When the temperature becomes too cool, lipids are locked into crystalline structures
and membranes lose their fluidity, which adversely affects solute transport and the
functions of other membrane proteins.
 One solution is to alter lipid composition in the membranes, increasing the proportion
of unsaturated fatty acids, which have shapes that keep membranes fluid at lower
temperatures.
 This response requires several hours to days, which is one reason rapid chilling is
generally more stressful than gradual seasonal cooling.
 Freezing is a more severe version of cold stress.
 At subfreezing temperatures, ice forms in the cell walls and intercellular spaces of
most plants.
 Solutes in the cytosol depress its freezing point.
 This lowers the extracellular water potential, causing water to leave the cytoplasm and,
therefore, causing dehydration.
 The resulting increase in the concentration of salt ions in the cytoplasm is also harmful
and can lead to cell death.
 Plants native to regions where winters are cold have special adaptations that enable them
to cope with freezing stress.
 This may involve an overall resistance to dehydration.
 In other cases, the cells of many frost-tolerant species increase their cytoplasmic levels
of specific solutes, such as sugars, which are better tolerated at high concentrations and
which help reduce water loss from the cell during extracellular freezing.

Concept 39.5 Plants defend themselves against herbivores and pathogens

 Plants do not exist in isolation, but interact with many other species in their communities.
 Some of these interspecific interactions—for example, associations with fungi in
mycorrhizae or with insect pollinators—are mutually beneficial.
 Most interactions that plants have with other organisms are not beneficial to the plant.
 As primary producers, plants are at the base of most food webs and are subject to
attack by a wide variety of plant-eating (herbivorous) animals.
 Plants are also subject to attacks by pathogenic viruses, bacteria, and fungi.
Plants deter herbivores with both physical and chemical defenses.
 Herbivory is a stress that plants face in any ecosystem.

Biology Chapter Notes

 Plants counter excess herbivory with both physical defenses, such as thorns, and chemical
defenses, such as the production of distasteful or toxic compounds.
 For example, some plants produce an unusual amino acid, canavanine, which resembles
arginine.
 If an insect eats a plant containing canavanine, canavanine is incorporated into the
insect’s proteins in place of arginine.
 Because canavanine is different enough from arginine to adversely affect the
conformation and, hence, the function of the proteins, the insect dies.
 Some plants even recruit predatory animals that help defend the plant against specific
herbivores.
 For example, a leaf damaged by caterpillars releases volatile compounds that attract
parasitoid wasps, hastening the destruction of the caterpillars.
 Parasitoid wasps inject their eggs into their prey, including herbivorous caterpillars.
 The eggs hatch within the caterpillars, and the larvae eat through their organic
containers from the inside out.
 These volatile molecules can also function as an “early warning system” for nearby plants
of the same species.
 Lima bean plants infested with spider mites release volatile chemicals that signal
“news” of the attack to neighboring, noninfested lima bean plants.
 The leaves of the noninfested plant activate defense genes whose expression patterns
are similar to that produced by exposure to jasmonic acid, an important plant defense
molecule.
 As a result, noninfested neighbors become less susceptible to spider mites and more
attractive to mites that prey on spider mites.
Plants use multiple lines of defense against pathogens.
 A plant’s first line of defense against infection is the physical barrier of the plant’s “skin,”
the epidermis of the primary plant body and the periderm of the secondary plant body.
 However, viruses, bacteria, and the spores and hyphae of fungi can enter the plant
through injuries or through natural openings in the epidermis, such as stomata.
 Once a pathogen invades, the plant mounts a chemical attack as a second line of
defense that kills the pathogens and prevents their spread from the site of infection.
 Plants are generally resistant to most pathogens.
 Plants have an innate ability to recognize invading pathogens and to mount successful
defenses.
 In a converse manner, successful pathogens cause disease because they are able to
evade recognition or suppress host defense mechanisms.
 Those few pathogens against which a plant has little specific defense are said to be
virulent.
 Avirulent pathogens gain enough access to their host to perpetuate themselves without
severely damaging or killing the plant.
 Specific resistance to a plant disease is based on what is called gene-for-gene
recognition.
 This involves recognition of pathogen-derived molecules by the protein products of
specific plant disease resistance (R) genes.
 There are many pathogens, and plants have many R genes.
 An R protein usually recognizes only a single corresponding pathogen molecule that is
encoded by an avirulence (Avr) gene.
Biology Chapter Notes
  Many Avr proteins play an active role in pathogenesis and are thought to redirect host
metabolism to the advantage of the pathogen.
 The simplest biochemical model for gene-for-gene recognition is the receptor-ligand
model.
 The R protein functions as a specific receptor protein that triggers resistance on
binding to the correct corresponding Avr protein.
 If the host lacks the R gene that counteracts the pathogen’s Avr gene, the pathogen can
invade and kill the plant.
 The “guard” hypothesis for gene-for-gene recognition proposes that R proteins function as
a surveillance system to detect changes in protein activity or conformation induced by Avr
proteins.
 Regardless of the mechanism, recognition of pathogen-derived molecules by R proteins
triggers a signal transduction pathway leading to a defense response in the infected plant
tissue.
 This defense includes an enhancement of the localized response at the site of infection
and a systemic response of the whole plant.
 Even if a plant is infected by a virulent strain of a pathogen—one for which that particular
plant has no genetic resistance—the plant is able to mount a localized chemical attack in
response to molecular signals released from cells damaged by infection.
 Molecules called elicitors, often cellulose fragments called oligosaccharins released
by cell wall damage, induce the production of antimicrobial compounds called
phytoalexins.
 Infection also activates genes that produce PR proteins (for pathogenesis-related).
 Some of these are antimicrobial and attack bacterial cell walls.
 Others spread “news” of the infection to nearby cells.
 Infection also stimulates cross-linking of molecules in the cell wall and deposition of
lignins.
 This sets up a local barricade that slows spread of the pathogen to other parts of the
plant.
 If the pathogen is avirulent based on an R-Avr match, the localized defense response is
more vigorous and is called a hypersensitive response (HR).
 There is an enhanced production of phytoalexins and PR proteins, and the “sealing”
response that contains the infection is more effective.
 After cells at the site of infection mount their chemical defense and seal off the area,
they destroy themselves.
 These areas are visible as lesions on a leaf or other infected organ, but the leaf or
organ will survive, and its defense response will help protect the rest of the plant.
 Part of the hypersensitive response includes production of chemical signals that spread
throughout the plant, stimulating production of phytoalexins and PR proteins.
 This response, called systemic acquired resistance (SAR), is nonspecific, providing
protection against a diversity of pathogens for days.
 A good candidate for one of the hormones responsible for activating SAR is salicylic
acid.
 A modified form of this compound, acetylsalicylic acid, is the active ingredient in
aspirin.

Biology Chapter Notes

  Centuries before aspirin was sold as a pain reliever, some cultures had learned that
chewing the bark of a willow tree (Salix) would lessen the pain of a toothache or
headache.
 In plants, salicylic acid also appears to have medicinal value, but only through the
stimulation of the systemic acquired resistance system.
 Plant biologists investigating disease resistance and other evolutionary adaptations of
plants are getting to the heart of how a plant responds to internal and external signals.

Biology Chapter Notes

 Chapter 40 Basic Principles of Animal Form and
Function
Chapter Notes

Overview: Diverse Forms, Common Challenges

 Animals inhabit almost every part of the biosphere.

 Despite their great diversity, all animals must solve a common set of problems.
 All animals must obtain oxygen, nourish themselves, excrete wastes, and move.
 Animals of diverse evolutionary histories and varying complexity must solve these
general challenges of life.
 Consider the long, tongue-like proboscis of a hawk moth, a structural adaptation for
feeding.
 Recoiled when not in use, the proboscis extends as a straw through which the moth can
suck nectar from deep within tube-shaped flowers.
 Analyzing the hawk moth’s proboscis gives clues about what it does and how it functions.
 Anatomy is the study of the structure of an organism.
 Physiology is the study of the functions an organism performs.
 Natural selection can fit structure to function by selecting, over many generations, the
best of the available variations in a population.
 Searching for food, generating body heat and regulating internal temperature, sensing and
responding to environmental stimuli, and all other animal activities require fuel in the
form of chemical energy.
 The concept of bioenergetics—how organisms obtain, process, and use energy
resources—is a connecting theme in the comparative study of animals.

Concept 40.1 Physical laws and the environment constrain animal size and shape
 An animal’s size and shape, features often called “body plans” or “designs,” are
fundamental aspects of form and function that significantly affect the way an animal
interacts with its environment.
 The terms plan and design do not mean that animal body forms are products of
conscious invention.
 The body plan or design of an animal results from a pattern of development
programmed by the genome, itself the product of millions of years of evolution due to
natural selection.
 Physical requirements constrain what natural selection can “invent.”
 An animal such as the mythical winged dragon cannot exist. No animal as large as a
dragon could generate enough lift to take off and fly.
 Similarly, the laws of hydrodynamics constrain the shapes that are possible for aquatic
organisms that swim very fast.
 Tunas, sharks, penguins, dolphins, seals, and whales are all fast swimmers.
Biology Chapter Notes
  All have the same basic fusiform shape, tapered at both ends.
 This shape minimizes drag in water, which is about a thousand times denser than air.
 The similar forms of speedy fishes, birds, and marine mammals are a consequence of
convergent evolution in the face of the universal laws of hydrodynamics.
 Convergence occurs because natural selection shapes similar adaptations when diverse
organisms face the same environmental challenge, such as the resistance of water to
fast travel.
Body size and shape affect interactions with the environment.
 An animal’s size and shape have a direct effect on how the animal exchanges energy and
materials with its surroundings.
 As a requirement for maintaining the fluid integrity of the plasma membrane of its cells,
an animal’s body must be arranged so that all of its living cells are bathed in an aqueous
medium.
 Exchange with the environment occurs as dissolved substances diffuse and are transported
across the plasma membranes between the cells and their aqueous surroundings.
 For example, a single-celled protist living in water has a sufficient surface area of
plasma membrane to service its entire volume of cytoplasm.
 Surface-to-volume ratio is one of the physical constraints on the size of single-celled
protists.
 Multicellular animals are composed of microscopic cells, each with its own plasma
membrane that acts as a loading and unloading platform for a modest volume of
cytoplasm.
 This only works if all the cells of the animal have access to a suitable aqueous
environment.
 For example, a hydra, built as a sac, has a body wall only two cell layers thick.
 Because its gastrovascular cavity opens to the exterior, both outer and inner layers of
cells are bathed in water.
 Another way to maximize exposure to the surrounding medium is to have a flat body.
 For instance, a parasitic tapeworm may be several meters long, but because it is very
thin, most of its cells are bathed in the intestinal fluid of the worm’s vertebrate host
from which it obtains nutrients.
 While two-layered sacs and flat shapes are designs that put a large surface area in contact
with the environment, these solutions do not permit much complexity in internal
organization.
 Most animals are more complex and are made up of compact masses of cells, producing
outer surfaces that are relatively small compared to the animal’s volume.
 Most organisms have extensively folded or branched internal surfaces specialized for
exchange with the environment.
 The circulatory system shuttles material among all the exchange surfaces within the
animal.
 Although exchange with the environment is a problem for animals whose cells are mostly
internal, complex forms have distinct benefits.
 A specialized outer covering can protect against predators; large muscles can enable
rapid movement; and internal digestive organs can break down food gradually,
controlling the release of stored energy.

Biology Chapter Notes

  Because the immediate environment for the cells is the internal body fluid, the
animal’s organ systems can control the composition of the solution bathing its cells.
 A complex body form is especially well suited to life on land, where the external
environment may be variable.

Concept 40.2 Animal form and function are correlated at all levels of organization
 Life is characterized by hierarchical levels of organization, each with emergent properties.
 Animals are multicellular organisms with their specialized cells grouped into tissues.
 In most animals, combinations of various tissues make up functional units called organs,
and groups of organs work together as organ systems.
 For example, the human digestive system consists of a stomach, small intestine, large
intestine, and several other organs, each a composite of different tissues.
 Tissues are groups of cells with a common structure and function.
 Different types of tissues have different structures that are suited to their functions.
 A tissue may be held together by a sticky extracellular matrix that coats the cells or
weaves them together in a fabric of fibers.
 The term tissue is from a Latin word meaning “weave.”
 Tissues are classified into four main categories: epithelial tissue, connective tissue,
nervous tissue, and muscle tissue.
 Occurring in sheets of tightly packed cells, epithelial tissue covers the outside of the body
and lines organs and cavities within the body.
 The cells of an epithelium are closely joined and in many epithelia, the cells are riveted
together by tight junctions.
 The epithelium functions as a barrier protecting against mechanical injury, invasive
microorganisms, and fluid loss.
 The cells at the base of an epithelial layer are attached to a basement membrane, a dense
mat of extracellular matrix.
 The free surface of the epithelium is exposed to air or fluid.
 Some epithelia, called glandular epithelia, absorb or secrete chemical solutions.
 The glandular epithelia that line the lumen of the digestive and respiratory tracts form
a mucous membrane that secretes a slimy solution called mucus that lubricates the
surface and keeps it moist.
 Epithelia are classified by the number of cell layers and the shape of the cells on the free
surface.
 A simple epithelium has a single layer of cells, and a stratified epithelium has
multiple tiers of cells.
 A “pseudostratified” epithelium is single-layered but appears stratified because the
cells vary in length.
 The shapes of cells on the exposed surface may be cuboidal (like dice), columnar (like
bricks on end), or squamous (flat like floor tiles).
 Connective tissue functions mainly to bind and support other tissues.
 Connective tissues have a sparse population of cells scattered through an extracellular
matrix.

Biology Chapter Notes

  The matrix generally consists of a web of fibers embedding in a uniform foundation
that may be liquid, jellylike, or solid.
 In most cases, the connective tissue cells secrete the matrix.
 There are three kinds of connective tissue fibers, which are all proteins: collagenous
fibers, elastic fibers, and reticular fibers.
 Collagenous fibers are made of collagen, the most abundant protein in the animal
kingdom.
 Collagenous fibers are nonelastic and do not tear easily when pulled lengthwise.
 Elastic fibers are long threads of elastin.
 Elastin fiber provides a rubbery quality that complements the nonelastic strength of
collagenous fibers.
 Reticular fibers are very thin and branched.
 Composed of collagen and continuous with collagenous fibers, they form a tightly
woven fabric that joins connective tissue to adjacent tissues.
 The major types of connective tissues in vertebrates are loose connective tissue, adipose
tissue, fibrous connective tissue, cartilage, bone, and blood.
 Each has a structure correlated with its specialized function.
 Loose connective tissue binds epithelia to underlying tissues and functions as packing
material, holding organs in place.
 Loose connective tissue has all three fiber types.
 Two cell types predominate in the fibrous mesh of loose connective tissue.
 Fibroblasts secrete the protein ingredients of the extracellular fibers.
 Macrophages are amoeboid cells that roam the maze of fibers, engulfing bacteria and
the debris of dead cells by phagocytosis.
 Adipose tissue is a specialized form of loose connective tissue that stores fat in adipose
cells distributed throughout the matrix.
 Adipose tissue pads and insulates the body and stores fuel as fat molecules.
 Each adipose cell contains a large fat droplet that swells when fat is stored and shrinks
when the body uses fat as fuel.
 Fibrous connective tissue is dense, due to its large number of collagenous fibers.
 The fibers are organized into parallel bundles, an arrangement that maximizes
nonelastic strength.
 This type of connective tissue forms tendons, attaching muscles to bones, and
ligaments, joining bones to bones at joints.
 Cartilage has an abundance of collagenous fibers embedded in a rubbery matrix made of
a substance called chondroitin sulfate, a protein-carbohydrate complex.
 Chondrocytes secrete collagen and chondroitin sulfate.
 The composite of collagenous fibers and chondroitin sulfate makes cartilage a strong
yet somewhat flexible support material.
 The skeleton of a shark and the embryonic skeletons of many vertebrates are
cartilaginous.
 We retain cartilage as flexible supports in certain locations, such as the nose, ears, and
intervertebral disks.
 The skeleton supporting most vertebrates is made of bone, a mineralized connective
tissue.
Biology Chapter Notes
  Bone-forming cells called osteoblasts deposit a matrix of collagen.
 Calcium, magnesium, and phosphate ions combine and harden within the matrix into
the mineral hydroxyapatite.
 The combination of hard mineral and flexible collagen makes bone harder than
cartilage without being brittle.
 The microscopic structure of hard mammalian bones consists of repeating units called
osteons.
 Each osteon has concentric layers of mineralized matrix deposited around a central
canal containing blood vessels and nerves that service the bone.
 Blood functions differently from other connective tissues, but it does have an extensive
extracellular matrix.
 The matrix is a liquid called plasma, consisting of water, salts, and a variety of
dissolved proteins.
 The liquid matrix enables rapid transport of blood cells, nutrients, and wastes.
 Suspended in the plasma are erythrocytes (red blood cells), leukocytes (white blood
cells), and cell fragments called platelets.
 Red cells carry oxygen.
 White cells function in defense against viruses, bacteria, and other invaders.
 Platelets aid in blood clotting.
 Muscle tissue is composed of long cells called muscle fibers that are capable of
contracting when stimulated by nerve impulses.
 Arranged in parallel within the cytoplasm of muscle fibers are large numbers of
myofibrils made of the contractile proteins actin and myosin.
 Muscle is the most abundant tissue in most animals, and muscle contraction accounts
for most of the energy-consuming cellular work in active animals.
 There are three types of muscle tissue in the vertebrate body: skeletal muscle, cardiac
muscle, and smooth muscle.
 Attached to bones by tendons, skeletal muscle is responsible for voluntary movements.
 Skeletal muscle consists of bundles of long cells called fibers.
 Each fiber is a bundle of strands called myofibrils.
 Skeletal muscle is also called striated muscle because the arrangement of contractile
units, or sarcomeres, gives the cells a striped (striated) appearance under the
microscope.
 Cardiac muscle forms the contractile wall of the heart.
 It is striated like skeletal muscle, and its contractile properties are similar to those of
skeletal muscle.
 Unlike skeletal muscle, cardiac muscle carries out the unconscious task of contraction
of the heart.
 Cardiac muscle fibers branch and interconnect via intercalated disks, which relay
signals from cell to cell during a heartbeat.
 Smooth muscle, which lacks striations, is found in the walls of the digestive tract, urinary
bladder, arteries, and other internal organs.
 The cells are spindle-shaped.
 They contract more slowly than skeletal muscles but can remain contracted longer.
 Controlled by different kinds of nerves than those controlling skeletal muscles, smooth
muscles are responsible for involuntary body activities.
Biology Chapter Notes
  These include churning of the stomach and constriction of arteries.
 Nervous tissue senses stimuli and transmits signals from one part of the animal to
another.
 The functional unit of nervous tissue is the neuron, or nerve cell, which is uniquely
specialized to transmit nerve impulses.
 A neuron consists of a cell body and two or more processes called dendrites and axons.
 Dendrites transmit impulses from their tips toward the rest of the neuron.
 Axons transmit impulses toward another neuron or toward an effector, such as a
muscle cell that carries out a body response.
 In many animals, nervous tissue is concentrated in the brain.
The organ systems of an animal are interdependent.
 In all but the simplest animals (sponges and some cnidarians) different tissues are
organized into organs.
 In some organs the tissues are arranged in layers.
 For example, the vertebrate stomach has four major tissue layers.
 A thick epithelium lines the lumen and secretes mucus and digestive juices.
 Outside this layer is a zone of connective tissue, surrounded by a thick layer of
smooth muscle.
 Another layer of connective tissue encases the entire stomach.
 Many vertebrate organs are suspended by sheets of connective tissues called mesenteries
in body cavities moistened or filled with fluid.
 Mammals have a thoracic cavity housing the lungs and heart that is separated from
the lower abdominal cavity by a sheet of muscle called the diaphragm.
 Organ systems carry out the major body functions of most animals.
 Each organ system consists of several organs and has specific functions.
 The efforts of all systems must be coordinated for the animal to survive.
 For instance, nutrients absorbed from the digestive tract are distributed throughout the
body by the circulatory system.
 The heart that pumps blood through the circulatory system depends on nutrients
absorbed by the digestive tract and also on oxygen obtained from the air or water by
the respiratory system.
 Any organism, whether single-celled or an assembly of organ systems, is a coordinated
living whole greater than the sum of its parts.

Concept 40.3 Animals use the chemical energy in food to sustain form and function
 All organisms require chemical energy for growth, physiological processes, maintenance
and repair, regulation, and reproduction.
 Plants use light energy to build energy-rich organic molecules from water and CO2,
and then they use those organic molecules for fuel.
 In contrast, animals are heterotrophs and must obtain their chemical energy in food,
which contains organic molecules synthesized by other organisms.
 The flow of energy through an animal—its bioenergetics—ultimately limits the animal’s
behavior, growth, and reproduction and determines how much food it needs.
 Studying an animal’s bioenergetics tells us a great deal about the animal’s adaptations.
Biology Chapter Notes
 Food is digested by enzymatic hydrolysis, and energy-containing food molecules are
absorbed by body cells.
 Most fuel molecules are used to generate ATP by the catabolic processes of cellular
respiration and fermentation.
 The chemical energy of ATP powers cellular work, enabling cells, organs, and organ
systems to perform the many functions that keep an animal alive.
 Since the production and use of ATP generates heat, an animal continuously loses heat
to its surroundings.
 After energetic needs of staying alive are met, any remaining food molecules can be used
in biosynthesis.
 This includes body growth and repair; synthesis of storage material such as fat; and
production of reproductive structures, including gametes.
 Biosynthesis requires both carbon skeletons for new structures and ATP to power their
assembly.
Metabolic rate provides clues to an animal’s bioenergetic “strategy.”
 The amount of energy an animal uses in a unit of time is called its metabolic rate—the
sum of all the energy-requiring biochemical reactions occurring over a given time
interval.
 Energy is measured in calories (cal) or kilocalories (kcal).
 A kilocalorie is 1,000 calories.
 The term Calorie, with a capital C, as used by many nutritionists, is actually a
kilocalorie.
 Metabolic rate can be determined several ways.
 Because nearly all the chemical energy used in cellular respiration eventually appears as
heat, metabolic rate can be measured by monitoring an animal’s heat loss.
 A small animal can be placed in a calorimeter, which is a closed, insulated chamber
equipped with a device that records the animal’s heat loss.
 A more indirect way to measure metabolic rate is to determine the amount of oxygen
consumed or carbon dioxide produced by an animal’s cellular respiration.
 These devices may measure changes in oxygen consumed or carbon dioxide produced
as activity changes.
 Over long periods, the rate of food consumption and the energy content of food can be
used to estimate metabolic rate.
 A gram of protein or carbohydrate contains about 4.5–5 kcal, and a gram of fat
contains 9 kcal.
 This method must account for the energy in food that cannot be used by the animal
(the energy lost in feces and urine).
 There are two basic bioenergetic “strategies” used by animals.
 Birds and mammals are mainly endothermic, maintaining their body temperature
within a narrow range by heat generated by metabolism.
 Endothermy is a high-energy strategy that permits intense, long-duration activity of
a wide range of environmental temperatures.
 Most fishes, amphibians, reptiles, and invertebrates are ectothermic, meaning they gain
their heat mostly from external sources.

Biology Chapter Notes

  The ectothermic strategy requires much less energy than is needed by endotherms,
because of the energy cost of heating (or cooling) an endothermic body.
 However, ectotherms are generally incapable of intense activity over long periods.
 In general, endotherms have higher metabolic rates than ectotherms.
Body size influences metabolic rate.
 The metabolic rates of animals are affected by many factors besides whether the animal is
an endotherm or an ectotherm.
 One of animal biology’s most intriguing, but largely unanswered, questions has to do with
the relationship between body size and metabolic rate.
 Physiologists have shown that the amount of energy it takes to maintain each gram of
body weight is inversely related to body size.
 For example, each gram of a mouse consumes about 20 times more calories than a
gram of an elephant.
 The higher metabolic rate of a smaller animal demands a proportionately greater delivery
rate of oxygen.
 A smaller animal also has a higher breathing rate, blood volume (relative to size), and
heart rate (pulse) and must eat much more food per unit of body mass.
 One hypothesis for the inverse relationship between metabolic rate and size is that the
smaller the size of an endotherm, the greater the energy cost of maintaining a stable body
temperature.
 The smaller the animal, the greater its surface-to-volume ratio, and thus the greater loss
of heat to (or gain from) the surroundings.
 However, this hypothesis fails to explain the inverse relationship between metabolism and
size in ectotherms, which do not use metabolic heat to maintain body temperature.
 Researchers continue to search for causes underlying this inverse relationship.
Animals adjust their metabolic rates as conditions change.
 Every animal has a range of metabolic rates.
 Minimal rates power the basic functions that support life, such as cell maintenance,
breathing, and heartbeat.
 The metabolic rate of a nongrowing endotherm at rest, with an empty stomach and
experiencing no stress, is called the basal metabolic rate (BMR).
 The BMR for humans averages about 1,600 to 1,800 kcal per day for adult males and
about 1,300 to 1,500 kcal per day for adult females.
 In ectotherms, body temperature changes with temperature of the surroundings, and so
does metabolic rate.
 Therefore, the minimal metabolic rate of an ectotherm must be determined at a specific
temperature.
 The metabolic rate of a resting, fasting, nonstressed ectotherm is called its standard
metabolic rate (SMR).
 For both ectotherms and endotherms, activity has a large effect on metabolic rate.
 Any behavior consumes energy beyond the BMR or SMR.
 Maximal metabolic rates (the highest rates of ATP utilization) occur during peak
activity, such as lifting heavy weights, all-out running, or high-speed swimming.

Biology Chapter Notes

 In general, an animal’s maximum metabolic rate is inversely related to the duration of
activity.
 Both an alligator (ectotherm) and a human (endotherm) are capable of intense exercise
in short spurts of a minute or less.
 These “sprints” are powered by the ATP present in muscle cells and ATP generated
anaerobically by glycolysis.
 Neither organism can maintain its maximum metabolic rate and peak activity level
over longer periods of exercise, although the endotherm has an advantage in endurance
tests.
 The BMR of a human is much higher than the SMR of an alligator.
 Both can reach high levels of maximum potential metabolic rates for short periods, but
metabolic rate drops as the duration of the activity increases and the source of energy
shifts toward aerobic respiration.
 Sustained activity depends on the aerobic process of cellular respiration for ATP supply.
 An endotherm’s respiration rate is about 10 times greater than an ectotherm’s.
 Only endotherms are capable of long-duration activities such as distance running.
 Between the extremes of BMR or SMR and maximal metabolic rate, many factors
influence energy requirements.
 These include age, sex, size, body and environmental temperatures, quality and
quantity of food, activity level, oxygen availability, hormonal balance, and time of day.
 Diurnal organisms, such as birds, humans, and many insects, are usually active and
have their highest metabolic rates during daylight hours.
 Nocturnal organisms, such as bats, mice, and many other mammals, are usually
active at night or near dawn and dusk and have their highest metabolic rates then.
 Metabolic rates measured when animals are performing a variety of activities give a better
idea of the energy costs of everyday life.
 For most terrestrial animals, the average daily rate of energy consumption is 2–4 times
BMR or SMR.
 Humans in most developed countries have an unusually low average daily
metabolic rate of about 1.5 times BMR—an indication of relatively sedentary
lifestyles.
Energy budgets reveal how animals use energy and materials.
 Different species of animals use the energy and materials in food in different ways,
depending on their environment, behavior, size, and basic energy strategy of endothermy
or ectothermy.
 For most animals, the majority of food is devoted to the production of ATP, and
relatively little goes to growth or reproduction.
 However, the amount of energy used for BMR (or SMR), activity, and temperature
control varies considerably between species.
 For example, the typical annual energy “budgets” of four vertebrates reinforces two
important concepts in bioenergetics.
 First, a small animal has a much greater energy demand per kg than does a large
animal of the same class.
 Second, an ectotherm requires much less energy per kg than does an endotherm of
equivalent size.
 Further, size and energy strategy has a great influence on how the total annual energy
expenditure is distributed among energetic needs.
Biology Chapter Notes
 A human female spends a large fraction of her energy budget for BMR and relatively little
for activity and body temperature regulation.
 The cost of nine months of pregnancy and several months of breast feeding amounts to
only 5–8% of the mother’s annual energy requirements.
 Growth amounts to about 1% of her annual energy budget.
 A male penguin spends a much larger fraction of his energy expenditures for activity
because he must swim to catch his food.
 Because the penguin is well insulated and fairly large, he has relatively low costs of
temperature regulation despite living in the cold Antarctic environment.
 His reproductive costs, about 6% of annual energy expenditures, mainly come from
incubating eggs and bringing food to his chicks.
 Penguins, like most birds, do not grow once they are adults.
 A female deer mouse spends a large fraction of her energy budget on temperature
regulation.
 Because of the high surface-to-volume ratio that goes with small size, mice lose body
heat rapidly to the environment and must constantly generate metabolic heat to
maintain body temperature.
 Female deer mice spend about 12% of their energy budget on reproduction.
 In contrast to endotherms, the ectothermic python has no temperature regulation costs.
 Like most reptiles, she grows continuously throughout life.
 In one year, she can add 750 g of new body tissue and produce about 650 g of eggs.
 Through the python’s economical ectothermic strategy, she expends only 1/40 of the
energy expended by the same-sized endothermic penguin.

Concept 40.4 Many animals regulate their internal environment within relatively
narrow limits
 More than a century ago, physiologist Claude Bernard made the distinction between
external environments surrounding an animal and the internal environment in which the
cells of the animal actually live.
 The internal environment of vertebrates is called the interstitial fluid.
 This fluid exchanges nutrients and wastes with blood contained in microscopic vessels
called capillaries.
 Bernard also recognized that many animals tend to maintain relatively constant conditions
in their internal environment, even when the external environment changes.
 While a pond-dwelling hydra is powerless to affect the temperature of the fluid that
bathes its cells, the human body can maintain its “internal pond” at a more or less
constant temperature of about 37°C.
 Similarly, our bodies control the pH of our blood and interstitial fluid to within a tenth
of a pH unit of 7.4.
 The amount of sugar in our blood does not fluctuate for long from a concentration of
about 90 mg of glucose per 100 mL of blood.
 There are times during the course of the development of an animal when major changes in
the internal environment are programmed to occur.
 For example, the balance of hormones in human blood is altered radically during
puberty and pregnancy.
 Still, the stability of the internal environment is remarkable.
Biology Chapter Notes
 Today, Bernard’s “constant internal milieu” is incorporated into the concept of
homeostasis, which means “steady state,” or internal balance.
 Actually the internal environment of an animal always fluctuates slightly.
 Homeostasis is a dynamic state, an interplay between outside forces that tend to
change the internal environment and internal control mechanisms that oppose such
changes.
Animals may be regulators or conformers for a particular environmental variable.
 Regulating and conforming are two extremes in how animals deal with environmental
fluctuations.
 An animal is a regulator for a particular environmental variable if it uses internal control
mechanisms to moderate internal change while external conditions fluctuate.
 For example, a freshwater fish maintains a stable internal concentration of solutes in its
blood that is higher than the water in which it lives.
 An animal is a conformer for a particular environmental variable if it allows its internal
conditions to vary as external conditions fluctuate.
 For example, many marine invertebrates live in environments where solute
concentration (salinity) is relatively stable.
 Unlike freshwater fishes, most marine invertebrates do not regulate their internal solute
concentration, but rather conform to the external environment.
 No organism is a perfect regulator or conformer.
 An animal may maintain homeostasis while regulating some internal conditions and
allowing others to conform to the environment.
 For example, most freshwater fishes regulate their internal solute concentration but
allow their internal temperature to conform to external water temperature.
Homeostasis depends on feedback circuits.
 Any homeostatic control system has three functional components: a receptor, a control
center, and an effector.
 The receptor detects a change in some variable in the animal’s internal environment,
such as a change in temperature.
 The control center processes the information it receives from the receptor and directs
an appropriate response by the effector.
 One type of control circuit, a negative-feedback system, can control the temperature in a
room.
 In this case, the control center, called a thermostat, also contains the receptor, a
thermometer.
 When room temperature falls, the thermostat switches on the heater, the effector.
 In such a negative-feedback system, a change in the variable being monitored triggers the
control mechanism to counteract further change in the same direction.
 Owing to a time lag between receptor and response, the variable drifts slightly above
and below the set point, but fluctuations are moderate.
 Negative-feedback mechanisms prevent small changes from becoming too large.
 Most homeostatic mechanisms in animals operate on this principle of negative feedback.
 Human body temperature is kept close to a set point of 37°C by the cooperation of
several negative-feedback circuits.

Biology Chapter Notes

 In contrast to negative feedback, positive feedback involves a change in some variable
that triggers mechanisms that amplify rather than reverse the change.
 For example, during childbirth, the pressure of the baby’s head against receptors near
the opening of the uterus stimulates uterine contractions.
 These cause greater pressure against the uterine opening, heightening the contractions,
which cause still greater pressure.
 Positive feedback brings childbirth to completion, a very different sort of process from
maintaining a steady state.
 While some aspects of the internal environment are maintained at a set point, regulated
change is essential to normal body functions.
 In some cases, the changes are cyclical, such as the changes in hormone levels
responsible for the menstrual cycle in women.
 In other cases, a regulated change is a reaction to a challenge to the body.
 For example, the human body reacts to certain infections by raising the set point for
temperature to a slightly higher level, and the resulting fever helps fight infection.
 Over the short term, homeostatic mechanisms can keep a process, such as body
temperature, close to a set point, whatever it is at that particular time.
 Over the longer term, homeostasis allows regulated change in the body’s internal
environment.
 Internal regulation is expensive.
 Animals use a considerable portion of their energy from the food they eat to maintain
favorable internal conditions.

Concept 40.5 Thermoregulation contributes to homeostasis and involves anatomy,

physiology, and behavior
 Thermoregulation is the process by which animals maintain an internal temperature
within a tolerable range.
 This ability is critical to survival, because most biochemical and physiological processes
are very sensitive to changes in body temperature.
 The rates of most enzyme-mediated reactions increase by a factor of 2 or 3 for every 10°C
temperature increase until temperature is high enough to begin to denature proteins.
 The properties of membranes also change with temperature.
 Although different species of animals are adapted to different environmental
temperatures, each species has an optimal temperature range.
 Thermoregulation helps keep body temperature within the optimal range, enabling
cells to function effectively as external temperature fluctuates.
Ectotherms and endotherms manage their heat budgets very differently.
 One way to classify the thermal characteristics of animals is to emphasize the role of
metabolic heat in determining body temperature.
 Ectotherms gain most of their heat from the environment.
 An ectotherm has such a low metabolic rate that the amount of heat it generates is too
small to have much effect on body temperature.
 Endotherms can use metabolic heat to regulate their body temperature.

Biology Chapter Notes

  In a cold environment, an endotherm’s high metabolic rate generates enough heat to
keep its body substantially higher than its surroundings.
 Many ectotherms can thermoregulate by behavioral means, such as basking in the sun or
seeking out shade.
 In general, ectotherms tolerate greater variation in internal temperature than do
endotherms.
 Animals are not classified as ectotherms or endotherms based on whether they have
variable or constant body temperatures.
 It is the source of heat used to maintain body temperature that distinguishes ectotherms
from endotherms.
 A different—and largely outdated—set of terms can be used to imply variable or constant
body temperature.
 A poikilotherm is an animal whose internal temperature varies widely.
 A homeotherm is an animal that maintains relatively stable internal temperatures.
 Another common misconception is the idea that ectotherms are “cold-blooded” and
endotherms are “warm-blooded.”
 Ectotherms do not necessarily have low body temperatures.
 While sitting in the sun, many ectothermic lizards have higher body temperatures than
mammals.
 Biologists avoid the terms cold-blooded and warm-blooded because they are so
misleading.
 Endothermy and ectothermy are not mutually exclusive thermoregulatory strategies.
 A bird is an endotherm but may warm itself in the sun on a cold morning, just as a
lizard does.
 Endothermy has several important advantages.
 Being able to generate a large amount of metabolic heat enables endotherms to
perform vigorous activity for much longer than is possible for most ectotherms.
 Sustained intense exercise, such as long-distance running or powered flight, is usually
only possible for endotherms.
 Terrestrial animals can maintain stable body temperatures despite temperature
fluctuations, which are more severe on land than in water.
 For example, no ectotherm can be active in below-freezing weather, but many
endotherms function well in such conditions.
 Endothermic vertebrates also have mechanisms for cooling their bodies in hot
environments, allowing them to withstand heat loads that would be intolerable for most
ectotherms.
 However, ectotherms can tolerate larger fluctuations in their internal temperatures.
 Being endothermic is energetically expensive.
 For example, at 20°C, a human at rest has a BMR or 1,300 to 1,800 kcal per day.
 An American alligator of similar weight has an SMR of only 60 kcal per day.
 As a result, ectotherms need to consume far more food than ectotherms of equivalent size.
 This is a serious disadvantage if food supplies are limited.
 Ectothermy is an extremely effective and successful strategy in most of Earth’s
environments, as is shown by the abundance and diversity of ectothermic animals.

Biology Chapter Notes

 Animals regulate the exchange of heat with their environment.
 Animals exchange heat with their external environment by four physical processes:
conduction, convection, radiation, and evaporation.
 Heat is always transferred from a hotter object to a cooler object.
 Endotherms and thermoregulating ectotherms must manage their heat budgets so that rates
of heat gain are equal to rates of heat loss.
 Five general categories of adaptations help animals thermoregulate.
 A major thermoregulatory adaptation in mammals and birds is insulation: hair, feathers,
or fat layers.
 Insulation reduces the flow of heat between an animal and its environment and lowers
the energy cost of keeping warm.
 In mammals, the insulating material is associated with the integumentary system, the
outer covering of the body.
 Skin is a key organ of the integumentary system.
 Skin functions as a thermoregulatory organ by housing nerves, sweat glands, blood
vessels, and hair follicles.
 It also protects internal body parts from mechanical injury, infection, and desiccation.
 Skin consists of two layers, the epidermis and the dermis, underlain by a tissue layer
called the hypodermis.
 The epidermis is the outer layer of skin, composed largely of dead epithelial cells.
 The dermis supports the epidermis and contains hair follicles, oil and sweat glands,
muscles, nerves, and blood vessels.
 Adipose tissue provides varying degrees of insulation, depending on the species.
 The insulating power of a layer of fur or feathers depends mostly on how much air the
layer traps.
 Hair loses most of its insulating power when wet.
 Land mammals and birds react to cold by raising their fur or feathers to trap a thicker
layer of air.
 Human goose bumps are a vestige of our hair-raising ancestors.
 Marine mammals have a very thick layer of insulating blubber just under their skin.
 The skin temperature of a marine mammal is close to water temperature.
 However, blubber insulation is so effective that marine mammals can maintain body
core temperatures of 36–38°C.
 Many endotherms and ectotherms can alter the amount of blood flow between the body
core and the skin.
 Elevated blood flow in the skin results from vasodilation, an increase in the diameter of
superficial blood vessels near the body surface.
 Vasodilation is triggered by nerve signals that relax the muscles of the vessel walls.
 In endotherms, vasodilation usually warms the skin, increasing the transfer of body
heat to a cool environment.
 The reverse process, vasoconstriction, reduces blood flow and heat transfer by decreasing
the diameter of superficial vessels.
 Another circulatory adaptation is an arrangement of blood vessels called a
countercurrent heat exchanger, which reduces heat loss.
Biology Chapter Notes
  In some species, blood can either go through the heat exchanger or bypass it.
 The relative amount of blood that flows through the two paths varies, adjusting the rate
of heat loss.
 Unlike most fishes, which are thermoconformers, some specialized endothermic bony
fishes and sharks have circulatory adaptations to retain metabolic heat.
 Endothermic fishes include bluefin tuna, swordfish, and great white sharks.
 Large arteries convey most of the cold blood from the gills to tissues just under the
skin.
 Branches deliver blood to the deep muscles, where small vessels are arranged into a
countercurrent heat exchanger.
 Endothermy enables vigorous, sustained activity that is characteristic of these animals.
 Some reptiles also have physiological adaptations to regulate heat loss.
 In the marine iguanas of the Galápagos Islands, body heat is conserved by
vasoconstriction of superficial blood vessels.
 Many endothermic insects (bumblebees, honeybees, some moths) have a countercurrent
heat exchanger that helps maintain a high temperature in the thorax, where the flight
muscles are located.
 In some insects, the countercurrent mechanism can be “shut down” to allow heat to be
shed during hot weather.
 A bumblebee queen uses this mechanism to incubate her eggs.
 She generates heat by shivering her flight muscles and then transfers the heat to her
abdomen, which she presses against her eggs.
 Many mammals and birds live in places where thermoregulation requires cooling as well
as warming.
 If environmental temperature is above body temperature, evaporation is the only way
to keep body temperature from rising.
 Terrestrial animals lose water by evaporation across the skin and when they breathe.
 Water absorbs considerable heat when it evaporates; it is 50 to 100 times more
effective than air in transferring heat.
 Some animals have adaptations to augment evaporative cooling.
 Panting is important in birds and many mammals.
 Some birds have a pouch richly supplied with blood vessels in the floor of the mouth.
 Birds flutter the pouch to increase evaporation.
 Sweating or bathing moistens the skin and enhances evaporative cooling.
 Many terrestrial mammals have sweat glands controlled by the nervous system.
 Other mechanisms to promote evaporative cooling include spreading saliva on skin or
regulating the amount of mucus secretion.
 Many endotherms and ectotherms use behavioral responses to control body temperature.
 Many ectotherms can maintain a constant body temperature by simple behaviors.
 Some animals hibernate or migrate to a more suitable climate.
 Amphibians regulate body temperature mainly by behavior, by moving to a location
where solar heat is available or by seeking shade.
 Reptiles also thermoregulate behaviorally.
 When cool, they seek warm places, orient themselves toward a heat source, and
expand the body surface exposed to the heat source.
Biology Chapter Notes
  When hot, they move to cool places or turn away from the heat source.
 Many terrestrial invertebrates use similar behavioral mechanisms.
 Honeybees use a thermoregulatory mechanism that depends on social behavior.
 In cold weather, they increase heat production and huddle together to retain heat.
 They maintain a relatively constant temperature by changing the density of the
huddling, and moving individuals between the cooler outer edges of the cluster and the
warmer center.
 Honeybees expend considerable energy to keep warm during long periods of cold
weather.
 This is the main function of the honey stored in the hive.
 Honeybees also cool the hive in hot weather by transporting water to it and fanning it
with their wings to promote evaporation and convection.
 Endotherms vary heat production to counteract constant heat loss.
 For example, heat production is increased by such muscle activity as moving or
shivering.
 Certain mammalian hormones can cause mitochondria to increase their metabolic activity
and produce heat instead of ATP.
 This nonshivering thermogenesis (NST) takes place throughout the body.
 Some mammals have brown fat that is specialized for rapid heat production.
 Through shivering and NST, mammals and birds may increase their metabolic heat
production to 5 or 10 times the minimal levels characteristic of warm weather.
 A few large reptiles can become endothermic in particular circumstances.
 For example, female pythons that are incubating eggs increase their metabolic rate by
shivering, generating enough heat to elevate egg temperatures by 5–7°C during
incubation.
 The smallest endotherms are flying insects such as bees and moths.
 These insects elevate body temperature by shivering before taking off.
 They contract their flight muscles in synchrony to produce only slight wing
movements but considerable heat.
 The regulation of body temperature in humans is a complex system facilitated by
feedback mechanisms.
 Nerve cells that control thermoregulation are concentrated in a brain region called the
hypothalamus.
 The hypothalamus contains a group of nerve cells that functions as a thermostat.
 Nerve cells that sense temperature are in the skin, in the hypothalamus itself, and in
other body regions.
 If the thermostat in the brain detects a decrease in the temperature of the blood
below the set point, it inhibits heat loss mechanisms and activates heat-saving ones
such as vasoconstriction of superficial vessels and erection of fur, while stimulating
heat-generating mechanisms such as shivering.
 If the thermostat in the brain detects a rise in the temperature of the blood above the
set point, it shuts down heat retention mechanisms and promotes body cooling by
vasodilation, sweating, or panting.
Animals can acclimatize to a new range of environmental temperatures.

Biology Chapter Notes

 Many animals can adjust to a new range of environmental temperatures by a physiological
response called acclimatization.
 Ectotherms and endotherms acclimatize differently.
 In birds and mammals, acclimatization includes adjusting the amount of insulation and
varying the capacity for metabolic heat production.
 Acclimatization in ectotherms involves compensating for temperature changes.
 Acclimatization responses in ectotherms often include adjustments at the cellular level.
 Cells may increase the production of certain enzymes or produce enzyme variants
with different temperature optima.
 Membranes also change the proportions of saturated and unsaturated lipids to keep
membranes fluid at different temperatures.
 Some ectotherms produce “antifreeze” compounds, or cryoprotectants, to prevent ice
formation in body cells.
 These compounds allow overwintering ectotherms such as frogs and arthropods to
withstand body temperatures well below zero.
 Arctic and antarctic fishes also have cryoprotectants to protect body tissues.
 Cells can make rapid adjustments to temperature changes.
 For example, mammalian cells grown in culture respond to increased temperature by
producing and accumulating stress-induced proteins, including heat-shock proteins.
 These molecules, found in bacteria, yeast, plants, and animals, help to maintain the
integrity of other proteins that would otherwise be denatured by severe heat.
 Stress-induced proteins help prevent cell death when an organism is challenged by
severe changes in cellular environment.
Animals may conserve energy through torpor.
 Some animals deal with severe conditions by an adaptation called torpor.
 Torpor is a physiological state in which activity is low and metabolism decreases.
 Hibernation is long-term torpor that is an adaptation to winter cold and food scarcity.
 When vertebrate endotherms enter torpor or hibernation, their body temperatures decline.
 Some hibernating mammals cool to 1–2°C, and a few drop slightly below 0°C in a
supercooled, unfrozen state.
 Metabolic rates during hibernation may be several hundred times lower than if animals
tried to maintain normal body temperatures.
 Hibernators can survive for very long periods on limited supplies of energy stored in
body tissues or as food cached in a burrow.
 Estivation, or summer torpor, is also characterized by slow metabolism or inactivity.
 Estivation allows animals to survive long periods of high temperatures and scarce
water supplies.
 Hibernation and estivation are often triggered by seasonal changes in the length of
daylight.
 Some hibernators prepare for winter by storing food in their burrows or by eating huge
quantities of food.
 Ground squirrels double their weight prior to hibernation.
 Many small mammals and birds exhibit a daily torpor that is adapted to their feeding
patterns.

Biology Chapter Notes

  For example, most bats and shrews feed at night and go into torpor during daylight
hours.
 Chickadees and hummingbirds feed during the day and go into torpor on cold nights.
 The body temperature of a hummingbird may drop by 25–30°C at night.
 An animal’s daily cycle of activity and torpor appears to be a built-in rhythm controlled
by its biological clock.
 Even if food is made available to a shrew, it will go through daily torpor.

Biology Chapter Notes

 Chapter 41 Animal Nutrition
Chapter Notes

Overview: The Need to Feed

 All animals eat other organisms—dead or alive, whole or by the piece (including
parasites).
 In general, animals fit into one of three dietary categories.
o Herbivores, such as gorillas, cows, hares, and many snails, eat mainly autotrophs
(plants and algae).
o Carnivores, such as sharks, hawks, spiders, and snakes, eat other animals.
o Omnivores, such as cockroaches, bears, raccoons, and humans, consume animal and
plant or algal matter.
 Humans evolved as hunters, scavengers, and gatherers.
 While the terms herbivore, carnivore, and omnivore represent the kinds of food that an
animal usually eats, most animals are opportunistic, eating foods that are outside their
main dietary category when these foods are available.
 For example, cattle and deer, which are herbivores, may occasionally eat small animals
or bird eggs.
 Most carnivores obtain some nutrients from plant materials that remain in the digestive
tract of the prey that they eat.
 All animals consume bacteria along with other types of food.
 For any animal, a nutritionally adequate diet must satisfy three nutritional needs:
o A balanced diet must provide fuel for cellular work.
o It must supply the organic raw materials needed to construct organic molecules.
o Essential nutrients that the animal cannot make from raw materials must be provided in
its food.

Concept 41.1 Homeostatic mechanisms manage an animal’s energy budget

 The flow of food energy into and out of an animal can be viewed as a “budget,” with the
production of ATP accounting for the largest fraction by far of the energy budget of most
animals.
 ATP powers basal or resting metabolism, as well as activity and, in endothermic
animals, thermoregulation.
 Nearly all ATP generation is based on the oxidation of organic fuel molecules—
carbohydrates, proteins, and fats—in cellular respiration.
 The monomers of any of these substances can be used as fuel.
 Fats are especially rich in energy, liberating about twice the energy liberated from an
equal amount of carbohydrate or protein during oxidation.
 When an animal takes in more calories than it needs to produce ATP, the excess can be
used for biosynthesis.
 This biosynthesis can be used to grow in size or for reproduction, or it can be stored in
energy depots.
Biology Chapter Notes
  In humans, the liver and muscle cells store energy as glycogen, a polymer made up of
many glucose units.
 Glucose is a major fuel molecule for cells, and its metabolism, regulated by
hormone action, is an important aspect of homeostasis.
 If glycogen stores are full and caloric intake still exceeds caloric expenditure, the
excess is usually stored as fat.
 When fewer calories are taken in than are expended—perhaps because of sustained
heavy exercise or lack of food—fuel is taken out of storage depots and oxidized.
 The human body expends liver glycogen first and then draws on muscle glycogen
and fat.
 Most healthy people—even if they are not obese—have enough stored fat to sustain
them through several weeks of starvation.
 The average human’s energy needs can be fueled by the oxidation of only 0.3 kg of
fat per day.
 Severe problems occur if the energy budget remains out of balance for long periods.
 If the diet of a person or other animal is chronically deficient in calories,
undernourishment results.
 The stores of glycogen and fat are used up, the body begins breaking down its own
proteins for fuel, muscles begin to decrease in size, and the brain can become protein-
deficient.
 If energy intake remains less than energy expenditure, death will eventually result, and
even if a seriously undernourished person survives, some damage may be irreversible.
 Because a diet of a single staple such as rice or corn can often provide sufficient calories,
undernourishment is generally common only where drought, war, or some other crisis has
severely disrupted the food supply.
 Another cause of undernourishment is anorexia nervosa, an eating disorder associated
with a compulsive aversion to body fat.
Obesity is a global health problem.
 Overnourishment, or obesity, the result of excessive food intake, is a common problem
in the United States and other affluent nations.
 The human body tends to store any excess fat molecules obtained from food instead of
using them for fuel.
 In contrast, when we eat an excess of carbohydrates, the body tends to increase its
rate of carbohydrate oxidation.
 Thus, the amount of fat in the diet can have a more direct effect on weight gain than
the amount of dietary carbohydrates.
 While fat hoarding can be a liability today, it probably provided a fitness advantage for
our hunting-and-gathering ancestors, enabling individuals with genes promoting the
storage of high-energy molecules during feasts to survive the eventual famines.
 The World Health Organization now recognizes obesity as a major global health problem.
 The increased availability of fattening foods in many countries combines with more
sedentary lifestyles to put excess weight on bodies.
 In the United States, the percentage of obese people has doubled to 30% over the past
20 years, and another 35% are overweight.
 Obesity contributes to health problems, including diabetes, cancer of the colon and breast,
and cardiovascular disease.
 Research on the causes and possible treatments for weight-control problems continues.
Biology Chapter Notes
  Over the long term, feedback circuits control the body’s storage and metabolism of fat.
 Several hormones regulate long-term and short-term appetite by affecting a “satiety
center” in the brain.
 Inheritance is a major factor in obesity.
 Most of the weight-regulating hormones are polypeptides.
 Dozens of genes that code for these hormones have been identified.
 In mammals, a hormone called leptin, produced by adipose cells, is a key player in a
complex feedback mechanism regulating fat storage and use.
 As adipose tissue increases, high leptin levels cue the brain to depress appetite and to
increase energy-consuming muscular activity and body-heat production.
 Conversely, loss of body fat decreases leptin levels in the blood, signaling the brain to
increase appetite and weight gain.
 Mice that inherit a defective gene for leptin become very obese.
 These mice can be treated by injection with leptin.
 However, very few obese people have defective leptin production.
 In fact, most obese humans have abnormally high leptin levels, due to their large
amounts of adipose tissue.
 For some reason, the brain’s satiety center does not respond to the high leptin levels in
many obese people.
 One hypothesis is that in humans, in contrast to other mammals, the leptin system
functions to stimulate appetite and prevent weight loss rather than to prevent weight
gain.
 Most humans crave fatty foods. Although fat hoarding is a health liability today, it may
have been advantageous in our evolutionary past.
 Our ancestors on the African savanna were hunter-gatherers who probably survived
mainly on plant materials, occasionally supplemented by meat.
 Natural selection may have favored those individuals with a physiology that induced
them to gorge on fatty foods on the rare occasions that they were available.
 Perhaps these individuals were more likely to survive famine.
 Obesity may be beneficial in certain species.
 Small seabirds called petrels fly long distances to find food that is rich in lipids.
 By bringing lipid-rich food to their chicks, the parents minimize the weight of food
that they must carry.
 However, because these foods are low in protein, young petrels have to consume more
calories than they burn in metabolism—and consequently they become obese.
 In some petrel species, chicks at the end of the growth period weigh much more their
parents, are too heavy to fly, and need to starve for several days to fly.
 The fat reserves help growing chicks to survive periods when parents are unable to
find food.

Concept 41.2 An animal’s diet must supply carbon skeletons and essential nutrients
 In addition to fuel for ATP production, an animal’s diet must supply all the raw materials
for biosynthesis.
 This requires organic precursors (carbon skeletons) from its food.

Biology Chapter Notes

  Given a source of organic carbon (such as sugar) and a source of organic nitrogen
(usually in amino acids from the digestion of proteins), animals can fabricate a great
variety of organic molecules—carbohydrates, proteins, and lipids.
 Besides fuel and carbon skeletons, an animal’s diet must also supply essential nutrients.
 These are materials that must be obtained in preassembled form because the animal’s
cells cannot make them from any raw material.
 Some materials are essential for all animals, but others are needed only by certain
species.
 For example, ascorbic acid (vitamin C) is an essential nutrient for humans and other
primates, guinea pigs, and some birds and snakes, but not for most other animals.
 An animal whose diet is missing one or more essential nutrients is said to be
malnourished.
 For example, many herbivores living where soils and plants are deficient in
phosphorus eat bones to obtain this essential nutrient.
 Malnutrition is much more common than undernourishment in human populations, and
it is even possible for an overnourished individual to be malnourished.
 There are four classes of essential nutrients: essential amino acids, essential fatty acids,
vitamins, and minerals.
 Animals require 20 amino acids to make proteins.
 Most animals can synthesize half of these if their diet includes organic nitrogen.
 The remaining essential amino acids must be obtained from food in prefabricated form.
 Eight amino acids are essential in the adult human with a ninth, histidine, being
essential for infants.
 The same amino acids are essential for most animals.
 A diet that provides insufficient amounts of one or more essential amino acids causes a
form of malnutrition known as protein deficiency.
 This is the most common type of malnutrition among humans.
 The victims are usually children, who, if they survive infancy, are likely to be retarded
in physical and perhaps mental development.
 In one variation of protein malnutrition, called kwashiorkor, the diet provides enough
calories but is severely deficient in protein.
 The protein in animal products, such as meat, eggs, and cheese, are “complete,” which
means that they provide all the essential amino acids in their proper proportions.
 Most plant proteins are “incomplete,” being deficient in one or more essential amino acid.
 For example, corn is deficient in the amino acid lysine.
 Individuals who are forced by economic necessity or other circumstances to obtain
nearly all their calories from corn would show symptoms of protein deficiency.
 This is true from any diet limited to a single plant source, including rice, wheat, and
potatoes.
 Protein deficiency from a vegetarian diet can be avoided by eating a combination of plant
foods that complement one another to supply all essential amino acids.
 For example, beans supply the lysine that is missing in corn, and corn provides the
methionine that is deficient in beans.
 Because the body cannot easily store amino acids, a diet with all essential amino acids
must be eaten each day, or protein synthesis is retarded.
Biology Chapter Notes
 Some animals have special adaptations that get them through periods where their bodies
demand extraordinary amounts of protein.
 For example, penguins use muscle proteins as a source of amino acids to make new
proteins during molting.
 While animals can synthesize most of the fatty acids they need, they cannot synthesize
essential fatty acids.
 These are certain unsaturated fatty acids, including linoleic acids, which are required
by humans.
 Most diets furnish ample quantities of essential fatty acids, and thus deficiencies are
rare.
 Vitamins are organic molecules required in the diet in quantities that are quite small
compared with the relatively large quantities of essential amino acids and fatty acids
animals need.
 While vitamins are required in tiny amounts—from about 0.01 mg to 100 mg per
day—depending on the vitamin, vitamin deficiency (or overdose in some cases) can
cause serious problems.
 So far, 13 vitamins essential to humans have been identified.
 These can be grouped into water-soluble vitamins and fat-soluble vitamins, with
extremely diverse physiological functions.
 The water-soluble vitamins include the B complex, which consists of several compounds
that function as coenzymes in key metabolic processes.
 Vitamin C, also water soluble, is required for the production of connective tissue.
 Excessive amounts of water-soluble vitamins are excreted in urine, and moderate
overdoses are probably harmless.
 The fat-soluble vitamins are A, D, E, and K.
 They have a wide variety of functions.
 Vitamin A is incorporated in the visual pigments of the eye.
 Vitamin D aids in calcium absorption and bone formation.
 Vitamin E seems to protect membrane phospholipids from oxidation.
 Vitamin K is required for blood clotting.
 Excess amounts of fat-soluble vitamins are not excreted but are deposited in body fat.
 Overconsumption may lead to toxic accumulations of these compounds.
 The subject of vitamin dosage has aroused heated scientific and popular debate.
 Some believe that it is sufficient to meet recommended daily allowances (RDAs), the
nutrient intake proposed by nutritionists to maintain health.
 Others argue that RDAs are set too low for some vitamins, and a fraction of these
people believe, probably mistakenly, that massive doses of vitamins confer health
benefits.
 Debate centers on the optimal doses of vitamins C and E.
 While research is ongoing, all that can be said with any certainty is that people who eat
a balanced diet are not likely to develop symptoms of vitamin deficiency.
 Minerals are simple inorganic nutrients, usually required in small amounts—from less
than 1 mg to about 2,500 mg per day.
 Mineral requirements vary with animal species.
 Humans and other vertebrates require relatively large quantities of calcium and
phosphorus for the construction and maintenance of bone.
Biology Chapter Notes
  Calcium is also necessary for the normal functioning of nerves and muscles.
 Phosphorus is a component of the cytochromes that function in cellular respiration.
 Iron is a component of the cytochromes that function in cellular respiration and of
hemoglobin, the oxygen-binding protein of red blood cells.
 Magnesium, iron, zinc, copper, manganese, selenium, and molybdenum are cofactors
built into the structure of certain enzymes.
 Magnesium, for example, is present in enzymes that split ATP.
 Iodine is required for thyroid hormones, which regulate metabolic rate.
 Sodium, potassium, and chloride are important in nerve function and have a major
influence on the osmotic balance between cells and the interstitial fluids.
 Excess consumption of salt (sodium chloride) is harmful.
 The average U.S. citizen eats enough salt to provide about 20 times the required
amount of sodium.
 Excess consumption of salt or several other minerals can upset homeostatic balance
and cause toxic side effects.
 For example, too much sodium is associated with high blood pressure, and excess iron
causes liver damage.

Concept 41.3 The main stages of food processing are ingestion, digestion, absorption,
and elimination
 Ingestion, the act of eating, is only the first stage of food processing.
 Food is “packaged” in bulk form and contains very complex arrays of molecules,
including large polymers and various substances that may be difficult to process or
even toxic.
 Animals cannot use macromolecules like proteins, fats, and carbohydrates in the form of
starch or other polysaccharides.
 First, polymers are too large to pass through membranes and enter the cells of the
animal.
 Second, the macromolecules that make up an animal are not identical to those of its
food.
 In building their macromolecules, however, all organisms use common monomers.
 For example, soybeans, fruit flies, and humans all assemble their proteins from the
same 20 amino acids.
 Digestion, the second stage of food processing, is the process of breaking food down into
molecules small enough for the body to absorb.
 Digestion cleaves macromolecules into their component monomers, which the animal
then uses to make its own molecules or as fuel for ATP production.
 Polysaccharides and disaccharides are split into simple sugars.
 Fats are digested to glycerol and fatty acids.
 Proteins are broken down into amino acids.
 Nucleic acids are cleaved into nucleotides.
 Digestion reverses the process that a cell uses to link together monomers to form
macromolecules.
 Rather than removing a molecule of water for each new covalent bond formed,
digestion breaks bonds with the addition of water via enzymatic hydrolysis.
Biology Chapter Notes
  A variety of hydrolytic enzymes catalyze the digestion of each of the classes of
macromolecules found in food.
 Chemical digestion is usually preceded by mechanical fragmentation of the food—by
chewing, for instance.
 Breaking food into smaller pieces increases the surface area exposed to digestive juices
containing hydrolytic enzymes.
 After the food is digested, the animal’s cells take up small molecules such as amino acids
and simple sugars from the digestive compartment, a process called absorption.
 During elimination, undigested material passes out of the digestive compartment.
Digestion occurs in specialized compartments.
 To avoid digesting their own cells and tissues, most organisms conduct digestion in
specialized compartments.
 The simplest digestive compartments are food vacuoles, organelles in which hydrolytic
enzymes break down food without digesting the cell’s own cytoplasm, a process termed
intracellular digestion.
 This process begins after a cell has engulfed food by phagocytosis or pinocytosis.
 Newly formed food vacuoles fuse with lysosomes, which are organelles containing
hydrolytic enzymes.
 Later the vacuole fuses with an anal pore, and its contents are eliminated.
 In most animals, at least some hydrolysis occurs by extracellular digestion, the
breakdown of food outside cells.
 Extracellular digestion occurs within compartments that are continuous with the
outside of the animal’s body.
 This enables organisms to devour much larger prey than can be ingested by
phagocytosis and digested intracellularly.
 Many animals with simple body plans, such as cnidarians and flatworms, have digestive
sacs with single openings, called gastrovascular cavities.
 These cavities function in both digestion and distribution of nutrients throughout the
body.
 For example, the cnidarians called hydras capture their prey with nematocysts and use
tentacles to stuff the prey through the mouth into the gastrovascular cavity.
 The prey is then partially digested by enzymes secreted by specialized gland cells
of the gastrodermis.
 Nutritive muscular cells in the gastrodermis engulf the food particles.
 Most of the actual hydrolysis of macromolecules occurs intracellularly.
 Undigested materials are eliminated through the mouth.
 In contrast to cnidarians and flatworms, most animals have digestive tubes extending
between a mouth and anus.
 These tubes are called complete digestive tracts or alimentary canals.
 Because food moves in one direction, the tube can be organized into specialized
regions that carry out digestion and nutrient absorption in a stepwise fashion.
 In addition, animals with alimentary canals can eat more food before the earlier meal is
completely digested.

Biology Chapter Notes

Concept 41.4 Each organ of the mammalian digestive system has specialized food-
processing functions
 The general principles of food processing are similar for a diversity of animals, including
the mammalian system that we will use as a representative example.
 The mammalian digestive system consists of the alimentary canal and various accessory
glands that secrete digestive juices into the canal through ducts.
 Peristalsis, rhythmic waves of contraction by smooth muscles in the walls of the canal,
pushes food along.
 Sphincters, muscular ring-like valves, regulate the passage of material between
specialized chambers of the canal.
 The accessory glands include the salivary glands, the pancreas, the liver, and the
gallbladder.
 After chewing and swallowing, it takes 5 to 10 seconds for food to pass down the
esophagus to the stomach, where it spends 2 to 6 hours being partially digested.
 Final digestion and nutrient absorption occur in the small intestine over a period of 5 to 6
hours.
 In 12 to 24 hours, any undigested material passes through the large intestine, and feces are
expelled through the anus.
The oral cavity, pharynx, and esophagus initiate food processing.
 Both physical and chemical digestion of food begins in the mouth.
 During chewing, teeth of various shapes cut, smash, and grind food, making it easier to
swallow and increasing its surface area.
 The presence of food in the oral cavity triggers a nervous reflex that causes the
salivary glands to deliver saliva through ducts to the oral cavity.
 Salivation may occur in anticipation because of learned associations between eating
and the time of day, cooking odors, or other stimuli.
 Saliva contains a slippery glycoprotein called mucin, which protects the soft lining of the
mouth from abrasion and lubricates the food for easier swallowing.
 Saliva also contains buffers that help prevent tooth decay by neutralizing acid in the
mouth.
 Antibacterial agents in saliva kill many bacteria that enter the mouth with food.
 Chemical digestion of carbohydrates, a main source of chemical energy, begins in the oral
cavity.
 Saliva contains salivary amylase, an enzyme that hydrolyzes starch and glycogen into
smaller polysaccharides and the disaccharide maltose.
 The tongue tastes food, manipulates it during chewing, and helps shape the food into a
ball called a bolus.
 During swallowing, the tongue pushes a bolus back into the oral cavity and into the
pharynx.
 The pharynx, also called the throat, is a junction that opens to both the esophagus and the
trachea (windpipe).
 When we swallow, the top of the windpipe moves up so that its opening, the glottis, is
blocked by a cartilaginous flap, the epiglottis.
 This mechanism normally ensures that a bolus will be guided into the entrance of the
esophagus and not directed down the windpipe.

Biology Chapter Notes

  When not swallowing, the esophageal sphincter muscles are contracted, the epiglottis
is up, and the glottis is open, allowing airflow to the lungs.
 When a food bolus reaches the pharynx, the larynx moves upward and the epiglottis
tips over the glottis, closing off the trachea.
 The esophageal sphincter relaxes and the bolus enters the esophagus.
 In the meantime, the larynx moves downward and the trachea is opened, and peristalsis
moves the bolus down the esophagus to the stomach.
 The esophagus conducts food from the pharynx down to the stomach by peristalsis.
 The muscles at the very top of the esophagus are striated and, therefore, under
voluntary control.
 Involuntary waves of contraction by smooth muscles in the rest of the esophagus then
take over.
The stomach stores food and performs preliminary digestion.
 The stomach is located in the upper abdominal cavity, just below the diaphragm.
 With accordion-like folds and a very elastic wall, the stomach can stretch to
accommodate about 2 L of food and fluid, storing an entire meal.
 The stomach also secretes a digestive fluid called gastric juice and mixes this
secretion with the food by the churning action of the smooth muscles in the stomach
wall.
 Gastric juice is secreted by the epithelium lining numerous deep pits in the stomach wall.
 With a high concentration of hydrochloric acid, the pH of the gastric juice is about 2—
acidic enough to digest iron nails.
 This acid disrupts the extracellular matrix that binds cells together.
 It kills most bacteria that are swallowed with food.
 Also present in gastric juice is pepsin, an enzyme that begins the hydrolysis of
proteins.
 Pepsin, which works well in strongly acidic environments, breaks peptide bonds
adjacent to specific amino acids, producing smaller polypeptides.
 Pepsin is secreted in an inactive form called pepsinogen by specialized chief cells
in gastric pits.
 Parietal cells, also in the pits, secrete hydrochloric acid that converts pepsinogen to the
active pepsin only when both reach the lumen of the stomach, minimizing self-
digestion.
 In a positive-feedback system, activated pepsin can activate more pepsinogen
molecules.
 The stomach’s second line of defense against self-digestion is a coating of mucus,
secreted by epithelial cells, that protects the stomach lining.
 Still, the epithelium is continually eroded, and the epithelium is completely replaced
by mitosis every three days.
 Gastric ulcers, lesions in the stomach lining, are caused by the acid-tolerant bacterium
Heliobacter pylori.
 Ulcers are often treated with antibiotics.
 About every 20 seconds, the stomach contents are mixed by the churning action of smooth
muscles.
 You may feel hunger pangs when your empty stomach churns.

Biology Chapter Notes

  Sensations of hunger are also associated with brain centers that monitor the blood’s
nutritional status and the levels of appetite-controlling hormones.
 As a result of mixing and enzyme action, what begins in the stomach as a recently
swallowed meal becomes a nutrient-rich broth known as acid chyme.
 Most of the time the stomach is closed off at either end.
 The opening from the esophagus to the stomach, the cardiac orifice, normally dilates
only when a bolus driven by peristalsis arrives.
 The occasional backflow of acid chyme from the stomach into the lower esophagus
causes heartburn.
 At the opening from the stomach to the small intestine is the pyloric sphincter, which
helps regulate the passage of chyme into the intestine.
 A squirt at a time, it takes about 2 to 6 hours after a meal for the stomach to empty.
The small intestine is the major organ of digestion and absorption.
 With a length of more than 6 m in humans, the small intestine is the longest section of the
alimentary canal.
 Most of the enzymatic hydrolysis of food macromolecules and most of the absorption of
nutrients into the blood occurs in the small intestine.
 In the first 25 cm or so of the small intestine, the duodenum, acid chyme from the
stomach mixes with digestive juices from the pancreas, liver, gall bladder, and gland cells
of the intestinal wall.
 The pancreas produces several hydrolytic enzymes and an alkaline solution rich in
bicarbonate that buffers the acidity of the chyme from the stomach.
 Pancreatic enzymes include protein-digesting enzymes (proteases) that are secreted
into the duodenum in inactive form.
 The pancreatic proteases are activated once they are in the extracellular space
within the duodenum.
 The liver performs a wide variety of important functions in the body, including the
production of bile.
 Bile is stored in the gallbladder until needed.
 It contains bile salts that act as detergents that aid in the digestion and absorption of
fats.
 Bile also contains pigments that are by-products of red blood cell destruction in the
liver.
 These bile pigments are eliminated from the body with the feces.
 The brush border of the epithelial lining of the duodenum produces several digestive
enzymes.
 Several enzymes are secreted into the lumen, while others are bound to the surface of
the epithelial cells.
 Enzymatic digestion is completed as peristalsis moves the mixture of chyme and digestive
juices along the small intestine.
 Most digestion is completed while the chyme is still in the duodenum.
 The remaining regions of the small intestine, the jejunum and ileum, function mainly in
the absorption of nutrients and water.
 To enter the body, nutrients in the lumen must pass the lining of the digestive tract.

Biology Chapter Notes

 A few nutrients are absorbed in the stomach and large intestine, but most absorption takes
place in the small intestine.
 The small intestine has a huge surface area—300 m2, roughly the size of a tennis court.
 The enormous surface of the small intestine is an adaptation that greatly increases the rate
of nutrient absorption.
 Large circular folds in the lining bear fingerlike projections called villi, and each
epithelial cell of a villus has many microscopic appendages called microvilli that are
exposed to the intestinal lumen.
 The microvilli are the basis of the term “brush border” for the intestinal epithelium.
 Penetrating the core of each villus is a net of microscopic blood vessels (capillaries) and a
single vessel of the lymphatic system called a lacteal.
 Nutrients are absorbed across the intestinal epithelium and then across the unicellular
epithelium of capillaries or lacteals.
 Only these two single layers of epithelial cells separate nutrients in the lumen of the
intestine from the bloodstream.
 In some cases, transport of nutrients across the epithelial cells is passive, as molecules
move down their concentration gradients from the lumen of the intestine into the epithelial
cells, and then into capillaries.
 Fructose, a simple sugar, moves by diffusion alone down its concentration gradient
from the lumen of the intestine into the epithelial cells and then into capillaries.
 Amino acids and sugars pass through the epithelium, enter capillaries, and are carried
away from the intestine by the bloodstream.
 Glycerol and fatty acids absorbed by epithelial cells are recombined into fats.
 The fats are mixed with cholesterol and coated with special proteins to form small
globules called chylomicrons.
 Chylomicrons are transported by exocytosis out of epithelial cells and into lacteals.
 The lacteals converge into the larger vessels of the lymphatic system, eventually
draining into large veins that return blood to the heart.
 The capillaries and veins that drain nutrients away from the villi converge into the
hepatic portal vein, which leads directly to the liver.
 Therefore, the liver, which has the metabolic versatility to interconvert various organic
molecules, has first access to amino acids and sugars absorbed after a meal is digested.
 The liver modifies and regulates this varied mix before releasing materials back into the
bloodstream.
 For example, the liver helps regulate the levels of glucose in the blood, ensuring that
blood exiting the liver usually has a glucose concentration very close to 0.1%,
regardless of carbohydrate content of the meal.
 From the liver, blood travels to the heart, which pumps the blood and nutrients to all parts
of the body.
Reclaiming water is a major function of the large intestine.
 The large intestine, or colon, is connected to the small intestine at a T-shaped junction
where a sphincter controls the movement of materials.
 One arm of the T is a pouch called the cecum.
 The relatively small cecum of humans has a fingerlike extension, the appendix, which
makes a minor contribution to body defense.

Biology Chapter Notes

  The main branch of the human colon is shaped like an upside-down U, about 1.5 m
long.
 A major function of the colon is to recover water that has entered the alimentary canal as
the solvent to various digestive juices.
 About 7 L of fluid are secreted into the lumen of the digestive tract of a person each
day.
 More than 90% of the water is reabsorbed, most in the small intestine, the rest in the
colon.
 Digestive wastes, the feces, become more solid as they are moved along the colon by
peristalsis.
 Movement in the colon is sluggish, requiring 12 to 24 hours for material to travel the
length of the organ.
 If the lining of the colon is irritated by a bacterial infection, less water than usual is
resorbed, resulting in diarrhea.
 If insufficient water is absorbed because peristalsis moves the feces too slowly, the
result is constipation.
 Living in the large intestine is a rich flora of mostly harmless bacteria.
 One of the most common inhabitants of the human colon is Escherichia coli, a favorite
research organism.
 As a by-product of their metabolism, many colon bacteria generate gases, including
methane and hydrogen sulfide.
 Some bacteria produce vitamins, including biotin, folic acid, vitamin K, and several B
vitamins, which supplement our dietary intake of vitamins.
 Feces contain masses of bacteria and undigested materials including cellulose.
 Although cellulose fibers have no caloric value to humans, their presence in the diet
helps move food along the digestive tract.
 The terminal portion of the colon is called the rectum, where feces are stored until they
can be eliminated.
 Between the rectum and the anus are two sphincters, one involuntary and one
voluntary.
 Once or more each day, strong contractions of the colon create an urge to defecate.

Concept 41.5 Evolutionary adaptations of vertebrate digestive systems are often

associated with diet
 The digestive systems of mammals and other vertebrates are variations on a common
plan.
 However, there are many intriguing variations, often associated with the animal’s diet.
 Dentition, an animal’s assortment of teeth, is one example of structural variation
reflecting diet.
 Particularly in mammals, evolutionary adaptation of teeth for processing different
kinds of food is one of the major reasons that mammals have been so successful.
 Nonmammalian vertebrates generally have less specialized dentition, but there are
exceptions.
 For example, poisonous snakes, such as rattlesnakes, have fangs, modified teeth that
inject venom into prey.
Biology Chapter Notes
  Some snakes have hollow fangs, like syringes, while others drip poison along
grooves in the tooth surface.
 All snakes have another important anatomic adaptation for feeding, the ability swallow
large prey whole.
 The lower jaw is loosely hinged to the skull by an elastic ligament that permits the
mouth and throat to open very wide for swallowing.
 Large, expandable stomachs are common in carnivores, which may go for a long time
between meals and, therefore, must eat as much as they can when they do catch prey.
 For example, a 200-kg African lion can consume 40 kg of meat in one meal.
 The length of the vertebrate digestive system is also correlated with diet.
 In general, herbivores and omnivores have longer alimentary canals relative to their body
sizes than do carnivores, providing more time for digestion and more surface areas for
absorption of nutrients.
 Vegetation is more difficult to digest than meat because it contains cells walls.
Symbiotic microorganisms help nourish many vertebrates.
 Much of the chemical energy in the diet of herbivorous animals is contained in the
cellulose of plant cell walls.
 However, animals do not produce enzymes that hydrolyze cellulose.
 Many vertebrates (and termites) solve this problem by housing large populations of
symbiotic bacteria and protists in special fermentation chambers in their alimentary
canals.
 These microorganisms do have enzymes that can digest cellulose to simple sugars that
the animal can absorb.
 The location of symbiotic microbes in herbivores’ digestive tracts varies depending on the
species.
 The hoatzin, an herbivorous bird that lives in South American rain forests, has a large,
muscular crop that houses symbiotic microorganisms.
 Many herbivorous mammals, including horses, house symbiotic microorganisms in a
large cecum, the pouch where the small and large intestines connect.
 The symbiotic bacteria of rabbits and some rodents live in the large intestine and
cecum.
 Since most nutrients are absorbed in the small intestine, these organisms recover
nutrients from fermentation in the large intestine by eating some of their feces and
passing food through a second time.
 The koala also has an enlarged cecum, where symbiotic bacteria ferment finely
shredded eucalyptus leaves.
 The most elaborate adaptations for a herbivorous diet have evolved in the ruminants,
which include deer, cattle, and sheep.
 When the cow first chews and swallows a mouthful of grass, boluses enter the rumen
and the reticulum.
 Symbiotic bacteria and protists digest this cellulose-rich meal, secreting fatty acids.
 Periodically, the cow regurgitates and rechews the cud, which further breaks down
the cellulose fibers.
 The cow then reswallows the cud to the omasum, where water is removed.
 The cud, with many microorganisms, passes to the abomasum for digestion by the
cow’s enzymes.
Biology Chapter Notes
 Chapter 42 Circulation and Gas Exchange
Chapter Notes

Overview: Trading with the Environment

 Every organism must exchange materials and energy with its environment, and this
exchange ultimately occurs at the cellular level.
 Cells live in aqueous environments.
 The resources that they need, such as nutrients and oxygen, move across the plasma
membrane to the cytoplasm.
 Metabolic wastes, such as carbon dioxide, move out of the cell.
 Most animals have organ systems specialized for exchanging materials with the
environment, and many have an internal transport system that conveys fluid (blood or
interstitial fluid) throughout the body.
 For aquatic organisms, structures such as gills present an expansive surface area to the
outside environment.
 Oxygen dissolved in the surrounding water diffuses across the thin epithelium covering
the gills and into a network of tiny blood vessels (capillaries).
 At the same time, carbon dioxide diffuses out into the water.

Concept 42.1 Circulatory systems reflect phylogeny

 Diffusion alone is not adequate for transporting substances over long distances in
animals—for example, for moving glucose from the digestive tract and oxygen from the
lungs to the brain of a mammal.
 Diffusion is insufficient over distances of more than a few millimeters, because the time it
takes for a substance to diffuse from one place to another is proportional to the square of
the distance.
 For example, if it takes 1 second for a given quantity of glucose to diffuse 100
microns, it will take 100 seconds for it to diffuse 1 mm and almost three hours to
diffuse 1 cm.
 The circulatory system solves this problem by ensuring that no substance must diffuse
very far to enter or leave a cell.
 The bulk transport of fluids throughout the body functionally connects the aqueous
environment of the body cells to the organs that exchange gases, absorb nutrients, and
dispose of wastes.
 For example, in the mammalian lung, oxygen from inhaled air diffuses across a thin
epithelium and into the blood, while carbon dioxide diffuses out.
 Bulk fluid movement in the circulatory system, powered by the heart, quickly carries
the oxygen-rich blood to all parts of the body.
 As the blood streams through the tissues within microscopic vessels called capillaries,
chemicals are exchanged between blood and the interstitial fluid that bathes the cells.
Most invertebrates have a gastrovascular cavity or a circulatory system for internal
transport.
 The body plan of a hydra and other cnidarians makes a circulatory system unnecessary.
Biology Chapter Notes
  A body wall only two cells thick encloses a central gastrovascular cavity that serves
for both digestion and for diffusion of substances throughout the body.
 The fluid inside the cavity is continuous with the water outside through a single
opening, the mouth.
 Thus, both the inner and outer tissue layers are bathed in fluid.
 In cnidarians such as Aurelia, the mouth leads to an elaborate gastrovascular cavity that
has branches radiating to and from the circular canal.
 The products of digestion in the gastrovascular cavity are directly available to the cells
of the inner layer, and it is only a short distance to diffuse to the cells of the outer
layer.
 Planarians and most other flatworms also have gastrovascular cavities that exchange
materials with the environment through a single opening.
 The flat shape of the body and the branching of the gastrovascular cavity throughout
the animal ensure that cells are bathed in a suitable medium and that diffusion
distances are short.
 For animals with many cell layers, gastrovascular cavities are insufficient for internal
distances because the diffusion transports are too great.
 In more complex animals, two types of circulatory systems that overcome the limitations
of diffusion have evolved: open circulatory systems and closed circulatory systems.
 Both have a circulatory fluid (blood), a set of tubes (blood vessels), and a muscular
pump (the heart).
 The heart powers circulation by using metabolic power to elevate the hydrostatic
pressure of the blood (blood pressure), which then flows down a pressure gradient
through its circuit back to the heart.
 In insects, other arthropods, and most molluscs, blood bathes organs directly in an open
circulatory system.
 There is no distinction between blood and interstitial fluid, collectively called
hemolymph.
 One or more hearts pump the hemolymph into interconnected sinuses surrounding the
organs, allowing exchange between hemolymph and body cells.
 In insects and other arthropods, the heart is an elongated dorsal tube.
 When the heart contracts, it pumps hemolymph through vessels out into sinuses.
 When the heart relaxes, it draws hemolymph into the circulatory system through pores
called ostia.
 Body movements that squeeze the sinuses help circulate the hemolymph.
 In a closed circulatory system, found in earthworms, squid, octopuses, and vertebrates,
blood is confined to vessels and is distinct from interstitial fluid.
 One or more hearts pump blood into large vessels that branch into smaller ones
coursing through organs.
 Materials are exchanged by diffusion between the blood and the interstitial fluid
bathing the cells.
 The fact that open and closed circulatory systems are both widespread in the animal
kingdom suggests that both systems offer advantages.
 The lower hydrostatic pressures associated with open circulatory systems make them
less costly than closed circulatory systems.

Biology Chapter Notes

  Because they lack an extensive system of blood vessels, open systems require less
energy to build and maintain.
 In molluscs and freshly molted aquatic arthropods, the open circulatory system
functions as a hydrostatic skeleton.
 What advantages are associated with closed circulatory systems?
 Closed systems with their higher blood pressure are more effective at transporting
circulatory fluids to meet the high metabolic demands of the tissues and cells of larger
and more active animals.
 Among the molluscs, only the large and active squid and octopuses have closed
circulatory systems.
Vertebrate phylogeny is reflected in adaptations of the cardiovascular system.
 The closed circulatory system of humans and other vertebrates is often called the
cardiovascular system.
 The heart consists of one atrium or two atria, the chambers that receive blood returning
to the heart, and one or two ventricles, the chambers that pump blood out of the heart.
 Arteries, veins, and capillaries are the three main kinds of blood vessels.
 Arteries carry blood away from the heart to organs.
 Within organs, arteries branch into arterioles, small vessels that convey blood to
capillaries.
 Capillaries with very thin, porous walls form networks called capillary beds, which
infiltrate each tissue.
 Chemicals, including dissolved gases, are exchanged across the thin walls of the
capillaries between the blood and interstitial fluid.
 At their “downstream” end, capillaries converge into venules, and venules converge
into veins, which (usually) return blood to the heart.
 Arteries and veins are distinguished by the direction in which they carry blood, not by the
characteristics of the blood they carry.
 All arteries carry blood from the heart toward capillaries.
 Veins return blood to the heart from capillaries.
 A significant exception is the hepatic portal vein that carries blood from capillary
beds in the digestive system to capillary beds in the liver.
 Metabolic rate is an important factor in the evolution of cardiovascular systems.
 In general, animals with high metabolic rates have more complex circulatory systems
and more powerful hearts than animals with low metabolic rates.
 Similarly, the complexity and number of blood vessels in a particular organ are
correlated with that organ’s metabolic requirements.
 Perhaps the most fundamental differences in cardiovascular adaptations are associated
with gill breathing in aquatic vertebrates compared with lung breathing in terrestrial
vertebrates.
 A fish heart has two main chambers, one atrium and one ventricle.
 Blood is pumped from the ventricle to the gills (the gill circulation) where it picks up
oxygen and disposes of carbon dioxide across the capillary walls.
 The gill capillaries converge into a vessel that carries oxygenated blood to capillary beds
in the other organs (the systemic circulation) and back via veins to the atrium of the
heart.

Biology Chapter Notes

 In fish, blood must pass through two capillary beds, the gill capillaries and systemic
capillaries.
 When blood flows through a capillary bed, blood pressure—the motive force for
circulation—drops substantially.
 Therefore, oxygen-rich blood leaving the gills flows to the systemic circulation quite
slowly (although the process is aided by body movements during swimming).
 This constrains the delivery of oxygen to body tissues and, hence, the maximum
aerobic metabolic rate of fishes.
 Frogs and other amphibians have a three-chambered heart with two atria and one
ventricle.
 The ventricle pumps blood into a forked artery that splits the ventricle’s output into the
pulmocutaneous and systemic circulations.
 The pulmocutaneous circulation leads to capillaries in the gas-exchange organs (the lungs
and skin of a frog), where the blood picks up O 2 and releases CO2 before returning to the
heart’s left atrium.
 Most of the returning oxygen-rich blood is pumped into the systemic circulation,
which supplies all body organs and then returns oxygen-poor blood to the right atrium
via the veins.
 This scheme, called double circulation, provides a vigorous flow of blood to the
brain, muscles, and other organs because the blood is pumped a second time after it
loses pressure in the capillary beds of the lung or skin.
 In the ventricle of the frog, some oxygen-rich blood from the lungs mixes with oxygen-
poor blood that has returned from the rest of the body.
 However, a ridge within the ventricle diverts most of the oxygen-rich blood from the
left atrium into the systemic circuit and most of the oxygen-poor blood from the right
atrium into the pulmocutaneous circuit.
 Nonbird reptiles also have double circulation with a pulmonary circuit (lungs) and a
systemic circuit.
 Turtles, snakes, and lizards have a three-chambered heart, although the ventricle is
partially blocked by a septum, which results in even less mixing of oxygen-rich and
oxygen-poor blood than in amphibians.
 All reptiles except birds have two arteries leading from the heart to the systemic
circuit, and arterial valves allow them to divert most of their blood from the pulmonary
circuit to the systemic circuit.
 In crocodilians, birds, and mammals, the ventricle is completely divided into separate
right and left chambers.
 In this arrangement, the left side of the heart receives and pumps only oxygen-rich
blood, while the right side handles only oxygen-poor blood.
 Double circulation restores pressure to the systemic circuit after blood has passed through
the lung capillaries and prevents mixing of oxygen-rich and oxygen-poor blood.
 The evolution of a powerful four-chambered heart was an essential adaptation to support
the endothermic way of life characteristic of birds and mammals.
 Endotherms use about ten times as much energy as ectotherms of the same size.
 Therefore, the endotherm circulatory system needs to deliver about ten times as much
fuel and O2 to their tissues and remove ten times as much wastes and CO2.
 Birds and mammals evolved from different reptilian ancestors, and their powerful
four-chambered hearts evolved independently—an example of convergent evolution.

Biology Chapter Notes

Concept 42.2 Double circulation in mammals depends on the anatomy and pumping
cycle of the heart
 In the mammalian cardiovascular system, the pulmonary and system circuits operate
simultaneously.
 The two ventricles pump almost in unison.
 While some blood is traveling in the pulmonary circuit, the rest of the blood is flowing
in the systemic circuit.
 To trace the double circulation pattern of the mammalian cardiovascular system, we’ll
start with the pulmonary (lung) circuit.
 The pulmonary circuit carries blood from the heart to the lungs and back again.
 The right ventricle pumps blood to the lungs via the pulmonary arteries.
 As blood flows through capillary beds in the right and left lungs, it loads O 2 and
unloads CO2.
 Oxygen-rich blood returns from the lungs via the pulmonary veins to the left atrium of
the heart.
 Next, the oxygen-rich blood flows to the left ventricle, as the ventricle opens and the
atrium contracts.
 The left ventricle pumps oxygen-rich blood out to the body tissues through the systemic
circuit.
 Blood leaves the left ventricle via the aorta, which conveys blood to arteries leading
throughout the body.
 The first branches from the aorta are the coronary arteries, which supply blood to
the heart muscle.
 The next branches lead to capillary beds in the head and arms.
 The aorta continues in a posterior direction, supplying oxygen-rich blood to arteries
leading to arterioles and capillary beds in the abdominal organs and legs.
 Within the capillaries, blood gives up much of its O2 and picks up CO2 produced by
cellular respiration.
 Venous return to the right side of the heart begins as capillaries rejoin to form venules and
then veins.
 Oxygen-poor blood from the head, neck, and forelimbs is channeled into a large vein
called the anterior (or superior) vena cava.
 Another large vein called the posterior (or inferior) vena cava drains blood from the
trunk and hind limbs.
 The two venae cavae empty their blood into the right atrium, from which the oxygen-
poor blood flows into the right ventricle.
 The mammalian heart is located beneath the breastbone (sternum) and consists mostly of
cardiac muscle.
 The two atria have relatively thin walls and function as collection chambers for blood
returning to the heart.
 The ventricles have thicker walls and contract much more strongly than the atria.
 A cardiac cycle is one complete sequence of pumping, as the heart contracts, and filling,
as it relaxes and its chambers fill with blood.
 The contraction phase is called systole, and the relaxation phase is called diastole.

Biology Chapter Notes

 For a human at rest with a pulse of about 75 beats per minute, one complete cardiac cycle
takes about 0.8 sec.
 During the relaxation phase (atria and ventricles in diastole) lasting about 0.4 sec,
blood returning from the large veins flows into atria and ventricles.
 A brief period (about 0.1 sec) of atrial systole forces all the remaining blood out of the
atria and into the ventricles.
 During the remaining 0.3 sec of the cycle, ventricular systole pumps blood into the
large arteries.
 Cardiac output is the volume of blood pumped per minute, and it depends on two
factors: the rate of contraction or heart rate (number of beats per second) and stroke
volume, the amount of blood pumped by the left ventricle in each contraction.
 The average stroke volume for a human is about 75 mL.
 The typical resting cardiac output, about 5.25 L/min, is equivalent to the total volume
of blood in the human body.
 Cardiac output can increase about fivefold during heavy exercise.
 Heart rate can be measured indirectly by measuring your pulse—the rhythmic
stretching of arteries caused by the pressure of blood pumped by the ventricles.
 Four valves in the heart, each consisting of flaps of connective tissue, prevent backflow
and keep blood moving in the correct direction.
 Between each atrium and ventricle is an atrioventricular (AV) valve, which keeps
blood from flowing back into the atria when the ventricles contract.
 The AV valves are anchored by strong fibers that prevent them from turning inside out.
 Two sets of semilunar valves, one between the left ventricle and the aorta and the
other between the right ventricle and the pulmonary artery, prevent backflow from
these vessels into the ventricles while they are relaxing.
 The heart sounds we can hear with a stethoscope are caused by the closing of the valves.
 The sound pattern is “lub-dup, lub-dup, lub-dup.”
 The first heart sound (“lub”) is created by the recoil of blood against the closed AV
valves.
 The second sound (“dup”) is the recoil of blood against the semilunar valves.
 A defect in one or more of the valves causes a heart murmur, which may be detectable
as a hissing sound when a stream of blood squirts backward through a valve.
 Some people are born with heart murmurs.
 Other murmurs are due to damage to the valves by infection.
 Most heart murmurs do not reduce the efficiency of blood flow enough to warrant
surgery.
 Because the timely delivery of oxygen to the body’s organs is critical for survival, several
mechanisms have evolved to assure continuity and control of the heartbeat.
 Certain cells of vertebrate cardiac muscle are self-excitable, meaning they contract
without any signal from the nervous system.
 Each cell has its own intrinsic contraction rhythm.
 However, these cells are synchronized by the sinoatrial (SA) node, or pacemaker,
which sets the rate and timing at which all cardiac muscle cells contract.
 The SA node is located in the wall of the right atrium.
 Because the vertebrate heart has a pacemaker made up of specialized muscle tissues
located within the heart itself, it is referred to as a myogenic heart.
Biology Chapter Notes
  In contrast, the pacemakers of most arthropod hearts originate in motor nerves arising
from the outside, an arrangement called a neurogenic heart.
 The cardiac cycle is regulated by electrical impulses that radiate throughout the heart.
 Cardiac muscle cells are electrically coupled by intercalated disks between adjacent
cells.
 The SA node generates electrical impulses, much like those produced by nerves that
spread rapidly through the wall of the atria, making them contract in unison.
 The impulse from the SA node is delayed by about 0.1 sec at the atrioventricular
(AV) node, the relay point to the ventricle, allowing the atria to empty completely
before the ventricles contract.
 Specialized muscle fibers called bundle branches and Purkinje fibers conduct the
signals to the apex of the heart and throughout the ventricular walls.
 This stimulates the ventricles to contract from the apex toward the atria, driving blood
into the large arteries.
 The impulses generated during the heart cycle produce electrical currents that are
conducted through body fluids to the skin.
 Here, the currents can be detected by electrodes and recorded as an electrocardiogram
(ECG or EKG).
 While the SA node sets the tempo for the entire heart, it is influenced by a variety of
physiological cues.
 Two sets of nerves affect heart rate, with one set speeding up the pacemaker and the
other set slowing it down.
 Heart rate is a compromise regulated by the opposing actions of these two sets of
nerves.
 The pacemaker is also influenced by hormones.
 For example, epinephrine from the adrenal glands increases heart rate.
 The rate of impulse generation by the pacemaker increases in response to increases in
body temperature and with exercise.

Concept 42.3 Physical principles govern blood circulation

 All blood vessels are built of similar tissues.
 The walls of both arteries and veins have three similar layers.
 On the outside, a layer of connective tissue with elastic fibers allows the vessel to
stretch and recoil.
 A middle layer has smooth muscle and more elastic fibers.
 Lining the lumen of all blood vessels, including capillaries, is an endothelium, a
single layer of flattened cells that minimizes resistance to blood flow.
 Structural differences correlate with the different functions of arteries, veins, and
capillaries.
 Capillaries lack the two outer layers, and their very thin walls consist only of
endothelium and its basement membrane, thus enhancing exchange.
 Arteries have thicker middle and outer layers than veins.
 The thicker walls of arteries provide strength to accommodate blood pumped rapidly
and at high pressure by the heart.

Biology Chapter Notes

  Their elasticity (elastic recoil) helps maintain blood pressure even when the heart
relaxes.
 The thinner-walled veins convey blood back to the heart at low velocity and pressure.
 Blood flows through the veins mainly because skeletal muscle contractions squeeze
blood in veins.
 Within larger veins, flaps of tissues act as one-way valves that allow blood to flow
only toward the heart.
Physical laws governing the movement of fluids through pipes affect blood flow and blood
pressure.
 The observation that blood travels more than a thousand times faster in the aorta than in
capillaries follows from the law of continuity, describing fluid movement through pipes.
 If a pipe’s diameter changes over its length, a fluid will flow through narrower
segments faster than it flows through wider segments because the volume of flow per
second must be constant throughout the entire pipe.
 Each artery conveys blood to such an enormous number of capillaries that the total cross-
sectional area is much greater in capillary beds than in any other part of the circulatory
system.
 The resulting slow flow rate and thin capillary walls enhance the exchange of substances
between the blood and interstitial fluid.
 As blood leaves the capillary beds and passes to venules and veins, it speeds up again as a
result of the reduction in total cross-sectional area.
 Fluids exert a force called hydrostatic pressure against surfaces they contact, and it is that
pressure that drives fluids through pipes.
 Fluids always flow from areas of high pressure to areas of lower pressure.
 Blood pressure, the hydrostatic force that blood exerts against vessel walls, is much
greater in arteries than in veins and is highest in arteries when the heart contracts
during ventricular systole, creating the systolic pressure.
 When you take your pulse by placing your fingers on your wrist, you can feel an artery
bulge with each heartbeat.
 The surge of pressure is partly due to the narrow openings of arterioles impeding the
exit of blood from the arteries, the peripheral resistance.
 Thus, when the heart contracts, blood enters the arteries faster than it can leave, and
the vessels stretch from the pressure.
 The elastic walls of the arteries snap back during diastole, but the heart contracts again
before enough blood has flowed into the arterioles to completely relieve pressure in the
arteries.
 As a consequence of the elastic arteries working against peripheral resistance, there is
substantial diastolic pressure even during diastole.
 Blood flows into arterioles and capillaries continuously.
 The arterial blood pressure of a healthy human oscillates between about 120 mm
Hg at systole and less than 80 mm Hg at diastole.
 Blood pressure is determined partly by cardiac output and partly by peripheral resistance.
 Contraction of smooth muscles in walls of arterioles constricts these vessels,
increasing peripheral resistance and increasing blood pressure upstream in the arteries.
 When the smooth muscles relax, the arterioles dilate, blood flow through arterioles
increases, and pressure in the arteries falls.
Biology Chapter Notes
  Nerve impulses, hormones, and other signals control the arteriole wall muscles.
 Stress, both physical and emotional, can raise blood pressure by triggering nervous and
hormonal responses that will constrict blood vessels.
 Cardiac output is adjusted in concert with changes in peripheral resistance.
 This coordination maintains adequate blood flow as the demands on the circulatory
system change.
 For example, during heavy exercise, arterioles in the working muscles dilate, admitting
a greater flow of oxygen-rich blood to the muscles and decreasing peripheral
resistance.
 At the same time, cardiac output increases, maintaining blood pressure and supporting
the necessary increase in blood flow.
 In large land animals, blood pressure is also affected by gravity.
 In addition to the peripheral resistance, additional pressure is necessary to push blood
to the level of the heart.
 In a standing human, it takes an extra 27 mm of Hg pressure to move blood from the
heart to the brain.
 In an organism like a giraffe, this extra force is about 190 mm Hg (for a total of 250
mm Hg).
 Special check valves and sinuses, as well as feedback mechanisms that reduce cardiac
output, prevent this high pressure from damaging the giraffe’s brain when it puts its
head down.
 By the time blood reaches the veins, its pressure is not affected much by the action of the
heart.
 The resistance of tiny arterioles and capillaries has dissipated the pressure generated by
the pumping heart.
 Rhythmic contractions of smooth muscles in the walls of veins and venules account for
some movement of blood.
 More important, the activity of skeletal muscles during exercise squeezes blood
through the veins.
 Also, inhalation changes pressure in the thoracic (chest) cavity, causing the venae
cavae and other large veins near the heart to expand and fill with blood.
Transfer of substances between the blood and the interstitial fluid occurs across the thin
walls of capillaries.
 At any given time, only about 5–10% of the body’s capillaries have blood flowing
through them.
 Capillaries in the brain, heart, kidneys, and liver are usually filled to capacity, but in
many other sites, the blood supply varies over times as blood is diverted.
 For example, after a meal, blood supply to the digestive tract increases.
 During strenuous exercise, blood is diverted from the digestive tract and supplied to
skeletal muscles.
 Two mechanisms, both dependent on smooth muscles controlled by nerve signals and
hormones, regulate the distribution of blood in capillary beds.
 In one mechanism, contraction of the smooth muscle layer in the wall of an arteriole
constricts the vessel, decreasing blood flow through it to a capillary bed.
 When the muscle layer relaxes, the arteriole dilates, allowing blood to enter the
capillaries.

Biology Chapter Notes

  In the other mechanism, rings of smooth muscles, called precapillary sphincters
because they are located at the entrance to capillary beds, control the flow of blood
between arterioles and venules.
 Some blood flows directly from arterioles to venules through thoroughfare channels
that are always open.
 The exchange of substances between the blood and interstitial fluid that bathes the cells
takes place across the thin endothelial walls of the capillaries.
 Some substances are carried across endothelial cells in vesicles that form by
endocytosis on one side and then release their contents by exocytosis on the other side.
 Others simply diffuse between the blood and the interstitial fluid across cells or
through the clefts between adjoining cells.
 Transport through these clefts occurs mainly by bulk flow due to fluid pressure.
 Blood pressure within the capillary pushes fluid, containing water and small solutes,
through the capillary clefts.
 This causes a net loss of fluid at the upstream end of the capillary.
 Blood cells and most proteins in the blood are too large and remain in the capillaries.
 As blood proceeds along the capillary, blood pressure continues to drop and the capillary
becomes hyperosmotic compared to the interstitial fluids.
 The resulting osmotic gradient pulls water into the capillary by osmosis near the
downstream end.
 About 85% of the fluid that leaves the blood at the arterial end of the capillary bed
reenters from the interstitial fluid at the venous end.
 The remaining 15% is eventually returned to the blood by the vessels of the lymphatic
system.
The lymphatic system returns fluid to the blood and aids in body defense.
 Fluids and some blood proteins that leak from the capillaries into the interstitial fluid are
returned to the blood via the lymphatic system.
 Fluid enters this system by diffusing into tiny lymph capillaries intermingled among
capillaries of the cardiovascular system.
 Once inside the lymphatic system, the fluid is called lymph, with a composition
similar to the interstitial fluid.
 The lymphatic system drains into the circulatory system near the junction of the venae
cavae with the right atrium.
 Lymph vessels, like veins, have valves that prevent the backflow of fluid toward the
capillaries.
 Rhythmic contraction of the vessel walls helps draw fluid into lymphatic capillaries.
 Like veins, lymph vessels depend mainly on the movement of skeletal muscle to
squeeze fluid toward the heart.
 Along lymph vessels are organs called lymph nodes.
 The lymph nodes filter the lymph and attack viruses and bacteria.
 Inside a lymph node is a honeycomb of connective tissue with spaces filled with white
blood cells specialized for defense.
 When the body is fighting an infection, these cells multiply, and the lymph nodes
become swollen.

Biology Chapter Notes

 In addition to defending against infection and maintaining the volume and protein
concentration of the blood, the lymphatic system transports fats from the digestive tract to
the circulatory system.

Concept 42.4 Blood is a connective tissue with cells suspended in plasma

 In invertebrates with open circulation, blood (hemolymph) is not different from interstitial
fluid.
 However, blood in the closed circulatory systems of vertebrates is a specialized
connective tissue consisting of several kinds of cells suspended in a liquid matrix called
plasma.
 The plasma includes the cellular elements (cells and cell fragments), which occupy about
45% of the blood volume, and transparent, straw-colored plasma.
 Plasma, about 55% of the blood volume, consists of water, ions, various plasma proteins,
nutrients, waste products, respiratory gases, and hormones, while the cellular elements
include red and white blood cells and platelets.
 Blood plasma is about 90% water.
 Dissolved in the plasma are a variety of ions, sometimes referred to as blood electrolytes.
 These are important in maintaining osmotic balance of the blood and help buffer the
blood at a pH of about 7.4.
 Also, proper functioning of muscles and nerves depends on the concentrations of key
ions in the interstitial fluid, which reflects concentrations in the plasma.
 Blood’s plasma proteins have many functions.
 Collectively, they act as buffers against pH changes, help maintain osmotic balance,
and contribute to the blood’s viscosity.
 Some specific proteins transport otherwise insoluble lipids in the blood.
 Other proteins—the immunoglobulins, or antibodies—help combat viruses and other
foreign agents that invade the body.
 Fibrinogen proteins help plug leaks when blood vessels are injured.
 Blood plasma with clotting factors removed is called serum.
 Plasma carries a wide variety of substances in transit from one part of the body to another,
including nutrients, metabolic wastes, respiratory gases, and hormones.
 Suspended in blood plasma are two classes of cells: red blood cells, which transport
oxygen, and white blood cells, which function in defense.
 A third cellular element, platelets, are pieces of cells that are involved in clotting.
 Red blood cells, or erythrocytes, are by far the most numerous blood cells.
 Each cubic millimeter of blood contains 5 to 6 million red cells, 5,000 to 10,000 white
blood cells, and 250,000 to 400,000 platelets.
 There are about 25 trillion red blood cells in the body’s 5 L of blood.
 The main function of red blood cells, oxygen transport, depends on rapid diffusion of
oxygen across the red blood cell’s plasma membranes.
 Human erythrocytes are small biconcave disks, presenting a large surface area.
 Mammalian erythrocytes lack nuclei, an unusual characteristic that leaves more space
in the tiny cells for hemoglobin, the iron-containing protein that transports oxygen.
 Red blood cells also lack mitochondria and generate ATP exclusively by anaerobic
metabolism.
Biology Chapter Notes
 An erythrocyte contains about 250 million molecules of hemoglobin.
 Each hemoglobin molecule binds up to four molecules of O2, so one erythrocyte can
transport a billion O2 molecules.
 As red blood cells pass through the capillary beds of lungs, gills, or other respiratory
organs, oxygen diffuses into the erythrocytes and hemoglobin binds O 2 and NO.
 In the systemic capillaries, hemoglobin unloads oxygen, which then diffuses into body
cells.
 NO relaxes the capillary walls, allowing them to expand and helping deliver O 2 to the
cells.
 There are five major types of white blood cells, or leukocytes: monocytes, neutrophils,
basophils, eosinophils, and lymphocytes.
 Their collective function is to fight infection.
 For example, monocytes and neutrophils are phagocytes, which engulf and digest
bacteria and debris from the body’s dead cells.
 Lymphocytes develop into specialized B cells and T cells, which produce the immune
response against foreign substances.
 White blood cells spend most of their time outside the circulatory system, patrolling
through interstitial fluid and the lymphatic system, fighting pathogens.
 A microliter of human blood normally has about 5,000 to 10,000 leukocytes, but their
numbers increase temporarily when the body is fighting infection.
 The third cellular element of blood, platelets, are fragments of cells about 2 to 3 microns
in diameter.
 They have no nuclei and originate as pinched-off cytoplasmic fragments of large cells
in the bone marrow.
 Platelets function in blood clotting.
 The cellular elements of blood wear out and are replaced constantly throughout a person’s
life.
 For example, erythrocytes usually circulate for only about 3 to 4 months and are then
destroyed by phagocytic cells in the liver and spleen.
 Enzymes digest the old cell’s macromolecules, and the monomers are recycled.
 Many of the iron atoms derived from hemoglobin in old red blood cells are
incorporated into new hemoglobin molecules.
 Erythrocytes, leukocytes, and platelets all develop from a single population of cells,
pluripotent stem cells, in the red marrow of bones, particularly the ribs, vertebrae,
breastbone, and pelvis.
 “Pluripotent” means that these cells have the potential to differentiate into any type of
blood cells or cells that produce platelets.
 This population arises in the early embryo and renews itself while replenishing the
blood with cellular elements.
 A negative-feedback mechanism, sensitive to the amount of oxygen reaching the tissues
via the blood, controls erythrocyte production.
 If the tissues do not produce enough oxygen, the kidney synthesizes and secretes a
hormone called erythropoietin (EPO), which stimulates production of erythrocytes.
 If blood is delivering more oxygen than the tissues can use, the level of erythropoietin
is reduced, and erythrocyte production slows.
 Physicians use synthetic EPO to treat people with anemia, a condition of low hemoglobin
levels.
Biology Chapter Notes
  Some athletes abuse EPO by injecting themselves with the drug to increase their
erythrocyte levels.
 This practice is known as blood doping. It is banned by the International Olympic
Committee and other sports federations.
 Through a recent breakthrough in isolating and culturing pluripotent stem cells,
researchers may soon have effective treatments for a number of human diseases, such as
leukemia.
 Individuals with leukemia have a cancerous line of stem cells that produce leukocytes.
 These cancerous cells crowd out cells that make red blood cells and produce an
unusually high number of leukocytes, many of which are abnormal.
 One strategy now being used experimentally for treating leukemia is to remove
pluripotent stem cells from a patient, destroy the patient’s bone marrow, and restock it
with noncancerous pluripotent cells.
 As few as 30 of these cells can repopulate the bone marrow.
 Blood contains a self-sealing material that plugs leaks from cuts and scrapes.
 A clot forms when the inactive form of the plasma protein fibrinogen is converted to
fibrin, which aggregates into threads that form the framework of the clot.
 The clotting mechanism begins with the release of clotting factors from platelets.
 An inherited defect in any step of the clotting process causes hemophilia, a disease
characterized by excessive bleeding from even minor cuts and bruises.
 The clotting process begins when the endothelium of a vessel is damaged and
connective tissue in the wall is exposed to blood.
 Platelets adhere to collagen fibers and release a substance that makes nearby
platelets sticky.
 The platelets form a plug.
 The seal is reinforced by a clot of fibrin when vessel damage is severe.
 More than a dozen clotting factors have been discovered, and the mechanism is still not
fully understood.
 A genetic mutation that affects any step of the clotting process causes hemophilia, a
disease characterized by excessive bleeding from even minor cuts.
 Anticlotting factors in the blood normally prevent spontaneous clotting in the absence of
injury.
 Sometimes, platelets clump and fibrin coagulates within a blood vessel, forming a clot
called a thrombus, and blocking the flow of blood.
 These potentially dangerous clots are more likely to form in individuals with
cardiovascular diseases, diseases of the heart and blood vessels.
Cardiovascular diseases are the leading cause of death in the United States and most other
developed nations.
 More than half of the deaths in the United States are caused by cardiovascular diseases,
diseases of the heart and blood vessels.
 The tendency to develop cardiovascular disease is inherited to some extent, but lifestyle
also plays a important role.
 Nongenetic factors include smoking, lack of exercise, a diet rich in animal fat, and
high levels of cholesterol in the blood.

Biology Chapter Notes

 One measure of an individual’s cardiovascular health or risk of arterial plaques can be
gauged by the ratio of low-density lipoproteins (LDLs) to high-density lipoproteins
(HDLs) in the blood.
 LDL is associated with depositing of cholesterol in arterial plaques.
 HDL may reduce cholesterol deposition.
 Exercise increases HDL concentration, while smoking increases LDL:HDL ratio.
 Healthy arteries have smooth inner linings that permit unimpeded blood flow.
 Deposition of cholesterol thickens and roughens this smooth lining.
 Growths called plaques develop in the inner wall of the arteries, narrowing their bore
and leading to a chronic cardiovascular disease known as atherosclerosis.
 At plaque sites, the smooth muscle layer of an artery thickens abnormally and becomes
infiltrated with fibrous connective tissue and lipids such as cholesterol.
 The rough lining of an atherosclerotic artery encourages the adhesion of platelets,
triggering the clotting process, and interfering with circulation.
 Hypertension (high blood pressure) promotes atherosclerosis and increases the risk of
heart disease and stroke.
 Atherosclerosis raises blood pressure by narrowing the vessels and reducing their
elasticity.
 According to one hypothesis, high blood pressure causes chronic damage to the
endothelium that lines the arteries, promoting plaque formation.
 Hypertension is simple to diagnose and can usually be controlled by diet, exercise,
medication, or a combination of these.
 A diastolic pressure over 90 is cause for concern, and extreme hypertension
(200/100) courts disaster.
 As atherosclerosis progresses, arteries become more and more clogged and the threat of
heart attack or stroke becomes much greater, but there may be warnings of this impending
threat.
 For example, if a coronary artery is partially blocked, a person may feel occasional
chest pains, a condition known as angina pectoris.
 This is a signal that part of the heart is not receiving enough blood, especially when the
heart is laboring because of physical or emotional stress.
 However, many people with atherosclerosis experience no warning signs and are unaware
of their disease until catastrophe strikes.
 The final blow is usually a heart attack or stroke.
 A heart attack is the death of cardiac muscle tissue resulting from prolonged blockage
of one or more coronary arteries, the vessels that supply oxygen-rich blood to the
heart.
 A stroke is the death of nervous tissue in the brain.
 Heart attacks and strokes frequently result from a thrombus that clogs a coronary artery or
an artery in the brain.
 A key process leading to the clogging of an artery is an inflammatory response triggered
by the accumulation of LDLs in the inner lining of an artery.
 Such an inflammation can cause plaques to rupture, releasing fragments that form a
thrombus.

Biology Chapter Notes

  The thrombus may originate at the site of blockage or it may develop elsewhere and be
transported (now called an embolus) until it becomes lodged in an artery too narrow
for it to pass.
 Cardiac or brain tissue downstream of the blockage may die from oxygen deprivation.
 If damage in the heart interrupts the conduction of electrical impulses through cardiac
muscle, heart rate may change drastically or the heart may stop beating altogether.
 Still, the victim may survive if a heartbeat is restored by cardiopulmonary resuscitation
(CPR) within a few minutes of the attack.
 The effects of a stroke and the individual’s chance of survival depend on the extent and
location of the damaged brain tissue.

Concept 42.5 Gas exchange occurs across specialized respiratory surfaces

 Gas exchange is the uptake of molecular oxygen (O2) from the environment and the
discharge of carbon dioxide (CO2) to the environment.
 While often called respiration, this process is distinct from, but linked to, the
production of ATP in cellular respiration.
 Gas exchange, in concert with the circulatory system, provides the oxygen necessary for
aerobic cellular respiration and removes the waste product, carbon dioxide.
 The source of oxygen, the respiratory medium, is air for terrestrial animals and water for
aquatic animals.
 The atmosphere is about 21% O2 (by volume).
 Dissolved oxygen levels in lakes, oceans, and other bodies of water vary considerably,
but are always much less than an equivalent volume of air.
 The part of an animal where gases are exchanged with the environment is the respiratory
surface.
 Movements of CO2 and O2 across the respiratory surface occur entirely by diffusion.
 The rate of diffusion is proportional to the surface area across which diffusion occurs,
and inversely proportional to the square of the distance through which molecules must
move.
 Therefore, respiratory surfaces tend to be thin and have large areas, maximizing the
rate of gas exchange.
 In addition, the respiratory surface of terrestrial and aquatic animals must be moist to
maintain the cell membranes.
 As a result, gases must dissolve in water before diffusing across respiratory
surfaces.
 Because the respiratory surface must supply O2 and expel CO2 for the entire body, the
structure of a respiratory surface depends mainly on the size of the organism, whether it
lives in water or on land, and on its metabolic demands.
 An endotherm requires a larger area of respiratory surface than a similar-sized
ectotherm.
 Gas exchange occurs over the entire surface area of protists and other unicellular
organisms.
 Similarly, for some relatively simple animals, such as sponges, cnidarians, and flatworms,
the plasma membrane of every cell in the body is close enough to the outside environment
for gases to diffuse in and out.

Biology Chapter Notes

 However, in most animals, the bulk of the body lacks direct access to the respiratory
medium.
 The respiratory surface is a thin, moist epithelium, separating the respiratory medium
from the blood or capillaries, which transport gases to and from the rest of the body.
 Some animals, such as earthworms and some amphibians, use the entire outer skin as a
respiratory organ.
 Just below the moist skin is a dense net of capillaries.
 However, because the respiratory surface must be moist, the possible habitats of these
animals are limited to water or damp places.
 Animals that use their moist skin as their only respiratory organ are usually small and
are either long and thin or flat in shape, with a high ratio of surface area to volume.
 For most other animals, the general body surface lacks sufficient area to exchange gases
for the entire body.
 The solution is a respiratory organ that is extensively folded or branched, enlarging the
surface area for gas exchange.
 Gills, tracheae, and lungs are the three most common respiratory organs.
Gills are respiratory adaptations of most aquatic animals.
 Gills are outfoldings of the body surface that are suspended in water.
 In some invertebrates, such as sea stars, gills have a simple shape and are distributed over
much of the body.
 Many segmented worms have flap-like gills that extend from each body segment, or long
feathery gills clustered at the head or tail.
 The gills of clams, crayfish, and many other animals are restricted to a local body region.
 The total surface area of gills is often much greater than that of the rest of the body.
 Water has both advantages and disadvantages as a respiratory medium.
 There is no problem keeping the cell membranes of the respiratory surface moist, since
the gills are surrounded by the aqueous environment.
 However, O2 concentrations in water are low, especially in warmer and saltier
environments.
 Thus, gills must be very effective to obtain enough oxygen.
 Ventilation, which increases the flow of the respiratory medium over the respiratory
surface, ensures that there is a strong diffusion gradient between the gill surface and the
environment.
 Without ventilation, a region of low O 2 and high CO2 concentrations can form around
the gill as it exchanges gas with the environment.
 Crayfish and lobsters have paddle-like appendages that drive a current of water over
their gills.
 Fish gills are ventilated by a current of water that enters the mouth, passes through slits
in the pharynx, flows over the gills, and exits the body.
 Because water is dense and contains little oxygen per unit volume, fishes must
expend considerable energy in ventilating their gills.
 Gas exchange at the gill surface is enhanced by the opposing flows of water and blood at
the gills.
 This flow pattern is countercurrent exchange.

Biology Chapter Notes

  As blood moves through a gill capillary, it becomes more and more loaded with
oxygen, but it simultaneously encounters water with even higher oxygen
concentrations because it is just beginning its passage over the gills.
 All along the gill capillary, there is a diffusion gradient favoring the transfer of oxygen
from water to blood.
 The countercurrent exchange mechanism is so efficient that the gills can remove more
than 80% of the oxygen from water to blood.
 Gills are generally unsuited for an animal living on land.
 An expansive surface of wet membrane exposed to air would lose too much water by
evaporation.
 In addition, the gills would collapse as their fine filaments, no longer supported by
water, cling together, reducing surface area for exchange.
 Most terrestrial animals have their respiratory surfaces within the body, opening to the
atmosphere through narrow tubes.
Tracheal systems and lungs are respiratory adaptations of terrestrial animals.
 As a respiratory medium, air has many advantages over water.
 Air has a much higher concentration of oxygen.
 Also, since O2 and CO2 diffuse much faster in air than in water, respiratory surfaces
exposed to air do not have to be ventilated as thoroughly as gills.
 When a terrestrial animal does ventilate, less energy is needed because air is far lighter
and much easier to pump than water and much less volume needs to be breathed to
obtain an equal amount of O2.
 Air does have problems as a respiratory medium.
 The respiratory surface, which must be large and moist, continuously loses water to the
air by evaporation.
 This problem is greatly reduced by a respiratory surface folded into the body.
 The tracheal system of insects is composed of air tubes that branch throughout the body.
 The largest tubes, called tracheae, open to the outside, and the finest branches extend
to the surface of nearly every cell where gas is exchanged by diffusion across the moist
epithelium that lines the terminal ends.
 The open circulatory system does not transport oxygen and carbon dioxide.
 For a small insect, diffusion through the trachea brings in enough O 2 and removes enough
CO2 to support cellular respiration.
 Larger insects with higher energy demands ventilate their tracheal systems with
rhythmic body movements that compress and expand the air tubes like bellows.
 An insect in flight has a very high metabolic rate, consuming 10 to 200 times more O 2
than it does at rest.
 Alternating contraction and relaxation of flight muscles compresses and expands the
body, rapidly pumping air through the tracheal system.
 The flight muscles are packed with mitochondria, and the tracheal tubes supply each
with ample oxygen.
 Unlike branching tracheal systems, lungs are restricted to one location.
 Because the respiratory surface of the lung is not in direct contact with all other parts
of the body, the circulatory system transports gases between the lungs and the rest of
the body.

Biology Chapter Notes

  Lungs have a dense net of capillaries just under the epithelium that forms the
respiratory surface.
 Lungs have evolved in spiders, terrestrial snails, and vertebrates.
 Among the vertebrates, amphibians have relatively small lungs that do not provide a large
surface, and many lack lungs altogether.
 They rely heavily on diffusion across other body surfaces, especially their moist skin,
for gas exchange.
 In contrast, most reptiles (including all birds) and all mammals rely entirely on lungs for
gas exchange.
 Turtles may supplement lung breathing with gas exchange across moist epithelial
surfaces in their mouth and anus.
 Lungs and air-breathing have evolved in a few fish species (lungfishes) as adaptations
to living in oxygen-poor water or to spending time exposed to air.
 In general, the size and complexity of lungs are correlated with an animal’s metabolic rate
(and hence rate of gas exchange).
 For example, the lungs of endotherms have a greater area of exchange surface than the
lungs of similar-sized ectotherms.
 Located in the thoracic (chest) cavity, the lungs of mammals have a spongy texture and
are honeycombed with a moist epithelium that functions as the respiratory surface.
 A system of branching ducts conveys air to the lungs.
 Air enters through the nostrils and is then filtered by hairs, warmed and humidified, and
sampled for odors as it flows through the nasal cavity.
 The nasal cavity leads to the pharynx, an intersection where the paths for air and food
cross.
 When food is swallowed, the larynx moves upward and tips the epiglottis over the
glottis.
 The rest of the time, the glottis is open, and air enters the upper part of the respiratory
tract.
 The wall of the larynx is reinforced by cartilage.
 In most mammals, the larynx is adapted as a voice box in which vibrations of a pair
of vocal cords produce sounds.
 These sounds are high-pitched when the vocal cords are stretched tight and vibrate
rapidly and low-pitched when the cords are less tense and vibrate slowly.
 From the larynx, air passes into the trachea, or windpipe, whose shape is maintained by
rings of cartilage.
 The trachea forks into two bronchi, one leading into each lung.
 Within the lung, each bronchus branches repeatedly into finer and finer tubes, called
bronchioles.
 The epithelium lining the major branches of the respiratory tree is covered by cilia and a
thin film of mucus.
 The mucus traps dust, pollen, and other particulate contaminants, and the beating cilia
move the mucus upward to the pharynx, where it is swallowed.
 At their tips, the tiniest bronchioles dead-end as a cluster of air sacs called alveoli.
 Gas exchange occurs across the thin epithelium of the lung’s millions of alveoli.
 These have a total surface area of about 100 m2 in humans, sufficient to carry out gas
exchange for the whole body.
Biology Chapter Notes
  Oxygen in the air entering the alveoli dissolves in the moist film and rapidly diffuses
across the epithelium into a web of capillaries that surrounds each alveolus.
 Carbon dioxide diffuses in the opposite direction.

Concept 42.6 Breathing ventilates the lungs

 The process of breathing, the alternate inhalation and exhalation of air, ventilates lungs.
 A frog ventilates its lungs by positive pressure breathing.
 During a breathing cycle, muscles lower the floor of the oral cavity, enlarging it and
drawing in air through the nostrils.
 With the nostrils and mouth closed, the floor of the oral cavity rises and air is forced
down the trachea.
 Elastic recoil of the lungs, together with compression of the muscular body wall, forces
air back out of the lungs during exhalation.
 In contrast, mammals ventilate their lungs by negative pressure breathing.
 This works like a suction pump, pulling air instead of pushing it into the lungs.
 Muscle action changes the volume of the rib cage and the chest cavity, and the lungs
follow suit.
 The lungs are enclosed by a double-walled sac, with the inner layer of the sac adhering to
the outside of the lungs and the outer layer adhering to the wall of the chest cavity.
 A thin space filled with fluid separates the two layers.
 Because of surface tension, the two layers behave like two plates of glass stuck
together by the adhesion and cohesion of a film of water.
 The layers can slide smoothly past each other, but they cannot be pulled apart easily.
 Surface tension couples movements of the lungs to movements of the rib cage.
 Lung volume increases as a result of the contraction of the rib muscles and diaphragm, a
sheet of skeletal muscle that forms the bottom wall of the chest cavity.
 Contraction of the rib muscles expands the rib cage by pulling the ribs upward and the
breastbone outward.
 At the same time, the diaphragm contracts and descends like a piston.
 These changes increase the lung volume, and as a result, air pressure within the alveoli
becomes lower than atmospheric pressure.
 Because air flows from higher pressure to lower pressure, air rushes into the
respiratory system.
 During exhalation, the rib muscles and diaphragm relax.
 This reduces lung volume and increases air pressure within the alveoli.
 This forces air up the breathing tubes and out through the nostrils.
 Actions of the rib muscles and diaphragm account for changes in lung volume during
shallow breathing, when a mammal is at rest.
 During vigorous exercise, other muscles of the neck, back, and chest further increase
ventilation volume by raising the rib cage even more.
 In some species, rhythmic movements during running cause visceral organs, including the
stomach and liver, to slide forward and backward in the body cavity with each stride.
 This “visceral pump” further increases ventilation volume by adding to the piston-like
action of the diaphragm.

Biology Chapter Notes

 The volume of air an animal inhales and exhales with each breath is called tidal volume.
 It averages about 500 mL in resting humans.
 The maximum tidal volume during forced breathing is the vital capacity, which is about
3.4 L and 4.8 L for college-age females and males, respectively.
 The lungs hold more air than the vital capacity, but some air, the residual volume,
remains in the lungs because the alveoli do not completely collapse.
 Since the lungs do not completely empty and refill with each breath cycle, newly inhaled
air is mixed with oxygen-depleted residual air.
 Therefore, the maximum oxygen concentration in the alveoli is considerably less than
in the atmosphere.
 Although this limits the effectiveness of gas exchange, the carbon dioxide in residual
air is critical for regulating the pH of blood and breathing rate in mammals.
 Ventilation is much more complex in birds than in mammals.
 Besides lungs, birds have eight or nine air sacs that do not function directly in gas
exchange, but act as bellows that keep air flowing through the lungs.
 The entire system—lungs and air sacs—is ventilated when the bird breathes.
 Air flows through the interconnected system in a circuit that passes through the lungs
in one direction only, regardless of whether the bird is inhaling or exhaling.
 Instead of alveoli, which are dead ends, the sites of gas exchange in bird lungs are tiny
channels called parabronchi, through which air flows in one direction.
 This system completely exchanges the air in the lungs with every breath.
 Therefore, the maximum lung oxygen concentrations are higher in birds than in
mammals.
 Partly because of this efficiency advantage, birds perform much better than mammals
at high altitude.
 For example, while human mountaineers experience tremendous difficulty
obtaining oxygen when climbing Earth’s highest peaks, several species of birds
easily fly over the same mountains during migration at altitudes of 9,000 m or
more.
Control centers in the brain regulate the rate and depth of breathing.
 While we can voluntarily hold our breath or breathe faster and deeper, most of the time
autonomic mechanisms regulate our breathing.
 This ensures that the work of the respiratory system is coordinated with that of the
cardiovascular system, and with the body’s metabolic demands for gas exchange.
 Our breathing control centers are located in two brain regions, the medulla oblongata
and the pons.
 Aided by the control center in the pons, the medulla’s center sets basic breathing
rhythm, triggering contraction of the diaphragm and rib muscles.
 A negative-feedback mechanism via stretch receptors prevents our lungs from
overexpanding by inhibiting the breathing center in the medulla.
 The medulla’s control center monitors the CO2 level of the blood and regulates breathing
activity appropriately.
 Its main cues about CO2 concentration come from slight changes in the pH of the
blood and cerebrospinal fluid bathing the brain.
 Carbon dioxide reacts with water to form carbonic acid, which lowers the pH.

Biology Chapter Notes

 When the control center registers a slight drop in pH, it increases the depth and rate of
breathing, and the excess CO2 is eliminated in exhaled air.
 Oxygen concentrations in the blood usually have little effect of the breathing control
centers.
 However, when the O2 level is severely depressed—at high altitudes, for example—O2
sensors in the aorta and carotid arteries in the neck send alarm signals to the breathing
control centers, which respond by increasing breathing rate.
 Normally, a rise in CO2 concentration is a good indicator of a fall in O 2 concentrations
because these are linked by the same process, cellular respiration.
 However, deep, rapid breathing (hyperventilation) purges the blood of so much CO 2
that the breathing center temporarily ceases sending impulses to the rib muscles and
diaphragm.
 The breathing center responds to a variety of nervous and chemical signals and adjusts the
rate and depth of breathing to meet the changing demands of the body.
 However, breathing control is only effective if it is coordinated with control of the
circulatory system, so that there is a good match between lung ventilation and the
amount of blood flowing through alveolar capillaries.
 For example, during exercise, cardiac output is matched to the increased breathing rate,
which enhances O2 uptake and CO2 removal as blood flows through the lungs.

Concept 42.7 Respiratory pigments bind and transport gases

Gases diffuse down pressure gradients in the lungs and other organs.
 For a gas, whether present in air or dissolved in water, diffusion depends on differences in
a quantity called partial pressure, the contribution of a particular gas to the overall total.
 At sea level, the atmosphere exerts a total pressure of 760 mm Hg.
 Since the atmosphere is 21% oxygen (by volume), the partial pressure of oxygen is
0.21 × 760, or about 160 mm Hg.
 The partial pressure of CO2 is only 0.23 mm Hg.
 When water is exposed to air, the amount of a gas that dissolves in water is proportional
to its partial pressure in the air and its solubility in water.
 An equilibrium is eventually reached when gas molecules enter and leave the solution
at the same rate.
 At this point, the gas is said to have the same partial pressure in the solution as it does
in the air.
 Thus, in a glass of water exposed to air at sea-level air pressure, the partial pressure of
O2 is 160 mm Hg and the partial pressure of CO2 is 0.23 mm Hg.
 A gas will always diffuse from a region of higher partial pressure to a region of lower
partial pressure.
 Blood arriving at the lungs via the pulmonary arteries has a lower partial pressure of O 2
and a higher partial pressure of CO2 than the air in the alveoli.
 As blood enters the alveolar capillaries, CO2 diffuses from blood to the air within the
alveoli, and oxygen in the alveolar air dissolves in the fluid that coats the epithelium
and diffuses across the surface into the blood.
 By the time blood leaves the lungs in the pulmonary veins, its partial pressure of O 2
has been raised and its partial pressure of CO2 has been lowered.
 In the tissue capillaries, gradients of partial pressure favor the diffusion of oxygen out of
the blood and carbon dioxide into the blood.
Biology Chapter Notes
  Cellular respiration removes oxygen from and adds carbon dioxide to the interstitial
fluid by diffusion.
 After the blood unloads oxygen and loads carbon dioxide, it is returned to the heart and
pumped to the lungs again, where it exchanges gases with air in the alveoli.
 The low solubility of oxygen in water is a fundamental problem for animals that rely on
the circulatory systems for oxygen delivery.
 For example, a person exercising consumes almost 2 L of O 2 per minute, but at normal
body temperature and air pressure, only 4.5 mL of O2 can dissolve in a liter of blood in
the lungs.
 If 80% of the dissolved O2 were delivered to the tissues (an unrealistically high
percentage), the heart would need to pump 500 L of blood per minute—a ton every 2
minutes.
 In fact, most animals transport most of the O2 bound to special proteins called respiratory
pigments instead of dissolved in solution.
 Respiratory pigments, often contained within specialized cells, circulate with the
blood.
 The presence of respiratory pigments increases the amount of oxygen that can be
carried in the blood to about 200 mL of O2 per liter of blood.
 For our exercising individual, the cardiac output would need to be a manageable 12.5
L of blood per minute to meet the oxygen demands of the systemic system.
 A diversity of respiratory pigments has evolved in various animal taxa to support their
normal energy metabolism.
 One example, hemocyanin, found in the hemolymph of arthropods and many
molluscs, has copper as its oxygen-binding component, coloring the blood bluish.
 The respiratory pigment of almost all vertebrates is the protein hemoglobin, contained
within red blood cells.
 Hemoglobin consists of four subunits, each with a cofactor called a heme group that
has an iron atom at its center.
 Because iron actually binds the O2, each hemoglobin molecule can carry four
molecules of O2.
 Like all respiratory pigments, hemoglobin must bind oxygen reversibly, loading oxygen at
the lungs or gills and unloading it in other parts of the body.
 Loading and unloading depend on cooperation among the subunits of the hemoglobin
molecule.
 The binding of O2 to one subunit induces the remaining subunits to change their shape
slightly such that their affinity for oxygen increases.
 When one subunit releases O2, the other three quickly follow suit as a conformational
change lowers their affinity for oxygen.
 Cooperative oxygen binding and release is evident in the dissociation curve for
hemoglobin.
 Where the dissociation curve has a steep slope, even a slight change in PO2 causes
hemoglobin to load or unload a substantial amount of O 2.
 This steep part corresponds to the range of partial pressures found in body tissues.
 Because of the effect of subunit cooperativity, a slight drop in P O2 causes a relatively
large increase in the amount of oxygen the blood unloads.
 As in all proteins, hemoglobin’s conformation is sensitive to a variety of factors.

Biology Chapter Notes

 For example, a drop in pH lowers the affinity of hemoglobin for O 2, an effect called the
Bohr shift.
 Because CO2 reacts with water to form carbonic acid, an active tissue will lower the pH of
its surroundings and induce hemoglobin to release more oxygen.
 In addition to oxygen transport, hemoglobin also helps transport carbon dioxide and
assists in buffering blood pH.
 About 7% of the CO2 released by respiring cells is transported in solution.
 Another 23% binds to amino groups of hemoglobin.
 About 70% is transported as bicarbonate ions.
 Carbon dioxide from respiring cells diffuses into the blood plasma and then into red blood
cells.
 The CO2 first reacts with water, assisted by the enzyme carbonic anhydrase, to form
H2CO3, which then dissociates into a hydrogen ion H+ and a bicarbonate ion (HCO3−)
 Most of the H+ attaches to hemoglobin and other proteins, minimizing the change in
blood pH.
 The HCO3− diffuses into the plasma.
 As blood flows through the lungs, the process is rapidly reversed as diffusion of CO 2 out
of the blood shifts the chemical equilibrium in favor of the conversion of HCO3− to CO2.
Elite animal athletes have adaptations that allow them to meet extreme oxygen demands.
 The elite animal marathon runner may be the antelope-like pronghorn that has roamed the
grasslands of North America for 4 million years.
 Pronghorns can run as fast as 100 km/hr, a speed second only to the cheetah.
 Pronghorns can sustain high speeds over long distances, unlike the cheetah.
 Stan Lindstedt and colleagues at the University of Wyoming and University of Bern
explored how pronghorns sustain their combination of great speed and great endurance:
through enhancements that supply increased oxygen to muscles, or through greater
energetic efficiency?
 Pronghorns consume O2 at a rate three times the rate expected for an animal of their
size.
 The rate of O2 consumption per gram of tissue by a pronghorn is the same as a mouse.
 The research team compared various physiological characteristics of pronghorns with
similar-sized domestic goats, which are adapted to climbing rather than running.
 The maximum rate of O2 consumption by pronghorns is five times that of goats.
 Why? Pronghorns have a larger surface area for diffusion in the lungs, nearly five
times the cardiac output, much higher muscle mass, and a higher volume and density
of mitochondria than goats.
 In addition, pronghorns maintain higher muscle temperatures.
 The pronghorn’s extreme O2 consumption rate, which underlies their ability to run at high
speeds over long distances, results from enhancements of the normal physiological
mechanisms present in other animals.
 These enhancements are the result of natural selection, perhaps exerted by the
predators that chased pronghorns on the open plains of North America for millions of
years.
 When an air-breathing animal swims underwater, it lacks access to its normal respiratory
medium.
Biology Chapter Notes
  Most humans can hold their breath for only 2 to 3 minutes and swim to depths of 20 m
or so.
 However, a variety of seals, sea turtles, and whales can stay submerged for much
longer times and reach much greater depths.
 The Weddell seal of Antarctica can plunge to depths of 200–500 m and remain there from
20 minutes to more than an hour.
 Elephant seals can dive to 1,500 m and stay submerged for up to 2 hours.
 One adaptation of these deep-divers, such as the Weddell seal, is an ability to store large
amounts of O2 in the tissues.
 Compared to a human, a seal can store about twice as much O 2 per kilogram of body
weight, mostly in the blood and muscles.
 About 36% of our total O2 is in our lungs, and 51% is in our blood.
 In contrast, the Weddell seal holds only about 5% of its O 2 in its small lungs and
stockpiles 70% in the blood.
 Several adaptations create these physiological differences between the seal and other
deep-divers in comparison to humans.
 First, the seal has about twice the volume of blood per kilogram of body weight as a
human.
 Second, the seal can store a large quantity of oxygenated blood in its huge spleen,
releasing this blood after the dive begins.
 The spleen can store about 24 L of blood.
 Third, diving mammals have a high concentration of an oxygen-storing protein called
myoglobin in their muscles.
 This enables a Weddell seal to store about 25% of its O 2 in muscle, compared to
only 13% in humans.
 Diving vertebrates not only start a dive with a relatively large O2 stockpile, but they also
have adaptations that conserve O2.
 They swim with little muscular effort and often use buoyancy changes to glide
passively upward or downward.
 Their heart rate and O2 consumption rate decrease during the dive, and most blood is
routed to the brain, spinal cord, eyes, adrenal glands, and placenta (in pregnant seals).
 Blood supply is restricted or even shut off to the muscles, and the muscles can
continue to derive ATP from fermentation after their internal O2 stores are depleted.
 During dives of more than 20 minutes, a Weddell seal’s muscles deplete the O 2 stored
in myoglobin and then derive ATP from fermentation instead of respiration.

Biology Chapter Notes

 Chapter 43 The Immune System
Chapter Notes

Overview: Reconnaissance, Recognition, and Response

 An animal must defend itself against unwelcome intruders—the many potentially

dangerous viruses, bacteria, and other pathogens it encounters in the air, in food, and in
water.
 It must also deal with abnormal body cells, which, in some cases, may develop into
cancer.
 Two major kinds of defense have evolved to counter these threats.
 The first kind of defense is innate immunity.
 Innate defenses are largely nonspecific, responding to a broad range of microbes.
 Innate immunity consists of external barriers formed by the skin and mucous
membranes, plus a set of internal cellular and chemical defenses that defend against
microbes that breach the external barriers.
 The internal defenses include macrophages and other phagocytic cells that ingest and
destroy pathogens.
 A second kind of defense is acquired immunity.
 Acquired immunity develops only after exposure to microbes, abnormal body cells, or
other foreign substances.
 Acquired defenses are highly specific and can distinguish one inducing agent from
another.
 This recognition is achieved by white blood cells called lymphocytes, which produce
two general types of immune responses.
 In the humoral response, cells derived from B-lymphocytes secrete defensive
proteins called antibodies that bind to microbes and target them for elimination.
 In the cell-mediated response, cytotoxic lymphocytes directly destroy infected body
cells, cancer cells, or foreign tissue.

Concept 43.1 Innate immunity provides broad defenses against infection

 An invading microbe must penetrate the external barrier formed by the skin and mucous
membranes, which cover the surface and line the openings of an animal’s body.
 If it succeeds, the pathogen encounters the second line of nonspecific defense, innate
cellular and chemical mechanisms that defend against the attacking foreign cell.
The skin and mucous membrane provide first-line barriers to infection.
 Intact skin is a barrier that cannot normally be penetrated by bacteria or viruses, although
even minute abrasions may allow their passage.
 Likewise, the mucous membranes that line the digestive, respiratory, and genitourinary
tracts bar the entry of potentially harmful microbes.
 Cells of these mucous membranes produce mucus, a viscous fluid that traps microbes
and other particles.
Biology Chapter Notes
  In the trachea, ciliated epithelial cells sweep out mucus with its trapped microbes,
preventing them from entering the lungs.
 Beyond their role as a physical barrier, the skin and mucous membranes counter
pathogens with chemical defenses.
 In humans, for example, secretions from sebaceous and sweat glands give the skin a
pH ranging from 3 to 5, which is acidic enough to prevent colonization by many
microbes.
 Microbial colonization is also inhibited by the washing action of saliva, tears, and
mucous secretions that continually bathe the exposed epithelium.
 All these secretions contain antimicrobial proteins.
 One of these, the enzyme lysozyme, digests the cell walls of many bacteria,
destroying them.
 Microbes present in food or water, or those in swallowed mucus, must contend with the
highly acidic environment of the stomach.
 The acid destroys many microbes before they can enter the intestinal tract.
 One exception, the virus hepatitis A, can survive gastric acidity and gain access to the
body via the digestive tract.
Phagocytic cells and antimicrobial proteins function early in infection.
 Microbes that penetrate the first line of defense face the second line of defense, which
depends mainly on phagocytosis, the ingestion of invading organisms by certain types of
white cells.
 Phagocyte function is intimately associated with an effective inflammatory response and
also with certain antimicrobial proteins.
 Phagocytes attach to their prey via surface receptors found on microbes but not normal
body cells.
 After attaching to the microbe, a phagocyte engulfs it, forming a vacuole that fuses with a
lysosome.
 Microbes are destroyed within lysosomes in two ways.
 Lysosomes contain nitric oxide and other toxic forms of oxygen, which act as
potent antimicrobial agents.
 Lysozymes and other enzymes degrade mitochondrial components.
 Some microbes have adaptations that allow them to evade destruction by phagocytes.
 The outer capsule of some bacterial cells hides their surface polysaccharides and
prevents phagocytes from attaching to them.
 Other bacteria are engulfed by phagocytes but resist digestion, growing and
reproducing within the cells.
 Four types of white blood cells are phagocytic.
 The phagocytic cells called neutrophils constitute about 60–70% of all white blood cells
(leukocytes).
 Cells damaged by invading microbes release chemical signals that attract neutrophils
from the blood.
 The neutrophils enter the infected tissue, engulfing and destroying microbes there.
 Neutrophils tend to self-destruct as they destroy foreign invaders, and their average life
span is only a few days.
 Monocytes, about 5% of leukocytes, provide an even more effective phagocytic defense.
Biology Chapter Notes
  After a few hours in the blood, they migrate into tissues and develop into
macrophages, which are large, long-lived phagocytes.
 Some macrophages migrate throughout the body, while others reside permanently in
certain tissues, including the lungs, liver, kidneys, connective tissues, brain, and
especially in lymph nodes and the spleen.
 The fixed macrophages in the spleen, lymph nodes, and other lymphatic tissues are
particularly well located to contact infectious agents.
 Microbes that enter the blood become trapped in the spleen, while microbes in
interstitial fluid flow into lymph and are trapped in lymph nodes.
 In either location, microbes soon encounter resident macrophages.
 Eosinophils, about 1.5% of all leukocytes, contribute to defense against large parasitic
invaders, such as the blood fluke, Schistosoma mansoni.
 Eosinophils position themselves against the external wall of a parasite and discharge
destructive enzymes from cytoplasmic granules.
 Dendritic cells can ingest microbes like macrophages. However, their primary role is to
stimulate the development of acquired immunity.
 A variety of proteins function in innate defense either by attacking microbes directly or by
impeding their reproduction.
 In addition to lysozyme, other antimicrobial agents include about 30 serum proteins,
known collectively as the complement system.
 Substances on the surface of many microbes can trigger a cascade of steps that
activate the complement system, leading to lysis of microbes.
 Another set of proteins that provide innate defenses are the interferons, which defend
against viral infection.
 These proteins are secreted by virus-infected body cells and induce uninfected
neighboring cells to produce substances that inhibit viral reproduction.
 Interferon limits cell-to-cell spread of viruses, helping to control viral infection.
 Because they are nonspecific, interferons produced in response to one virus may confer
short-term resistance to unrelated viruses.
 One type of interferon activates phagocytes.
 Interferons can be produced by recombinant DNA technology and are being tested for
the treatment of viral infections and cancer.
 Damage to tissue by a physical injury or the entry of microbes leads to the release of
chemical signals that trigger a localized inflammatory response.
 One of the chemical signals of the inflammatory response is histamine, which is stored in
mast cells in connective tissues.
 When injured, mast cells release their histamine.
 Histamine triggers both dilation and increased permeability of nearby capillaries.
 Leukocytes and damaged tissue cells also discharge prostaglandins and other
substances that promote blood flow to the site of injury.
 Increased local blood supply leads to the characteristic swelling, redness, and heat of
inflammation.
 Blood-engorged leak fluid into neighboring tissue, causing swelling.
 Enhanced blood flow and vessel permeability have several effects.
 First, they aid in delivering clotting elements to the injured area.

Biology Chapter Notes

  Clotting marks the beginning of the repair process and helps block the spread of
microbes elsewhere.
 Second, increased blood flow and vessel permeability increase the migration of
phagocytic cells from the blood into the injured tissues.
 Phagocyte migration usually begins within an hour after injury.
 Chemokines secreted by many cells, including blood vessel endothelial cells and
monocytes, attract phagocytes to the area.
 The body may also mount a systemic response to severe tissue damage or infection.
 Injured cells secrete chemicals that stimulate the release of additional neutrophils from
the bone marrow.
 In a severe infection, the number of white blood cells may increase significantly within
hours of the initial inflammation.
 Another systemic response to infection is fever, which may occur when substances
released by activated macrophages set the body’s thermostat at a higher temperature.
 Moderate fever may facilitate phagocytosis and hasten tissue repair.
 Certain bacterial infections can induce an overwhelming systemic inflammatory response
leading to a condition known as septic shock.
 Characterized by high fever and low blood pressure, septic shock is the most common
cause of death in U.S. critical care units.
 Clearly, while local inflammation is an essential step toward healing, widespread
inflammation can be devastating.
 Natural killer (NK) cells do not attack microorganisms directly but destroy virus-
infected body cells.
 They also attack abnormal body cells that could become cancerous.
 NK cells attach to a target cell and release chemicals that bring about apoptosis, or
programmed cell death.
 To summarize the nonspecific defense systems, the first line of defense, the skin and
mucous membranes, prevents most microbes from entering the body.
 The second line of defense uses phagocytes, natural killer cells, inflammation, and
antimicrobial proteins to defend against microbes that have managed to enter the body.
 These two lines of defense are nonspecific in that they do not distinguish among
pathogens.
Invertebrates also have highly effective innate defenses.
 Insect hemolymph contains circulating cells called hemocytes.
 Some hemocytes can phagocytose microbes, while others can form a cellular capsule
around large parasites.
 Other hemocytes secrete antimicrobial peptides that bind to and destroy pathogens.
 Current evidence suggests that invertebrates lack cells analogous to lymphocytes, the
white blood cells responsible for acquired, specific immunity in vertebrates.
 Certain invertebrate defenses do exhibit some features characteristic of acquired
immunity.
 Sponge cells can distinguish self from nonself cells.
 Phagocytic cells of earthworms show immunological memory, responding more
quickly to a particular foreign tissue the second time it is encountered.

Biology Chapter Notes

Concept 43.2 In acquired immunity, lymphocytes provide specific defenses against
infection
 While microorganisms are under assault by phagocytic cells, the inflammatory response,
and antimicrobial proteins, they inevitably encounter lymphocytes, the key cells of
acquired immunity, the body’s second major kind of defense.
 As macrophages and dendritic cells phagocytose microbes, they secrete certain cytokines
that help activate lymphocytes and other cells of the immune system.
 Thus the innate and acquired defenses interact and cooperate with each other.
 Any foreign molecule that is recognized by and elicits a response from lymphocytes is
called an antigen.
 Most antigens are large molecules such as proteins or polysaccharides.
 Most are cell-associated molecules that protrude from the surface of pathogens or
transplanted cells.
 A lymphocyte actually recognizes and binds to a small portion of an antigen called an
epitope.
Lymphocytes provide the specificity and diversity of the immune system.
 The vertebrate body is populated by two main types of lymphocytes: B lymphocytes (B
cells) and T lymphocytes (T cells).
 Both types of lymphocytes circulate throughout the blood and lymph and are
concentrated in the spleen, lymph nodes, and other lymphatic tissue.
 B and T cells recognize antigens by means of antigen-specific receptors embedded in their
plasma membranes.
 A single B or T cell bears about 100,000 identical antigen receptors.
 Because lymphocytes recognize and respond to particular microbes and foreign
molecules, they are said to display specificity for a particular epitope on an antigen.
 Each B cell receptor for an antigen is a Y-shaped molecule consisting of four polypeptide
chains: two identical heavy chains and two identical light chains linked by disulfide
bridges.
 A region in the tail portion of the molecule, the transmembrane region, anchors the
receptor in the cell’s plasma membrane.
 A short region at the end of the tail extends into the cytoplasm.
 At the two tips of the Y-shaped molecules are the light- and heavy-chain variable (V)
regions whose amino acid sequences vary from one B cell to another.
 The remainder of the molecule is made up of the constant (C) regions, which do not vary
from cell to cell.
 Each B cell receptor has two identical antigen-binding sites formed from part of a heavy-
chain V region and part of a light-chain V region.
 The interaction between an antigen-binding site and its corresponding antigen is stabilized
by multiple noncovalent bonds.
 Secreted antibodies, or immunoglobulins, are structurally similar to B cell receptors but
lack the transmembrane regions that anchor receptors in the cell membrane.
 B cell receptors are often called membrane antibodies or membrane immunoglobulins.

Biology Chapter Notes

 Each T cell receptor for an antigen consists of two different polypeptide chains: an alpha
chain and a beta chain, linked by a disulfide bridge.
 Near the base of the molecule is a transmembrane region that anchors the molecule in the
cell’s plasma membrane.
 At the outer tip of the molecule, the alpha and beta chain variable (V) regions form a
single antigen-binding site.
 The remainder of the molecule is made up of the constant (C) regions.
 T cell receptors recognize and bind with antigens with the same specificity as B cell
receptors.
 However, while the receptors on B cells recognize intact antigens, the receptors on T cells
recognize small fragments of antigens that are bound to normal cell-surface proteins
called MHC molecules.
 MHC molecules are encoded by a family of genes called the major histocompatibility
complex (MHC).
 As a newly synthesized MHC molecule is transported toward the plasma membrane, it
binds with a fragment of antigen within the cell and brings it to the cell surface, a process
called antigen presentation.
 There are two ways in which foreign antigens can end up inside cells of the body.
 Depending on their source, peptide antigens are handled by a different class of MHC
molecule and recognized by a particular subgroup of T cells.
 Class I MHC molecules, found on almost all nucleated cells of the body, bind
peptides derived from foreign antigens that have been synthesized within the cell.
 Any body cell that becomes infected or cancerous can display such peptide
antigens by virtue of its class I MHC molecules.
 Class I MHC molecules displaying bound peptide antigens are recognized by a
subgroup of T cells called cytotoxic T cells.
 Class II MHC molecules are made by dendritic cells, macrophages, and B cells.
 In these cells, class II MHC molecules bind peptides derived from foreign materials
that have been internalized and fragmented by phagocytosis.
 For each vertebrate species, there are numerous different alleles for each class I and class
II MHC gene, producing the most polymorphic proteins known.
 As a result of the large number of different alleles in the human population, most of us
are heterozygous for every one of our MHC genes.
 Moreover, it is unlikely that any two people, except identical twins, will have exactly
the same set of MHC molecules.
 The MHC provides a biochemical fingerprint virtually unique to each individual that
marks body cells as “self.”
Lymphocyte development gives rise to an immune system that distinguishes self from
nonself.
 Lymphocytes, like all blood cells, originate from pluripotent stem cells in the bone
marrow or liver of a developing fetus.
 Early lymphocytes are all alike, but they later develop into T cells or B cells, depending
on where they continue their maturation.
 Lymphocytes that migrate from the bone marrow to the thymus develop into T cells.

Biology Chapter Notes

 Lymphocytes that remain in the bone marrow and continue their maturation there
become B cells.
 There are three key events in the life of a lymphocyte.
 The first two events take place as a lymphocyte matures, before it has contact with any
antigen.
 The third event occurs when a mature lymphocyte encounters and binds a specific
antigen, leading to its activation, proliferation, and differentiation—a process called
clonal selection.
 The variable regions at the tip of each antigen receptor chain, which form the antigen-
binding site, account for the diversity of lymphocytes.
 The variability of these regions is enormous.
 Each person has as many as a million different B cells and 10 million different T cells,
each with a specific antigen-binding ability.
 At the core of lymphocyte diversity are the unique genes that encode the antigen receptor
chains.
 These genes consist of numerous coding gene segments that undergo random,
permanent rearrangement, forming functional genes that can be expressed as receptor
chains.
 Genes for the light chain of the B cell receptor and for the alpha and beta chains of the
T cell receptor undergo similar rearrangements, but we will consider only the gene
coding for the light chain of the B cell receptor.
 The immunoglobulin light-chain gene contains a series of 40 variable (V) gene
segments separated by a long stretch of DNA from 5 joining (J) gene segments.
 Beyond the J gene segments is an intron, followed by a single exon that codes for the
constant region of the light chain.
 In this state, the light-chain gene is not functional.
 However, early in B cell development, a set of enzymes called recombinase link one V
gene segment to one J gene segment, forming a single exon that is part V and part J.
 Recombinase acts randomly and can link any one of 40 V gene segments to any one
of 5 J gene segments.
 For the light-chain gene, there are 200 possible gene products (20 V × 5 J).
 Once V-J rearrangement has occurred, the gene is transcribed and translated into a
light chain with a variable and constant region. The light chains combine randomly
with the heavy chains that are similarly produced.
 The random rearrangements of antigen receptor genes may produce antigen receptors
that are specific for the body’s own molecules.
 As B and T cells mature, their antigen receptors are tested for potential self-reactivity.
 Lymphocytes bearing receptors specific for molecules present in the body are either
destroyed by apoptosis or rendered nonfunctional.
 Failure to do this can lead to autoimmune diseases such as multiple sclerosis.
Antigens interact with specific lymphocytes, inducing immune responses and
immunological memory.
 Although it encounters a large repertoire of B cells and T cells, a microorganism interacts
only with lymphocytes bearing receptors specific for its various antigenic molecules.
 A lymphocyte is “selected” when it encounters a microbe with epitopes matching its
receptors.

Biology Chapter Notes

  Selection activates the lymphocyte, stimulating it to divide and differentiate, and
eventually to produce two clones of cells.
 One clone consists of a large number of effector cells, short-lived cells that combat the
same antigen.
 The other clone consists of memory cells, long-lived cells bearing receptors for the
same antigen.
 This antigen-driven cloning of lymphocytes is called clonal selection and is fundamental
to acquired immunity.
 Each antigen, by binding selectively to specific receptors, activates a tiny fraction of
cells from the body’s diverse pool of lymphocytes.
 This relatively small number of selected cells gives rise to clones of thousands of cells,
all specific for and dedicated to eliminating that antigen.
 The selective proliferation and differentiation of lymphocytes that occur the first time the
body is exposed to an antigen is the primary immune response.
 About 10 to 17 days are required from the initial exposure for the maximum effector
cell response.
 During this period, selected B cells and T cells generate antibody-producing effector B
cells called plasma cells, and effector T cells, respectively.
 While this response is developing, a stricken individual may become ill, but symptoms
of the illness diminish and disappear as antibodies and effector T cells clear the antigen
from the body.
 A second exposure to the same antigen at some later time elicits the secondary immune
response.
 This response is faster (only 2 to 7 days), of greater magnitude, and more prolonged.
 In addition, the antibodies produced in the secondary response tend to have greater
affinity for the antigen than those secreted in the primary response.
 Measures of antibody concentrations in the blood serum over time show the difference
between primary and secondary immune responses.
 The immune system’s capacity to generate secondary immune responses is called
immunological memory, based not only on effector cells, but also on clones of long-
lived T and B memory cells.
 These memory cells proliferate and differentiate rapidly when they later contact the
same antigen.

Concept 43.3 Humoral and cell-mediated immunity defend against different types of
threats
 The immune system can mount two types of responses to antigens: a humoral response
and a cell-mediated response.
 Humoral immunity involves B cell activation and clonal selection and results in the
production of antibodies that circulate in the blood plasma and lymph.
 Circulating antibodies defend mainly against free bacteria, toxins, and viruses in the
body fluids.
 In cell-mediated immunity, activation and clonal selection of cytotoxic T
lymphocytes allows these cells to directly destroy certain target cells, including
“nonself” cancer and transplant cells.

Biology Chapter Notes

 The humoral and cell-mediated immune responses are linked by cell-signaling
interactions, especially via helper T cells.
Helper T lymphocytes function in both humoral and cell-mediated immunity.
 When a helper T cell recognizes a class II MHC molecule-antigen complex on an antigen-
presenting cell, the helper T cell proliferates and differentiates into a clone of activated
helper T cells and memory helper T cells.
 A surface protein called CD4 binds the side of the class II MHC molecule.
 This interaction helps keep the helper T cell and the antigen-presenting cell joined while
activation of the helper T cell proceeds.
 Activated helper T cells secrete several different cytokines that stimulate other
lymphocytes, thereby promoting cell-mediated and humoral responses.
 Dendritic cells are important in triggering a primary immune response.
 They capture antigens, migrate to the lymphoid tissues, and present antigens, via class
II MHC molecules, to helper T cells.
 Macrophages present antigens to memory helper T cells, while B cells primarily present
antigens to helper T cells in the course of the humoral response.
In the cell-mediated response, cytotoxic T cells counter intracellular pathogens.
 Antigen-activated cytotoxic T lymphocytes kill cancer cells and cells infected by viruses
and other intracellular pathogens.
 Fragments of nonself proteins synthesized in such target cells associate with class I MHC
molecules and are displayed on the cell surface, where they can be recognized by
cytotoxic T cells.
 This interaction is greatly enhanced by the T surface protein CD8 that helps keep the
cells together while the cytotoxic T cell is activated.
 When a cytotoxic T cell is activated by specific contacts with class I MHC-antigen
complexes on an infected cell, the activated cytotoxic T cell differentiates into an active
killer, which kills its target cell—the antigen-presenting cell—primarily by secreting
proteins that act on the bound cell.
 The death of the infected cell not only deprives the pathogen of a place to reproduce,
but also exposes it to circulating antibodies, which mark it for disposal.
 Once activated, cytotoxic T cells kill other cells infected with the same pathogen.
 In the same way, cytotoxic T cells defend against malignant tumors.
 Because tumor cells carry distinctive molecules not found on normal cells, they are
identified as foreign by the immune system.
 Class I MHC molecules on a tumor cell present fragments of tumor antigens to
cytotoxic T cells.
 Interestingly, certain cancers and viruses actively reduce the amount of class I MHC
protein on affected cells so that they escape detection by cytotoxic T cells.
 The body has a backup defense in the form of natural killer cells, part of the
nonspecific defenses, which lyse virus-infected and cancer cells.
In the humoral response, B cells make antibodies against extracellular pathogens.
 Antigens that elicit a humoral immune response are typically proteins and polysaccharides
present on the surface of bacteria or transplanted tissue.

Biology Chapter Notes

 The activation of B cells is aided by cytokines secreted by helper T cells activated by the
same antigen.
 These B cells proliferate and differentiate into a clone of antibody-secreting plasma
cells and a clone of memory B cells.
 When antigen first binds to receptors on the surface of a B cell, the cell takes in a few of
the foreign molecules by receptor-mediated endocytosis.
 The B cell then presents antigen fragments to a helper B cell.
 Many antigens (primarily proteins), called T-dependent antigens, can trigger a humoral
immune response by B cells only with the participation of helper T cells.
 Other antigens, such as polysaccharides and proteins with many identical polypeptides,
function as T-independent antigens.
 These include the polysaccharides of many bacterial capsules and the proteins of the
bacterial flagella.
 These antigens bind simultaneously to a number of membrane antibodies on the B cell
surface.
 This stimulates the B cell to generate antibody-secreting plasma cells without the help
of cytokines.
 While this response is an important defense against many bacteria, it generates a
weaker response than T-dependent antigens and generates no memory cells.
 Any given humoral response stimulates a variety of different B cells, with each giving rise
to a clone of thousands of plasma cells.
 Each plasma cell is estimated to secrete about 2,000 antibody molecules per second
over the cell’s 4- to 5-day life span.
 A secreted antibody has the same general Y-shaped structure as a B cell receptor, but
lacks a transmembrane region that would anchor it to a plasma membrane.
 Antigens that elicit a humoral immune response are typically the protein and
polysaccharide surface components of microbes, incompatible transplanted tissues, or
incompatible transfused cells.
 In addition, for some humans, the proteins of foreign substances such as pollen or bee
venom act as antigens that induce an allergic, or hypersensitive, humoral response.
 Antibodies constitute a group of globular serum proteins called immunoglobins (Igs).
 There are five major types of heavy-chain constant regions, determining the five major
classes of antibodies.
 Two classes exist primarily as polymers of the basic antibody molecule: IgM as a
pentamer and IgA as a dimmer.
 The other three classes—IgG, IgE, and IgD—exist exclusively as monomers,
 The power of antibody specificity and antigen-antibody binding has been applied in
laboratory research, clinical diagnosis, and disease treatment.
 Some antibody tools are polyclonal, the products of many different clones of B cells,
each specific for a different epitope.
 Others are monoclonal, prepared from a single clone of B cells grown in culture.
 These cells produce monoclonal antibodies, specific for the same epitope on an
antigen.
 These have been used to tag specific molecules.
 For example, toxin-linked antibodies search and destroy tumor cells.

Biology Chapter Notes

 The binding of antibodies to antigens is also the basis of several antigen disposal
mechanisms.
 In viral neutralization, antibodies bind to proteins on the surface of a virus, blocking
the virus’s ability to infect a host cell.
 In opsonization, the bound antibodies enhance macrophage attachment to and
phagocytosis of the microbes. Neither the B cell receptor for an antigen nor the
secreted antibody actually binds to an entire antigen molecule.
 Antibody-mediated agglutination of bacteria or viruses effectively neutralizes and
opsonizes the microbes.
 Agglutination is possible because each antibody molecule has at least two antigen-
binding sites.
 IgM can link together five or more viruses or bacteria.
 These large complexes are readily phagocytosed by macrophages.
 In precipitation, the cross-linking of soluble antigen molecules—molecules dissolved in
body fluids—forms immobile precipitates that are disposed of by phagocytosis.
 The complement system participates in the antibody-mediated disposal of microbes and
transplanted body cells.
 The pathway begins when IgM or IgG antibodies bind to a pathogen, such as a bacterium.
 The first complement component links two bound antibodies and is activated, initiating
the cascade.
 Ultimately, complement proteins generate a membrane attack complex (MAC),
which forms a pore in the bacterial membrane, resulting in cell lysis.
 Whether activated as part of innate or acquired defenses, the complement cascade
results in the lysis of microbes and produces activated complement proteins that
promote inflammation or stimulate phagocytosis.
Immunity can be achieved naturally or artificially.
 Immunity conferred by recovering from an infectious disease such as chicken pox is
called active immunity because it depends on the response of the infected person’s own
immune system.
 Active immunity can be acquired naturally or artificially, by immunization, also
known as vaccination.
 Vaccines include inactivated bacterial toxins, killed microbes, parts of microbes, viable
but weakened microbes, and even genes encoding microbial proteins.
 These agents can act as antigens, stimulating an immune response and, more
important, producing immunological memory.
 A vaccinated person who encounters the actual pathogen will have the same quick
secondary response based on memory cells as a person who has had the disease.
 Routine immunization of infants and children has dramatically reduced the incidence
of infectious diseases such as measles and whooping cough, and has led to the
eradication of smallpox, a viral disease.
 Unfortunately, not all infectious agents are easily managed by vaccination.
 For example, the emergence of new strains of pathogens with slightly altered
surface antigens complicates development of vaccines against some microbes, such
as the parasite that causes malaria.
 Antibodies can be transferred from one individual to another, providing passive
immunity.

Biology Chapter Notes

  This occurs naturally when IgG antibodies of a pregnant woman cross the placenta to
her fetus.
 In addition, IgA antibodies are passed from mother to nursing infant in breast milk.
 Passive immunity persists as long as these antibodies last, a few weeks to a few
months.
 This protects the infant from infections until the baby’s own immune system has
matured.
 Passive immunity can be transferred artificially by injecting antibodies from an animal
that is already immune to a disease into another animal.
 This confers short-term, but immediate, protection against that disease.
 For example, a person bitten by a rabid animal may be injected with antibodies against
rabies virus because rabies may progress rapidly, and the response to an active
immunization could take too long to save the life of the victim.
 Most people infected with rabies virus are given both passive immunizations (the
immediate defense) and active immunizations (a longer-term defense).

Concept 43.4 The immune system’s ability to distinguish self from nonself limits tissue
transplantation
 In addition to attacking pathogens, the immune system will also attack cells from other
individuals.
 For example, a skin graft from one person to a nonidentical individual will look
healthy for a day or two, but it will then be destroyed by immune responses.
 Interestingly, a pregnant woman does not reject the fetus as a foreign body.
Apparently, the structure of the placenta is the key to this acceptance.
 One source of potential problems with blood transfusions is an immune reaction from
individuals with incompatible blood types.
 In the ABO blood groups, an individual with type A blood has A antigens on the
surface of red blood cells.
 This is not recognized as an antigen by the “owner,” but it can be identified as
foreign if placed in the body of another individual.
 B antigens are found on type B red blood cells.
 Both A and B antigens are found on type AB red blood cells.
 Neither antigen is found on type O red blood cells.
 A person with type A blood already has antibodies to the B antigen, even if the person has
never been exposed to type B blood.
 These antibodies arise in response to bacteria (normal flora) that have epitopes very
similar to blood group antigens.
 Thus, an individual with type A blood does not make antibodies to A-like bacterial
epitopes—these are considered self—but that person does make antibodies to B-like
bacterial epitopes.
 If a person with type A blood receives a transfusion of type B blood, the preexisting
anti-B antibodies will induce an immediate and devastating transfusion reaction.
 Because blood group antigens are polysaccharides, they induce T-independent responses,
which elicit no memory cells.
 Each response is like a primary response, and it generates IgM anti-blood-group
antibodies, not IgG.
Biology Chapter Notes
  This is fortunate, because IgM antibodies do not cross the placenta, where they may
harm a developing fetus with a blood type different from its mother’s.
 However, another blood group antigen, the Rh factor, can cause mother-fetus problems
because antibodies produced for it are IgG.
 This situation arises when a mother that is Rh-negative (lacks the Rh factor) has a fetus
that is Rh-positive, having inherited the factor from the father.
 If small amounts of fetal blood cross the placenta late in pregnancy or during delivery,
the mother mounts a humoral response against the Rh factor.
 The danger occurs in subsequent Rh-positive pregnancies, when the mother’s Rh-
specific memory B cells produce IgG antibodies that can cross the placenta and destroy
the red blood cells of the fetus.
 To prevent this, the mother is injected with anti-Rh antibodies after delivering her first
Rh-positive baby.
 She is, in effect, passively immunized (artificially) to eliminate the Rh antigen before
her own immune system responds and generates immunological memory against the
Rh factor, endangering her future Rh-positive babies.
 Major histocompatibility complex (MHC) molecules are responsible for stimulating
rejection of tissue grafts and organ transplants.
 Because MHC creates a unique protein fingerprint for each individual, foreign MHC
molecules are antigenic, inducing immune responses against the donated tissue or
organ.
 To minimize rejection, attempts are made to match MHC of tissue donor and recipient
as closely as possible.
 In the absence of identical twins, siblings usually provide the closest tissue-type
match.
 In addition to MHC matching, various medicines are used to suppress the immune
response to the transplant.
 However, this strategy leaves the recipient more susceptible to infection and cancer
during the course of treatment.
 More selective drugs, which suppress helper T cell activation without crippling
nonspecific defense or T-independent humoral responses, have greatly improved the
success of organ transplants.
 In bone marrow transplants, it is the graft itself, rather than the recipient, which is the
source of potential immune rejection.
 Bone marrow transplants are used to treat leukemia and other cancers as well as
various hematological diseases.
 Prior to the transplant, the recipient is typically treated with irradiation to eliminate the
recipient’s immune system, eliminating all abnormal cells and leaving little chance of
graft rejection.
 However, the donated marrow, containing lymphocytes, may react against the
recipient, producing graft versus host reaction, unless well matched.

Concept 43.5 Exaggerated, self-directed, or diminished immune responses can cause

disease
 Malfunctions of the immune system can produce effects ranging from the minor
inconvenience of some allergies to the serious and often fatal consequences of certain
autoimmune and immunodeficiency diseases.
Biology Chapter Notes
 Allergies are hypersensitive (exaggerated) responses to certain environmental antigens,
called allergens.
 One hypothesis to explain the origin of allergies is that they are evolutionary remnants
of the immune system’s response to parasitic worms.
 The humoral mechanism that combats worms is similar to the allergic response that
causes such disorders as hay fever and allergic asthma.
 The most common allergies involve antibodies of the IgE class.
 Hay fever, for example, occurs when plasma cells secrete IgE specific for pollen
allergens.
 Some IgE antibodies attach by their tails to mast cells present in connective tissue,
without binding to the pollen.
 Later, when pollen grains enter the body, they attach to the antigen-binding sites of
mast cell-associated IgE, cross-linking adjacent antibody molecules.
 This event triggers the mast cell to degranulate—that is, to release histamines and other
inflammatory agents from vesicles called granules.
 High levels of histamines cause dilation and increased permeability of small blood
vessels.
 These inflammatory events lead to typical allergy symptoms: sneezing, runny nose,
tearing eyes, and smooth muscle contractions that can result in breathing difficulty.
 Antihistamines diminish allergy symptoms by blocking receptors for histamine.
 Sometimes, an acute allergic response can result in anaphylactic shock, a life-threatening
reaction to injected or ingested allergens.
 Anaphylactic shock results when widespread mast cell degranulation triggers abrupt
dilation of peripheral blood vessels, causing a precipitous drop in blood pressure.
 Death may occur within minutes.
 Triggers of anaphylactic shock in susceptible individuals include bee venom,
penicillin, or foods such as peanuts or fish.
 Some hypersensitive individuals carry syringes with epinephrine, which counteracts
this allergic response.
 Sometimes the immune system loses tolerance for self and turns against certain molecules
of the body, causing one of many autoimmune diseases.
 In systemic lupus erythematosus (lupus), the immune system generates antibodies
against various self-molecules, including histones and DNA released by the normal
breakdown of body cells.
 Lupus is characterized by skin rashes, fever, arthritis, and kidney dysfunction.
 Rheumatoid arthritis leads to damage and painful inflammation of the cartilage and
bone of joints.
 In insulin-dependent diabetes mellitus, the insulin-producing beta cells of the pancreas
are the targets of autoimmune cytotoxic T cells.
 Multiple sclerosis (MS) is the most common chronic neurological disease in developed
countries.
 In MS, T cells reactive against myelin infiltrate the central nervous system and destroy
the myelin sheath that surrounds some neurons.
 People with MS experience a number of serious neurological abnormalities.
 The mechanisms that lead to autoimmunity are not fully understood.
 It was thought that people with autoimmune diseases had self-reactive lymphocytes
that escaped elimination during their development.
Biology Chapter Notes
  We now know that healthy people also have lymphocytes with the capacity to react
against self, but these cells are inhibited from inducing an autoimmune reaction by
several regulatory mechanisms.
 Autoimmune disease likely arises from some failure in immune regulation, perhaps
linked with particular MHC alleles.
 In immunodeficiency diseases, the function of either the humoral or cell-mediated
immune defense is compromised.
 An immunodeficiency disease caused by a genetic or developmental defect in the immune
system is called an inborn or primary immunodeficiency.
 An immunodeficiency defect in the immune system that develops later in life, following
exposure to a chemical or biological agent, is called an acquired or secondary
immunodeficiency.
 In severe combined immunodeficiency (SCID), both branches of the immune system fail to
function.
 For individuals with this disease, long-term survival requires a bone marrow transplant
that will continue to supply functional lymphocytes.
 Several gene therapy approaches are in clinical trials to attempt to reverse SCID.
 Recent successes include a child with SCID who received gene therapy in 2002 when
she was 2 years old. In 2004, her T cells and B cells were still functioning normally.
 Immunodeficiency may also develop later in life.
 For example, certain cancers suppress the immune system. An example is Hodgkin’s
disease, which damages the lymphatic system.
 AIDS is another acquired immune deficiency.
 Healthy immune system function appears to depend on both the endocrine system and the
nervous system.
 For example, hormones secreted by the adrenal glands during stress affect the number
of white blood cells and may suppress the immune system in other ways.
 Similarly, some neurotransmitters secreted when we are relaxed and happy may
enhance immunity.
 Physiological evidence also points to an immune system–nervous system link based on
the presence of neurotransmitter receptors on the surfaces of lymphocytes and a
network of nerve fibers that penetrates deep into the thymus.
AIDS is an immunodeficiency disease caused by a virus.
 In 1981, increased rates of two rare diseases, Kaposi’s sarcoma, a cancer of the skin and
blood vessels, and pneumonia caused by the protozoan Pneumocystis carinii, were the
first signals to the medical community of a new threat to humans, later known as
acquired immunodeficiency syndrome, or AIDS.
 Both conditions were previously known to occur mainly in severely
immunosuppressed individuals.
 People with AIDS are susceptible to opportunistic diseases.
 Because AIDS arises from the loss of helper T cells, both humoral and cell-mediated
immune responses are impaired.
 In 1983, a retrovirus, now called human immunodeficiency virus (HIV), was identified
as the causative agent of AIDS.
 HIV gains entry into cells by making use of proteins that participate in normal immune
responses.
Biology Chapter Notes
  The main receptor for HIV on helper T cells is the cell’s CD4 molecule.
 In addition to CD4, HIV requires a second cell-surface protein, a coreceptor.
 Once inside the cell, the HIV RNA is reverse-transcribed, and the product DNA is
integrated into the host cell’s genome.
 In this form, the viral genome can direct the production of new viral particles.
 The death of helper T cells in HIV infection is due to the damaging effects of viral
reproduction, coupled with inappropriately timed apoptosis triggered by the virus.
 HIV infection cannot yet be cured, although certain drugs slow HIV reproduction and the
progression to AIDS.
 However, these drugs are very expensive and not available to all infected people,
especially in developing countries.
 In addition, the mutational changes that occur with each round of virus reproduction
can generate drug-resistant strains of HIV.
 Transmission of HIV requires the transfer of body fluids containing infected cells, such
as semen or blood, from person to person.
 In December 2003, the Joint UN Program on AIDS estimated that 40 million people
worldwide are living with HIV/AIDS. The best approach for slowing the spread of
HIV is to educate people about the practices that lead to transmission, such as using
dirty needles or having unprotected intercourse.

Biology Chapter Notes

 Chapter 44 Osmoregulation and Excretion
Chapter Notes

Overview: A Balancing Act

 The physiological systems of animals operate within a fluid environment.

 The relative concentrations of water and solutes must be maintained within narrow
limits, despite variations in the animal’s external environment.
 Metabolism also poses the problem of disposal of wastes.
 The breakdown of proteins and nucleic acids is problematic because ammonia, the
primary metabolic waste from breakdown of these molecules, is very toxic.
 An organism maintains a physiological favorable environment by osmoregulation,
regulating solute balance and the gain and loss of water and excretion, the removal of
nitrogen-containing waste products of metabolism.

Concept 44.1 Osmoregulation balances the uptake and loss of water and solutes
 All animals face the same central problem of osmoregulation.
 Over time, the rates of water uptake and loss must balance.
 Animal cells—which lack cell walls—swell and burst if there is a continuous net
uptake of water, or shrivel and die if there is a substantial net loss of water.
 Water enters and leaves cells by osmosis, the movement of water across a selectively
permeable membrane.
 Osmosis occurs whenever two solutions separated by a membrane differ in osmotic
pressure, or osmolarity (moles of solute per liter of solution).
 The unit of measurement of osmolarity is milliosmoles per liter (mosm/L).
 1 mosm/L is equivalent to a total solute concentration of 10−3 M.
 The osmolarity of human blood is about 300 mosm/L, while seawater has an
osmolarity of about 1,000 mosm/L.
 If two solutions separated by a selectively permeable membrane have the same
osmolarity, they are said to be isoosmotic.
 There is no net movement of water by osmosis between isoosmotic solutions, although
water molecules do cross at equal rates in both directions.
 When two solutions differ in osmolarity, the one with the greater concentration of
solutes is referred to as hyperosmotic, and the more dilute solution is hypoosmotic.
 Water flows by osmosis from a hypoosmotic solution to a hyperosmotic one.
Osmoregulators expend energy to control their internal osmolarity; osmoconformers are
isoosmotic with their surroundings.
 There are two basic solutions to the problem of balancing water gain with water loss.
 One—available only to marine animals—is to be isoosmotic to the surroundings as an
osmoconformer.
 Although they do not compensate for changes in external osmolarity,
osmoconformers often live in water that has a very stable composition and, hence,
they have a very constant internal osmolarity.
Biology Chapter Notes
 In contrast, an osmoregulator is an animal that must control its internal osmolarity
because its body fluids are not isoosmotic with the outside environment.
 An osmoregulator must discharge excess water if it lives in a hypoosmotic
environment or take in water to offset osmotic loss if it inhabits a hyperosmotic
environment.
 Osmoregulation enables animals to live in environments that are uninhabitable to
osmoconformers, such as freshwater and terrestrial habitats.
 It also enables many marine animals to maintain internal osmolarities different from
that of seawater.
 Whenever animals maintain an osmolarity difference between the body and the external
environment, osmoregulation has an energy cost.
 Because diffusion tends to equalize concentrations in a system, osmoregulators must
expend energy to maintain the osmotic gradients via active transport.
 The energy costs depend mainly on how different an animal’s osmolarity is from its
surroundings, how easily water and solutes can move across the animal’s surface, and
how much membrane-transport work is required to pump solutes.
 Osmoregulation accounts for nearly 5% of the resting metabolic rate of many marine
and freshwater bony fishes.
 Most animals, whether osmoconformers or osmoregulators, cannot tolerate substantial
changes in external osmolarity and are said to be stenohaline.
 In contrast, euryhaline animals—which include both some osmoregulators and
osmoconformers—can survive large fluctuations in external osmolarity.
 For example, various species of salmon migrate back and forth between freshwater and
marine environments.
 The food fish, tilapia, is an extreme example, capable of adjusting to any salt
concentration between freshwater and 2,000 mosm/L, twice that of seawater.
 Most marine invertebrates are osmoconformers.
 Their osmolarity is the same as seawater.
 However, they differ considerably from seawater in their concentrations of most
specific solutes.
 Thus, even an animal that conforms to the osmolarity of its surroundings does regulate
its internal composition.
 Marine vertebrates and some marine invertebrates are osmoregulators.
 For most of these animals, the ocean is a strongly dehydrating environment because it
is much saltier than internal fluids, and water is lost from their bodies by osmosis.
 Marine bony fishes, such as cod, are hypoosmotic to seawater and constantly lose
water by osmosis and gain salt by diffusion and from the food they eat.
 The fishes balance water loss by drinking seawater and actively transporting chloride
ions out through their skin and gills.
 Sodium ions follow passively.
 They produce very little urine.
 Marine sharks and most other cartilaginous fishes (chondrichthyans) use a different
osmoregulatory “strategy.”
 Like bony fishes, salts diffuse into the body from seawater, and these salts are removed
by the kidneys, a special organ called the rectal gland, or in feces.

Biology Chapter Notes

  Unlike bony fishes, marine sharks do not experience a continuous osmotic loss because
high concentrations of urea and trimethylamine oxide (TMAO) in body fluids leads to
an osmolarity slightly higher than seawater.
 TMAO protects proteins from damage by urea.
 Consequently, water slowly enters the shark’s body by osmosis and in food, and is
removed in urine.
 In contrast to marine organisms, freshwater animals are constantly gaining water by
osmosis and losing salts by diffusion.
 This happens because the osmolarity of their internal fluids is much higher than that of
their surroundings.
 However, the body fluids of most freshwater animals have lower solute concentrations
than those of marine animals, an adaptation to their low-salinity freshwater habitat.
 Many freshwater animals, including fish such as perch, maintain water balance by
excreting large amounts of very dilute urine, and regaining lost salts in food and by
active uptake of salts from their surroundings.
 Salmon and other euryhaline fishes that migrate between seawater and freshwater undergo
dramatic and rapid changes in osmoregulatory status.
 While in the ocean, salmon osmoregulate as other marine fishes do, by drinking
seawater and excreting excess salt from the gills.
 When they migrate to fresh water, salmon cease drinking, begin to produce lots of
dilute urine, and their gills start taking up salt from the dilute environment—the same
as fishes that spend their entire lives in fresh water.
 Dehydration dooms most animals, but some aquatic invertebrates living in temporary
ponds and films of water around soil particles can lose almost all their body water and
survive in a dormant state, called anhydrobiosis, when their habitats dry up.
 For example, tardigrades, or water bears, contain about 85% of their weight in water
when hydrated but can dehydrate to less than 2% water and survive in an inactive state
for a decade until revived by water.
 Anhydrobiotic animals must have adaptations that keep their cell membranes intact.
 While the mechanism that tardigrades use is still under investigation, researchers do
know that anhydrobiotic nematodes contain large amounts of sugars, especially the
disaccharide trehalose.
 Trehalose, a dimer of glucose, seems to protect cells by replacing water associated
with membranes and proteins.
 Many insects that survive freezing in the winter also use trehalose as a membrane
protectant.
 The threat of desiccation is perhaps the largest regulatory problem confronting terrestrial
plants and animals.
 Humans die if they lose about 12% of their body water.
 Camels can withstand twice that level of dehydration.
 Adaptations that reduce water loss are key to survival on land.
 Most terrestrial animals have body coverings that help prevent dehydration.
 These include waxy layers in insect exoskeletons, the shells of land snails, and the
multiple layers of dead, keratinized skin cells of most terrestrial vertebrates.
 Being nocturnal also reduces evaporative water loss.
 Despite these adaptations, most terrestrial animals lose considerable water from moist
surfaces in their gas exchange organs, in urine and feces, and across the skin.
Biology Chapter Notes
  Land animals balance their water budgets by drinking and eating moist foods and by
using metabolic water from aerobic respiration.
 Some animals are so well adapted for minimizing water loss that they can survive in
deserts without drinking.
 For example, kangaroo rats lose so little water that they can recover 90% of the loss
from metabolic water and gain the remaining 10% in their diet of seeds.
 These and many other desert animals do not drink.
Water balance and waste disposal depend on transport epithelia.
 The ultimate function of osmoregulation is to maintain the composition of cellular
cytoplasm, but most animals do this indirectly by managing the composition of an internal
body fluid that bathes the cells.
 In animals with an open circulatory system, this fluid is hemolymph.
 In vertebrates and other animals with a closed circulatory system, the cells are bathed
in an interstitial fluid that is controlled through the composition of the blood.
 The maintenance of fluid composition depends on specialized structures ranging from
cells that regulate solute movement to complex organs such as the vertebrate kidney.
 In most animals, osmotic regulation and metabolic waste disposal depend on the ability of
a layer or layers of transport epithelium to move specific solutes in controlled amounts
in specific directions.
 Some transport epithelia directly face the outside environment, while others line
channels connected to the outside by an opening on the body surface.
 The cells of the epithelium are joined by impermeable tight junctions that form a
barrier at the tissue-environment barrier.
 In most animals, transport epithelia are arranged into complex tubular networks with
extensive surface area.
 For example, the salt-secreting glands of some marine birds, such as the albatross,
secrete an excretory fluid that is much more salty than the ocean.
 The counter-current system in these glands removes salt from the blood, allowing these
organisms to drink seawater during their months at sea.
 The molecular structure of plasma membranes determines the kinds and directions of
solutes that move across the transport epithelium.
 For example, the salt-excreting glands of the albatross remove excess sodium chloride
from the blood.
 By contrast, transport epithelia in the gills of freshwater fishes actively pump salts
from the dilute water passing by the gill filaments into the blood.
 Transport epithelia in excretory organs often have the dual functions of maintaining
water balance and disposing of metabolic wastes.

Concept 44.2 An animal’s nitrogenous wastes reflect its phylogeny and habitat
 Because most metabolic wastes must be dissolved in water when they are removed from
the body, the type and quantity of waste products may have a large impact on water
balance.
 Nitrogenous breakdown products of proteins and nucleic acids are among the most
important wastes in terms of their effect on osmoregulation.
 During their breakdown, enzymes remove nitrogen in the form of ammonia, a small
and very toxic molecule.
Biology Chapter Notes
  Some animals excrete ammonia directly, but many species first convert the ammonia
to other compounds that are less toxic but costly to produce.
 Animals that excrete nitrogenous wastes as ammonia need access to lots of water.
 This is because ammonia is very soluble but can be tolerated only at very low
concentrations.
 Therefore, ammonia excretion is most common in aquatic species.
 Many invertebrates release ammonia across the whole body surface.
 In fishes, most of the ammonia is lost as ammonium ions (NH4+) at the gill epithelium.
 Freshwater fishes +are able to exchange NH4+ for Na+ from the environment, which
helps maintain Na concentrations in body fluids.
 Ammonia excretion is much less suitable for land animals.
 Because ammonia is so toxic, it can be transported and excreted only in large volumes
of very dilute solutions.
 Most terrestrial animals and many marine organisms (which tend to lose water to their
environment by osmosis) do not have access to sufficient water.
 Instead, mammals, most adult amphibians, sharks, and some marine bony fishes and
turtles excrete mainly urea.
 Urea is synthesized in the liver by combining ammonia with carbon dioxide and is
excreted by the kidneys.
 The main advantage of urea is its low toxicity, about 100,000 times less than that of
ammonia.
 Urea can be transported and stored safely at high concentrations.
 This reduces the amount of water needed for nitrogen excretion when releasing a
concentrated solution of urea rather than a dilute solution of ammonia.
 The main disadvantage of urea is that animals must expend energy to produce it from
ammonia.
 In weighing the relative advantages of urea versus ammonia as the form of nitrogenous
waste, it makes sense that many amphibians excrete mainly ammonia when they are
aquatic tadpoles.
 They switch largely to urea when they are land-dwelling adults.
 Land snails, insects, birds, and many reptiles excrete uric acid as the main nitrogenous
waste.
 Like urea, uric acid is relatively nontoxic.
 But unlike either ammonia or urea, uric acid is largely insoluble in water and can be
excreted as a semisolid paste with very little water loss.
 While saving even more water than urea, it is even more energetically expensive to
produce.
 Uric acid and urea represent different adaptations for excreting nitrogenous wastes with
minimal water loss.
 Mode of reproduction appears to have been important in choosing among these
alternatives.
 Soluble wastes can diffuse out of a shell-less amphibian egg (ammonia) or be carried
away by the mother’s blood in a mammalian embryo (urea).
 However, the shelled eggs of birds and reptiles are not permeable to liquids, which
means that soluble nitrogenous wastes trapped within the egg could accumulate to
dangerous levels.
Biology Chapter Notes
  Even urea is toxic at very high concentrations.
 Uric acid precipitates out of solution and can be stored within the egg as a harmless
solid left behind when the animal hatches.
 The type of nitrogenous waste also depends on habitat.
 For example, terrestrial turtles (which often live in dry areas) excrete mainly uric acid,
while aquatic turtles excrete both urea and ammonia.
 In some species, individuals can change their nitrogenous wastes when environmental
conditions change.
 For example, certain tortoises that usually produce urea shift to uric acid when
temperature increases and water becomes less available.
 Excretion of nitrogenous wastes is a good illustration of how response to the environment
occurs on two levels.
 Over generations, evolution determines the limits of physiological responses for a
species.
 During their lives, individual organisms make adjustments within these evolutionary
constraints.
 The amount of nitrogenous waste produced is coupled to the energy budget and depends
on how much and what kind of food an animal eats.
 Because they use energy at high rates, endotherms eat more food—and thus produce
more nitrogenous wastes—per unit volume than ectotherms.
 Carnivores (which derive much of their energy from dietary proteins) excrete more
nitrogen than animals that obtain most of their energy from lipids or carbohydrates.

Concept 44.3 Diverse excretory systems are variations on a tubular theme

 Although the problems of water balance on land or in salt water or fresh water are very
different, the solutions all depend on the regulation of solute movements between internal
fluids and the external environment.
 Much of this is handled by excretory systems, which are central to homeostasis
because they dispose of metabolic wastes and control body fluid composition by
adjusting the rates of loss of particular solutes.
Most excretory systems produce urine by refining a filtrate derived from body fluids.
 While excretory systems are diverse, nearly all produce urine in a process that involves
several steps.
 First, body fluid (blood, coelomic fluid, or hemolymph) is collected.
 The initial fluid collection usually involves filtration through selectively permeable
membranes consisting of a single layer of transport epithelium.
 Hydrostatic pressure forces water and small solutes into the excretory system.
 This fluid is called the filtrate.
 Filtration is largely nonselective.
 It is important to recover small molecules from the filtrate and return them to the
body fluids.
 Excretory systems use active transport to reabsorb valuable solutes in a process of
selective reabsorption.
 Nonessential solutes and wastes are left in the filtrate or added to it by selective
secretion, which also uses active transport.
Biology Chapter Notes
  The pumping of various solutes also adjusts the osmotic movement of water into or out
of the filtrate.
 The processed filtrate is excreted as urine.
 Flatworms have an excretory system called protonephridia, consisting of a branching
network of dead-end tubules.
 These are capped by a flame bulb with a tuft of cilia that draws water and solutes from
the interstitial fluid, through the flame bulb, and into the tubule system.
 The urine in the tubules exits through openings called nephridiopores.
 Excreted urine is very dilute in freshwater flatworms.
 Apparently, the tubules reabsorb most solutes before the urine exits the body.
 In these freshwater flatworms, the major function of the flame-bulb system is
osmoregulation, while most metabolic wastes diffuse across the body surface or are
excreted into the gastrovascular cavity.
 However, in some parasitic flatworms, protonephridia do dispose of nitrogenous
wastes.
 Protonephridia are also found in rotifers, some annelids, larval molluscs, and lancelets.
 Metanephridia, another tubular excretory system, consist of internal openings that collect
body fluids from the coelom through a ciliated funnel, the nephrostome, and release the
fluid to the outside through the nephridiopore.
 Each segment of an annelid worm has a pair of metanephridia.
 An earthworm’s metanephridia have both excretory and osmoregulatory functions.
 As urine moves along the tubule, the transport epithelium bordering the lumen
reabsorbs most solutes and returns them to the blood in the capillaries.
 Nitrogenous wastes remain in the tubule and are dumped outside.
 Because earthworms experience a net uptake of water from damp soil, their
metanephridia balance water influx by producing dilute urine.
 Insects and other terrestrial arthropods have organs called Malpighian tubules that
remove nitrogenous wastes and also function in osmoregulation.
 These open into the digestive system and dead-end at tips that are immersed in the
hemolymph.
 The transport epithelium lining the tubules secretes certain solutes, including nitrogenous
wastes, from the hemolymph into the lumen of the tubule.
 Water follows the solutes into the tubule by osmosis, and the fluid then passes back to
the rectum, where most of the solutes are pumped back into the hemolymph.
 Water again follows the solutes, and the nitrogenous wastes, primarily insoluble uric
acid, are eliminated along with the feces.
 This system is highly effective in conserving water and is one of several key
adaptations contributing to the tremendous success of insects on land.
 The kidneys of vertebrates usually function in both osmoregulation and excretion.
 Like the excretory organs of most animal phyla, kidneys are built of tubules.
 The osmoconforming hagfishes, which are not vertebrates but are among the most
primitive living chordates, have kidneys with segmentally arranged excretory tubules.
 This suggests that the excretory segments of vertebrate ancestors were segmented.
 However, the kidneys of most vertebrates are compact, nonsegmented organs
containing numerous tubules arranged in a highly organized manner.

Biology Chapter Notes

  The vertebrate excretory system includes a dense network of capillaries intimately
associated with the tubules, along with ducts and other structures that carry urine out of
the tubules and kidney and eventually out of the body.

Concept 44.4 Nephrons and associated blood vessels are the functional units of the
mammalian kidney
 Mammals have a pair of bean-shaped kidneys.
 Each kidney is supplied with blood by a renal artery and drained by a renal vein.
 In humans, the kidneys account for less than 1% of body weight, but they receive
about 20% of resting cardiac output.
 Urine exits each kidney through a duct called the ureter, and both ureters drain through a
common urinary bladder.
 During urination, urine is expelled from the urinary bladder through a tube called the
urethra, which empties to the outside near the vagina in females or through the penis
in males.
 Sphincter muscles near the junction of the urethra and the bladder control urination.
 The mammalian kidney has two distinct regions, an outer renal cortex and an inner renal
medulla.
 Both regions are packed with microscopic excretory tubules, nephrons, and their
associated blood vessels.
 Each nephron consists of a single long tubule and a ball of capillaries, called the
glomerulus.
 The blind end of the tubule forms a cup-shaped swelling, called Bowman’s capsule,
that surrounds the glomerulus.
 Each human kidney contains about a million nephrons, with a total tubule length of 80
km.
 Filtration occurs as blood pressure forces fluid from the blood in the glomerulus into the
lumen of Bowman’s capsule.
 The porous capillaries, along with specialized capsule cells called podocytes, are
permeable to water and small solutes but not to blood cells or large molecules such as
plasma proteins.
 The filtrate in Bowman’s capsule contains salt, glucose, amino acids, vitamins,
nitrogenous wastes such as urea, and other small molecules.
 From Bowman’s capsule, the filtrate passes through three regions of the nephron: the
proximal tubule; the loop of Henle, a hairpin turn with a descending limb and an
ascending limb; and the distal tubule.
 The distal tubule empties into a collecting duct, which receives processed filtrate from
many nephrons.
 The many collecting ducts empty into the renal pelvis, which is drained by the ureter.
 In the human kidney, about 80% of the nephrons, the cortical nephrons, have reduced
loops of Henle and are almost entirely confined to the renal cortex.
 The other 20%, the juxtamedullary nephrons, have well-developed loops that extend
deeply into the renal medulla.
 Only mammals and birds have juxtamedullary nephrons; the nephrons of other
vertebrates lack loops of Henle.

Biology Chapter Notes

  It is the juxtamedullary nephrons that enable mammals to produce urine that is
hyperosmotic to body fluids, conserving water.
 The nephron and the collecting duct are lined by a transport epithelium that processes the
filtrate to form the urine.
 Their most important task is to reabsorb solutes and water.
 The nephrons and collecting ducts reabsorb nearly all of the sugar, vitamins, and other
organic nutrients from the initial filtrate and about 99% of the water.
 This reduces 180 L of initial filtrate to about 1.5 L of urine to be voided.
 Each nephron is supplied with blood by an afferent arteriole, a branch of the renal artery
that subdivides into the capillaries of the glomerulus.
 The capillaries converge as they leave the glomerulus, forming an efferent arteriole.
 This vessel subdivides again into the peritubular capillaries, which surround the
proximal and distal tubules.
 Additional capillaries extend downward to form the vasa recta, a loop of capillaries
that serves the loop of Henle.
 The tubules and capillaries are immersed in interstitial fluid, through which substances
diffuse.
 Although the excretory tubules and their surrounding capillaries are closely associated,
they do not exchange materials directly.
 The tubules and capillaries are immersed in interstitial fluid, through which various
materials diffuse between the plasma in the capillaries and the filtrate within the
nephron tubule.
 Filtrate from Bowman’s capsule flows through the nephron and collecting ducts as it
becomes urine.
 Secretion and reabsorption in the proximal tubule substantially alter the volume and
composition of filtrate.
 For example, the cells of the transport epithelium help maintain a constant pH in body
fluids by controlled secretions of hydrogen ions or ammonia.
 The cells also synthesize and secrete ammonia, which neutralizes the acid.
 The proximal tubules reabsorb about 90% of the important buffer bicarbonate
(HCO3−).
 Drugs and other poisons that have been processed in the liver pass from the peritubular
capillaries into the interstitial fluid and then across the epithelium to the nephron’s
lumen.
 Valuable nutrients, including glucose, amino acids, and K +, are actively or passively
absorbed from filtrate.
 One of the most important functions of the proximal tubule is reabsorption of most of the
NaCl and water from the initial filtrate volume.
 Salt in the filtrate diffuses into the cells of the transport epithelium.
 The epithelial cells actively transport Na+ into the interstitial fluid.
 This transfer of positive charge is balanced by the passive transport of Cl − out of the
tubule.
 As salt moves from the filtrate to the interstitial fluid, water follows by osmosis.
 The exterior side of the epithelium has a much smaller surface area than the side facing
the lumen, which minimizes leakage of salt and water back into the tubule, and instead
they diffuse into the peritubular capillaries.

Biology Chapter Notes

 Reabsorption of water continues as the filtrate moves into the descending limb of the
loop of Henle.
 This transport epithelium is freely permeable to water but not very permeable to salt
and other small solutes.
 For water to move out of the tubule by osmosis, the interstitial fluid bathing the tubule
must be hyperosmotic to the filtrate.
 Because the osmolarity of the interstitial fluid becomes progressively greater from the
outer cortex to the inner medulla, the filtrate moving within the descending loop of
Henle continues to lose water.
 In contrast to the descending limb, the transport epithelium of the ascending limb of the
loop of Henle is permeable to salt, not water.
 As filtrate ascends the thin segment of the ascending limb, NaCl diffuses out of the
permeable tubule into the interstitial fluid, increasing the osmolarity of the medulla.
 The active transport of salt from the filtrate into the interstitial fluid continues in the
thick segment of the ascending limb.
 By losing salt without giving up water, the filtrate becomes progressively more dilute
as it moves up to the cortex in the ascending limb of the loop.
 The distal tubule plays a key role+ in regulating the K+ and NaCl concentrations in body
fluids by varying the amount of K that is secreted into the filtrate and the amount of NaCl
reabsorbed from the filtrate.
 Like the proximal tubule, the distal tubule also contributes to pH regulation by
controlled secretion of H+ and the reabsorption of bicarbonate (HCO3−).
 By actively reabsorbing NaCl, the transport epithelium of the collecting duct plays a
large role in determining how much salt is actually excreted in the urine.
 Though the degree of its permeability is under hormonal control, the epithelium is
permeable to water but not to salt or (in the renal cortex) to urea.
 As the collecting duct traverses the gradient of osmolarity in the kidney, the filtrate
becomes increasingly concentrated as it loses more and more water by osmosis to the
hyperosmotic interstitial fluid.
 In the inner medulla, the duct becomes permeable to urea.
 Because of the high urea concentration in the filtrate at this point, some urea
diffuses out of the duct and into the interstitial fluid.
 Along with NaCl, this urea contributes to the high osmolarity of the interstitial fluid
in the medulla.
 This high osmolarity enables the mammalian kidney to conserve water by excreting
urine that is hyperosmotic to general body fluids.

Concept 44.5 The mammalian kidney’s ability to conserve water is a key terrestrial
adaptation
 The osmolarity of human blood is about 300 mosm/L, but the kidney can excrete urine up
to four times as concentrated—about 1,200 mosm/L.
 At an extreme of water conservation, Australian hopping mice, which live in desert
regions, can produce urine concentrated to 9,300 mosm/L—25 times as concentrated
as their body fluid.
 In a mammalian kidney, the cooperative action and precise arrangement of the loops of
Henle and the collecting ducts are largely responsible for the osmotic gradients that
concentrate the urine.
Biology Chapter Notes
  In addition, the maintenance of osmotic differences and the production of
hyperosmotic urine are only possible because considerable energy is expended by the
active transport of solutes against concentration gradients.
 In essence, the nephrons can be thought of as tiny energy-consuming machines whose
function is to produce a region of high osmolarity in the kidney, which can then extract
water from the urine in the collecting duct.
 The two primary solutes in this osmolarity gradient are NaCl and urea.
 The juxtamedullary nephrons, which maintain an osmotic gradient in the kidney and use
that gradient to excrete a hyperosmotic urine, are the key to understanding the physiology
of the mammalian kidney as a water-conserving organ.
 Filtrate passing from Bowman’s capsule to the proximal tubule has an osmolarity of
about 300 mosm/L.
 As the filtrate flows through the proximal tubule in the renal cortex, large amounts of
water and salt are reabsorbed.
 The volume of the filtrate decreases substantially, but its osmolarity remains about the
same.
 The ability of the mammalian kidney to convert interstitial fluid at 300 mosm/L to 1,200
mosm/L as urine depends on a countercurrent multiplier between the ascending and
descending limbs of the loop of Henle.
 As the filtrate flows from the cortex to the medulla in the descending limb of the loop of
Henle, water leaves the tubule by osmosis.
 The osmolarity of the filtrate increases as solutes, including NaCl, become more
concentrated.
 The highest molarity occurs at the elbow of the loop of Henle.
 This maximizes the diffusion of salt out of the tubule as the filtrate rounds the curve
and enters the ascending limb, which is permeable to salt but not to water.
 The descending limb produces progressively saltier filtrate, and the ascending limb
exploits this concentration of NaCl to help maintain a high osmolarity in the interstitial
fluid of the renal medulla.
 The loop of Henle has several qualities of a countercurrent system.
 Although the two limbs of the loop are not in direct contact, they are close enough to
exchange substances through the interstitial fluid.
 The nephron can concentrate salt in the inner medulla largely because exchange
between opposing flows in the descending and ascending limbs overcomes the
tendency for diffusion to even out salt concentrations throughout the kidney’s
interstitial fluid.
 The vasa recta is also a countercurrent system, with descending and ascending vessels
carrying blood in opposite directions through the kidney’s osmolarity gradient.
 As the descending vessel conveys blood toward the inner medulla, water is lost from
the blood and NaCl diffuses into it.
 These fluxes are reversed as blood flows back toward the cortex in the ascending
vessel.
 Thus, the vasa recta can supply the kidney with nutrients and other important
substances without interfering with the osmolarity gradient necessary to excrete a
hyperosmotic urine.
 The countercurrent-like characteristics of the loop of Henle and the vasa recta maintain
the steep osmotic gradient between the medulla and the cortex.

Biology Chapter Notes

  This gradient is initially created by active transport of NaCl out of the thick segment of
the ascending limb of the loop of Henle into the interstitial fluid.
 This active transport and other active transport systems in the kidney consume
considerable ATP, requiring the kidney to have one of the highest relative metabolic
rates of any organ.
 By the time the filtrate reaches the distal tubule, it is actually hypoosmotic to body fluids
because of active transport of NaCl out of the thick segment of the ascending limb.
 As the filtrate descends again toward the medulla in the collecting duct, water is
extracted by osmosis into the hyperosmotic interstitial fluids, but salts cannot diffuse in
because the epithelium is impermeable to salt.
 This concentrates salt, urea, and other solutes in the filtrate.
 Some urea leaks out of the lower portion of the collecting duct, contributing to the high
interstitial osmolarity of the inner medulla.
 Before leaving the kidney, the urine may obtain the osmolarity of the interstitial fluid in
the inner medulla, which can be as high as 1,200 mosm/L.
 Although isoosmotic to the inner medulla’s interstitial fluid, the urine is hyperosmotic
to blood and interstitial fluid elsewhere in the body.
 This high osmolarity allows the solutes remaining in the urine to be secreted from the
body with minimal water loss.
 The juxtamedullary nephron is a key adaptation to terrestrial life, enabling mammals to
get rid of salts and nitrogenous wastes without squandering water.
 The remarkable ability of the mammalian kidney to produce hyperosmotic urine is
completely dependent on the precise arrangement of the tubules and collecting ducts in
the renal cortex and medulla.
 The kidney is one of the clearest examples of how the function of an organ is
inseparably linked to its structure.
 One important aspect of the mammalian kidney is its ability to adjust both the volume and
osmolarity of urine, depending on the animal’s water and salt balance and the rate of urea
production.
 With high salt intake and low water availability, a mammal can excrete urea and salt
with minimal water loss in small volumes of hyperosmotic urine.
 If salt is scarce and fluid intake is high, the kidney can get rid of excess water with
little salt loss by producing large volumes of hypoosmotic urine (as dilute as 70
mosm/L).
 This versatility in osmoregulatory function is managed with a combination of nervous
and hormonal controls.
 Regulation of blood osmolarity is maintained by hormonal control of the kidney by
negative feedback circuits.
 One hormone important in regulating water balance is antidiuretic hormone (ADH).
 ADH is produced in the hypothalamus of the brain and stored in and released from the
pituitary gland, which lies just below the hypothalamus.
 Osmoreceptor cells in the hypothalamus monitor the osmolarity of the blood.
 When blood osmolarity rises above a set point of 300 mosm/L, more ADH is released into
the bloodstream and reaches the kidney.
 ADH induces the epithelium of the distal tubules and collecting ducts to become more
permeable to water.
 This amplifies water reabsorption.
Biology Chapter Notes
  This reduces urine volume and helps prevent further increase of blood osmolarity
above the set point.
 By negative feedback, the subsiding osmolarity of the blood reduces the activity of
osmoreceptor cells in the hypothalamus, and less ADH is secreted.
 Only a gain of additional water in food and drink can bring osmolarity all the way back
down to 300 mosm/L.
 ADH alone only prevents further movements away from the set point.
 Conversely, if a large intake of water has reduced blood osmolarity below the set point,
very little ADH is released.
 This decreases the permeability of the distal tubules and collecting ducts, so water
reabsorption is reduced, resulting in an increased discharge of dilute urine.
 Alcohol can disturb water balance by inhibiting the release of ADH, causing excessive
urinary water loss and dehydration (causing some symptoms of a hangover).
 Normally, blood osmolarity, ADH release, and water reabsorption in the kidney are all
linked in a feedback loop that contributes to homeostasis.
 A second regulatory mechanism involves a special tissue called the juxtaglomerular
apparatus (JGA), located near the afferent arteriole that supplies blood to the
glomerulus.
 When blood pressure or blood volume in the afferent arteriole drops, the enzyme renin
initiates chemical reactions that convert a plasma protein angiotensinogen to a peptide
called angiotensin II.
 Acting as a hormone, angiotensin II increases blood pressure and blood volume in several
ways.
 It raises blood pressure by constricting arterioles, decreasing blood flow to many
capillaries, including those of the kidney.
 It also stimulates the proximal tubules to reabsorb more NaCl and water.
 This reduces the amount of salt and water excreted and, consequently, raises blood
pressure and volume.
 It also stimulates the adrenal glands, located atop the kidneys, to release a hormone
called aldosterone.
 This acts on the distal tubules, which reabsorb Na + and water, increasing blood
volume and pressure.
 In summary, the renin-angiotensin-aldosterone system (RAAS) is part of a complex
feedback circuit that functions in homeostasis.
 A drop in blood pressure triggers a release of renin from the JGA.
 In turn, the rise in blood pressure and volume resulting from the various actions of
angiotensin II and aldosterone reduce the release of renin.
 While both ADH and RAAS increase water reabsorption, they counter different
osmoregulatory problems.
 The release of ADH is a response to an increase in the osmolarity of the blood, as
when the body is dehydrated from excessive loss or inadequate intake of water.
 However, a situation that causes excessive loss of salt and body fluids—an injury or
severe diarrhea, for example—will reduce blood volume without increasing
osmolarity.
 The RAAS will detect the fall in blood volume and pressure and respond by increasing
water and Na+ reabsorption.
 Normally, ADH and the RAAS are partners in homeostasis.
Biology Chapter Notes
  ADH alone would lower blood Na+ concentration by stimulating water reabsorption in
the kidney.
 But the RAAS helps maintain balance by stimulating Na + reabsorption.
 Still another hormone, atrial natriuretic factor (ANF), opposes the RAAS.
 The walls of the atria release ANF in response to an increase in blood volume and
pressure.
 ANF inhibits the release of renin from the JGA, inhibits NaCl reabsorption by the
collecting ducts, and reduces aldosterone release from the adrenal glands.
 These actions lower blood pressure and volume.
 Thus, the ADH, the RAAS, and ANF provide an elaborate system of checks and
balances that regulates the kidney’s ability to control the osmolarity, salt concentration,
volume, and pressure of blood.
 The South American vampire bat, Desmodus rotundas, illustrates the flexibility of the
mammalian kidney to adjust rapidly to contrasting osmoregulatory and excretory
problems.
 This species feeds on the blood of large birds and mammals by making an incision in
the victim’s skin and then lapping up blood from the wound.
 Because they fly long distances to locate a suitable victim, they benefit from consuming
as much blood as possible when they do find prey—so much so that a bat would be too
heavy to fly after feeding.
 The bat uses its kidneys to offload much of the water absorbed from a blood meal by
excreting large volumes of dilute urine as it feeds.
 Having lost enough water to fly, the bat returns to its roost in a cave or hollow tree,
where it spends the day.
 In the roost, the bat faces a very different regulatory problem.
 Its food is mostly protein, which generates large quantities of urea, but roosting bats
don’t have access to drinking water.
 Their kidneys shift to producing small quantities of highly concentrated urine,
disposing of the urea load while conserving as much water as possible.
 The vampire bat’s ability to alternate rapidly between producing large amounts of
dilute urine and small amounts of very hyperosmotic urine is an essential part of its
adaptation to an unusual food source.

Concept 44.6 Diverse adaptations of the vertebrate kidney have evolved in different
environments
 Variations in nephron structure and function equip the kidneys of different vertebrates for
osmoregulation in their various habitats.
 Mammals that excrete the most hyperosmotic urine, such as hopping mice and other
desert mammals, have exceptionally long loops of Henle.
 This maintains steep osmotic gradients, resulting in very concentrated urine.
 In contrast, beavers, which rarely face problems of dehydration, have nephrons with
short loops, resulting in a much lower ability to concentrate urine.
 Birds, like mammals, have kidneys with juxtamedullary nephrons that specialize in
conserving water.
 However, the nephrons of birds have much shorter loops of Henle than do mammalian
nephrons.
Biology Chapter Notes
  Bird kidneys cannot concentrate urine to the osmolarities achieved by mammalian
kidneys.
 The main water conservation adaptation of birds is the use of uric acid as the nitrogen
excretion molecule.
 The kidneys of other reptiles, having only cortical nephrons, produce urine that is, at
most, isoosmotic to body fluids.
 However, the epithelium of the cloaca helps conserve fluid by reabsorbing some of the
water present in urine and feces.
 Also, like birds, most other terrestrial reptiles excrete nitrogenous wastes as uric acid.
 In contrast to mammals and birds, a freshwater fish must excrete excess water because the
animal is hyperosmotic to its surroundings.
 Instead of conserving water, the nephrons produce a large volume of very dilute urine.
 Freshwater fishes conserve salts by reabsorption of ions from the filtrate in the
nephrons.
 Amphibian kidneys function much like those of freshwater fishes.
 When in fresh water, the skin of the frog accumulates certain salts from the water by
active transport, and the kidneys excrete dilute urine.
 On land, where dehydration is the most pressing problem, frogs conserve body fluid by
reabsorbing water across the epithelium of the urinary bladder.
 Marine bony fishes, being hypoosmotic to their surroundings, have the opposite problem
of their freshwater relatives.
 In many species, nephrons have small glomeruli or lack glomeruli altogether.
 Concentrated urine is produced by secreting ions into excretory tubules.
 The kidneys of marine fishes excrete very little urine and function mainly to get rid of
divalent ions such as Ca2+, Mg2+, and SO42−, which the fish takes in by its incessant
drinking of seawater.
 Its gills excrete mainly monovalent ions +
such as Na + and Cl− and the bulk of its
nitrogenous wastes in the form of NH4 .

Biology Chapter Notes

 Chapter 45 Hormones and the Endocrine System
Chapter Notes

Overview: The Body’s Long-Distance Regulators

 An animal hormone is a chemical signal that is secreted into the circulatory system that
communicates regulatory messages within the body.
 A hormone may reach all parts of the body, but only specific target cells respond to
specific hormones.
 A given hormone traveling in the bloodstream elicits specific responses from its target
cells, while other cell types ignore that particular hormone.

Concept 45.1 The endocrine system and the nervous system act individually and
together in regulating an animal’s physiology
 Animals have two systems of internal communication and regulation, the nervous system
and the endocrine system.
 Collectively, all of an animal’s hormone-secreting cells constitute its endocrine system.
 Hormones coordinate slow but long-acting responses to stimuli such as stress,
dehydration, and low blood glucose levels.
 Hormones also regulate long-term developmental processes such as growth and
development of primary and secondary sexual characteristics.
 Hormone-secreting organs called endocrine glands secrete hormones directly into the
extracellular fluid, where they diffuse into the blood.
 The nervous and endocrine systems overlap to some extent.
 Certain specialized nerve cells known as neurosecretory cells release hormones into
the blood.
 The hormones produced by these cells are sometimes called neurohormones.
 Chemicals such as epinephrine serve as both hormones of the endocrine system and
neurotransmitters in the nervous system.
 The nervous system plays a role in certain sustained responses—controlling day/night
cycles and reproductive cycles in many animals, for example—often by increasing or
decreasing secretions from endocrine glands.
 The fundamental concepts of biological control systems are important in regulation by
hormones.
 A receptor, or sensor, detects a stimulus and sends information to a control center.
 After comparing the incoming information to a set point, the control center sends out a
signal that directs an effector to respond.
 In endocrine and neuroendocrine pathways, this outgoing signal, called an efferent
system, is a hormone or neurohormone, which acts on particular effector tissues and
elicits specific physiological or developmental changes.
 The three types of simple hormonal pathways (simple endocrine pathway, simple
neurohormone pathway, and simple neuroendocrine pathway) include these basic
functional components.

Biology Chapter Notes

 A common feature of control pathways is a feedback loop connecting the response to the
initial stimulus.
 In negative feedback, the effector response reduces the initial stimulus, and eventually
the response ceases.
 This prevents overreaction by the system.
 Negative feedback regulates many endocrine and nervous mechanisms.
 Positive feedback reinforces the stimulus and leads to an even greater response.
 The neurohormone pathway that regulates the release of milk by a nursing mother is an
example of positive feedback.
 Suckling stimulates sensory nerve cells in the nipples, which send nervous signals
that reach the hypothalamus, the control center.
 The hypothalamus triggers the release of the neurohormone oxytocin from the
posterior pituitary gland.
 Oxytocin causes the mammary glands to secrete milk.
 The release of milk in turn leads to more suckling and stimulation of the pathway,
until the baby is satisfied.

Concept 45.2 Hormones and other chemical signals bind to target cell receptors,
initiating pathways that culminate in specific cell responses
 Hormones convey information via the bloodstream to target cells throughout the body.
 Other chemical signals—local regulators—transmit information to target cells near the
secreting cells.
 Pheromones carry messages to different individuals of a species.
 Three major classes of molecules function as hormones in vertebrates: proteins and
peptides, amines, and steroids.
 Most protein/peptides and amine hormones are water-soluble, unlike steroid hormones.
 Signaling by all hormones involves three key events: reception, signal transduction, and
response.
 Reception of the signal occurs when the signal molecule binds to a specific receptor
protein in or on the target cell.
 Binding of a signal molecule to a receptor protein triggers signal transduction within
the target cell that results in a response, a change in the cell’s behavior.
 Cells that lack receptors for a particular chemical signal are unresponsive to that
signal.
Water-soluble hormones have cell-surface receptors.
 The receptors for water-soluble hormones are embedded in the plasma membrane.
 Binding of a hormone to its receptor initiates a signal transduction pathway, a series of
changes in cellular proteins that converts an extracellular chemical signal to a specific
intracellular response.
 The response may be the activation of an enzyme, a change in uptake or secretion of
specific molecules, or rearrangement of the cytoskeleton.
 Signal transduction from some cell-surface receptors activates proteins in the
cytoplasm that move into the nucleus and directly or indirectly regulate gene
transcription.

Biology Chapter Notes

 An example of the role of cell-surface receptors involves changes in a frog’s skin color,
an adaptation that helps camouflage the frog in changing light.
 Skin cells called melanocytes contain the dark pigment melanin in cytoplasmic
organelles called melanosomes.
 The frog’s skin appears light when melanosomes cluster tightly around the cell
nuclei and darker when they spread out in the cytoplasm.
 A peptide hormone called melanocyte-stimulating hormone controls the arrangement
of melanosomes and, thus, skin color.
 Adding melanocyte-stimulating hormone to the interstitial fluid containing the
pigment-containing cells causes the melanosomes to disperse.
 However, direct microinjection of melanocyte-stimulating hormone into individual
melanocytes has no effect.
 This provides evidence that interaction between the hormone and a surface receptor is
required for hormone action.
 A particular hormone may cause diverse responses in target cells having different
receptors for the hormone, different signal transduction pathways, and/or different
proteins for carrying out the response.
Lipid-soluble hormones have intracellular receptors.
 Evidence for intracellular receptors for steroid hormones came in the 1960s.
 Researchers demonstrated that estrogen and progesterone accumulate within the nuclei
of cells in the reproductive tract of female rats but not in the nuclei of cells in tissues
that do not respond to estrogen.
 These observations led to the hypothesis that cells sensitive to steroid hormones
contain internal receptor molecules that bind the hormones.
 Researchers have since identified the intracellular protein receptors for steroid hormones,
thyroid hormones, and the hormonal form of vitamin D.
 All these hormones are small, nonpolar molecules that diffuse through the
phospholipid interior of cell membranes.
 Intracellular receptors usually perform the entire task of transducing the signal within the
target cell.
 The chemical signal activates the receptor, which directly triggers the cell’s response.
 In almost every case, the intracellular receptor activated by a lipid-soluble hormone is
a transcription factor, and the response is a change in gene expression.
 Most intracellular receptors are located in the nucleus.
 The hormone-receptor complexes bind to specific sites in the cell’s DNA and stimulate
the transcription of specific genes.
 Some steroid hormone receptors are trapped in the cytoplasm when no hormone is
present.
 Binding of a steroid hormone to its cytoplasmic receptor forms a hormone-receptor
complex that can move into the nucleus and stimulate transcription of specific genes.
 In both cases, mRNA produced in response to hormone stimulation is translated into new
protein in the cytoplasm.
 For example, estrogen induces cells in the reproductive system of a female bird to
synthesize large amount of ovalbumin, the main protein of egg white.
 As with hormones that bind to cell-surface receptors, hormones that bind to intracellular
receptors may exert different effects on different target cells.
Biology Chapter Notes
 A variety of local regulators affect neighboring target cells.
 Local regulators convey messages between neighboring cells, a process referred to as
paracrine signaling.
 Local regulators can act on nearby target cells within seconds or milliseconds, eliciting
responses more quickly than hormones can.
 Some local regulators have cell-surface receptors; others have intracellular receptors.
 Binding of local regulators to their receptors triggers events within target cells similar
to those elicited by hormones.
 Several types of chemical compounds function as local regulators.
 Among peptide/protein local regulators are cytokines, which play a role in immune
responses, and most growth factors, which stimulate cell proliferation and
differentiation.
 Another important local regulator is the gas nitric oxide (NO).
 When blood oxygen level falls, endothelial cells synthesize and release NO.
 NO activates an enzyme that relaxes neighboring smooth muscle cells, dilating the
walls of blood vessels and improving blood flow to tissues.
 Nitric oxide also plays a role in male sexual function, increasing blood flow to the
penis to produce an erection.
 Highly reactive and potentially toxic, NO usually triggers changes in the target cell
within a few seconds of contact and then breaks down.
 Viagra sustains an erection by interfering with the breakdown of NO.
 When secreted by neurons, NO acts as a neurotransmitter.
 When secreted by white blood cells, it kills bacteria and cancer cells.
 Local regulators called prostaglandins (PGs) are modified fatty acids derived from lipids
in the plasma membrane.
 Released by most types of cells into interstitial fluids, prostaglandins regulate nearby
cells in various ways, depending on the tissue.
 In semen that reaches the female reproductive tract, prostaglandins trigger the
contraction of the smooth muscles of the uterine wall, helping sperm to reach the egg.
 PGs secreted by the placenta cause the uterine muscles to become more excitable,
helping to induce uterine contractions during childbirth.
 Other PGs help induce fever and inflammation, and intensify the sensation of pain.
 These responses contribute to the body’s defense.
 The anti-inflammatory effects of aspirin and ibuprofen are due to the drugs’
inhibition of prostaglandin synthesis.
 Prostaglandins also help regulate the aggregation of platelets, an early stage in the
formation of blood clots.
 This is why people at risk for a heart attack may take daily low doses of aspirin.
 In the respiratory system, two prostaglandins have opposite effects on the smooth
muscle cells in the walls of blood vessels serving the lungs.
 Prostaglandin E signals the muscle cells to relax, dilating the blood vessels and
promoting oxygenation of the blood.
 Prostaglandin F signals the muscle cells to contract, constricting the vessels and
reducing blood flow through the lungs.

Biology Chapter Notes

Concept 45.3 The hypothalamus and pituitary integrate many functions of the
vertebrate endocrine system
 The hypothalamus integrates vertebrate endocrine and nervous function.
 This region of the lower brain receives information from nerves throughout the body and
from other parts of the brain then initiates endocrine signals appropriate to environmental
conditions.
 The hypothalamus contains two sets of neurosecretory cells whose hormonal secretions
are stored in or regulate the activity of the pituitary gland, located at the base of the
hypothalamus.
 The posterior pituitary (neurohypophysis) stores and secretes two hormones produced
by the hypothalamus.
 The long axons of these cells carry the hormones to the posterior pituitary.
 The anterior pituitary (adenohypophysis) consists of endocrine cells that synthesize and
secrete at least six different hormones directly into the blood.
 Several of these hormones have other endocrine glands as their targets.
 Hormones that regulate the function of endocrine glands are called tropic
hormones.
 They are particularly important in coordinating endocrine signaling throughout the
body.
 The anterior pituitary itself is regulated by tropic hormones produced by a set of
neurosecretory cells in the hypothalamus.
 Some hypothalamic tropic hormones (releasing hormones) stimulate the anterior
pituitary to release its hormones.
 Others (inhibiting hormones) inhibit hormone secretion.
 Hypothalamic releasing and inhibiting hormones are secreted into capillaries at the base
of the hypothalamus.
 The capillaries drain into portal vessels that subdivide into a second capillary bed
within the anterior pituitary.
 Every anterior pituitary hormone is controlled by at least one releasing hormone.
 Some have both a releasing hormone and an inhibiting hormone.
 The posterior pituitary releases two hormones, oxytocin and antidiuretic hormone.
 Both are peptides made by neurosecretory cells in the hypothalamus and, thus, are
neurohormones.
 Oxytocin induces contraction of the uterus during childbirth and causes mammary glands
to eject milk during nursing.
 Oxytocin signaling in both cases exhibits positive feedback.
 Antidiuretic hormone (ADH) promotes retention of water by the kidneys, decreasing
urine volume.
 ADH helps regulate osmolarity of the blood via negative feedback.
 Secretion is regulated by water/salt balance.
 The anterior pituitary produces many different hormones.
 Four function as tropic hormones, stimulating the synthesis and release of hormones
from the thyroid gland, adrenal glands, and gonads.
 Several others exert only direct, nontropic effects on nonendocrine organs.
 One, growth hormone, has both tropic and nontropic actions.
Biology Chapter Notes
 Three of the tropic hormones secreted by the anterior pituitary are closely related in their
chemical structures.
 Follicle-stimulating hormone (FSH), luteinizing hormone (LH), and thyroid-
stimulating hormone (TSH) are similar glycoproteins.
 FSH and LH are also called gonadotropins because they stimulate the activities of
the gonads.
 TSH promotes normal development of the thyroid gland and the production of
thyroid hormones.
 Adrenocorticotropic hormone (ACTH) is a peptide hormone that stimulates the
production and secretion of steroid hormones by the adrenal cortex.
 All four anterior pituitary tropic hormones participate in complex neuroendocrine
pathways.
 In each pathway, signals to the brain stimulate release of an anterior pituitary tropic
hormone.
 The tropic hormone then acts on its target endocrine tissue, stimulating secretion of a
hormone that exerts systemic metabolic or developmental effects.
 Nontropic hormones produced by the anterior pituitary include prolactin, melanocyte-
stimulating hormone (MSH), and ß-endorphin.
 These peptide/protein hormones, whose secretion is controlled by hypothalamic
hormones, function in simple neuroendocrine pathways.
 Prolactin (PRL) stimulates mammary gland growth and milk production and secretion
in mammals.
 It regulates fat metabolism and reproduction in birds, delays metamorphosis in
amphibians (where it may also function as a larval growth hormone), and regulates
salt and water balance in freshwater fishes.
 This suggests that prolactin is an ancient hormone whose functions have diversified
during the evolution of various vertebrate groups.
 Secretion is regulated by hypothalamic hormones.
 Melanocyte-stimulating hormone (MSH) regulates the activity of pigment-
containing cells in the skin of some fishes, amphibians, and reptiles.
 In mammals, MSH acts on neurons in the brain, inhibiting hunger.
 ß-endorphin belongs to a class of chemical signals called endorphins.
 All the endorphins bind to receptors in the brain and dull the perception of pain.
 Both MSH and ß-endorphin are formed by cleavage of the same precursor protein that
gives rise to ACTH.
 Growth hormone (GH) is so similar structurally to prolactin that scientists hypothesize
the genes directing their production evolved from the same ancestral gene.
 GH acts on a wide variety of target tissues with both tropic and nontropic effects.
 Its major tropic action is to signal the liver to release insulin-like growth factors
(IGFs), which circulate in the blood and directly stimulate bone and cartilage growth.
 In the absence of GH, the skeleton of an immature animal stops growing.
 GH also exerts diverse metabolic effects that raise blood glucose, opposing the effects
of insulin.
 Abnormal production of GH can produce several disorders.
 Gigantism is caused by excessive GH production during development.
 Acromegaly is caused by excessive GH production during adulthood.

Biology Chapter Notes

  Pituitary dwarfism is caused by childhood GH deficiency, and can be treated by
therapy with genetically engineered GH.

Concept 45.4 Nonpituitary hormones help regulate metabolism, homeostasis,

development, and behavior
Thyroid hormones function in development, bioenergetics, and homeostasis.
 The thyroid gland of mammals consists of two lobes located on the ventral surface of the
trachea.
 The thyroid gland produces two very similar hormones derived from the amino acid
tyrosine: triiodothyronine (T3), which contains three iodine atoms, and thyroxin (T4),
which contains four iodine atoms.
 In mammals, the thyroid secretes mainly T4, but target cells convert most of it to T 3 by
removing one iodine atom.
 Although the same receptor molecule in the cell nucleus binds both hormones, the
receptor has greater affinity for T3 than for T4.
 It is primarily T3 that brings about responses in target cells.
 This process involves a complex neuroendocrine pathway with two negative feedback
loops.
 The thyroid plays a crucial role in vertebrate development and maturation.
 Thyroid controls metamorphosis of a tadpole into a frog, which involves massive
reorganization of many different tissues.
 The thyroid is equally important in human development.
 Cretinism, an inherited condition of thyroid deficiency, retards skeletal growth and
mental development.
 The thyroid gland has important homeostatic functions.
 In adult mammals, thyroid hormones help to maintain normal blood pressure, heart
rate, muscle tone, digestion, and reproductive functions.
 Throughout the body, T3 and T4 are important in bioenergetics, increasing the rate of
oxygen consumption and cellular metabolism.
 Too much or too little of these hormones can cause serious metabolic disorders.
 Hyperthyroidism is the excessive secretion of thyroid hormones, leading to high body
temperature, profuse sweating, weight loss, irritability, and high blood pressure.
 An insufficient amount of thyroid hormones is known as hypothyroidism.
 This condition can cause cretinism in infants.
 Adult symptoms include weight gain, lethargy, and cold intolerance.
 A deficiency of iodine in the diet can result in goiter, an enlargement of the thyroid
gland.
 Without sufficient iodine, the thyroid gland cannot synthesize adequate amounts of
T3 and T4.
 The resulting low blood levels of these hormones cannot exert negative
feedback on the hypothalamus and anterior pituitary.
 The pituitary continues to secrete TSH, elevating TSH levels and enlarging the
thyroid.
 In addition to cells that produce T3 and T4, the mammalian thyroid gland produces
calcitonin.
Biology Chapter Notes
  This hormone acts in conjunction with parathyroid hormone to maintain calcium
homeostasis.
Parathyroid hormone and calcitonin balance blood calcium.
 Rigorous homeostatic control of blood calcium level is critical because calcium ions
(Ca2+) are essential to the normal functioning of all cells.
 If blood Ca2+ falls substantially, skeletal muscles begin to contract convulsively, a
potentially fatal condition called tetany.
 In mammals, parathyroid hormone and calcitonin play a major role in maintaining
blood Ca2+ near a set point of about 10 mg/100 mL.
 When blood Ca2+ falls below the set point, parathyroid hormone (PTH) is released from
four small structures, the parathyroid glands, embedded on the surface of the thyroid.
 PTH raises the level of blood Ca2+ by direct and indirect effects.
 In bone, PTH induces specialized cells called osteoclasts to decompose the mineralized
matrix of bone and release Ca2+ into the blood.
 In the kidneys, it promotes the conversion of vitamin D to its active hormonal form.
 An inactive form of vitamin D is obtained from food or synthesized in the skin.
 The+ active form of vitamin D acts directly on the intestines, stimulating the uptake of
Ca2 from food.
 A rise in blood Ca2+ above the set point promotes release of calcitonin from the
thyroid gland.
 Calcitonin+ exerts effects on bone and kidneys opposite those of PTH and thus lowers
blood Ca2 levels.
 The regulation of blood Ca2+ levels illustrates how two hormones with opposite effects
(PTH and calcitonin) balance each other, exerting tight regulation and maintaining
homeostasis.
 Each hormone functions in a simple endocrine pathway in which the hormone-secreting
cells themselves monitor the variable being regulated.
 In classic feedback, the response to one hormone triggers release of the antagonistic
hormone, minimizing fluctuations in the concentration of Ca 2+ levels in the blood.
Endocrine tissues of the pancreas secrete insulin and glucagon, antagonistic hormones
that regulate blood glucose.
 The pancreas has both endocrine and exocrine functions.
 Its exocrine function is the secretion of bicarbonate ions and digestive enzymes, which
are released into small ducts and carried to the small intestine via the pancreatic duct.
 Tissues and glands that discharge secretions into ducts are described as exocrine.
 Clusters of endocrine cells, the islets of Langerhans, are scattered throughout the
exocrine tissues of the pancreas.
 Each islet has a population of alpha cells, which produce the hormone glucagon, and a
population of beta cells, which produce the hormone insulin.
 Both hormones are secreted directly into the circulatory system.
 Insulin and glucagon are antagonistic hormones that regulate the concentration of glucose
in the blood.
 This is a critical bioenergetic and homeostatic function, because glucose is a major fuel
for cellular respiration and a key source of carbon skeletons for the synthesis of other
organic compounds.
Biology Chapter Notes
 Metabolic balance depends on maintaining blood glucose concentrations near a set point
of about 90 mg/100 mL in humans.
 When blood glucose exceeds this level, insulin is released and lowers blood glucose.
 When blood glucose falls below this level, glucagon is released and its effects increase
blood glucose concentration.
 Each hormone operates in a simple endocrine pathway regulated by negative feedback.
 Insulin lowers blood glucose levels by stimulating all body cells (except brain cells) to
take up glucose from the blood.
 Brain cells can take up glucose without insulin and, thus, have access to circulating
fuel at all times.
 Insulin also decreases blood glucose by slowing glycogen breakdown in the liver and
inhibiting the conversion of amino acids and glycerol to glucose.
 The liver, skeletal muscles, and adipose tissues store large amounts of fuel and are
especially important in bioenergetics.
 The liver and muscles store sugar as glycogen, whereas adipose tissue cells convert
sugars to fats.
 The liver is a key fuel-processing center because only liver cells are sensitive to
glucagon.
 The antagonistic effects of glucagon and insulin are vital to glucose homeostasis and
regulation of fuel storage and fuel consumption by body cells.
 The liver’s ability to perform its vital roles in glucose homeostasis results from the
metabolic versatility of its cells and its access to absorbed nutrients via the hepatic portal
vein.
 Diabetes mellitus is perhaps the best-known endocrine disorder.
 It is caused by a deficiency of insulin or a depressed response to insulin in target
tissues.
 There are two types of diabetes mellitus with very different causes, but each is
marked by high blood glucose.
 In people with diabetes, elevated blood glucose exceeds the reabsorption capacity of
the kidneys, causing them to excrete glucose.
 As glucose is concentrated in the urine, more water is excreted with it, resulting in
excessive volumes of water and persistent thirst.
 Without sufficient glucose to meet the needs of most body cells, fat becomes the main
substrate for cellular respiration.
 In severe cases of diabetes, acidic metabolites formed during fat breakdown
accumulate in the blood, threatening life by lowering blood pH.
 Type I diabetes mellitus (insulin-dependent diabetes) is an autoimmune disorder in which
the immune system destroys the beta cells of the pancreas.
 Type I diabetes usually appears in childhood and destroys the person’s ability to
produce insulin.
 The treatment is insulin injections, usually several times a day.
 Human insulin is available from genetically engineered bacteria.
 Type II diabetes mellitus (non-insulin-dependent diabetes) is characterized by deficiency
of insulin or, more commonly, by a decreased responsiveness to insulin in target cells, due
to some change in insulin receptors.
 This form of diabetes occurs after age 40, and the risk increases with age.
Biology Chapter Notes
  Although heredity can play a role in type II diabetes, excess body weight and lack of
exercise significantly increase the risk.
 Type II diabetes accounts for more than 90% of diabetes cases.
 Many type II diabetics can manage their blood glucose with regular exercise and a
healthful diet, although some require insulin injections.
The adrenal medulla and adrenal cortex help the body manage stress.
 The adrenal glands are located adjacent to the kidneys.
 In mammals, each adrenal gland is actually made up of two glands with different cell
types, functions, and embryonic origins.
 The adrenal cortex is the outer portion, and the adrenal medulla is the central portion.
 Like the pituitary, the adrenal gland is a fused endocrine and neuroendocrine gland.
 The adrenal cortex consists of true endocrine cells, while the secretory cells of the
adrenal medulla derive from the neural crest during embryonic development.
 The adrenal medulla produces two hormones, epinephrine (adrenaline) and
norepinephrine (noradrenaline).
 These hormones are members of a class of hormones, the catecholamines, amines that
are synthesized from the amino acid tyrosine.
 Both are also neurotransmitters in the nervous system.
 Either positive or negative stress stimulates secretion of epinephrine and
norepinephrine from the adrenal medulla.
 These hormones act directly on several target tissues to give the body a rapid
bioenergetic boost.
 They increase the rate of glycogen breakdown in the liver and skeletal muscles,
promote glucose release into the blood by liver cells, and stimulate the release of
fatty acids from fat cells.
 The released glucose and fatty acids circulate in the blood and can be used by
the body as fuel.
 Epinephrine and norepinephrine also exert profound effects on the cardiovascular and
respiratory systems.
 They increase heart rate and stroke volume of the heartbeat and dilate the
bronchioles in the lungs to increase the rate of oxygen delivery to body cells.
 Catecholamines also act to shunt blood away from skin, digestive organs, and
kidneys, and increase blood supply to the heart, brain, and skeletal muscles.
 Epinephrine generally has a greater effect on heart and metabolic rates, while the primary
role of norepinephrine is in sustaining blood pressure.
 Secretion of these hormones by the adrenal medulla is stimulated by nerve signals carried
from the brain via the sympathetic division of the autonomic nervous system.
 In response to a stressful situation, nerve impulses from the hypothalamus travel to the
adrenal medulla, where they trigger the release of epinephrine.
 Norepinephrine is released independently.
 The adrenal medulla hormones act in a simple neurohormone pathway.
 The neurosecretory cells are modified peripheral nerve cells.
 Hormones from the adrenal cortex also function in the body’s response to stress.
 Stressful stimuli cause the hypothalamus to secrete a releasing hormone that stimulates
the anterior pituitary to release the tropic hormone ACTH.
Biology Chapter Notes
 When ACTH reaches the adrenal cortex via the bloodstream, it stimulates the endocrine
cells to synthesize and secrete a family of steroids called corticosteroids.
 Elevated levels of corticosteroids in the blood suppress the secretion of ACTH.
 The two main types of corticosteroids in humans are the glucocorticoids, such as cortisol,
and the mineralocorticoids, such as aldosterone.
 Both hormones help maintain homeostasis when stress is experienced over a long
period of time.
 The primary effect of glucocorticoids is on bioenergetics, specifically on glucose
metabolism.
 Glucocorticoids make more glucose available as fuel.
 They act on skeletal muscle, causing a breakdown of muscle proteins.
 The synthesis of glucose from muscle proteins is a homeostatic mechanism providing
circulating fuel when body activities require more than the liver can metabolize from
its metabolic stores.
 Cortisol and other glucocorticoids also suppress certain components of the body’s
immune system.
 Because of their anti-inflammatory effect, glucocorticoids have been used to treat
inflammatory diseases such as arthritis.
 However, long-term use of these hormones can have serious side effects due to their
metabolic actions and can also increase susceptibility to infection.
 Mineralocorticoids act principally on salt and water balance.
 Aldosterone stimulates cells in the kidneys to reabsorb Na + and water from filtrate,
raising blood pressure and volume.
 Aldosterone secretion is stimulated primarily by angiotensin II, as part of the
regulatory pathway that controls the kidney’s ability to maintain ion and water
homeostasis of the blood.
 When an individual is under severe stress, the resulting rise in blood ACTH levels can
increase the rate at which the adrenal cortex secretes aldosterone as well as
glucocorticoids.
 A third group of corticosteroids is composed of sex hormones.
 All the steroid hormones are secreted from cholesterol, and their structures differ in minor
ways.
 However, these differences are associated with major differences in their effects.
 The sex hormones produced by the adrenal cortex are mainly male hormones (androgens)
with small amounts of female hormones (estrogens and progestins)
 Androgens secreted by the adrenal cortex may account for the female sex drive.
Gonadal steroids regulate growth, development, reproductive cycles, and sexual behavior.
 The gonads are the primary source of the sex hormones.
 The gonads produce and secrete three major categories of steroid hormones: androgens,
estrogens, and progestins.
 All three types are found in males and females but in different proportions.
 Sex hormones affect growth and development and regulate reproductive cycles and sexual
behavior.
 The testes primarily synthesize androgens, the main one being testosterone.
 Androgens promote development and maintenance of male sex characteristics.
Biology Chapter Notes
  Androgens produced early in development determine whether a fetus develops as a
male or a female.
 At puberty, high levels of androgens are responsible for the development of male
secondary sex characteristics, including male patterns of hair growth, a low voice, and
increased muscle mass and bone mass typical of males.
 The muscle-building action of testosterone and other anabolic steroids has led some
athletes to take them as supplements.
 Abuse of these hormones carries many health risks, and they are banned in most
competitive sports.
 Estrogens, the most important of which is estradiol, are responsible for the development
and maintenance of the female reproductive system and the development of female
secondary sex characteristics.
 In mammals, progestins, which include progesterone, are involved in promoting uterine
lining growth to support the growth and development of an embryo.
 Both estrogens and androgens are components of complex neuroendocrine pathways.
 Their secretion is controlled by gonadotropins (FSH and LH) from the anterior
pituitary gland.
 FSH and LH production is controlled by a releasing hormone from the hypothalamus,
GnRH (gonadotropin-releasing hormone).
The pineal gland is involved in biorhythms.
 The pineal gland is a small mass of tissue near the center of the mammalian brain.
 The pineal gland synthesizes and secretes the hormone melatonin, an amine.
 Depending on the species, the pineal gland contains light-sensitive cells or has nervous
connections from the eyes that control its secretory activity.
 Melatonin regulates functions related to light and to seasons marked by changes in day
length.
 Its primary functions are related to biological rhythms associated with reproduction.
 Melatonin secretion is regulated by light/dark cycles.
 Melatonin is secreted at night, and the amount secreted depends on the length of the
night.
 Thus, melatonin production is a link between a biological clock and daily or
seasonal activities such as reproduction.
 Recent evidence suggests that the main target cells of melatonin are the part of the
brain called the suprachiasmatic nucleus (SCN), which functions as a biological clock.
 Melatonin seems to decrease the activity of neurons in the SCN, and this may be
related to its role in mediating rhythms.
 Much remains to be learned about the precise role of melatonin and about biological
clocks in general.

Concept 45.5 Invertebrate regulatory systems also involve endocrine and nervous
system interactions
 Invertebrates produce a variety of hormones in endocrine and neurosecretory cells.
 Some invertebrate hormones have homeostatic functions, such as regulation of water
balance.
 Others function in reproduction and development.
Biology Chapter Notes
  In hydras, one hormone functions in growth and budding (asexual reproduction) but
prevents sexual reproduction.
 In the mollusc Aplysia, specialized nerve cells secrete a neurohormone that stimulates
the laying of thousands of eggs and inhibits feeding and locomotion, activities that
interfere with reproduction.
 All groups of arthropods have extensive endocrine systems.
 Crustaceans have hormones for growth and reproduction, water balance, movement of
pigments in the integument and eyes, and regulation of metabolism.
 Crustaceans and insects grow in spurts, shedding the old exoskeleton and secreting a new
one with each molt.
 Insects acquire their adult characteristics in a single terminal molt.
 In all arthropods with exoskeletons, molting is triggered by a hormone.
 The hormonal control of insect development is well understood.
 Brain hormone, produced by neurosecretory cells in the brain, stimulates the release of
ecdysone from the prothoracic glands, a pair of endocrine glands behind the head.
 Ecdysone promotes molting and the development of adult characteristics.
 Brain hormone and ecdysone are balanced by juvenile hormone, secreted by the corpora
allata, a pair of small endocrine glands that are somewhat analogous to the anterior
pituitary of vertebrates.
 As the name suggests, juvenile hormone promotes the retention of larval (juvenile)
characteristics.
 In the presence of a high concentration of juvenile hormone, ecdysone still stimulates
molting, but the product is simply a larger larva.
 Only when the level of juvenile hormone declines can ecdysone-induced molting produce
a pupa.
 Within the pupa, metamorphosis produces the adult form.
 Synthetic juvenile hormone is used as insecticide to prevent insects from maturing to
reproductive adults.

Biology Chapter Notes

 Chapter 46 Animal Reproduction
Chapter Notes

Overview: Doubling Up for Sexual Reproduction

Concept 46.1 Both asexual and sexual reproduction occur in the animal kingdom
 Asexual reproduction involves the formation of individuals whose genes come from a
single parent.
 There is no fusion of sperm and egg.
 Sexual reproduction is the formation of offspring by the fusion of haploid gametes to
form a diploid zygote.
 The female gamete, the unfertilized egg, or ovum, is usually large and nonmotile.
 The male gamete is the sperm, which is usually small and motile.
 Sexual reproduction increases genetic variation among offspring by generating unique
combinations of genes inherited from two parents.
Diverse mechanisms of asexual reproduction enable animals to produce identical
offspring rapidly.
 Many invertebrates can reproduce asexually by fission, in which a parent separates into
two or more approximately equal-sized individuals.
 Budding is also common among invertebrates. This is a form of asexual reproduction
in which new individuals split off from existing ones.
 In fragmentation, the body breaks into several pieces, some or all of which develop
into complete adults.
 Reproducing in this way requires regeneration of lost body parts.
 Many animals can also replace new appendages by regeneration.
 Asexual reproduction has a number of advantages.
 It allows isolated animals to reproduce without needing to find a mate.
 It can create numerous offspring in a short period of time.
 In stable environments, it allows for the perpetuation of successful genotypes.

Reproductive cycles and patterns vary extensively among mammals.

 Most animals exhibit cycles in reproductive activity, usually related to changing seasons.
 This allows animals to conserve resources and reproduce when more energy is
available and when environmental conditions favor the survival of offspring.
 Reproductive cycles are controlled by a combination of environmental and hormonal
cues.
 Environmental cues may include seasonal temperature, rainfall, day length, and lunar
cycles.
 Animals may reproduce exclusively asexually or sexually or they may alternate between
the two modes, depending on environmental conditions.
Biology Chapter Notes
  Daphnia reproduce by parthenogenesis under favorable conditions and sexually during
times of environmental stress.
 Parthenogenesis is the process by which an unfertilized egg develops without being
fertilized.
 Parthenogenesis plays a role in the social organization of some bees, wasps, and ants.
 Male honeybees (drones) are haploid, and female honeybees (queens and workers)
are diploid.
 Several genera of fishes, amphibians, and lizards reproduce by a form of
parthenogenesis that produces diploid “zygotes.”
 Fifteen species of whiptail lizards reproduce exclusively by parthenogenesis.
 There are no males in this species, but the lizards imitate courtship and mating
behavior typical of sexual species of the same genus.
 Sexual reproduction presents a problem for sessile or burrowing animals or parasites that
may have difficulty encountering a member of the opposite sex.
 One solution is hermaphroditism, in which one individual functions as both a male
and a female.
 Some hermaphrodites can self-fertilize, but most mate with another member of the
same species.
 In such matings, each individual receives and donates sperm.
 This results in twice as many offspring as would be produced if only one set of
eggs were fertilized.
 In sequential hermaphroditism, an individual reverses its sex during its lifetime.
 In some species, the sequential hermaphrodite is female first.
 In other species, the sequential hermaphrodite is male first.

Concept 46.2 Fertilization depends on mechanisms that help sperm meet eggs of the
same species
 The mechanisms of fertilization, the union of sperm and egg, play an important part in
sexual reproduction.
 In external fertilization, eggs are released by the female into a wet environment,
where they are fertilized by the male.
 In species with internal fertilization, sperm are deposited in or near the female
reproductive tract, and fertilization occurs within the tract.
 A moist habitat is almost always required for external fertilization, both to prevent
gametes from drying out and to allow the sperm to swim to the eggs.
 In species with external fertilization, timing is crucial to ensure that mature sperm
encounter ripe eggs.
 Environmental cues such as temperature or day length may cause gamete release by
the whole population.
 Individuals may engage in courtship behavior that leads to fertilization of the eggs of
one female by one male.
 Internal fertilization is an adaptation to terrestrial life that enables sperm to reach an egg
in a dry environment.
 Internal fertilization requires sophisticated reproductive systems, including copulatory
organs that deliver sperm and receptacles for their storage and transport to ripe eggs.

Biology Chapter Notes

 Mating animals may use pheromones, chemical signals released by one organism that
influence the behavior or physiology of other individuals of the same species.
 Pheromones are small, volatile, or water-soluble molecules that disperse into the
environment.
 Like hormones, pheromones are active in minute amounts.
 Many pheromones act as male attractants.
 All species produce more offspring than can survive to reproduce.
 Internal fertilization usually involves the production of fewer zygotes than does external
fertilization.
 However, the survival rate is higher for internal fertilization.
 Major types of protection include tough eggshells, development of the embryo within
the reproductive tract of the mother, and parental care of the eggs and offspring.
 Marsupial mammals retain their embryos for only a short period in the uterus.
 The embryos crawl out and complete fetal development attached to a mammary gland
in the mother’s pouch.
 The embryos of eutherian mammals develop entirely within the uterus, nourished through
the placenta.
 Parental care of offspring can occur regardless of whether fertilization is external or
internal.
Reproductive systems produce gametes and make them available to gametes of the
opposite sex.
 The least complex reproductive systems lack gonads, the organs that produce gametes in
most animals.
 Polychaete worms lack gonads. Eggs and sperm develop from undifferentiated cells
lining the coelom.
 As the gametes mature, they are released from the body wall and fill the coelom.
 In some species, the body splits open to release the gametes, killing the parent.
 Some reproductive systems, such as those of parasitic flatworms, are very complex.
 Most insects have separate sexes with complex reproductive systems.
 In many species, the female reproductive system includes a spermatheca, a sac in
which sperm may be stored for a year or more.
 The basic plan of all vertebrate reproductive systems is very similar.
 However, there are variations.
 In many nonmammalian vertebrates, the digestive, excretory, and reproductive
systems share a common opening to the outside, the cloaca.
 Mammals have separate openings for the digestive and reproductive systems.
 Female mammals also have separate openings for the excretory and reproductive
systems.
 The uterus of most vertebrates is partly or completely divided into two chambers.
 Male reproductive systems differ mainly in copulatory organs.
 Many mammalian vertebrates do not have a well-developed penis and simply
turn the cloaca inside out to ejaculate.

Biology Chapter Notes

Concept 46.3 Reproductive organs produce and transport gametes: focus on humans
Human reproduction involves intricate anatomy and complex behavior.
 The reproductive anatomy of the human female includes external and internal
reproductive structures.
 External reproductive structures consist of two sets of labia surrounding the clitoris
and vaginal opening.
 Internal reproductive organs consist of a pair of gonads and a system of ducts and
chambers.
 The role of the ducts and chambers is to conduct the gametes and house the embryo
and fetus.
 The ovaries, the female gonads, lie in the abdominal cavity, attached to the uterus by a
mesentery.
 Each ovary is enclosed in a tough protective capsule and contains many follicles.
 Each follicle consists of one egg cell surrounded by one or more layers of follicle cells.
 A woman is born with about 400,000 follicles.
 Only several hundred of these will release eggs during a female’s reproductive
years.
 Follicles produce the primary female sex hormones, estrogens.
 Usually one follicle matures and releases its egg during each menstrual cycle in the
process of ovulation.
 After ovulation, the remaining follicular tissue develops into the corpus luteum.
 The corpus luteum secretes additional estrogens and progesterone, hormones that help
maintain the uterine lining during pregnancy.
 If pregnancy does not occur, the corpus luteum disintegrates and a new follicle matures
during the next cycle.
 At ovulation, the egg is released into the abdominal cavity near the opening of the
oviduct.
 The cilia-lined funnel-like opening of the oviduct draws in the egg.
 Cilia convey the egg through the oviduct to the uterus.
 The highly vascularized inner lining of the uterus is called the endometrium.
 The neck of the uterus, the cervix, opens into the vagina.
 The vagina is a thin-walled chamber that forms the birth canal and is the repository for
sperm during copulation.
 It opens to the outside at the vulva, the collective term for the external female
genitalia.
 The vaginal opening is partially covered by a thin sheet of tissue called the hymen.
 The vaginal and urethral openings are located within a recess called the vestibule.
 The vestibule is surrounded by a pair of slender folds called the labia minora.
 The labia majora enclose and protect the labia minora and vestibule.
 The clitoris is found at the front edge of the vestibule.
 During sexual arousal, the clitoris, vagina, and labia engorge with blood and enlarge.
 During sexual arousal, Bartholin’s glands secrete mucus into the vestibule, providing
lubrication and facilitating intercourse.
 Mammary glands are present in both males and females but normally function only in
females.
Biology Chapter Notes
  They are not a component of the human reproductive system but are important to
mammalian reproduction.
 Within the glands, small sacs of epithelial tissue secrete milk, which drains into a
series of ducts opening at the nipple.
 Adipose tissue forms the main mass of the mammary gland of a nonlactating mammal.
 The low estrogen level in males prevents the development of the sensory apparatus and fat
deposits, so that male breasts remain small, with nipples unconnected to the ducts.
 The male’s external reproductive organs consist of the scrotum and penis.
 The internal reproductive organs consist of gonads that produce sperm and hormones,
accessory glands that secrete products essential to sperm movement, and ducts to carry the
sperm and glandular secretions.
 The male gonads, or testes, consist of highly coiled tubes surrounded by layers of
connective tissue.
 The tubes are seminiferous tubules, where sperm are produced.
 Leydig cells scattered between the seminiferous tubules produce testosterone and other
androgens.
 The scrotum, a fold in the body wall, holds the testes outside the body cavity at a
temperature about 2°C below that of the abdomen.
 This keeps testicular temperature cooler than that in the body cavity.
 The testes develop in the body cavity and descend into the scrotum just before birth.
 From the seminiferous tubules of the testes, the sperm pass through the coiled tubules of
the epididymis.
 As they pass through this duct, sperm become motile and gain the ability to fertilize an
egg.
 Ejaculation propels sperm from the epididymis to the vas deferens.
 The vas deferens run from the scrotum and behind the urinary bladder.
 Each vas deferens joins with a duct from the seminal vesicle to form an ejaculatory
duct.
 The ejaculatory ducts open into the urethra.
 The urethra drains both the excretory and reproductive systems.
 Accessory sex glands add secretions to semen.
 A pair of seminal vesicles contributes about 60% of total semen volume.
 Seminal fluid is thick, yellowish, and alkaline.
 It contains mucus, fructose, a coagulating enzyme, ascorbic acid, and
prostaglandins.
 The prostate gland secretes directly into the urethra.
 Prostatic fluid is thin and milky.
 This fluid contains anticoagulant enzymes and citrate.
 Prostate problems are common in males older than 40.
 Benign prostate enlargement occurs in virtually all males older than 70.
 Prostate cancer is one of the most common cancers in men.
 The bulbourethral glands are a pair of small glands along the urethra below the prostate.
 Prior to ejaculation, they secrete clear mucus that neutralizes any acidic urine
remaining in the urethra.
 Bulbourethral fluid also carries some sperm released before ejaculation.
Biology Chapter Notes
  This is one of the reasons the withdrawal method of birth control has a high failure
rate.
 A male usually ejaculates about 2–5 mL of semen, with each milliliter containing about
50–130 million sperm.
 Once in the female reproductive tract, prostaglandins in semen thin the mucus at the
opening of the uterus and stimulate uterine contractions that help move the semen.
 When ejaculated, semen coagulates, making it easier for uterine contractions to move
it along.
 Anticoagulants then liquefy the semen, and the sperm begin swimming.
 The alkalinity of semen helps neutralize the acidic environment of the vagina,
protecting the sperm and increasing their motility.
 The human penis is composed of three layers of spongy erectile tissue.
 During sexual arousal, the erectile tissue fills with blood from arteries.
 The resultant increased pressure seals off the veins that drain the penis, causing it to
engorge with blood.
 The engorgement of the penis with blood causes an erection, which is essential
for the insertion of the penis into the vagina.
 The penis of some mammals possesses a baculum, a bone that helps stiffen the penis.
 Temporary impotence can result from the consumption of alcohol or other drugs, and
from emotional problems.
 Irreversible impotence due to nervous system or circulatory problems can be treated with
drugs and penile implant devices.
 The oral drug Viagra acts by promoting the action of nitric oxide, enhancing relaxation
of smooth muscles in the blood vessels of the penis.
 This allows blood to enter the erectile tissue and sustain an erection.
 The main shaft of the penis is covered by relatively thick skin.
 The sensitive head, or glans penis, is covered by thinner skin.
 The glans is covered by the foreskin, or prepuce, which may be removed by
circumcision.
 There is no verifiable health benefit to circumcision, which arose from religious
tradition.
Human sexual response is very complex.
 Human arousal involves a variety of psychological and physical factors.
 Human sexual response is characterized by a common physiological pattern.
 Two types of physiological reaction predominate in both sexes:
o Vasocongestion, filling of tissue with blood, is caused by increased blood flow.
o Myotonia is increased muscle tension.
 Both smooth and skeletal muscle may show sustained or rhythmic contractions.

 The sexual response can be divided into four phases: excitement, plateau, orgasm, and
resolution.
 Excitement prepares the vagina and penis for coitus.
 Vasocongestion is evident in the erection of the penis and clitoris; the enlargement of
the testes, labia, and breasts; and vaginal lubrication.
 Myotonia may result in nipple erection or tension in the arms and legs.
Biology Chapter Notes
 In the plateau phase, these responses continue.
 Stimulation by the autonomic nervous system increases breathing and heart rate.
 In females, plateau includes vasocongestion of the outer third of the vagina, expansion
of the inner two-thirds of the vagina, and elevation of the uterus to form a depression
that receives sperm at the back of the vagina.
 Orgasm is the shortest phase of the sexual response cycle.
 It is characterized by rhythmic, involuntary contractions of the reproductive structures
in both sexes.
 In male orgasm, emission is the contraction of the glands and ducts of the reproductive
tract, which forces semen into the urethra.
 Ejaculation occurs with the contraction of the urethra and expulsion of semen.
 In female orgasm, the uterus and outer vagina contract.
 Resolution completes the cycle and reverses the responses of earlier stages.
 Vasocongested organs return to their normal sizes and colors; muscles relax.

Concept 46.4 In humans and other mammals, a complex interplay of hormones

regulates gametogenesis
Spermatogenesis and oogenesis both involve meiosis but differ in three significant ways.
 Gametogenesis is based on meiosis.
 Spermatogenesis is the production of mature sperm cells from spermatogonia.
 Spermatogenesis is a continuous and prolific process in the adult male.
 Each ejaculation contains 100–650 million sperm.
 Spermatogenesis occurs in seminiferous tubules.
 Primordial germ cells of the embryonic testes differentiate into spermatogonia, the
stem cells that give rise to sperm.
 As spermatogonia differentiate into spermatocytes and then into spermatids, meiosis
reduces the chromosome number from diploid to haploid.
 As spermatogenesis progresses, the developing sperm cells move from the wall to the
lumen of a seminiferous tubule and then to the epididymis, where they become motile.
 The structure of sperm fits its function.
 A head containing the haploid nucleus is tipped with an acrosome, which contains
enzymes that help the sperm penetrate to the egg.
 Behind the head are a large number of mitochondria (or a single large one) that provide
ATP to power the flagellum.
 Oogenesis is the production of ova from oogonia.
 Oogenesis differs from spermatogenesis in three major ways.
o At birth an ovary may contain all of the primary oocytes it will ever have.
 However, in 2004, researchers reported that multiplying oogonia exist in the ovaries
of adult mice.
 Researchers are looking for similar cells in human ovaries.
 Sperm are produced from spermatogonia throughout a man’s life.
o Unequal cytokinesis during meiosis results in the formation of a single large
secondary oocyte and three small polar bodies.
 The secondary oocyte becomes the ovum, while the polar bodies degenerate.
Biology Chapter Notes
  In spermatogenesis, all four products of meiosis become mature sperm.
o Oogenesis has long “resting” periods.
 Spermatogenesis produces mature sperm from spermatogonia in an uninterrupted
sequence.
 Oogenesis begins in the female embryo with differentiation of primordial germ cells into
oogonia, ovary-specific stem cells.
 An oogonium multiplies by mitosis and begins meiosis, but the process stops at
prophase I.
 The primary oocytes remain quiescent within small follicles until puberty.
 Beginning at puberty, follicle-stimulating hormone (FSH) stimulates a follicle to grow
and induces its primary oocyte to complete meiosis I and start meiosis II.
 It is arrested at metaphase II as a secondary oocyte.
 The secondary oocyte is released when the follicle breaks open at ovulation.
 Meiosis is completed when a sperm penetrates the oocyte.
 Oogenesis is completed, producing an ovum.
 The haploid nuclei of the sperm and ovum fuse in fertilization.
 The ruptured follicle develops into the corpus luteum.
 If the released oocyte is not fertilized, the corpus luteum degenerates.
 In females, the secretion of hormones and the reproductive events they regulate are cyclic.
 Hormonal control of the female cycle is complex.
 Humans and many other primates have menstrual cycles.
 If pregnancy does not occur, the endometrium is shed through the cervix and vagina in
menstruation.
 Other mammals have estrous cycles.
 If pregnancy does not occur, the uterus reabsorbs the endometrium.
 Estrous cycles are associated with more pronounced behavioral cycles than are
menstrual cycles.
 The period of sexual activity, estrus, is the only time the condition of the vagina
permits mating.
 Human females may be sexually receptive throughout their menstrual cycle.
 The term menstrual cycle refers specifically to the changes that occur in the uterus, and is
also called the uterine cycle.
 It is caused by cyclic events that occur in the ovaries, the ovarian cycle.
 The cycle begins with the release from the hypothalamus of GnRH or gonadotropin-
releasing hormone, which stimulates the pituitary to secrete small amounts of FSH and
LH.
 FSH stimulates follicle growth, aided by LH, or luteinizing hormone, and the cells of
the growing follicles start to make estrogen.
 There is a slow rise in estrogen secreted during the follicular phase, the part of the
ovarian cycle in which follicles are growing and oocytes maturing.
 The low level of estrogen inhibits secretion of the pituitary hormones, keeping FSH and
LH levels low.
 The levels of FSH and LH shoot up when the secretion of estrogen by the growing
follicle rises sharply.

Biology Chapter Notes

  The high concentration of estrogen stimulates the secretion of gonadotropins by
acting on the hypothalamus to increase its output of GnRH.
 This stimulates the secretion of FSH and LH.
 LH secretion is especially high, because the high concentration of estrogen
increases the sensitivity of LH-releasing cells in the pituitary to GnRH.
 LH induces the final maturation of the follicle and ovulation.
 The follicle and adjacent wall of the ovary rupture, releasing the secondary oocyte.
 Following ovulation, during the luteal phase of the ovarian cycle, LH stimulates the
transformation of the follicle into the corpus luteum, a glandular structure.
 Under the continued stimulation by LH during this phase, the corpus luteum secretes
progesterone and estrogen.
 As the levels of these hormones rise, they exert negative feedback on the
hypothalamus and pituitary, inhibiting the secretion of LH and FSH.
 Near the end of the luteal phase, the corpus luteum disintegrates, causing concentrations
of estrogen and progesterone to decline.
 The pituitary and hypothalamus are liberated from the inhibitory effects of these
hormones.
 The pituitary begins to secrete enough FSH to stimulate the growth of new follicles in
the ovary, initiating the next ovarian cycle.
 The follicular phase of the ovarian cycle is coordinated with the proliferative phase of
the menstrual cycle.
 Secretion of estrogens during the follicular phase stimulates endometrial thickening.
 The estrogen and progesterone of the luteal phase stimulate development and
maintenance of the endometrium, including the enlargement of arteries and the growth
of endometrial glands.
 The glands secrete a nutrient fluid that can sustain an early embryo before it
implants in the uterine lining.
 Thus, the luteal phase of the ovarian cycle is coordinated with the secretory phase
of the uterine cycle.
 The rapid drop in ovarian hormones as the corpus luteum disintegrates causes spasms in
the uterine lining, depriving it of blood.
 The upper two-thirds of the endometrium disintegrates, resulting in menstruation, or the
menstrual flow phase of the uterine cycle, and the beginning of a new cycle.
 During menstruation, new ovarian follicles begin to grow.
 Estrogen is also responsible for female secondary sex characteristics, including
deposition of fat in the breasts and hips, increased water retention, and stimulation of
breast development.
 It also influences sexual behavior.
 Menopause, the cessation of ovarian and menstrual cycles, usually occurs between ages
46 and 54.
 During these years, the ovaries lose their responsiveness to FSH and LH, and
menopause results from a decline in estrogen production by the ovary.
 Menopause is an unusual phenomenon.
 In most species, females and males retain their reproductive capacity throughout life.
 There might be an evolutionary explanation for menopause.

Biology Chapter Notes

  One hypothesis proposes that cessation of reproduction allowed a woman to provide
better care for her children and grandchildren, increasing the survival of individuals
bearing her genes and increasing her fitness.
The principle sex hormones in the male are the androgens.
 The male sex hormones, androgens, are steroid hormones produced mainly by the Leydig
cells of the testes, interstitial cells near the seminiferous tubules.
 Testosterone, the most important male androgen, and other androgens are responsible for
the primary and secondary male sex characteristics.
 Primary sex characteristics are associated with the development of the vas deferens
and other ducts, development of the external reproductive structures, and sperm
production.
 Secondary sex characteristics are features not directly related to the reproductive
system, including deepening of the voice, distribution of facial and pubic hair, and
muscle growth.
 Androgens also affect behavior.
 In addition to specific sexual behaviors and sex drive, androgens increase general
aggressiveness.
 They are responsible for vocal behavior, like singing in birds and calling by frogs.
 Hormones from the anterior pituitary and hypothalamus control androgen secretion and
sperm production by the testes.

Concept 46.5 In humans and other placental mammals, an embryo grows into a
newborn in the mother’s uterus
 In placental mammals, pregnancy or gestation is the condition of carrying one or more
embryos.
 A human pregnancy averages 266 days.
 Many rodents have gestation periods of 21 days. Cows have a gestation of 27 days, and
elephant gestation lasts 600 days.
 Fertilization or conception occurs in the oviduct.
 Twenty-four hours later, cleavage begins.
 Three to four days after fertilization, the embryo reaches the uterus as a ball of cells.
 By one week past fertilization, the blastocyst forms as a sphere of cells containing a
cavity.
 After a few more days, the blastocyst implants in the endometrium.
 The embryo secretes hormones to signal its presence and control the mother’s
reproductive system.
 Human chorionic gonadotropin (HCG) acts like pituitary LH to maintain secretion
of progesterone and estrogens by the corpus luteum for the first few weeks of
pregnancy.
 Some HCG is excreted in the urine, where it is detected by pregnancy tests.
 Human gestation is divided into three trimesters of three months each.
 For the first 2–4 weeks of development, the embryo obtains nutrients from the
endometrium.
 The outer layer of the blastocyst, called the trophoblast invades the endometrium,
eventually helping to form the placenta.
Biology Chapter Notes
  The placenta allows diffusion of material between maternal and embryonic
circulations, providing nutrients, exchanging respiratory gases, and disposing of
metabolic wastes for the embryo.
 Blood from the embryo travels to the placenta and returns via the umbilical vein.
 Organogenesis occurs during the first trimester.
 By the end of week four, the heart is beating.
 By the end of week eight, all the major structures of the adult are present in
rudimentary form.
 The rapidity of development makes this a time when the embryo is especially
sensitive to environmental insults such as radiation or drugs.
 High levels of progesterone initiate changes in the maternal reproductive system.
 These include increased mucus in the cervix to form a protective plug, growth of
the maternal part of the placenta, enlargement of the uterus, and cessation of
ovarian and menstrual cycling.
 The breasts enlarge rapidly and may be very tender.
 During the second trimester, the fetus grows rapidly to 30 cm and is very active.
 The mother may feel movements during the early part of the second trimester.
 Hormonal levels stabilize as HCG declines, the corpus luteum deteriorates, and the
placenta takes over the secretion of progesterone, which maintains the pregnancy.
 During the third trimester, the fetus grows rapidly to about 3–4 kg in weight and 50 cm in
length.
 Fetal activity may decrease as the fetus fills the space available to it.
 Maternal abdominal organs become compressed and displaced, leading to frequent
urination, digestive blockages, and back strain.
 A complex interplay of local regulators (prostaglandins) and hormones (estrogen and
oxytocin) induces and regulates labor.
 The mechanism that triggers labor is not fully understood.
 In one possible model, high levels of estrogen induce the formation of oxytocin
receptors on the uterus.
 Oxytocin, produced by the fetus and the mother’s posterior pituitary, stimulates
powerful contractions by the smooth muscles of the uterus.
 Oxytocin also stimulates the placenta to secrete prostaglandins, which enhance the
contractions.
 The physical and emotional stress associated with the contractions stimulate the release
of more oxytocin and prostaglandins, a positive feedback system that underlies the
process of labor.
 Birth, or parturition, is brought about by strong, rhythmic uterine contractions.
 The process of labor has three stages.
 The first stage is the opening up and thinning of the cervix, ending in complete
dilation.
 The second stage is the expulsion of the baby as a result of strong uterine
contractions.
 The third stage is the expulsion of the placenta.
 Lactation is unique to mammals.
 After birth, decreasing levels of progesterone free the anterior pituitary from negative
feedback and allow prolactin secretion.
Biology Chapter Notes
  Prolactin stimulates milk production 2–3 days after birth.
 The release of milk from the mammary glands is controlled by oxytocin.
 Reproductive immunologists are working to understand why mammalian mothers do not
reject the embryo as a foreign body, despite its paternal antigens.
 The trophoblast may inhibit a maternal immune response against the embryo by
releasing signal molecules with immunosuppressive effects.
 These include HCG, a variety of protein “factors,” a prostaglandin, several
interleukins, and an interferon.
 Some combination of these substances may interfere with immune rejection by
acting on the mother’s T lymphocytes.
 A different hypothesis suggests that the trophoblast and later the placenta secrete an
enzyme that rapidly breaks down local supplies of tryptophan, an amino acid necessary
for T cell survival and function.
 This enzyme is essential for maintaining pregnancy in mice.
 Another possibility is the absence of certain histocompatibility antigens on placenta
cells and the secretion of a hormone that induces synthesis of a “death activator”
protein (FasL) on placental cells.
 Activated T cells have a complementary “death receptor” (Fas), and the binding of
FasL to Fas causes the T cells to self-destruct by apoptosis.
 Contraception can be achieved in several ways.
 Some methods prevent the release of mature secondary oocytes and sperm from
gonads, others prevent fertilization by keeping sperm and egg apart, and still others
prevent implantation of an embryo.
 Fertilization can be prevented by abstinence from sexual intercourse or by any of
several barriers that keep sperm and egg apart.
 Temporary abstinence is called the rhythm method of birth control.
 This means of natural family planning depends on refraining from intercourse
when conception is most likely.
 Ovulation can be detected by noting changes in cervical mucus and body
temperature during the menstrual cycle.
 Natural family planning brings a pregnancy rate of 10–20%.
 As a method of preventing fertilization, coitus interruptus, or withdrawal (removal of
the penis from the vagina before ejaculation), is unreliable.
 Sperm may be present in secretions that precede ejaculation.
 The several barrier methods of contraception that block sperm from meeting the egg
have pregnancy rates of less than 10%.
 The condom used by the male is a thin latex or natural membrane sheath that fits over
the penis to collect the semen.
 The diaphragm is a dome-shaped rubber cap that fits into the upper portion of the
vagina before intercourse.
 Both methods are more effective when used in conjunction with a spermicide.
 Birth control pills are chemical contraceptives with a pregnancy rate of less than 1%.
 The most commonly used birth control pills are a combination of a synthetic estrogen
and progestin (progesterone-like hormone).
 This combination acts by negative feedback to stop the release of GnRH by the
hypothalamus and, thus, of FSH and LH by the pituitary.
 The prevention of LH release prevents ovulation.
Biology Chapter Notes
  As a backup mechanism, the inhibition of FSH secretion by the low dose of
estrogen in the pills prevents follicles from developing.
 A second type of birth control pill, the minipill, contains only progestin.
 It does not effectively block ovulation, and it is not as effective a contraceptive as the
combination pill.
 The minipill prevents fertilization mainly by causing thickening of a woman’s
cervical mucus so it blocks sperm from entering the uterus.
 It also causes changes in the endometrium that interfere with implantation.
 Combination pills carry a slightly elevated risk of abnormal blood clotting, high blood
pressure, heart attack, and stroke.
 However, they decrease the risk of ovarian and endometrial cancers.
 Sterilization is the permanent prevention of gamete release.
 Tubal ligation in women involves cauterization or ligation of a section of the
oviducts to prevent the eggs from traveling into the uterus.
 Vasectomy in men is the cutting of each vas deferens to prevent sperm from
entering the urethra.
 Abortion is the termination of a pregnancy.
 Spontaneous abortion or miscarriage occurs in as many of one-third of all
pregnancies.
 In addition, 1.5 million American women choose abortions performed by
physicians each year.
 A drug called mifepristone, or RU-486, enables a woman to terminate pregnancy
nonsurgically within the first seven weeks.
 An analogue of progesterone, RU-486 blocks progesterone reception in the
uterus, preventing progesterone from maintaining pregnancy.
 It is taken with a small amount of prostaglandin to induce uterine contractions.

Modern technology offers solutions for some reproductive problems.

 It is now possible to diagnose many genetic and congenital abnormalities while the fetus
is in the uterus.
 Amniocentesis and chorionic villus sampling are invasive techniques in which amniotic
fluid or fetal cells are obtained for genetic analysis.
 Commonly used noninvasive techniques use ultrasound imaging to detect fetal conditions.
 A newer noninvasive method uses the fact that maternal blood contains fetal blood
cells that can be tested.
 A maternal blood sample yields fetal cells that can be identified by specific antibodies
and tested for genetic disorders.
 Reproductive technology can help with infertility treatments.
 Hormone therapy can increase sperm and egg production.
 Surgery can correct blocked oviducts.
 Many infertile couples use assisted reproductive technology (ART).
 These procedures involve surgical removal of secondary oocytes from a woman’s
body, fertilizing them, and returning them to the woman’s body.
 With in vitro fertilization, the most common ART procedure, the oocytes are
mixed with sperm in culture dishes and inserted in the woman’s uterus at the eight-
cell stage or beyond.

Biology Chapter Notes

  In ZIFT (zygote intrafallopian transfer), eggs are also fertilized in vitro, but zygotes
are transferred immediately to the woman’s fallopian tubes.
 In GIFT (gamete intrafallopian transfer), the eggs are not fertilized in vitro.
 Instead, the eggs and sperm are placed in the woman’s oviducts in the hope that
fertilization will occur there.
 These techniques are performed throughout the world and have resulted in thousands of
children.

Biology Chapter Notes

 Chapter 47 Animal Development
Chapter Notes

Overview: A Body-Building Plan for Animals

From egg to organism, an animal’s form develops gradually.

 The question of how a zygote becomes an animal has been asked for centuries.
 As recently as the 18th century, the prevailing idea was preformation, the notion that an
egg or sperm contains an embryo that is a preformed miniature adult.
 The competing theory is epigenesis, proposed 2,000 years earlier by Aristotle.
 According to epigenesis, the form of an animal emerges from a relatively formless egg.
 As microscopy improved in the 19th century, biologists could see that embryos took
shape in a series of progressive steps.
 Epigenesis displaced preformation as the favored explanation among embryologists.
 Both preformation and epigenesis have some legitimacy.
 Although the embryo’s form emerges gradually as it develops, aspects of the
developmental plan are already in place in the eggs of many species.
 An organism’s development is primarily determined by the genome of the zygote and
also by differences that arise between early embryonic cells.
 These differences set the stage for the expression of different genes in different cells.
 In some species, early embryonic cells become different because of the uneven
distribution within the unfertilized egg of maternal substances called cytoplasmic
determinants.
 These substances affect development of the cells that inherit them during the early
mitotic divisions of the embryo.
 In other species, the differences between cells are due to their location in the developing
embryo.
 Most species establish differences between early embryonic cells by a combination of
these two mechanisms.
 As development continues, selective gene expression leads to cell differentiation, the
specialization of cells in structure and function.
 Along with cell division and differentiation, development involves morphogenesis, the
process by which an animal takes shape.

Concept 47.1 After fertilization, embryonic development proceeds through cleavage,

gastrulation, and organogenesis
Fertilization activates the egg and brings together the nuclei of sperm and egg.
 The gametes (egg and sperm) are both highly specialized cell types.
 Fertilization combines haploid sets of chromosomes from two individuals into a single
diploid cell, the zygote.
 Another key function of fertilization is activation of the egg.
Biology Chapter Notes
  Contact of the sperm with the egg’s surface initiates metabolic reactions within the egg
that trigger the onset of embryonic development.
 Sea urchin fertilization has been extensively studied.
 Sea urchin egg and sperm encounter each other after the animals release their gametes
into seawater.
 The jelly coat of the egg attracts the sperm, which swims toward the egg.
 When the head of the sperm comes into contact with the jelly coat, the acrosomal
reaction is triggered, and the acrosome, a specialized vesicle at the tip of the sperm,
discharges its contents by exocytosis.
 Hydrolytic enzymes enable the acrosomal process to penetrate the egg’s jelly coat.
 The tip of the acrosomal process adheres to special receptor proteins on the egg’s
surface.
 These receptors extend through the vitelline layer, just external to the egg’s plasma
membrane.
 This lock-and-key recognition ensures that eggs will be fertilized only by sperm of the
same species.
 The sperm and egg plasma membranes fuse, and the sperm nucleus enters the egg’s
cytoplasm.
 Na+ channels in the egg’s plasma membrane open.
 Na+ flows into the egg, and the membrane depolarizes, changing the membrane
potential of the egg.
 Such depolarization is common in animals.
 Occurring within 1–3 seconds after the sperm binds to the egg, depolarization prevents
additional sperm from fusing with the egg’s plasma membrane.
 This fast block to polyspermy prevents polyspermy, the fertilization of the egg by
multiple sperm.
 Fusion of egg and sperm plasma membranes triggers a signal-transduction pathway.
 Ca2+ from the egg’s endoplasmic reticulum is released into the cytosol and propagates
as a wave across the fertilized egg.
 High concentrations of Ca2+ cause cortical granules to fuse with the plasma membrane
and release their contents into the perivitelline space, the space between the plasma
membrane and the vitelline layer.
 The vitelline layer separates from the plasma membrane.
 An osmotic gradient draws water into the perivitelline space, swelling it and pushing it
away from the plasma membrane.
 The vitelline layer hardens into a fertilization envelope, which resists the entry of
additional sperm.
 The fertilization envelope and other changes in the egg’s surface function together as a
long-term slow block to polyspermy.
 The plasma membrane returns to normal, and the fast block to polyspermy no longer
functions.
 High concentrations of Ca2+ in the egg stimulate an increase in the rates of cellular
respiration and protein synthesis, activating the egg.
 Unfertilized eggs can be activated artificially by the injection of Ca 2+ or by a variety of
mildly injurious treatments, such as temperature shock.
 It is even possible to activate an egg that has had its nucleus removed.
Biology Chapter Notes
  Evidently, proteins and mRNAs present in the cytoplasm of the unfertilized egg are
sufficient for egg activation.
 As the metabolism of the activated egg increases, the sperm nucleus swells and merges
with the egg nucleus, creating the diploid nucleus of the zygote.
 DNA synthesis begins and the first cell division occurs about 90 minutes after
fertilization.
 Fertilization in terrestrial animals, including mammals, is generally internal.
 Secretions in the mammalian female reproductive tract alter certain molecules on the
surface of sperm cells and increase sperm motility.
 The mammalian egg is surrounded by follicle cells also released during ovulation.
 A sperm must migrate through a layer of follicle cells before it reaches the zona
pellucida, the extracellular matrix of the egg.
 Binding of the sperm cell to a receptor on the zona pellucida induces an acrosomal
reaction similar to that seen in the sea urchin.
 Enzymes from the acrosome enable the sperm cell to penetrate the zona pellucida and
bind to the egg’s plasma membrane.
 The binding of the sperm cell to the egg triggers changes within the egg, leading to a
cortical reaction, the release of enzymes from cortical granules to the outside via
exocytosis.
 The released enzymes catalyze alteration of the zona pellucida, which functions as a
slow block to polyspermy.
 The entire sperm, tail and all, enters the egg.
 A centrosome forms around the centriole that acted as the basal body of the sperm’s
flagellum.
 This centrosome duplicates to form the two centrosomes of the zygote.
 These will generate the mitotic spindle for the first cell division.
 The envelopes of both egg and sperm nuclei disperse.
 The chromosomes from the two gametes share a common spindle apparatus during the
first mitotic division of the zygote.
 Only after the first division, as diploid nuclei form in the two daughter cells, do the
chromosomes from the two parents come together in a common nucleus.
 Fertilization is much slower in mammals than in the sea urchin.
 The first cell division occurs 12–36 hours after sperm binding in mammals.
Cleavage partitions the zygote into many smaller cells.
 A succession of rapid cell divisions called cleavage follows fertilization.
 During this period, cells go through the S (DNA synthesis) and M (mitosis) phases of
the cell cycle but may skip the G1 and G2 phases.
 As a result, little or no protein synthesis occurs.
 The first five to seven divisions form a cluster of cells known as the morula.
 A fluid-filled cavity called the blastocoel forms within the morula, which becomes a
hollow ball of cells called the blastula.
 The zygote is partitioned into many smaller cells called blastomeres.
 Each blastomere contains different regions of the undivided cytoplasm and, thus,
may contain different cytoplasmic determinants.

Biology Chapter Notes

 Most animals have both eggs and zygotes with a definite polarity.
 Thus, the planes of division follow a specific pattern relative to the poles of the zygote.
 Polarity is defined by the heterogeneous distribution of substances such as mRNA,
proteins, and yolk.
 Yolk is most concentrated at the vegetal pole and least concentrated at the animal
pole.
 In amphibians, a rearrangement of the egg cytoplasm occurs at the time of fertilization.
 The plasma membrane and cortex rotate toward the point of sperm entry.
 The gray crescent is exposed, marking the dorsal surface of the embryo.
 Molecules in the vegetal cortex are now able to interact with inner cytoplasmic
molecules in the animal hemisphere, leading to the formation of cytoplasmic
determinants that will later initiate development of dorsal structures.
 Thus, cortical rotation establishes the dorsal-ventral (back-belly) axis of the zygote.
 In frogs, the first two cleavages are vertical and result in four blastomeres of equal size.
 The third division is horizontal, producing an eight-celled embryo with two tiers of
four cells.
 The unequal division of yolk displaces the mitotic apparatus and cytokinesis toward
the animal end of the dividing cells in equatorial divisions.
 As a result, animal blastomeres are smaller than those in the vegetal hemisphere.
 Continued cleavage produces a morula and then a blastula.
 Because of unequal cell division, the blastocoel is located in the animal hemisphere.
 Animals with less yolk (such as the sea urchin) also have an animal-vegetal axis.
 However, the blastomeres are similar in size, and the blastocoel is centrally located.
 Yolk has its most pronounced effect on cleavage in the eggs of reptiles, many fishes, and
insects.
 The yolk of a chicken egg is actually an egg cell, swollen with yolk nutrients.
 Cleavage of a fertilized bird’s egg is restricted to a small disk of yolk-free cytoplasm,
while yolk remains uncleaved.
 The incomplete division of a yolk-rich egg is meroblastic cleavage.
 It contrasts with holoblastic cleavage, the complete cleavage of eggs with little or
moderate yolk.
 Early cleavage in a bird embryo produces a cap of cells called the blastoderm, which
rests on undivided egg yolk.
 The blastomeres sort into upper and lower layers, the epiblast and the hypoblast.
 The cavity between these two layers is the avian version of the blastocoel.
 This stage is the avian equivalent of the blastula.
 In insects, the zygote’s nucleus is located within the mass of yolk.
 Cleavage begins with the nucleus undergoing mitotic divisions, unaccompanied by
cytokinesis.
 These mitotic divisions produce several hundred nuclei, which migrate to the outer
edge of the embryo.
 After several more rounds of mitosis, plasma membranes form around each nucleus,
and the embryo, the equivalent of a blastula, consists of a single layer of 6,000 cells
surrounding a mass of yolk.

Biology Chapter Notes

 Gastrulation rearranges the blastula to form a three-layered embryo with a primitive gut.
 Gastrulation rearranges the embryo into a triploblastic gastrula.
 The embryonic germ layers are the ectoderm, the outer layer of the gastrula; the
mesoderm, which fills the space between ectoderm and endoderm; and the endoderm,
which lines the embryonic gut.
 Sea urchin gastrulation begins at the vegetal pole where individual cells detach from the
blastula wall and enter the blastocoel as migratory mesenchyme cells.
 The remaining cells flatten to form a vegetal plate that buckles inward in a process
called invagination.
 The buckled vegetal plate undergoes extensive rearrangement of its cells,
transforming the shallow invagination into a primitive gut, or archenteron.
 The open end, the blastopore, will become the anus.
 An opening at the other end of the archenteron will form the mouth of the
digestive tube.
 Frog gastrulation produces a triploblastic embryo with an archenteron.
 Where the gray crescent was located, invagination forms the dorsal lip of the
blastopore.
 Cells on the dorsal surface roll over the edge of the dorsal lip and into the interior of
the embryo, a process called involution.
 Once inside the embryo, these cells move away from the blastopore and become
organized into layers of endoderm and mesoderm, with endoderm on the inside.
 As the process is completed, the lip of the blastopore encircles a yolk plug.
 Gastrulation in the chick is similar to frog gastrulation in that it involves cells moving
from the surface of the embryo to an interior location.
 In birds, the inward movement of cells is affected by the large mass of yolk.
 All the cells that will form the embryo come from the epiblast.
 During gastrulation, some epiblast cells move toward the midline of the blastoderm
then detach and move inward toward the yolk.
 These cells produce a thickening called the primitive streak, which runs along
what will become the bird’s anterior-posterior axis.
 The primitive steak is the functional equivalent of the frog blastopore.
 Some of the inward-moving epiblast cells displace hypoblast cells and form the
endoderm.
 Other epiblast cells move laterally into the blastocoel, forming the mesoderm.
 The epiblast cells that remain on the surface form ectoderm.

 The hypoblast is required for normal development and seems to help direct the formation
of the primitive streak.
 Some hypoblast cells later form portions of the yolk sac.
In organogenesis, the organs of the animal body form from the three embryonic germ
layers.
 Various regions of the three embryonic germ layers develop into the rudiments of organs
during the process of organogenesis.
 While gastrulation involves mass cell movements, organogenesis involves more localized
morphogenetic changes in tissue and cell shape.
 The first organs to form in the frog are the neural tube and notochord.
Biology Chapter Notes
  The notochord is formed from dorsal mesoderm that condenses above the archenteron.
 Signals sent from the notochord to the overlying ectoderm cause that region of notochord
to become neural plate.
 This process is often seen in organogenesis: one germ layer signaling another to
determine the fate of the second layer.
 The neural plate curves inward, rolling itself into a neural tube that runs along the
anterior-posterior axis of the embryo.
 The neural tube becomes the brain and spinal cord.
 Unique to vertebrate embryos is a band of cells called the neural crest, which develops
along the border where the neural tube pinches off from the ectoderm.
 Neural crest cells migrate throughout the embryo, forming many cell types.
 Some have proposed calling neural crest cells the “fourth germ layer.”
 Somites form in strips of mesoderm lateral to the notochord.
 The somites are arranged serially on both sides along the length of the notochord.
 Mesenchyme cells migrate from the somites to new locations.
 The notochord is the core around which the vertebrae form.
 Parts of the notochord persist into adulthood as the inner portions of vertebral disks.
 Somite cells also form the muscles associated with the axial skeleton.
 Lateral to the somites, the mesoderm splits into two layers that form the lining of the
coelom.
 As organogenesis progresses, morphogenesis and cell differentiation refine the organs that
form from the three germ layers.
 Embryonic development leads to an aquatic, herbivorous tadpole larva, which later
metamorphoses into a terrestrial, carnivorous adult frog.
 The derivatives of the ectoderm germ layer include epidermis of skin and its derivatives,
epithelial lining of the mouth and rectum, cornea and lens of the eyes, the nervous system,
adrenal medulla, tooth enamel, and the epithelium of the pineal and pituitary glands.
 The endoderm germ layer contributes to the epithelial linings of the digestive tract (except
the mouth and rectum), respiratory system, pancreas, thyroid, parathyroids, thymus,
urethra, urinary bladder, and reproductive system.
 Derivatives of the mesoderm germ layer are the notochord, the skeletal and muscular
systems, the circulatory and lymphatic systems, the excretory system, the reproductive
system (except germ cells), the dermis of skin, the lining of the body cavity, and the
adrenal cortex.
Amniote embryos develop in a fluid-filled sac within a shell or uterus.
 The amniote embryo is the solution to reproduction in a dry environment.
 The shelled eggs of birds and other reptiles, as well as monotreme mammals, and the
uterus of placental mammals provide an aqueous environment for development.
 Within the shell or uterus, the embryos of these animals are surrounded by fluid within
a sac formed by a membrane called the amnion.
 Reptiles (including birds) and mammals are thus amniotes.
 Amniote development includes the formation of four extraembryonic membranes: yolk
sac, amnion, chorion, and allantois.
 The cells of the yolk sac digest yolk, providing nutrients to the embryo.
Biology Chapter Notes
  The amnion encloses the embryo in a fluid-filled amniotic sac that protects the embryo
from drying out.
 The chorion cushions the embryo against mechanical shocks and works with the
allantois to exchange gases between the embryo and the surrounding air.
 The allantois functions as a disposal sac for uric acid and functions with the chorion as
a respiratory organ.
Mammalian development has some unique features.
 The eggs of most mammals are very small, storing little food.
 Early cleavage is relatively slow in mammals.
 In humans, the first division is complete after 36 hours, the second division after 60
hours, and the third division after 72 hours.
 Relatively slow cleavage produces equal-sized blastomeres.
 At the eight-cell stage, the blastomeres become tightly adhered to one another, causing
the outer surface to appear smooth.
 At completion of cleavage, the embryo has more than 100 cells arranged around a
central cavity.
 The blastocyst travels down the oviduct to reach the uterus.
 Clustered at one end of the blastocyst is a group of cells called the inner cell mass that
develops into the embryo and contributes to all the extraembryonic membranes.
 The trophoblast, the outer epithelium of the blastocyst, secretes enzymes that break down
the endometrium to facilitate implantation of the blastocyst.
 The trophoblast thickens, projecting fingerlike projections into the surrounding
maternal tissue, which is rich in vascular tissue.
 Invasion by the trophoblast leads to erosion of the capillaries in the surrounding
endometrium, causing the blood to spill out and bathe trophoblast tissue.
 At the time of implantation, the inner cell mass forms a flat disk with an upper layer of
cells, the epiblast, and a lower layer, the hypoblast.
 As in birds, the human embryo develops almost entirely from the epiblast.
 As implantation is completed, gastrulation begins.
 Cells move inward from the epiblast through the primitive streak to form mesoderm
and endoderm.
 At the same time, extraembryonic membranes develop.
 The trophoblast continues to expand into the endometrium.
 The invading trophoblast, mesodermal cells derived from the epiblast, and adjacent
endometrial tissue all contribute to the formation of the placenta.
 The embryonic membranes of mammals are homologous with those of birds and other
mammals.
 The chorion, which completely surrounds the embryo and other embryonic
membranes, functions in gas exchange.
 The amnion encloses the embryo in a fluid-filled amniotic cavity.
 The yolk sac encloses another fluid-filled cavity, which contains no yolk.
 The yolk sac membrane of mammals is the site of early formation of blood cells,
which later migrate to the embryo.
 The fourth extraembryonic membrane, the allantois, is incorporated into the umbilical
cord, where it forms blood vessels that transport oxygen and nutrients from the
placenta to the embryo and rid the embryo of carbon dioxide and nitrogenous wastes.
Biology Chapter Notes
 The extraembryonic membranes of reptiles, where embryos are nourished with yolk, were
conserved as mammals diverged in the course of evolution but with modifications adapted
to development within the reproductive tract of the mother.
 The completion of gastrulation is followed by the first events of organogenesis: the
formation of the neural tube, notochord, and somites.

Concept 47.2 Morphogenesis in animals involves specific changes in cell shape, position,
and adhesion
 Morphogenesis is a major aspect of development in plants and animals, but only in
animals does it involve cell movement.
 Movement of parts of a cell can bring about changes in cell shape.
 It can also enable a cell to migrate from one place to another within the embryo.
 Changes in cell shape and cell position are involved in cleavage, gastrulation, and
organogenesis.
 Changes in the shape of a cell usually involve the reorganization of the cytoskeleton.
 Consider how the cells of the neural plate form the neural tube.
 First, the microtubules oriented parallel to the dorsal-ventral axis of the embryo help to
lengthen the cells in that direction.
 At the dorsal end of each cell is a parallel array of actin filaments oriented crosswise.
 These contract, giving the cells a wedge shape that bends the ectoderm inward.
 Similar changes in cell shape occur during other invaginations and evaginations of
tissue layers throughout development.
 The cytoskeleton is also drives cell migration.
 Cells “crawl” within the embryo by extending cytoplasmic fibers to form cellular
protrusions, in a manner akin to amoeboid movement.
 The cellular protrusions of migrating embryonic cells are usually flat sheets
(lamellipodia) or spikes (filopodia).
 During gastrulation, invagination is initiated by the wedging of cells on the surface of
the blastula, but the movement of cells deeper into the embryo involves the extension
of filopodia by cells at the leading edge of the migrating tissue.
 The cells that first move through the blastopore and along the inside of the
blastocoel drag others along behind them as a sheet of cells.
 This involuted sheet of cells forms the endoderm and mesoderm of the embryo.
 Cell crawling is also involved in convergent extension, a type of morphogenetic
movement in which the cells of a tissue layer rearrange themselves so the sheet
converges and extends, becoming narrower but longer.
 Convergent extension allows the archenteron to elongate in the sea urchin and frog
and is responsible for the change in shape of a frog embryo from spherical to
submarine shaped.
 The movements of convergent extension probably involve the extracellular matrix
(ECM), a mixture of secreted glycoproteins lying outside the plasma membrane.
 ECM fibers may direct cell movement by functioning as tracks, directing migrating
cells along particular routes.
 Some ECM substances, such as fibronectins, help cells migrate by providing
anchorage for crawling.
 Other ECM substances may inhibit migration in certain directions.
Biology Chapter Notes
 In frog gastrulation, fibronectin fibers line the roof of the blastocoel.
 As the future mesoderm moves into the interior of the embryo, cells at the free edge of
the mesodermal sheet migrate along these fibers.
 Researchers can prevent the attachment of cells to fibronectin (and prevent inward
movement of the mesoderm) by injecting embryos with antifibronectin antibodies.
 As migrating cells move along specific paths through the embryo, receptor proteins on
their surfaces pick up directional cues from the immediate environment.
 Such signals from the ECM can direct the orientation of cytoskeletal elements to
propel the cell in the proper direction.
 Cell adhesion molecules (CAMs), located on cell surfaces, bind to CAMs on other cells.
 CAMs vary in amount and chemical identity with cell type.
 These differences help to regulate morphogenetic movement and tissue binding.
 Cadherins are also involved in cell-to-cell adhesion.
 Cadherins require the presence of calcium for proper function.
 There are many cadherins, and the gene for each cadherin is expressed in specific
locations at specific times during embryonic development.

Concept 47.3 The developmental fate of cells depends on their history and on inductive
signals
 Development requires the timely differentiation of cells in specific locations.
 Two general principles integrate the current understanding of the genetic and cellular
mechanisms that underlie differentiation during embryonic development.
 First, during early cleavage divisions, embryonic cells must somehow become different
from one another.
 In many animal species, initial differences result from uneven distribution of
cytoplasmic determinants (mRNAs, proteins, and other molecules) in the unfertilized
egg.
 The resulting differences in the cytoplasmic composition of cells help specify body
axes and influence the expression of genes that affect the developmental fate of cells.
 For example, the cells of the inner cell mass are located internally in the early
human embryo, while trophoblast cells are located on the outer surface of the
blastocyst.
 The difference in cell environment determines the fate of these cells.
 Second, once initial cell asymmetries are set up, subsequent interactions among the
embryonic cells influence their fate, usually by causing changes in gene expression.
 This mechanism is termed induction.
 Induction, which brings about the differentiation of many specialized cell types, is
mediated by diffusible chemical signals or by cell-surface interactions.
Fate mapping can reveal cell genealogies in chordate embryos.
 Fate maps illustrate the developmental history of cells.
 In classic experiments in the 1920s, German embryologist Vogt charted fate maps for
different regions of early amphibian embryos.
 His work provided evidence that the lineage of cells making up the three germ layers
created by gastrulation is traceable to cells in the blastula, before gastrulation begins.
Biology Chapter Notes
 Developmental biologists have combined fate-mapping studies with experimental
manipulation of parts of embryos.
 Two important conclusions have emerged.
 “Founder cells” give rise to specific tissues in older embryos.
 As development proceeds, a cell’s developmental potential (the range of structures it
can form) becomes restricted.
The eggs of most vertebrates have cytoplasmic determinants that help establish the body
axes.
 A bilaterally symmetrical animal has an anterior-posterior axis, a dorsal-ventral axis, and
left and right sides.
 Establishing this basic body plan is a first step in morphogenesis and a prerequisite for
the development of tissues and organs.
 In frogs, locations of melanin and yolk define the animal and vegetal hemispheres
respectively.
 The animal-vegetal axis indirectly determines the anterior-posterior body axis.
 Fertilization in frogs triggers cortical rotation, which establishes the dorsal-ventral axis
and leads to the appearance of the gray crescent, whose position marks the dorsal side.
 Once any two axes are established, the third (right-left) is specified by default.
 Molecular mechanisms then carry out the program associated with that axis.
 In amniotes, body axes are not fully established until later.
 In chicks, gravity is involved in establishing the anterior-posterior axis as the egg
travels down the oviduct before being laid.
 Later, pH differences between the two sides of the blastoderm establish the dorsal-
ventral axis.
 In mammals, no polarity is obvious until after cleavage, although recent research suggests
that the orientation of the egg and sperm nuclei before fusion may play a role in
determining the axes.
 In many species with cytoplasmic determinants, only the zygote is totipotent, capable of
developing into all cell types found in the adult.
 The fate of embryonic cells is affected by both the distribution of cytoplasmic
determinants and cleavage pattern.
 In frogs, the first cleavage occurs along an axis that produces two identical blastomeres
with identical developmental potential.
 The cells of the mammalian embryo remain totipotent until the 16-cell stage, when they
become arranged into the precursors of the trophoblast and inner cell mass of the
blastocyst.
 At that time, location determines cell fate.
 At the 8-cell stage, each of the blastomeres of the mammalian embryo can form a
complete embryo if isolated.
 The progressive restriction of potency is a general feature of development in animals.
 In some species, the cells of the early gastrula retain the capacity to give rise to more
than one kind of cell, although they are no longer totipotent.
 In general, the tissue-specific fates of cells in the late gastrula are fixed.
 Even if manipulated experimentally, they will give rise to the same type of cells as
in a normal embryo.
Biology Chapter Notes
 Inductive signals play an important role in cell fate determination and pattern formation.
 Once embryonic cell division creates cells that are different from one another, the cells
begin to influence each other’s fates by induction.
 At the molecular level, the effect of induction is usually the switching on of a set of
genes that make the receiving cells differentiate into a specific tissue.
 In the 1920s, Hans Spemann and Hilde Mangold carried out a set of transplantation
experiments.
 These experiments showed that the dorsal lip of the blastopore in an early gastrula
serves as an organizer of the embryo by initiating a chain of inductions that results in
the formation of the notochord, neural tube, and other organs.
 Developmental biologists are working to identify the molecular basis of induction by
Spemann’s organizer (also called the gastrula organizer or simply the organizer).
 A growth factor called bone morphogenetic protein 4 (BMP-4) is active exclusively in
cells on the ventral side of the amphibian gastrula.
 BMP-4 induces those cells to form ventral structures.
 Organizer cells inactivate BMP-4 on the dorsal side of the embryo by producing
proteins that bind to BMP-4, rendering it unable to signal.
 This allows formation of dorsal structures such as the notochord and neural tube.
 Proteins related to BMP-4 and its inhibitors are also found in other animals, suggesting
that they evolved long ago and may participate in development in many different
organisms.
 Many inductions involve a sequence of inductive steps that progressively determine the
fate of cells.
 In late gastrula of the frog, ectoderm cells destined to form the lenses of the eyes
receive inductive signals from the ectodermal cells that will form the neural plate.
 Later, inductive signals from the optic cup, an outgrowth of the developing brain,
complete the determination of lens-forming cells.
 Inductive signals play a major role in pattern formation, the development of an animal’s
spatial information.
 Positional information, supplied by molecular cues, tells a cell where it is relative to
the animal’s body axes.
 Limb development in chicks serves as a model of pattern formation.
 Wings and legs of chicks begin as bumps of tissue called limb buds.
 Each component of a chick limb develops with a precise location and orientation
relative to three axes, the proximal-distal axis (shoulder-to-fingertip), the anterior-
posterior axis (thumb-to-little-finger), and the dorsal-ventral axis (knuckle-to-palm).
 A limb bud consists of a core of mesodermal tissue covered by a layer of ectoderm.
 Two critical organizer regions are present in all vertebrate limb buds.
 The cells of these regions secrete proteins that provide key positional information to
the other cells of the bud.
 One limb-bud organizer region is the apical ectodermal ridge (AER), a thickened area of
ectoderm at the tip of the bud.
 The AER is required for the outgrowth of the limb along the proximal-distal axis and
for patterning along this axis.
 The cells of the AER produce several secreted protein signals, belonging to the
fibroblast growth factor (FGF) family.
Biology Chapter Notes
  These signals promote limb-bud outgrowth.
 If the AER is surgically removed and beads soaked in FGF are put in its place, a nearly
normal limb will develop.
 The AER (and other limb-bud ectoderms) also appears to guide pattern formation along
the limb’s dorsal-ventral axis.
 If the ectoderm of the limb bud, including the AER, is detached from the mesoderm
and rotated 180° back-to-front, the limb elements that form have reversed dorsal-
ventral orientation.
 The second major limb-bud organizer region is the zone of polarizing activity (ZPA), a
block of mesodermal tissue located underneath the ectoderm where the posterior side of
the bud is attached to the body.
 The ZPA is necessary for proper pattern formation along the anterior-posterior axis of
the limb.
 Cells nearest the ZPA give rise to posterior structures (such as our little finger); cells
farthest from the ZPA form anterior structures (such as our thumb).
 Tissue transplantation experiments support the hypothesis that the ZPA produces an
inductive signal that conveys positional information indicating “posterior.”
 The cells of the ZPA secrete a protein growth factor called Sonic hedgehog.
 If cells genetically engineered to produce large amounts of Sonic hedgehog are
implanted in the anterior region of a normal limb bud, a mirror-image limb bud
results.
 Extra toes and fingers in mice (and maybe humans) result from the production
of Sonic hedgehog in the wrong part of the limb bud.
 We can conclude from these experiments that pattern formation requires cells to receive
and interpret environmental cues that vary with location.
 These cues tell cells where they are in the 3-D realm of a developing organ.
 Organizers such as the AER and the ZPA function as signaling centers.
 The AER and ZPA also interact with each other via signaling molecules and signaling
pathways, to influence each other’s developmental fates.
 What determines whether a limb bud develops into a forelimb or a hindlimb?
 The cells receiving signals from the AER and ZPA respond according to their own
developmental histories.
 Earlier developmental signals have set up patterns of gene expression that distinguish
future forelimbs from future hindlimbs.
 Construction of a fully formed animal involves a sequence of events that include many
steps of signaling and differentiation.
 Initial cell asymmetries allow different types of cells to influence each other to express
specific sets of genes.
 The products of these genes direct cells to differentiate into specific types.
 Coordinated with morphogenesis, various pathways of pattern formation occur in all
the different parts of the developing embryo.
 These processes produce a complex arrangement of multiple tissues and organs, each
functioning in the appropriate location to form a coordinated organism.

Biology Chapter Notes

 Chapter 48 Nervous Systems
Chapter Notes

Overview: Command and Control Center

 The human brain contains an estimated 1011 (100 billion) neurons.

 Each neuron may communicate with thousands of other neurons in complex
information-processing circuits.
 Recently developed technologies can record brain activity from outside the skull.
 One technique is functional magnetic resonance imaging (fMRI), which reconstructs a
3-D map of the subject’s brain activity.
 The results of brain imaging and other research methods show that groups of neurons
function in specialized circuits dedicated to different tasks.
The ability of cells to respond to the environment has evolved over billions of years.
 The ability to sense and react originated billions of years ago with prokaryotes that could
detect changes in their environment and respond in ways that enhanced their survival and
reproductive success.
 Such cells could locate food sources by chemotaxis.
 Later, modification of this simple process provided multicellular organisms with a
mechanism for communication between cells of the body.
 By the time of the Cambrian explosion, systems of neurons that allowed animals to sense
and move rapidly had evolved in essentially modern form.

Concept 48.1 Nervous systems consist of circuits of neurons and supporting cells
Nervous systems show diverse patterns of organization.
 All animals except sponges have some type of nervous system.
 What distinguishes nervous systems of different animal groups is how the neurons are
organized into circuits.
 Cnidarians have radially symmetrical bodies organized around a gastrovascular cavity.
 In hydras, neurons controlling the contraction and expansion of the gastrovascular
cavity are arranged in diffuse nerve nets.
 The nervous systems of more complex animals contain nerve nets, as well as nerves,
which are bundles of fiberlike extensions of neurons.
 With cephalization come more complex nervous systems.
 Neurons are clustered in a brain near the anterior end in animals with elongated,
bilaterally symmetrical bodies.
 In simple cephalized animals such as the planarian, a small brain and longitudinal nerve
cords form a simple central nervous system (CNS).
 In more complex invertebrates, such as annelids and arthropods, behavior is regulated by
more complicated brains and ventral nerve cords containing segmentally arranged clusters
of neurons called ganglia.

Biology Chapter Notes

  Nerves that connect the CNS with the rest of the animal’s body make up the
peripheral nervous system (PNS).
 The nervous systems of molluscs correlate with lifestyle.
 Clams and chitons have little or no cephalization and simple sense organs.
 Squids and octopuses have the most sophisticated nervous systems of any
invertebrates, rivaling those of some vertebrates.
 The large brain and image-forming eyes of cephalopods support an active,
predatory lifestyle.
Nervous systems consist of circuits of neurons and supporting cells.
 In general, there are three stages in the processing of information by nervous systems:
sensory input, integration, and motor output.
 Sensory neurons transmit information from sensors that detect external stimuli (light,
heat, touch) and internal conditions (blood pressure, muscle tension).
 Sensory input is conveyed to the CNS, where interneurons integrate the sensory
input.
 Motor output leaves the CNS via motor neurons, which communicate with effector cells
(muscle or endocrine cells).
 Effector cells carry out the body’s response to a stimulus.
 The stages of sensory input, integration, and motor output are easy to study in the simple
nerve circuits that produce reflexes, the body’s automatic responses to stimuli.
Networks of neurons with intricate connections form nervous systems.
 The neuron is the structural and functional unit of the nervous system.
 The neuron’s nucleus is located in the cell body.
 Arising from the cell body are two types of extensions: numerous dendrites and a single
axon.
 Dendrites are highly branched extensions that receive signals from other neurons.
 An axon is a longer extension that transmits signals to neurons or effector cells.
 The axon joins the cell body at the axon hillock, where signals that travel down the
axon are generated.
 Many axons are enclosed in a myelin sheath.
 Near its end, axons divide into several branches, each of which ends in a synaptic
terminal.
 The site of communication between a synaptic terminal and another cell is called a
synapse.
 At most synapses, information is passed from the transmitting neuron (the presynaptic
cell) to the receiving cell (the postsynaptic cell) by means of chemical messengers
called neurotransmitters.
 Glia are supporting cells that are essential for the structural integrity of the nervous
system and for the normal functioning of neurons.
 There are several types of glia in the brain and spinal cord.
 Astrocytes are found within the CNS.
 They provide structural support for neurons and regulate the extracellular
concentrations of ions and neurotransmitters.

Biology Chapter Notes

  Some astrocytes respond to activity in neighboring neurons by facilitating
information transfer at those neuron’s synapses.
 By inducing the formation of tight junctions between capillary cells, astrocytes help
form the blood-brain barrier, which restricts the passage of substances into the
CNS.
 In an embryo, radial glia form tracks along which newly formed neurons migrate from
the neural tube.
 Both radial glia and astrocytes can also act as stem cells, generating neurons and
other glia.
 Oligodendrocytes (in the CNS) and Schwann cells (in the PNS) are glia that form
myelin sheaths around the axons of vertebrate neurons.
 These sheaths provide electrical insulation of the axon.
 In multiple sclerosis, myelin sheaths gradually deteriorate, resulting in a
progressive loss of body function due to the disruption of nerve signal transmission.

Concept 48.2 Ion pumps and ion channels maintain the resting potential of a neuron
Every cell has a voltage, or membrane potential, across its plasma membrane.
 All cells have an electrical potential difference (voltage) across their plasma membrane).
 This voltage is called the membrane potential.
 In neurons, the membrane potential is typically between −60 and −80 mV when the
cell is not transmitting signals.
 The membrane potential of a neuron that is not transmitting signals is called the resting
potential.
 In all neurons, the resting potential depends on the ionic gradients that exist across the
plasma membrane.
 In mammals,+
the extracellular fluid has a Na+ concentration of 150 millimolar (mM)
and a K of 5 mM.
 In the cytosol, Na+ concentration is 15 mM, and K+ concentration is 150 mM.
 These gradients are maintained by the sodium-potassium pump.
 The magnitude of the membrane voltage at equilibrium, called the equilibrium potential
(Eion), is given by a formula called the Nernst equation.
 For an ion with a net charge of +1, the Nernst equation is:
 Eion = 62mV (log [ion]outside/[ion]inside)
 The Nernst equation applies to any membrane that is permeable to a single type of ion.
 In our model, the membrane is only permeable to K+ +, and the Nernst equation can be
used to calculate EK, the equilibrium potential for K .
 With this K+ concentration gradient, K+ is at equilibrium when the inside of the
membrane is 92 mV more negative than the outside.
 Assume that the membrane is only permeable to Na+.
 ENa, the equilibrium potential+
for Na+, is +62 mV, indicating that, with this Na+
concentration gradient, Na is at equilibrium when the inside of the membrane is 62
mV more positive than the outside.
 How does a real mammalian neuron differ from these model neurons?
 The plasma membrane of a real neuron at rest has many open potassium channels, but it
also has a relatively small number of open sodium channels.
Biology Chapter Notes
 Consequently, the resting potential is around −60 to −80 mV, between EK and ENa.
 Neither K+ nor Na + is at equilibrium, and there is a net flow of each ion (a current)
across the membrane at rest.
 The resting membrane potential remains steady, which means that the K + and Na+ currents
are equal and opposite.
 The reason the +resting potential is closer to E K than to ENa is that the membrane is more
permeable to K than to Na+.
 If something causes the membrane’s permeability to Na + to increase, the membrane
potential will move toward ENa and away from EK.
 This is the basis of nearly all electrical signals in the nervous system.
 The membrane potential can change from its resting value when the membrane’s
permeability to particular ions changes.
 Sodium and potassium play major roles, but there are also important roles for chloride and
calcium ions.
 The resting potential results from the diffusion of K + and Na+ through ion channels that
are always open.
 These channels are ungated.
 Neurons also have gated ion channels, which open or close in response to one of three
types of stimuli.
 Stretch-gated ion channels are found in cells that sense stretch, and open when the
membrane is mechanically deformed.
 Ligand-gated ion channels are found at synapses and open or close when a specific
chemical, such as a neurotransmitter, binds to the channel.
 Voltage-gated ion channels are found in axons (and in the dendrites and cell bodies of
some neurons, as well as in some other types of cells) and open or close in response to
a change in membrane potential.

Concept 48.3 Action potentials are the signals conducted by axons

 Gated ion channels are responsible for generating the signals of the nervous system.
 If a cell has gated ion channels, its membrane potential may change in response to
stimuli that open or close those channels.
 Some stimuli trigger a hyperpolarization, an increase in the magnitude of the membrane
potential.
 Gated K+ channels open, K+ diffuses out of the cell, and the inside of the membrane
becomes more negative.
 Other stimuli trigger a depolarization, a reduction in the magnitude of the membrane
potential.
 Gated Na+ channels open, Na+ diffuses into the cell, and the inside of the membrane
becomes less negative.
 These changes in membrane potential are called graded potentials because the magnitude
of the change—either hyperpolarization or depolarization—varies with the strength of the
stimulus.
 A larger stimulus causes a larger change in membrane permeability and, thus, a larger
change in membrane potential.

Biology Chapter Notes

 In most neurons, depolarizations are graded only up to a certain membrane voltage, called
the threshold.
 A stimulus strong enough to produce a depolarization that reaches the threshold triggers a
different type of response, called an action potential.
 An action potential is an all-or-none phenomenon.
 Once triggered, it has a magnitude that is independent of the strength of the triggering
stimulus.
 Action potentials of neurons are very brief—only 1–2 milliseconds in duration.
 This allows a neuron to produce them at high frequency.
 Both voltage-gated Na+ channels and voltage-gated K+ channels are involved in the
production of an action potential.
 Both types of channels are opened+ by depolarizing the membrane, but they respond
independently and sequentially: Na channels open before K+ channels.
 Each voltage-gated Na+ channel has two gates, an activation gate and an inactivation gate,
and both must be open for Na+ to diffuse through the channel.
 At the resting potential, the activation gate is closed and the inactivation gate is open
on most Na+ channels.
 Depolarization of the membrane rapidly opens the activation gate and slowly closes the
inactivation gate.
 Each voltage-gated K+ channel has just one gate, an activation gate.
 At the resting potential, the activation gate on most K+ channels is closed.
 Depolarization of the membrane slowly opens the K+ channel’s activation gate.
 How do these channel properties contribute to the production of an action potential?
 When a stimulus depolarizes +
the membrane, the activation gates on some Na + channels
open, allowing more Na to diffuse into the cell.
 The Na++ influx causes further depolarization, which opens the activation gates on still
more Na channels, and so on.
 Once the threshold is crossed, this positive-feedback cycle rapidly brings the membrane
potential close to ENa during the rising phase.
 However, two events prevent the membrane potential from actually reaching E Na.
 The inactivation gates on most Na+ channels close, halting Na+ influx.
 The activation gates on most K+ channels open, causing a rapid efflux of K+.
 Both events quickly bring the membrane potential back toward E K during the falling
phase.
 In fact, in the final+ phase of an action potential, called the undershoot, the membrane’s
permeability to K is higher than at rest, so the membrane potential is closer to EK than
it is at the resting potential.
 The K+ channels’ activation gates eventually close, and the membrane potential returns to
the resting potential.
 The Na+ channels’ inactivation gates remain closed during the falling phase and the early
part of the undershoot.
 As a result, if a second depolarizing stimulus occurs during this refractory period, it
will be unable to trigger an action potential.
Nerve impulses propagate themselves along an axon.
Biology Chapter Notes
 The action potential is repeatedly regenerated along the length of the axon.
 An action potential achieved at one region of the membrane is sufficient to depolarize
a neighboring region above the threshold level, thus triggering a new action potential.
 Immediately behind the+ traveling zone of depolarization due to Na+ influx is a zone of
repolarization due to K efflux.
 In the repolarized zone, the activation gates of Na+ channels are still closed.
 Consequently, the inward current that depolarizes the axon membrane ahead of the
action potential cannot produce another action potential behind it.
 Once an action potential starts, it normally moves in only one direction—toward the
synaptic terminals.
 Several factors affect the speed at which action potentials are conducted along an axon.
 One factor is the diameter of the axon: the larger the axon’s diameter, the faster the
conduction.
 In the myelinated neurons of vertebrates, voltage-gated Na+ and K+ channels are
concentrated at gaps in the myelin sheath called nodes of Ranvier.
 Only these unmyelinated regions of the axon depolarize.
 Thus, the impulse moves faster than in unmyelinated neurons.
 This mechanism is called saltatory conduction.

Concept 48.4 Neurons communicate with other cells at synapses

 When an action potential reaches the terminal of the axon, it generally stops there.
 However, information is transmitted from a neuron to another cell at the synapse.
 Some synapses, called electrical synapses, contain gap junctions that do allow electrical
current to flow directly from cell to cell.
 Action potentials travel directly from the presynaptic to the postsynaptic cell.
 In both vertebrates and invertebrates, electrical synapses synchronize the activity of
neurons responsible for rapid, stereotypical behaviors.
 The vast majority of synapses are chemical synapses, which involve the release of
chemical neurotransmitter by the presynaptic neuron.
 The presynaptic neuron synthesizes the neurotransmitter and packages it in synaptic
vesicles, which are stored in the neuron’s synaptic terminals.
 When an action potential reaches a terminal, it depolarizes the terminal membrane,
opening voltage-gated calcium channels in the membrane.
 Calcium ions (Ca2+) then diffuse into the terminal, and the rise in Ca 2+ concentration in the
terminal causes some of the synaptic vesicles to fuse with the terminal membrane,
releasing the neurotransmitter by exocytosis.
 The neurotransmitter diffuses across the narrow gap, called the synaptic cleft, which
separates the presynaptic neuron from the postsynaptic cell.
 The effect of the neurotransmitter on the postsynaptic cell may be direct or indirect.
 Information transfer at the synapse can be modified in response to environmental
conditions.
 Such modification may form the basis for learning or memory.
Neural integration occurs at the cellular level.

Biology Chapter Notes

 At many chemical synapses, ligand-gated ion channels capable of binding to the
neurotransmitter are clustered in the membrane of the postsynaptic cell, directly opposite
the synaptic terminal.
 Binding of the neurotransmitter to the receptor opens the channel and allows specific ions
to diffuse across the postsynaptic membrane.
 This mechanism of information transfer is called direct synaptic transmission.
 The result is generally a postsynaptic potential, a change in the membrane potential of
the postsynaptic cell.
 Excitatory postsynaptic potentials (EPSPs) depolarize the postsynaptic neuron.
 The binding of neurotransmitter to postsynaptic receptors opens gated channels that
allow Na+ to diffuse into and K+ to diffuse out of the cell.
 Inhibitory postsynaptic potential (IPSP) hyperpolarizes the postsynaptic neuron.
 The binding of neurotransmitter to postsynaptic receptors open gated channels that
allow K+ to diffuse out of the cell and/or Cl− to diffuse into the cell.
 Various mechanisms end the effect of neurotransmitters on postsynaptic cells.
 The neurotransmitter may simply diffuse out of the synaptic cleft.
 The neurotransmitter may be taken up by the presynaptic neuron through active
transport and repackaged into synaptic vesicles.
 Glia actively take up the neurotransmitter at some synapses and metabolize it as fuel.
 The neurotransmitter acetylcholine is degraded by acetylcholinesterase, an enzyme in
the synaptic cleft.
 Postsynaptic potentials are graded; their magnitude varies with a number of factors,
including the amount of neurotransmitter released by the presynaptic neuron.
 Postsynaptic potentials do not regenerate but diminish with distance from the synapse.
 Most synapses on a neuron are located on its dendrites or cell body, whereas action
potentials are generally initiated at the axon hillock.
 Therefore, a single EPSP is usually too small to trigger an action potential in a
postsynaptic neuron.
 Graded potentials (EPSPs and IPSPs) are summed to either depolarize or hyperpolarize a
postsynaptic neuron.
 Two EPSPs produced in rapid succession at the same synapse can be added in an effect
called temporal summation.
 Two EPSPs produced nearly simultaneously by different synapses on the same
postsynaptic neuron can be added, in an effect called spatial summation.
 Summation also applies to IPSPs.
 This interplay between multiple excitatory and inhibitory inputs is the essence of
integration in the nervous system.
 The axon hillock is the neuron’s integrating center, where the membrane potential at
any instant represents the summed effect of all EPSPs and IPSPs.
 Whenever the membrane potential at the axon hillock reaches the threshold, an action
potential is generated and travels along the axon to its synaptic terminals.
 In indirect synaptic transmission, a neurotransmitter binds to a receptor that is not part of
an ion channel.
 This binding activates a signal transduction pathway involving a second messenger in
the postsynaptic cell.
 This form of transmission has a slower onset, but its effects have a longer duration.
Biology Chapter Notes
 cAMP acts as a secondary messenger in indirect synaptic transmission.
 When the neurotransmitter norepinephrine binds to its receptor, the neurotransmitter-
receptor complex activates a G-protein, which in turn activates adenylyl cyclase, the
enzyme that converts ATP to cAMP.
 cAMP activates protein kinase A, which phosphorylates specific channel proteins in
the postsynaptic membrane, causing them to open or close.
 Because of the amplifying effect of the signal transduction pathway, the binding of a
neurotransmitter to a single receptor can open or close many channels.
The same neurotransmitter can produce different effects on different types of cells.
 Each of the known neurotransmitters binds to a specific group of receptors.
 Some neurotransmitters have a dozen or more receptors, which can produce very
different effects in postsynaptic cells.
 Acetylcholine is one of the most common neurotransmitters in both invertebrates and
vertebrates.
 In the vertebrate CNS, it can be inhibitory or excitatory, depending on the type of
receptor.
 At the vertebrate neuromuscular junction, acetylcholine released by the motor neuron
binds to receptors on ligand-gated channels in the muscle cell, producing an EPSP via
direct synaptic transmission.
 Nicotine binds to the same receptors.
 Acetylcholine is inhibitory to cardiac muscle cell contraction.
 Biogenic amines are neurotransmitters derived from amino acids.
 One group, known as catecholamines, consists of neurotransmitters produced from the
amino acid tyrosine.
 This group includes epinephrine and norepinephrine and a closely related compound
called dopamine.
 Another biogenic amine, serotonin, is synthesized from the amino acid tryptophan.
 The biogenic amines are usually involved in indirect synaptic transmission, most
commonly in the CNS.
 Dopamine and serotonin affect sleep, mood, attention, and learning.
 Imbalances in these neurotransmitters are associated with several disorders.
 Parkinson’s disease is associated with a lack of dopamine in the brain.
 LSD and mescaline produce hallucinations by binding to brain receptors for
serotonin and dopamine.
 Depression is treated with drugs that increase the brain concentrations of biogenic
amines such as norepinephrine and serotonin.
 Prozac inhibits the uptake of serotonin after its release, increasing its effect.
 Four amino acids function as neurotransmitters in the CNS: gamma aminobutyric acid
(GABA), glycine, glutamate, and aspartate.
 GABA is the neurotransmitter at most inhibitory synapses in the brain, where it
produces IPSPs.
 Several neuropeptides, relatively short chains of amino acids, serve as neurotransmitters.
 Most neurons release one or more neuropeptides as well as a nonpeptide
neurotransmitter.
 Neuropeptides usually operate via signal transduction pathways.

Biology Chapter Notes

  The neuropeptide substance P is a key excitatory neurotransmitter that mediates our
perception of pain.
 Other neuropeptides, endorphins, act as natural analgesics.
 Opiates such as morphine and heroin bind to receptors on brain neurons by
mimicking endorphins, which are produced in the brain under times of physical or
emotional stress.
 Some neurons of the vertebrate PNS and CNS release dissolved gases, especially nitric
oxide and carbon monoxide, which act as local regulators.
 During male sexual arousal, certain neurons release NO into the erectile tissue of the
penis.
 In response, smooth muscle cells in the blood vessel walls of the erectile tissue relax,
allowing the blood vessels to dilate and fill the spongy erectile tissue with blood,
producing an erection.
 Viagra inhibits an enzyme that slows the muscle-releasing effects of NO.
 Carbon monoxide is synthesized by the enzyme heme oxygenase.
 In the brain, CO regulates the release of hypothalamic hormones.
 In the PNS, it acts as an inhibitory neurotransmitter that hyperpolarizes intestinal
smooth muscle cells.
 NO and CO are synthesized by cells as needed.
 They diffuse into neighboring target cells, produce an effect, and are broken down, all
within a few seconds.

Concept 48.5 The vertebrate nervous system is regionally specialized

Vertebrate nervous systems have central and peripheral components.
 In all vertebrates, the nervous system shows a high degree of cephalization and has
distinct CNS and PNS components.
 The brain provides integrative power that underlies the complex behavior of
vertebrates.
 The spinal cord integrates simple responses to certain kinds of stimuli and conveys
information to and from the brain.
 The vertebrate CNS is derived from the dorsal embryonic nerve cord, which is hollow.
 In the adult, this feature persists as the narrow central canal of the spinal cord and the
four ventricles of the brain.
 Both the canal and the ventricles are filled with cerebrospinal fluid, which is formed
in the brain by filtration of the blood.
 Cerebrospinal fluid circulates through the central canal and ventricles and then drains
into the veins, assisting in the supply of nutrients and hormone and the removal of
wastes.
 In mammals, the fluid cushions the brain and spinal cord by circulating between two of
the meninges, layers of connective tissue that surround the CNS.
 White matter of the CNS is composed of bundles of myelinated axons.
 Gray matter consists of unmyelinated axons, nuclei, and dendrites.
The divisions of the peripheral nervous system interact in maintaining homeostasis.

Biology Chapter Notes

 The PNS transmits information to and from the CNS and plays an important role in
regulating the movement and internal environment of a vertebrate.
 The vertebrate PNS consists of left-right pairs of cranial and spinal nerves and their
associated ganglia.
 Paired cranial nerves originate in the brain and innervate the head and upper body.
 Paired spinal nerves originate in the spinal cord and innervate the entire body.
 The PNS can be divided into two functional components: the somatic nervous system and
the autonomic nervous system.
 The somatic nervous system carries signals to and from skeletal muscle, mainly in
response to external stimuli.
 It is subject to conscious control, but much skeletal muscle activity is actually
controlled by reflexes mediated by the spinal cord or the brainstem.
 The autonomic nervous system regulates the internal environment by controlling smooth
and cardiac muscles and the organs of the digestive, cardiovascular, excretory, and
endocrine systems.
 Three divisions make up the autonomic nervous system: sympathetic, parasympathetic,
and enteric.
 Activation of the sympathetic division correlates with arousal and energy
generation—the “flight or fight” response.
 Activation of the parasympathetic division generally promotes calming and a
return to self-maintenance functions—“rest and digest.”
 When sympathetic and parasympathetic neurons innervate the same organ, they
often have antagonistic effects.
 The enteric division consists of complex networks of neurons in the digestive tract,
pancreas, and gallbladder.
 The enteric networks control the secretions of these organs as well as activity in
the smooth muscles that produce peristalsis.
 The sympathetic and parasympathetic divisions normally regulate the enteric
division.
 The somatic and autonomic nervous systems often cooperate in maintaining
homeostasis.
Embryonic development of the vertebrate brain reflects its evolution from three anterior
bulges of the neural tube.
 In all vertebrates, three bilaterally symmetrical, anterior bulges of the neural tube form the
forebrain, midbrain, and hindbrain during embryonic development.
 Over vertebrate evolution, the brain became further divided structurally and functionally,
providing additional complex integration.
 The forebrain is particularly enlarged in birds and mammals.
 Five brain regions form by the fifth week of human embryonic development.
 The telencephalon and diencephalon develop from the forebrain.
 The mesencephalon develops from the midbrain.
 The metencephalon and myelencephalon develop from the hindbrain.
 The telencephalon gives rise to the cerebrum.
 Rapid growth of the telencephalon during the second month of human development
causes the outer portion of the cerebrum, the cerebral cortex, to extend over the rest
of the brain.
Biology Chapter Notes
 The adult brainstem consists of the midbrain (derived from the mesencephalon), the pons
(derived from the metencephalon), and the medulla oblongata (derived from the
myelencephalon).
 The metencephalon also gives rise to the cerebellum.
Evolutionarily older structures of the vertebrate brain regulate essential automatic and
integrative functions.
 The brainstem is one of the evolutionarily older parts of the brain.
 Sometimes called the “lower brain,” it consists of the medulla oblongata, pons, and
midbrain.
 The brain stem functions in homeostasis, coordination of movement, and conduction of
impulses to higher brain centers.
 Centers in the brainstem contain neuron cell bodies that send axons to many areas of the
cerebral cortex and cerebellum, releasing neurotransmitters.
 Signals in these pathways cause changes in attention, alertness, appetite, and
motivation.
 The medulla oblongata contains centers that control visceral (autonomic, homeostatic)
functions, including breathing, heart and blood vessel activity, swallowing, vomiting, and
digestion.
 The pons also participates in some of these activities.
 It regulates the breathing centers in the medulla.
 Information transmission to and from higher brain regions is one of the most important
functions of the medulla and pons.
 The two regions also help coordinate large-scale body movements.
 Axons carrying instructions about movement from the midbrain and forebrain to the
spinal cord cross from one side of the CNS to the other in the medulla.
 The right side of the brain controls the movement of the left side of the body, and vice
versa.
 The midbrain contains centers involved in the receipt and integration of sensory
information.
 Superior colliculi are involved in the regulation of visual reflexes.
 Inferior colliculi are involved in the regulation of auditory reflexes.
 The midbrain relays information to and from higher brain centers.
 The reticular activating system (RAS) of the reticular formation regulates sleep and
arousal.
 Acting as a sensory filter, the RAS selects which information reaches the cerebral
cortex.
 The more information the cortex receives, the more alert and aware the person is.
 The brain can ignore some stimuli while actively processing other input.
 Sleep and wakefulness are regulated by specific parts of the brainstem.
 The pons and medulla contain centers that cause sleep when stimulated, and the
midbrain has a center that causes arousal.
 Serotonin may be the neurotransmitter of the sleep-producing centers.
 All birds and mammals show characteristic sleep/wake cycles.
 Melatonin, a hormone produced by the pineal gland, appears to play an important
role in these cycles.
Biology Chapter Notes
  The function of sleep is still not fully understood.
 One hypothesis is that sleep is involved in the consolidation of learning and
memory, and experiments show that regions of the brain activated during a learning
task can become active again during sleep.
 The cerebellum develops from part of the metencephalon.
 It functions to error-check and coordinate motor activities, and perceptual and
cognitive functions.
 The cerebellum is involved in learning and remembering motor skills.
 It relays sensory information about joints, muscles, sight, and sound to the cerebrum.
 The cerebellum also coordinates motor commands issued by the cerebrum.
 The embryonic diencephalon develops into three adult brain regions: the epithalamus,
thalamus, and hypothalamus.
 The epithalamus includes the pineal gland and the choroid plexus, one of several
clusters of capillaries that produce cerebrospinal fluid from blood.
 The thalamus relays all sensory information to the cerebrum and relays motor
information from the cerebrum.
 Incoming information from all the senses is sorted in the thalamus and sent to the
appropriate cerebral centers for further processing.
 The thalamus also receives input from the cerebrum and other parts of the brain that
regulate emotion and arousal.
 Although it weighs only a few grams, the hypothalamus is a crucial brain region for
homeostatic regulation.
 It is the source of posterior pituitary hormones and releasing hormones that act on
the anterior pituitary.
 The hypothalamus also contains centers involved in thermoregulation, hunger,
thirst, sexual and mating behavior, and pleasure.
 Animals exhibit circadian rhythms, one being the sleep/wake cycle.
 The biological clock is an internal timekeeper that regulates a variety of physiological
phenomena, including hormone release, hunger, and sensitivity to external stimuli.
 In mammals, the hypothalamic suprachiasmatic nuclei (SCN) function as a biological
clock.
 The clock’s rhythm requires external cues to remain synchronized with
environmental cycles.
 Experiments in which humans have been deprived of external cues have shown that
the human biological clock has a period of 24 hours and 11 minutes.
The cerebrum is the most highly developed structure of the mammalian brain.
 The cerebrum is derived from the embryonic telencephalon and is divided into left and
right cerebral hemispheres.
 Each hemisphere consists of an outer covering of gray matter, the cerebral cortex; internal
white matter; and groups of neurons deep within the white matter called basal nuclei.
 The basal nuclei are important centers for planning and learning movement sequences.
 In humans, the largest and most complex part of the brain is the cerebral cortex.
 It is here that sensory information is analyzed, motor commands are issued, and
language is generated.
 The cerebral cortex underwent a dramatic expansion when the ancestors of mammals
diverged from reptiles.
Biology Chapter Notes
 Mammals have a region of the cerebral cortex known as the neocortex.
 The neocortex forms the outermost part of the mammalian cerebrum, consisting of six
parallel layers of neurons running tangential to the brain surface.
 The human neocortex is highly convoluted, allowing the region to have a large surface
area and still fit inside the skull.
 Although less than 5 mm thick, the human neocortex has a surface area of about
0.5m2 and accounts for about 80% of the total brain mass.
 Nonhuman primates and cetaceans also have exceptionally large, convoluted
neocortices.
 The surface area relative to body size of a porpoise’s neocortex is second only to
that of a human.
 The cerebral cortex is divided into right and left sides.
 The left hemisphere is primarily responsible for the right side of the body.
 The right hemisphere is primarily responsible for the left side of the body.
 A thick band of axons known as the corpus callosum is the major connection between the
two hemispheres.
 Damage to one area of the cerebrum early in development can frequently cause
redirection of its normal functions to other areas.

Concept 48.6 The cerebral cortex controls voluntary movement and cognitive functions
 The cerebrum is divided into frontal, temporal, occipital, and parietal lobes.
 Researchers have identified a number of functional areas within each lobe.
 These areas include primary sensory areas, each of which receives and processes a
specific type of sensory information, and association areas, which integrate the
information from various parts of the brain.
 The major increase in the size of the neocortex that occurred during mammalian evolution
was mostly an expansion of the association areas that integrate higher cognitive functions
and make more complex behavior and learning possible.
 Most sensory information coming into the cortex is directed via the thalamus to primary
sensory areas within the lobes: visual information to the occipital lobe; auditory input to
the temporal lobe; and somatosensory information about touch, pain, pressure,
temperature, and position of limbs and muscles to the parietal lobe.
 In mammals, olfactory information is first sent to regions in the cortex that are similar
in mammals and reptiles, and then via the thalamus to an interior part of the frontal
lobe.
 Based on the integrated sensory information, the cerebral cortex can generate motor
commands that cause specific behaviors.
 These commands consist of action potentials produced by neurons in the primary
motor cortex, which lies at the rear of the frontal lobe.
 The action potentials travel along axons to the brainstem and spinal cord, where they
excite motor neurons, which in turn excite skeletal muscle cells.
 In both the somatosensory cortex and the motor cortex, neurons are distributed in an
orderly fashion according to the part of the body that generates the sensory input or
receives the motor command.
 The cortical surface area devoted to each body part is not related to the size of the part.

Biology Chapter Notes

  Instead it is related to the number of sensory neurons that innervate that part (for the
somatosensory cortex) or the amount of skill needed to control muscles in that part (for
the motor cortex).
 During brain development, competing functions segregate and displace each other in the
cortex of the left and right cerebral hemispheres, resulting in lateralization of brain
function.
 The left hemisphere specializes in language, math, logic operations, and the processing
of serial sequences of information, and fine visual and auditory details.
 It specializes in detailed activities required for motor control.
 The right hemisphere specializes in pattern recognition, spatial relationships, nonverbal
ideation, emotional processing, and the parallel processing of information.
 Understanding and generating the stress and intonation patterns of speech that
convey its emotional content is primarily a right-hemisphere function, as is musical
appreciation.
 The right hemisphere specializes in perceiving the relationship between images and the
whole context in which they occur, whereas the left hemisphere is better at focused
perception.
 The two hemispheres work together, exchanging information through the fibers of the
corpus callosum.
 Broca’s area, located in the left hemisphere’s frontal lobe, is responsible for speech
production.
 Wernicke’s area, located in the right hemisphere’s temporal lobe, is responsible for
speech comprehension.
 Studies of brain activity using fMRI and positron-emission tomography (PET) confirm
that Broca’s area is active during the generation of speech, while Wernicke’s area is
active when speech is heard.
 These areas are part of a larger network of brain regions involved in language,
including the visual cortex (for reading) and frontal and temporal areas that are
involved in generating verbs to match nouns and grouping together related words and
concepts.
 Emotions are the result of a complex interplay of many regions of the brain.
 The limbic system is a ring of structures around the brainstem, including three parts of
the cerebral cortex—the amygdala, hippocampus, and olfactory bulb—along with some
inner portions of the cortex’s lobes, and parts of the thalamus and hypothalamus.
 These structures interact with sensory areas of the neocortex to mediate primary
emotions that result in laughing or crying.
 It also attaches emotional “feelings” to basic, survival-level functions controlled by the
brainstem, including aggression, feeding, and sexuality.
 The limbic system is central to crucial mammalian behaviors involved in emotional
bonding and extended nurturing of infants.
 The amygdala, a structure in the temporal lobe, is central in recognizing the emotional
content of facial expression and laying down emotional memories.
 This emotional memory system seems to appear earlier in development than the
system that supports explicit recall of events, which requires the hippocampus.
 As children develop, primary emotions such as pleasure and fear are associated with
different situations in a process that requires portions of the neocortex, especially the
prefrontal cortex.

Biology Chapter Notes

  Damage to regions of the frontal cortex may leave the patient’s intelligence and
memories intact, but destroy their motivation, foresight, goal formation, and decision
making.
 Frontal lobotomy was a widely performed surgical procedure in which the connection
between the prefrontal cortex and the limbic system was disrupted.
 This technique was used to treat severe emotional problems.
 It resulted in docility and the loss of ability to concentrate, plan, and work toward
goals.
 Drug therapy has replaced frontal lobotomy.
 Short-term memories are stored in the frontal lobes and released as they become
irrelevant.
 Should we wish to retain knowledge of short-term memories, long-term memories are
established by mechanisms involving the hippocampus.
 The transfer of information from short-term to long-term memory is enhanced by
repetition (“practice makes perfect”), positive or negative emotional states mediated by
the amygdala, and the association of the new data with previously stored information.
 Many sensory and motor association areas of the cerebral cortex outside Broca’s area and
Wernicke’s area are involved in storing and retrieving words and images.
 The memorization of information can be very rapid and may rely mainly on rapid changes
in the strength of existing neural connections.
 In contrast, the slow learning and remembering of skills and procedures appear to
involve the formation of new connections between neurons, by cellular mechanisms
similar to those responsible for brain growth and development.
 Motor skills are usually learned by repetition.
 It is possible to perform such skills without consciously recalling the individual steps
involved.
 Nobel laureate Eric Kandel and his colleagues at Columbia University studied the cellular
basis of learning using the sea hare, Aplysia californica.
 They were able to explain the mechanism of simple forms of learning in the mollusc in
terms of changes in the strength of synaptic transmission between specific sensory and
motor neurons.
 In the vertebrate brain, a form of learning called long-term potentiation (LTP) involves
an increase in the strength of synaptic transmission that occurs when presynaptic neurons
produce a brief, high-frequency series of action potentials.
 LTP can last for days or weeks and may be a fundamental process by which memories
are stored or learning takes place.
 The cellular mechanism of LTP has been studied most thoroughly at synapses in the
hippocampus, where presynaptic neurons release the excitatory neurotransmitter
glutamate.
 The postsynaptic neurons possess two types of glutamate receptors: AMPA receptors and
NMDA receptors.
 AMPA receptors are part of ligand-gated ion channels.
 When glutamate binds to them, Na+ and K+ diffuse through the channels, and the
postsynaptic membrane depolarizes.
 NMDA receptors are part of channels that are both ligand-gated and voltage-gated.
 The channels open only if glutamate is bound and the membrane is depolarized.
Biology Chapter Notes
 The binding of glutamate to these two types of receptors can lead to LTP through changes
in both the presynaptic and postsynaptic neurons.
 Neuroscientists have begun studying human consciousness using brain-imaging
techniques such as fMRI.
 Brain imaging can show neural activity associated with conscious perceptual choices
and unconscious processing of sensory information.
 Such studies offer an increasingly detailed picture of how neural activity correlates
with conscious experience.
 There is a growing consensus that consciousness is an emergent property of the brain, one
that recruits activities in many areas of the cerebral cortex.
 Several models suggest a scanning mechanism that repetitively sweeps across the brain,
integrating widespread activity into a unified, conscious moment.

Concept 48.7 CNS injuries and diseases are the focus of much research
 Unlike the PNS, the mammalian CNS does not have the ability to repair itself when
damaged or injured by disease.
 Surviving neurons in the brain can make new connections and sometimes compensate for
damage.
 Generally speaking, brain and spinal cord injuries, strokes, and diseases that destroy
CNS neurons have devastating effects.
 Research on nerve cell development and neural stem cells may be the future of treatment
for damage to the CNS.
 Researchers are investigating how neurons “find their way” during CNS development.
 To reach their target cells, axons must elongate from a few micrometers to a meter or
more.
 Molecular signposts along the way direct and redirect the growing axon in a series of
mid-course connections that result in a meandering, but not random, elongation.
 The responsive region at the leading edge of the neuron is called the growth cone.
 Signal molecules released by cells along the growth route bind to receptors on the
plasma membrane of the growth cone, triggering a signal transduction pathway.
 The axon may respond by growing toward the source of the signal molecules
(attraction) or away from it (repulsion).
 Cell adhesion molecules on the axon’s growth cone also play a role by attaching to
complementary molecules on surrounding cells that provide tracks for the growing
axon to follow.
 Nerve growth factor released by astrocytes and growth-promoting proteins produced
by the neurons themselves contribute to the process by simulating axonal elongation.
 The growing axon expresses different genes as it develops, and it is influenced by
surrounding cells that it moves away from.
 This complex process has been conserved during millions of years of evolution, for
the genes, gene products, and mechanisms of axon guidance are remarkably similar
in humans, nematode worms, and insects.
 In 1998, it was discovered that a adult human brain does produce new neurons.
 New neurons have been found in the hippocampus.

Biology Chapter Notes

  The function of these new neurons is not clear, but it is known that mice living
in stimulating conditions have more new neurons in their hippocampus than
those that receive little stimulation.
 Since mature human brain cells cannot undergo cell division, the new cells must
have arisen from stem cells.
 In 2001, Fred Gage of the Salk Institute announced that they had cultured neural
progenitor cells from adult human brains.
 The term progenitor means that these stem cells are committed to develop as
neurons or glia.
 In culture, the cells divided 30 to 70 times and differentiated into neurons and
astrocytes.
The nervous system has a number of diseases and disorders.
 About 1% of the world’s population suffers from schizophrenia, a severe mental
disturbance characterized by psychotic episodes.
 The symptoms of schizophrenia include hallucinations and delusions, blunted
emotions, distractibility, lack of initiative, and poverty of speech.
 The cause of schizophrenia is unknown, although the disease has a strong genetic
component.
 There is an active effort to find the mutant genes that predispose a person to
schizophrenia.
 Multiple genes must be involved because inheritance does not follow a simple
Mendelian pattern.
 Available treatments for schizophrenia focus on the use of dopamine as a
neurotransmitter.
 Two lines of evidence suggest that this approach is suitable.
 First, amphetamine, which stimulates dopamine release, can produce symptoms
identical to those of schizophrenia.
 Second, many of the drugs that alleviate the symptoms block dopamine receptors.
 Additional neurotransmitters may also be involved because other drugs successful in
treating schizophrenia have stronger effects on serotonin and/or norepinephrine
transmitters.
 There are other indications that glutamate receptors may play a role in schizophrenia.
 The street drug PCP blocks glutamate receptors and induces strong schizophrenia-like
symptoms.
 Many current schizophrenia medications have severe side effects.
 Twenty-five percent of schizophrenics on chronic drug therapy develop tardive
dyskinesia, in which the patient has uncontrolled facial writhing movements.
 Two broad forms of depressive illness are known: bipolar disorder and major depression.
 Bipolar disorder involves swings in mood from high to low and affects about 1% of the
world’s population.
 People with major depression have a low mood most of time.
 Five percent of the population suffers from major depression.
 In bipolar disorder, the manic phase is characterized by high self-esteem, increased
energy, a flow of ideas, and risky behaviors such as promiscuity and reckless spending.
 In the depressive phase, symptoms include lowered ability to feel pleasure, loss of
interest, sleep disturbances, feelings of worthlessness, and risk of suicide.
Biology Chapter Notes
 Both bipolar disorder and major depression have a genetic component, as identical twins
have a 50% chance of sharing this mental illness.
 It is likely that childhood stress is also an important factor.
 Several treatments for depression are available, including Prozac, electroconvulsive shock
therapy, lithium administration, and talk therapy.
 Alzheimer’s disease is a mental deterioration or dementia.
 It is characterized by confusion, memory loss, and a variety of other symptoms.
 Its incidence is age related, rising from 10% at age 65 to 35% at age 85.
 The disease is progressive, with patients losing the ability to live alone and take care of
themselves.
 There are also personality changes, almost always for the worse.
 It is difficult to diagnose Alzheimer’s disease while the patient is still alive.
 However, it results in characteristic brain pathology.
 Neurons die in huge areas of the brain, often leading to shrinkage of brain tissue.
 The diagnostic features are neurofibrillary tangles and senile plaques in the remaining
brain tissue.
 Neurofibrillary tangles are bundles of degenerated neuronal and glial processes.
 Senile plaques are aggregates of ß-amyloid, an insoluble peptide that is cleaved
from a membrane protein normally found in neurons.
 Membrane enzymes, called secretases, catalyze the cleavage, causing ß-amyloid to
accumulate outside the neurons and to aggregate in the form of plaques.
 The plaques seem to trigger the death of the surrounding neurons.

 In 2004, a team of researchers at Northwestern University used genetic engineering to

eliminate one of the secretases in a strain of mice prone to Alzheimer’s disease.
 The genetically engineered mice accumulated less ß-amyloid and did not experience
the age-related memory deficits typical of mice of that strain.
 Other drugs are being developed to prevent the development of senile plaques, which
form before overt symptoms of Alzheimer’s disease develop.
 Approximately 1 million people in the United States suffer from Parkinson’s disease, a
motor disease characterized by difficulty in initiating movement, slowness of movement,
and rigidity.
 Like Alzheimer’s disease, Parkinson’s disease results from death of neurons in a midbrain
nucleus called the substantia nigra.
 These neurons normally release dopamine from their synaptic terminals in the basal
nuclei.
 The degeneration of dopamine neurons is associated with the accumulation of protein
aggregates containing a protein typically found in presynaptic nerve terminals.
 Most cases of Parkinson’s disease lack a clearly identifiable cause.
 The consensus among scientists is that it results from a combination of environmental
and genetic factors.
 At present, there is no cure for Parkinson’s disease, although various approaches are used
to manage the symptoms, including brain surgery; deep-brain stimulation; and drugs such
as L-dopa, a dopamine precursor that can cross the blood-brain barrier.
 One potential cure is to implant dopamine-secreting neurons, either in the substantia
nigra or in the basal ganglia.
Biology Chapter Notes
  Embryonic stem cells can be stimulated or genetically engineered to develop into
dopamine-secreting neurons.
 Transplantation of these cells into rats with an experimentally induced condition
that mimics Parkinson’s disease has led to a recovery of motor control.
It remains to be seen whether this kind of regenerative medicine will work in humans.

Biology Chapter Notes

 Chapter 49 Sensory and Motor Mechanisms
Chapter Notes

Overview: Sensing and Acting

 The origins of sensing date back to the appearance in prokaryotes of cellular structures
that sense pressure and chemicals in the environment and direct movement in an
appropriate direction.
 These structures have been transformed during the course of evolution into diverse
mechanisms that sense various types of energy and generate many different levels of
physical movement in response.
 The detection and processing of sensory information and the generation of motor output
provide the physiological basis for all animal behavior.

Concept 49.1 Sensory receptors transduce stimulus energy and transmit signals to the
central nervous system
o The brain’s processing of sensory input and motor output is cyclical rather than
linear.
 Sensing, brain analysis, and action are ongoing and overlapping processes.
 Information is transmitted through the nervous system in the form of all-or-nothing action
potentials.
 What matters is where action potentials go.
 Sensations begin as different forms of energy detected by sensory receptors.
 This energy is converted to action potentials that travel to appropriate regions of the
brain.
 Once the brain is aware of sensations, it interprets them, giving the perception of
stimuli.
 Perceptions such as colors, smells, sounds, and tastes are constructions formed in the
brain and do not exist outside of it.
o Sensory receptors transduce stimulus energy and transmit signals to the nervous
system.
 Sensory reception begins with the detection of stimulus energy by sensory receptors.
 Most sensory receptors are specialized neurons or epithelial cells that exist singly or in
groups with other cell types in sensory organs, such as eyes or ears.
 Exteroreceptors detect stimuli originating outside the body, such as heat, light,
pressure, and chemicals.
 Interoreceptors detect stimuli originating inside the body, such as blood pressure and
body position.
 Sensory receptors convey the energy of stimuli into membrane potentials and transmit
signals to the nervous system.
 Sensory receptors perform four functions in this process: sensory transduction,
amplification, transmission, and integration.
Biology Chapter Notes
  The conversion of stimulus energy into a change in membrane potential of a sensory
receptor is sensory transduction.
 The change in membrane potential itself is receptor potential.
 Receptor potentials are graded potentials; their magnitude varies with the strength
of the stimulus.
 All receptor potentials result from the opening or closing of ion channels in the
sensory receptor’s plasma membrane.
 Many sensory receptors are extremely sensitive.
 Most light receptors can detect a single photon of light.
 Hair cells of the inner ear can detect motion of only a fraction of a nanometer.
 Chemical receptors can detect a single molecule.
 The strengthening of stimulus energy by cells in sensory pathways is called
amplification.
 An action potential conducted from the eye to the brain has about 100,000 times as
much energy as the few photons of light that triggered it.
 Some amplification occurs in the sensory receptors, and signal transduction
pathways involving second messengers often contribute to it.
 Amplification can also take place in the accessory structures of a complex sense
organ.
 The conduction of sensory impulses to the CNS is transmission.
 Some sensory receptors transmit chemical signals to sensory neurons.
 The strength of the stimulus and receptor potential affects the amount of excitatory
neurotransmitter released by the sensory receptor.
 Some sensory receptors are sensory neurons.
 The intensity of the receptor potential affects the frequency of action potentials.
 Many sensory neurons spontaneously generate action potentials at a low rate.
 Therefore, a stimulus does not switch the production of action potentials on or off
in these neurons.
 Rather, it modulates action potential frequency.
 The processing, or integration, of sensory information begins as soon as the information
is received.
 Receptor potentials produced by stimuli delivered to different parts of a sensory
receptor are integrated through summation, as are postsynaptic potentials in sensory
neurons that synapse with multiple receptors.
 Another type of integration by receptors is sensory adaptation, a decrease in
responsiveness to continued stimulation.
 The integration of sensory information occurs at all levels within the nervous system.
 Complex sensory structures such as eyes have higher levels of integration, and the
CNS further processes all incoming signals.
o Sensory receptors are categorized by the type of energy they transduce.
 Mechanoreceptors respond to mechanical energy such as pressure, touch, stretch,
motion, and sound.
 Bending or stretching of a mechanoreceptor’s plasma membrane increases the
membrane’s permeability to sodium and potassium ions.
 The crayfish stretch receptor, the vertebrate hair cell, and the vertebrate stretch receptor
are examples of mechanoreceptors.
Biology Chapter Notes
  Muscle spindles respond to the stretching of skeletal muscle, depolarizing sensory
neurons and triggering action potentials that are transmitted to the spinal cord.
 Muscle spindles and the sensory neurons that innervate them are part of the nerve
circuits that underlie reflexes.
 The mammalian sense of touch also relies on mechanoreceptors that are the dendrites
of sensory neurons, embedded in layers of connective tissue.
 Receptors that detect light touch are close to the surface of the skin, while receptors
responding to strong pressure and vibrations are in deep skin layers.
 Chemoreceptors respond to chemical stimuli.
 General chemoreceptors transmit information about total solute concentration of a
solution, while specific chemoreceptors respond to specific types of molecules.
 Osmoreceptors in the mammalian brain are general receptors that detect changes in
solute concentration of the blood and stimulate thirst when osmolarity increases.
 Internal chemoreceptors respond to glucose, O2, CO2, and amino acids.
 Two of the most sensitive and specific chemoreceptors known are present in the
antennae of the male silkworm moth.
 They detect the two chemical components of the female moth sex pheromone.
 In each example, the stimulus molecule binds to a specific site on the membrane of the
receptor cell and initiates changes in membrane permeability.
 Electromagnetic receptors respond to various forms of electromagnetic energy such as
visible light, electricity, and magnetism.
 Photoreceptors respond to the radiation we know as visible light and are often
organized into eyes.
 Some snakes have infrared detectors that detect body heat of prey.
 Some fishes generate electric currents and use electroreceptors to locate prey that
disrupt those currents.
 Many animals use Earth’s magnetic field lines to orient themselves as they migrate.
 The iron-containing mineral magnetite is found in the skulls of many vertebrates, in
the abdomen of bees, in the teeth of some molluscs, and in certain protists and
prokaryotes that orient to Earth’s magnetic field.
 Thermoreceptors respond to heat or cold and help regulate body temperature by
signaling surface and body core temperature.
 Thermoreceptors in the skin and in the anterior hypothalamus send information to the
body’s thermostat, located in the posterior hypothalamus.
 Pain receptors, or nociceptors, are a class of naked dendrites in the epidermis.
 Most animals experience pain, although we cannot say what perceptions other animals
associate with stimulation of pain receptors.
 Pain is an important sensation, because the stimulus leads to a defensive reaction.
 Different types of pain receptors respond to different types of pain, such as excess
heat, pressure, or chemicals released from damaged or inflamed tissues.
 Prostaglandins increase pain by sensitizing receptors, lowering their threshold.
 Aspirin and ibuprofen reduce pain by inhibiting prostaglandin synthesis.

o Concept 49.2 The mechanoreceptors involved with hearing and equilibrium

detect settling particles or moving fluid
 Hearing and balance are related in most animals.
Biology Chapter Notes
 Both involve mechanoreceptors that produce receptor potentials when some part of the
membrane is bent by settling particles or moving fluid.
 Statocysts are mechanoreceptors that function in an invertebrate’s sense of equilibrium.
 A common type of statocyst consists of a layer of ciliated receptor cells surrounding a
chamber that contains one or more statoliths, grains of sand or other dense granules.
 Gravity causes the statoliths to settle to a low point in the chamber, stimulating
receptors in that location.
 Many jellies have statocysts at the fringe of their bell, giving them an indication of
body position.
 Many invertebrates have a general sensitivity to sound, although specialized structures for
hearing are less common than gravity sensors.
 Sound sensitivity in insects depends on body hairs that vibrate in response to sound
waves.
 Different hairs respond to different frequencies.
 Many insects have localized “ears,” with a tympanic membrane stretched over an
internal air chamber.
 Sound waves vibrate the tympanic membrane, stimulating receptor cells attached to
the inside of the membrane and resulting in nerve impulses that are transmitted to
the brain.
 Some moths can hear the high-pitched sounds that bats produce for sonar, and undertake
escape maneuvers.
o In mammals, the sensory organs for hearing and equilibrium are associated with
the ear.
 The outer ear includes the external pinna and the auditory canal, which collects sound
waves and channels them to the tympanic membrane.
 From the tympanic membrane, sound waves are transmitted through the middle ear.
 In the middle ear, three small bones, the malleus, incus, and stapes, transmit
vibrations to the oval window and on to the inner ear.
 The Eustachian tube connects the middle ear with the pharynx and equalizes
pressure between the middle ear and the atmosphere.
 The inner ear consists of a labyrinth of fluid-filled channels housed within the temporal
bone of the skull.
 The cochlea is the part of the inner ear concerned with hearing.
 Structurally, it consists of the upper vestibular canal and the lower tympanic canal,
which are separated by the cochlear duct.
 The vestibular and tympanic canals are filled with perilymph.
 The cochlear duct is filled with endolymph.
 The organ of Corti, which rests on the basilar membrane, contains the
mechanoreceptors of the ear, hair cells with hairs projecting into the cochlear duct.
 Many of the hairs are attached to the tectorial membrane, which rests atop the hair
cells of the organ of Corti like a shelf.
 Sound waves make the basilar membrane vibrate, which results in bending of the
hairs and depolarization of the hair cells.
 How does the ear convert the energy of pressure waves traveling through air into nerve
impulses that the brain perceives as sound?
 Vibrating objects create percussion waves in the surrounding air.
Biology Chapter Notes
  These waves cause the tympanic membrane to vibrate with the same frequency as the
sound.
 The three bones of the middle ear transmit the vibrations to the oval window, a membrane
in the cochlea’s surface.
 The stapes vibrates against the oval window, creating pressure waves in the cochlear
fluid.
 The round window functions to dissipate the vibrations.
 Vibrations in the cochlear fluid cause the basilar membrane to vibrate.
 The hair cells brush against the tectorial membrane, generating an action potential in a
sensory neuron.
 Pitch is based on the location of the hair cells that depolarize.
 The basilar membrane is not uniform along its length.
 Every region of the basilar membrane is most affected by a particular vibration
frequency.
 The actual perception of pitch occurs in the brain.
 Volume is determined by the amplitude of the sound wave.
 A large amplitude sound wave causes a more vigorous vibration of the basilar
membrane, a greater bending of the hairs on the hair cells, and more action potentials
in the sensory neurons.
o The inner ear also contains the organs of equilibrium.
 Behind the oval window is a vestibule that contains two chambers, the utricle and
saccule.
 The utricle opens into three semicircular canals.
 The utricle and saccule respond to changes in head position relative to gravity and
movement in one direction.
 Hair cells are arranged in clusters and project into a gelatinous material containing
otoliths.
 When the head’s orientation changes, the hair cells are tugged on, sending nerve
impulse along a sensory neuron.
 The mechanism is similar to the function of statocysts in invertebrates, and the
utricle and saccule are considered specialized types of statocysts.
 The semicircular canals respond to rotation or angular movements of the head.
 The mechanism is similar to that associated with the utricle and saccule.
o A lateral line system and inner ear detect pressure waves in most fishes and aquatic
amphibians.
 Fishes and amphibians lack cochleae, eardrums, and openings to the outside.
 However, they have saccules, utricles, and semicircular canals, structures homologous
to the equilibrium sensors of human ears.
 Vibrations of the water caused by sound waves are conducted through the skeleton of the
head to the inner ears, setting the otoliths in motion and stimulating the hair cells.
 The fish’s air-filled swim bladder may contribute to the transfer of sound to the inner ear.
 Catfishes and minnows have a series of bones, called the Weberian apparatus, which
conducts vibrations from the swim bladder to the inner ear.

Biology Chapter Notes

 Most fishes and aquatic amphibians have a lateral line system along both sides of their
body.
 The system contains mechanoreceptors that detect low-frequency waves by a
mechanism similar to the function of a mammalian inner ear.
 Water enters the lateral line system through numerous pores and flows along a tube
past the mechanoreceptors.
 The receptor units, called neuromasts, resemble the ampullae in our semicircular
canals.
 Each neuromast has a cluster of hair cells whose hairs are embedded in a gelatinous
cupula.
 Water movement bends the cupula, depolarizing the hair cells and leading to action
potentials that are transmitted along the axons of sensory neurons to the brain.
 This provides a fish with information concerning its movement through water or the
direction and velocity of water flowing over its body.
 In terrestrial vertebrates, the inner ear has evolved as the main organ of hearing and
equilibrium.
 Some amphibians have a lateral line as tadpoles, but not as terrestrial adults.
 In frogs and toads, sound vibrations are conducted to the inner ear by a tympanic
membrane on the body surface and a single middle ear bone.
 A small side pocket on the saccule functions as the main hearing organ of the frog.
 This outgrowth of the saccule gave rise to the more elaborate cochlea during
mammalian evolution.
 Birds also have a cochlea.
 As in amphibians, sound is conducted from the tympanic membrane by a single
bone, the stapes.
o
o Concept 49.3 The senses of taste and smell are closely related in most animals
 Many animals use their chemical senses to find mates, to recognize territory that has been
marked by some chemical substance, and to help navigate during migration.
 Chemical conversation is especially important for animals, such as ants and bees, which
live in large social groups.
 The perceptions of gustation (taste) and olfaction (smell) are both dependent on
chemoreceptors that detect specific chemicals in the environment.
 In all animals, chemical senses are important in feeding behavior.
 In terrestrial animals, taste is the detection of chemicals in solution and smell is the
detection of chemicals in the air.
 There is no distinction between taste and smell in aquatic animals.
 Taste receptors in insects are located on their feet and in mouthparts, within sensory hairs
called sensilla.
 A tasting hair contains chemoreceptors responsive to particular classes of chemical
stimuli.
 Insects also have olfactory hairs on their antennae.
o Human receptor cells for taste are organized into taste buds.
 In mammals, taste receptors are located in taste buds, most of which are on the surface of
the tongue.
Biology Chapter Notes
  Most taste buds are associated with nipple-shaped projections called papillae.
 Each taste receptor responds to a wide array of chemicals, but is most responsive to a
particular type of substance.
 It is the pattern of taste receptor response that determines perceived flavor.
 Transduction in taste receptors occurs by several mechanisms.
 Chemoreceptors that detect saltiness (mainly Na +) and sourness (H+ generated by
acids) have channels in their plasma membrane though which these ions can diffuse.
 The influx of Na+ or H+ depolarizes the cell.
 In chemoreceptors that detect bitter substances, the substance binds to K+ channels and
closes them.
 The resulting decrease in potassium permeability depolarizes the cell.
 The mechanism for umami (glutamate) receptors may involve the binding of glutamate
to Na+ channels.
 When the glutamate is bound, the channels open, Na+ diffuses into the cell, and it
depolarizes.
 Sweetness is detected by chemoreceptors that have receptor proteins for sugars.
 Binding of a sugar molecule to a receptor protein triggers a signal transduction
pathway that results in depolarization.
 In all taste receptors, depolarization causes the smell to release neurotransmitters onto a
sensory neuron, which transmits action potentials to the brain.
o Olfactory receptor cells line the upper portion of the nasal cavity.
 In mammals, olfactory receptors line the upper portion of the nasal cavity.
 The receptive ends of the cells contain cilia that extend into the layer of mucus coating the
nasal cavity.
 The binding of odor molecules to olfactory receptors initiates signal-transduction
pathways involving a G-protein-signaling pathway and, often, adenylyl cyclase and
second messenger cyclic AMP.
 The second messenger opens channels in the plasma membrane that are permeable to
both sodium and calcium ions.
 The influx of these ions depolarizes the membrane, causing the receptor cell to
generate action potentials.
 Humans can distinguish thousands of different odors, each caused by a structurally
distinct odorant.
 There are more than 1,000 odorant receptor genes, accounting for approximately 3% of
all genes in the human genome.
 Each olfactory receptor cell expresses only one or a few odorant receptor genes.
 Cells with different odorant selectivities are interspersed in the nasal cavity, but their
axons sort themselves out in the olfactory bulb of the brain.
 Taste and smell interact with each other, although the receptors and brain pathways for the
two senses are independent.

Concept 49.4 Similar mechanisms underlie vision throughout the animal kingdom
 Many types of light detectors have evolved in the animal kingdom, from simple clusters
of cells that detect only direction and intensity of light to complex image-forming eyes.
Biology Chapter Notes
 All photoreceptors contain similar pigment molecules that absorb light.
 Most, if not all, animal photoreceptors may be homologous.
 All animals with vision share genes associated with the embryonic development of
photoreceptors.
 The genetic underpinnings of all photoreceptors may have evolved in the earliest
bilateral animals.
 The specific types of eyes that form in an animal depend on developmental patterns
regulated by genetic mechanisms that evolved later, superimposed on the common
ancestral mechanism.
o A diversity of photoreceptors has evolved among invertebrates.
 The eye cups of planarians are among the simplest photoreceptors.
 These structures detect light intensity and direction, but do not provide image
formation.
 The movement of a planarian is integrated with photoreception.
 Two major types of image-forming eyes have evolved in invertebrates.
 One type of eye is the compound eye of insects and crustaceans.
 Each eye consists of ommatidia, each with its own light-focusing lens.
 Each ommatidium detects light from a tiny portion of the visual field.
 This type of eye is very good at detecting movement.
 Insects have excellent color vision, and some can see ultraviolet light.
 Single-lens eyes are found in some invertebrates such as jellies, polychaetes, spiders, and
molluscs.
 The eye of an octopus works much like a camera and is similar to the vertebrate eye.
 Light enters through the pupil, with the iris changing the diameter.
 Behind the pupil, a single lens focuses light on a layer of photoreceptors.
 Muscles in an invertebrate’s single-lens eye move the lens to focus at different
distances.
o Vertebrates have single-lens eyes.
 Vertebrate eyes are structurally analogous to the invertebrate single-lens eye.
 The globe of the vertebrate eye (the eyeball) consists of a tough, white outer layer of
connective tissue called the sclera and a thin, pigmented inner layer called the choroid.
 A delicate layer of epithelial cells forms a mucus membrane, the conjunctiva, which
covers the external cover of the sclera and keeps the eye moist.
 At the front of the eye is a transparent cornea, which lets light into the eye and acts as
a fixed lens.
 The conjunctiva does not cover the cornea.
 The anterior choroid prevents light rays from scattering and distorting the image.
 Anteriorly, it forms the iris, which gives the eye its color.
 The iris regulates the size of the pupil.
 Inside the choroid, the retina lines the interior surface of the choroid.
 The retina contains photoreceptors, except at the optic disk (where the optic nerve
attaches).
 The lens (a transparent protein disk) and ciliary body divide the eye into two cavities.
Biology Chapter Notes
  The anterior cavity is filled with aqueous humor produced by the ciliary body.
 Glaucoma results when the ducts that drain aqueous humor are blocked.
 The posterior cavity is filled with vitreous humor.
 The lens, the aqueous humor, and the vitreous humor all play a role in focusing light onto
the retina.
 In squids, octopuses, and many fishes, this is accomplished by moving the lens
forward and backward.
 In mammals, focus is accomplished by changing the shape of the lens.
 The lens is flattened for focusing on distant objects.
 The lens is rounded for focusing on near objects.
 When focusing on a close object, the lens becomes almost spherical, a change called
accommodation.
 The retina contains about 125 million rod cells, which are light sensitive but do not
distinguish colors, and about 6 million cone cells, which are not as light sensitive as rods
but provide color vision.
 These cells account for 70% of the sensory receptors in the body.
 Rods are most highly concentrated at the peripheral regions of the retina and are
completely absent from the fovea, the center of the visual field.
 Cones are most dense at the fovea, which has 150,000 cones per square millimeter.
o The light-absorbing pigment rhodopsin triggers a signal-transduction pathway.
 Each rod or cone in the vertebrate retina contains visual pigments consisting of light-
absorbing molecules called retinal bonded to membrane proteins called opsin.
 Rhodopsin (retinal + opsin) is the visual pigment of rods.
 The absorption of light by rhodopsin initiates a signal-transduction pathway.
 Color reception is more complex than the rhodopsin mechanism.
 There are three subclasses of cone cells, each with its own type of photopsin.
 Color perception is based on the brain’s analysis of the relative responses of each
type of cone.
 In humans, colorblindness is due to a deficiency, or absence, of one or more
photopsins.
 It is inherited as an X-linked trait and is more common in males than females.
o The retina assists the cerebral cortex in processing visual information.
 Visual processing begins with rods and cones synapsing with neurons called bipolar cells.
 In the dark, rods and cones are depolarized, and they continually release the
neurotransmitter glutamate at these synapses.
 This steady glutamate release depolarizes some bipolar cells and hyperpolarizes others.
 In the light, rods and cones hyperpolarize, shutting off the release of glutamate.
 In response, the bipolar cells that are depolarized by glutamate hyperpolarize, and
those that are hyperpolarized by glutamate depolarize.
 Three other types of neurons contribute to information processing in the retina: ganglion
cells, horizontal cells, and amacrine cells.
 Bipolar cells synapse with ganglion cells and transmit action potentials to the brain via
axons in the optic nerve.

Biology Chapter Notes

  Horizontal cells and amacrine cells help integrate the information before it is sent to
the brain.
 Signals from the rods or cones may follow a vertical or a lateral path in the retina.
 In the vertical pathway, information passes from photoreceptors to bipolar cells to
ganglion cells.
 In the lateral pathway, horizontal cells carry signals from one rod or cone to other
photoreceptors and to several bipolar cells, and amacrine cells distribute information
from one bipolar cell to several ganglion cells.
 This form of integration results in lateral inhibition.
 More distant photoreceptors and bipolar cells are inhibited, which sharpens
edges and enhances contrast in the image.
 All the rods or cones that feed information to one ganglion cell form the receptive field for
that cell.
 A larger receptive field results in a less sharp image than a smaller receptive field,
because the larger field provides less information about exactly where the light struck
the retina.
 The optic nerves of the two eyes meet at the optic chiasm near the center of the base of
the cerebral cortex.
 At the optic chiasm, sensations from the left visual field of both eyes are transmitted to
the right side of the brain.
 Sensations from the right visual field of both eyes are transmitted to the left side of the
brain.
 Ganglion cell axons lead to the lateral geniculate nuclei of the thalamus.
 Neurons then convey information to the primary visual cortex in the occipital lobe of
the cerebrum.
 Additional interneurons carry the information to higher-order visual processing and
integrating centers elsewhere in the cortex.
 Point-by-point information in the visual field is projected along neurons onto the visual
cortex.
 How does the cortex convert a complex set of action potentials representing two-
dimensional images focused on our retina into 3-D perceptions of our surroundings?
 Thirty percent of the cerebral cortex—hundreds of millions of interneurons in dozens
of integrating centers—take part in formulating what we actually “see.”

Concept 49.5 Animal skeletons function in support, protection, and movement

 Locomotion is active movement from one place to another.
 Swimming, crawling, running, hopping, and flying all result from muscles working
against some type of skeleton.
 A hydrostatic skeleton consists of fluid held under pressure in a closed body
compartment.
 Form and movement is controlled by changing the shape of this compartment.
 Among the cnidarians, a hydra can elongate by closing its mouth and using contractile
cells in the body wall to constrict the central gastrovascular cavity.
 Because water cannot be compressed very much, decreasing the diameter of the
cavity forces it to increase in length.
Biology Chapter Notes
  The interstitial fluid functions as the main hydrostatic skeleton in flatworms.
 Nematodes hold fluid in their pseudocoelom.
 The fluid is under high pressure, and contractions of the longitudinal muscles result
in thrashing movements.
 The coelomic fluid of earthworms acts as a hydrostatic skeleton.
 The coelomic cavity is divided into segments by septa, allowing the animal to
change the shape of each segment individually, using both circular and longitudinal
muscles.
 Earthworms use their hydrostatic skeletons to move by peristalsis.
 Hydrostatic skeletons are advantageous in aquatic environments and can support
crawling and burrowing.
 However, they do not allow the body to be held off the ground for running or
walking.
 An exoskeleton is a hard encasement deposited on the surface of an animal.
 Many molluscs are enclosed in a calcareous exoskeleton secreted by the mantle.
 The jointed exoskeleton of arthropods is composed of a cuticle.
 Regions of the cuticle vary in hardness and degree of flexibility.
 About 30–50% of the cuticle consists of chitin.
 Muscles attach to the interior surface of the cuticle.
 This type of exoskeleton must be molted to allow for growth.
 Endoskeletons consist of hard supporting elements within the soft tissues of the animal.
 Sponges are reinforced by hard spicules of inorganic material.
 Echinoderms have an endoskeleton of hard plates composed of magnesium carbonate
and calcium carbonate, bound together by protein fibers.
 Chordate endoskeletons are composed of cartilage, bone, or some combination of the
two.
 Some of the bones of the mammalian skeleton are connected at joints by ligaments,
while others are fused together.
o Physical support on land depends on adaptations of body proportions and posture.
 A large animal has very different body proportions than a small animal.
 Larger animals need proportionately stronger bones to support their large mass.
 In the support of body weight, posture may be more important than body proportions.
 Muscles and tendons (connective tissue that join muscles to bone) hold the legs of
large animals relatively straight and positioned under the body and bear most of the
load.
o
o Concept 49.6 Muscles move skeletal parts by contracting
 Muscles come in antagonistic pairs.
 Humans flex the arm by contracting the biceps, and extend it by contracting the triceps
and relaxing the biceps.
 Vertebrate skeletal muscle is responsible for voluntary muscle movement in the body.
 A skeletal muscle consists of a bundle of long fibers running parallel to the length of the
muscle.
Biology Chapter Notes
  Each fiber is a single cell with multiple nuclei.
 A fiber is a bundle of smaller myofibrils arranged longitudinally.
 The myofibrils are composed of two kinds of myofilaments: thin and thick filaments.
 Thin filaments consist of two strands of actin and one strand of regulatory protein
coiled about each other.
 Thick filaments consist of myosin molecules.
o Interactions between myosin and actin generate force during muscle contractions.
 The sarcomere is the functional unit of muscle contraction.
 The borders of the sarcomere, the Z lines, are lined up in adjacent myofibrils and form the
striations.
 Thin filaments are attached to the Z lines and project toward the center of the
sarcomere, while the thick filaments are centered in the sarcomere.
 In a muscle fiber at rest, thick and thin filaments do not overlap completely, and the
area near the edge of the sarcomere where there are only thin filaments is called the I
band.
 The A band is the broad region that corresponds to the length of the thick filaments.
 The thin filaments do not extend completely across the sarcomere, so the H zone in the
center of the A band contains only thick filaments.
 According to the sliding-filament model of muscle contraction, neither the thin nor the
thick filaments change in length when the sarcomere shortens.
 Instead, the filaments slide past each other longitudinally, producing more overlap
between the thick and thin filaments.
 As a result, both the region occupied only by thin filaments (the I band) and the
region occupied only by thick filaments (the H band) shrink.
 The sliding is based on the interaction between the actin and myosin molecules that make
up the thick and thin filaments.
 Each myosin molecule has a long tail region and a globular head region.
 The tail adheres to the tails of other myosin molecules.
 The head binds and hydrolyzes ATP and is the center of the bioenergetic reactions that
power muscle contraction.
 Hydrolysis of ATP triggers steps in which myosin binds to actin, forming a cross-bridge
and pulling the thin filament toward the center of the sarcomere.
 The cross-bridge is broken when a new molecule of ATP binds to the myosin head.
 The free head cleaves the new ATP and attaches to a new binding site on another actin
molecule farther along the thin filament.
 A typical muscle fiber at rest contains only enough ATP for a few contractions.
 The energy required for continued contractions is stored in creatine phosphate and
glycogen.
 Creatine phosphate can transfer a phosphate group to ADP to make ATP.
 The resting supply of creatine phosphate is sufficient to sustain contractions for
about 15 seconds.
 Glycogen is broken down to glucose, which can generate ATP via glycolysis or
aerobic respiration.

Biology Chapter Notes

  Using glucose from a typical muscle fiber’s glycogen store, glycolysis can support
about 1 minute of sustained contractions, while aerobic respiration can power
contractions for nearly an hour.
o Calcium ions and regulatory proteins control muscle contraction.
 At rest, tropomyosin blocks the myosin binding sites on actin.
 When calcium binds to the troponin complex, a conformational change results in the
movement of the tropomyosin-troponin complex and exposure of actin’s myosin binding
sites.
 When Ca2+ is present in the cytosol, the thick and thin filaments slide by each other, and
the muscle fiber contracts.
 An action potential in a motor neuron that makes a synapse with a muscle fiber is the
initial stimulus for muscle contraction.
 The synaptic terminal of the motor neuron releases the neurotransmitter acetylcholine,
depolarizing the muscle fiber and causing it to produce an action potential.
 The action potential spreads deep into the muscle fiber along infoldings of the plasma
membrane called transverse (T) tubules.
 The T tubules meet the muscle cell’s sarcoplasmic reticulum (SR), and stored Ca2+ is
released into the cytosol.
 Ca2+ bind to the troponin complex, triggering contractions of the muscle fiber.
 Contraction stops when the SR pumps Ca2+ out of the cytosol, and tropomyosin
again blocks the myosin-binding sites on the thin filaments.
 In amyotrophic lateral sclerosis (ALS), motor neurons in the spinal cord and brainstem
degenerate, and the muscle fibers with which they synapse atrophy.
 ALS is progressive and usually fatal; there is no cure.
 Botulism results from consumption of an exotoxin from the bacterium Clostridium
botulinum in improperly preserved foods.
 The toxin paralyzes muscles by blocking the release of acetylcholine from motor
neurons.
o Diverse body movements require variation in muscle activity.
 An individual muscle cell either contracts completely or not all.
 A muscle fiber contracts with a brief contraction called a twitch.
 A whole muscle, composed of many individual muscle fibers, can contract to varying
degrees.
 Contraction is graded; we can voluntarily alter the extent and strength of a contraction.
 This is due to variation in the number of muscle fibers that contract and variation in the
rate at which muscle fibers are stimulated.
 Each motor neuron may synapse with many motor fibers.
 Hundreds of motor neurons control a muscle, each with its own pool of muscle
fibers scattered throughout the muscle.
 A motor unit consists of a single motor unit and all the muscle fibers it controls.
 When a motor neuron produces an action potential, all the muscle fibers in its motor
unit contract as a group.
 The strength of the contraction depends on how many muscle fibers the motor neuron
controls, from a few to hundreds.

Biology Chapter Notes

  The nervous system can thus regulate the strength of contraction in a whole muscle
by determining how many motor units are activated at a given instant and by
selecting large or small motor units to activate.
 As more and more of the motor neurons controlling the muscle are activated, a process
of recruitment increases the force developed by the muscle.
 Prolonged contraction of muscles can result in fatigue, caused by depletion of ATP,
dissipation of ion gradients, and accumulation of lactate.
 The nervous system may alternate activation among the motor units in a muscle,
allowing different motor units to take turns maintaining a prolonged contraction.
 The second mechanism by which the nervous system produces graded whole-muscle
contractions is by varying the rate of muscle fiber stimulation.
 Summation of action potentials will increase muscle fiber tension.
 If the rate of stimulation is fast enough that the muscle does not relax between stimuli,
the twitches fuse into a smooth sustained contraction called tetanus.
 During tetanus, elastic structures (tendons and connective tissue) are fully stretched
and all the tension generated by the muscle fiber is transmitted to the bones.
 Muscle fibers are specialized.
 Fast muscle fibers are adapted for rapid, powerful contraction, but fatigue relatively
quickly.
 Slow muscle fibers are adapted for sustained contraction.
 Relative to fast fibers, slow fibers have less sarcoplasmic reticulum, so Ca 2+ remains in
the cytosol longer.
 Fibers that rely on glycolysis are called glycolytic fibers.
 Oxidative fibers rely mostly on aerobic respiration.
 They have more mitochondria, a better blood supply, and a large amount of an
oxygen-storing protein called myoglobin.
 There are three main types of skeletal muscle fibers: slow oxidative, fast oxidative, and
fast glycolytic.
 In addition to skeletal muscle, vertebrates have cardiac and smooth muscle.
 Cardiac muscle is similar to skeletal muscle, with striations.
 Cardiac muscle cells can generate their own action potentials.
 Intercalated discs facilitate the coordinated contraction of cardiac muscle cells.
 Action potentials of cardiac muscles can last up to twenty times longer than those
of skeletal muscle fibers.
 Smooth muscle lacks the striations seen in both skeletal and cardiac muscle.
 Smooth muscle lacks troponin complexes and T tubules and has poorly developed SR.
 Small amounts of Ca2+ enter the cytosol via the plasma membrane.
 Smooth muscles have slow contractions but have more control over contraction
strength than skeletal muscles.
 These involuntary muscles are found lining the walls of hollow organs.
 Invertebrate muscle cells are similar to vertebrate skeletal and smooth muscle cells.
 The flight muscles of insects are capable of independent, rhythmic contraction, so the
wings of some insects can actually beat faster than the action potentials can arrive from
the central nervous system.
o
o Concept 49.7 Locomotion requires energy to overcome friction and gravity
Biology Chapter Notes
 Most animals are mobile and spend a considerable portion of their time actively searching
for food.
 Different modes of locomotion vary in energy costs.
 In all its modes, locomotion requires that an animal expend energy to overcome two
forces that tend to keep it stationary: friction and gravity.
 Since water is buoyant, gravity poses less of a problem for swimming than for other
modes of locomotion.
 However, since water is dense, friction is more of a problem.
 Fast swimmers have fusiform bodies.
 Animals swim in diverse ways.
 For instance, many insects and four-legged vertebrates use their legs as oars to push
against the water.
 Squids and scallops are jet-propelled, taking in and squirting out water.
 Sharks and bony fishes move their bodies and tails from side to side, while whales
undulate their bodies and tails up and down.
 For locomotion on land, powerful muscles and skeletal support are more important than a
streamlined shape.
 When hopping, the tendons in a kangaroo’s legs store and release energy like a spring
that is compressed and released.
 The tail helps in the maintenance of balance.
 When walking, having three feet (or one foot, for bipeds) on the ground helps in the
maintenance of balance.
 When running, momentum—more than foot contact—helps keep the body upright.
 Crawling requires a considerable expenditure of energy to overcome friction, but
maintaining balance is not a problem.
 Earthworms crawl by peristalsis.
 Many snakes undulate the entire body from side to side, assisted in movement by
large, moveable scales on the underside of the body.
 Gravity poses a major problem when flying, because wings must develop enough lift
to overcome gravity’s downward force. The key to flight is the aerodynamic shape of
wings as airfoils.
 Flying animals are light, with body masses ranging from less than a gram for some
insects to 20 kg for the largest flying birds.
 Birds have hollow, air-filled bones and no teeth.
 The energetic cost of locomotion depends on the mode of locomotion and the
environment.
 Running animals generally expend more energy per meter than equivalent-sized
animals specialized for swimming, partly because running or walking requires energy
to overcome gravity.
 Swimming is the most energy efficient mode of locomotion, assuming that the animal
is specialized for swimming.
 Flying animals use more energy than swimming or running animals with the same
body mass.
 Larger animals travel more efficiently than smaller animals specialized for the same mode
of transportation.

Biology Chapter Notes

 An animal’s use of energy to move determines how much energy in food is available for
other activities, such as growth and reproduction.
 Thus, structural and behavioral adaptations that maximize the efficiency of locomotion
increase an animal’s evolutionary fitness.

Biology Chapter Notes

 Chapter 50 An Introduction to Ecology and the
Biosphere
Chapter Notes

Overview: The Scope of Ecology

 Ecology is the scientific study of the interactions between organisms and their
environment.

Concept 50.1 Ecology is the study of interactions between organisms and the
environment
 Ecologists ask questions about factors affecting the distribution and abundance of
organisms.
 Ecologists might study how interactions between organisms and the environment affect
the number of species living in an area, the cycling of nutrients, or the growth of
populations.
Ecology and evolutionary biology are closely related sciences.
 Ecology has a long history as a descriptive science.
 Modern ecology is also a rigorous experimental science.
 Ecology and evolutionary biology are closely related sciences.
 Events that occur over ecological time (minutes to years) translate into effects over
evolutionary time (decades to millennia).
 For example, hawks feeding on field mice kill certain individuals (over ecological
time), reducing population size (an ecological effect), altering the gene pool (an
evolutionary effect), and selecting for mice with fur color that camouflages them in
their environment (over evolutionary time).
Ecological research ranges from the adaptations of individual organisms to the dynamics
of the biosphere.
 The environment of any organism includes the following components:
 Abiotic components: nonliving chemical and physical factors such as temperature,
light, water, and nutrients.
 Biotic components: all living organisms in the individual’s environment.
 Ecology can be divided into a number of areas of study.
 Organismal ecology is concerned with the behavioral, physiological, and morphological
ways individuals interact with the environment.
 A population is a group of individuals of the same species living in a particular
geographic area. Population ecology examines factors that affect population size and
composition.
 A community consists of all the organisms of all the species that inhabit a particular area.
Community ecology examines the interactions between species and considers how
Biology Chapter Notes
 factors such as predation, competition, disease, and disturbance affect community
structure and organization.
 An ecosystem consists of all the abiotic factors in addition to the entire community of
species that exist in a certain area. Ecosystem ecology studies energy flow and cycling of
chemicals among the various abiotic and biotic components.
 A landscape or seascape consists of several different ecosystems linked by exchanges of
energy, materials, and organisms. Landscape ecology deals with arrays of ecosystems
and their arrangement in a geographic region.
 Each landscape or seascape consists of a mosaic of different types of patches, an
environmental characteristic ecologists refer to as patchiness. Landscape ecological
research focuses on the factors controlling exchanges of energy, materials, and
organisms among ecosystem patches.
 The biosphere is the global ecosystem, the sum of all of the planet’s ecosystems. The
biosphere includes the entire portion of Earth inhabited by life, ranging from the
atmosphere to a height of several kilometers to the oceans and water bearing rocks to a
depth of several kilometers.
Ecology provides a scientific context for evaluating environmental issues.
 It is important to clarify the difference between ecology, the scientific study of the
distribution and abundance of organisms, and environmentalism, advocacy for the
protection or preservation of the natural environment.
 To address environmental problems, we need to understand the interactions of organisms
and the environment.
 The science of ecology provides that understanding.
 In 1962, Rachel Carson’s book Silent Spring warned that the use of pesticides such as
DDT was causing population declines in many nontarget organisms.
 Today, acid precipitation, land misuse, toxic wastes, habitat destruction, and the growing
list of endangered or extinct species are just a few of the problems that threaten the Earth.
 Many influential ecologists feel a responsibility to educate legislators and the general
public about decisions that affect the environment.
 It is important to communicate the scientific complexity of environmental issues.
 Our ecological information is always incomplete. The precautionary principle
(essentially “an ounce of prevention is worth a pound of cure”) can guide decision making
on environmental issues.

Concept 50.2 Interactions between organisms and the environment limit the
distribution of species
 Ecologists have long recognized distinct global and regional patterns in the distribution of
organisms.
 Biogeography is the study of past and present distributions of individual species in the
context of evolutionary theory.
 Ecologists ask a series of questions to determine what limits the geographical distribution
of any species.
Species dispersal contributes to the distribution of organisms.

Biology Chapter Notes

 The movement of individuals away from centers of high population density or from their
area of origin is called dispersal.
 The dispersal of organisms is crucial to understanding geographic isolation in evolution
and the broad patterns of geographic distribution of species.
 One way to determine if dispersal is a key factor limiting distribution is to observe the
results when humans have accidentally or intentionally transplanted a species to areas
where it was previously absent.
 For the transplant to be considered successful, the organisms must not only survive in
the new area, but also reproduce there.
 If the transplant is successful, then the potential range of the species is larger than its
actual range.
 Species introduced to new geographic locations may disrupt the communities and
ecosystems to which they are introduced.
 Consequently, ecologists rarely conduct transplant experiments today.
 Instead, they study the outcome when a species has been transplanted accidentally or
for another purpose.
Behavior and habitat selection contribute to the distribution of organisms.
 Sometimes organisms do not occupy all of their potential range but select particular
habitats.
 Does behavior play a role in limiting distribution in such cases?
 Habitat selection is one of the least-understood ecological processes, but it appears to play
an important role in limiting the distribution of many species.
Biotic factors affect the distribution of organisms.
 Do biotic factors limit the distribution of species?
 Negative interactions with other organisms in the form of predation, parasitism,
disease, or competition may limit the ability of organisms to survive and reproduce.
 Predator-removal experiments can provide information about how predators limit
distribution of prey species.
 Absence of other species may also limit distribution of a species.
 For example, the absence of a specific pollinator or prey species may limit
distribution of an organism.
Abiotic factors affect the distribution of organisms.
 The global distribution of organisms broadly reflects the influence of abiotic factors such
as temperature, water, and sunlight.
 The environment is characterized by spatial and temporal heterogeneity.
 Environmental temperature is an important factor in the distribution of organisms because
of its effect on biological processes.
 Very few organisms can maintain an active metabolism at very high or very low
temperatures.
 Some organisms have extraordinary adaptations to allow them to live outside the
temperature range habitable for most other living things.
 The variation in water availability among habitats is an important factor in species
distribution.
 Most aquatic organisms are restricted to either freshwater or marine environments.
Biology Chapter Notes
  Terrestrial organisms face a nearly constant threat of desiccation and have adaptations
to allow them to obtain and conserve water.
 Sunlight provides the energy that drives nearly all ecosystems.
 Intensity of light is not the most important factor limiting plant growth in most
terrestrial environments, although shading by a forest canopy makes competition for
light in the understory intense.
 In aquatic environments, light intensity limits distribution of photosynthetic organisms.
 Every meter of water depth selectively absorbs 45% of red light and 2% of blue
light passing through it.
 As a result, most photosynthesis in aquatic environments occurs near the surface.
 Photoperiod, the relative length of daytime and nighttime, is a reliable indicator of
seasonal events and is an important cue for the development or behavior of many
organisms.
 Wind amplifies the effects of temperature by increasing heat loss due to evaporation and
convection. It also increases water loss by increasing the rate of evaporative cooling in
animals and transpiration in plants.
 The physical structure, pH, and mineral composition of soils and rocks limit distribution
of plants and, thus, of the animals that feed upon them, contributing to the patchiness of
terrestrial ecosystems.
 In streams and rivers, substrate composition can affect water chemistry, affecting
distribution of organisms.
 In marine environments, the structure of substrates in the intertidal areas or seafloor limits
the organisms that can attach to or burrow in those habitats.
Four abiotic factors are the major components of climate.
 Climate is the prevailing weather conditions in an area.
 Four abiotic factors—temperature, water, sunlight, and wind—are the major
components of climate.
 Climatic factors, especially temperature and water, have a major influence on the
distribution of organisms.
 Climate patterns can be described on two scales. Macroclimate patterns are on global,
regional, or local levels, and microclimate patterns are very fine patterns such as the
conditions experienced by a community of organisms under a fallen log.
 Climate determines the makeup of biomes, the major types of ecosystems.
 Annual means for temperature and rainfall are reasonably well correlated with the
biomes found in different regions.
 Global climate patterns are determined by sunlight and Earth’s movement in space.
 The sun’s warming effect on the atmosphere, land, and water establishes the
temperature variations, cycles of air movement, and evaporation of water that are
responsible for latitudinal variations in climate.
 Bodies of water and topographic features such as mountain ranges create regional climatic
variations, while smaller features of the landscape affect local climates.
 Ocean currents influence climate along the coast by heating or cooling overlying air
masses, which may pass over land.
 Coastal regions are generally moister than inland areas at the same latitude.
 In general, oceans and large lakes moderate the climate of nearby terrestrial
environments.
Biology Chapter Notes
  In certain regions, cool, dry ocean breezes are warmed when they move over land,
absorbing moisture and creating a hot, rainless climate slightly inland.
 This Mediterranean climate pattern occurs inland from the Mediterranean Sea.
 Ocean currents also influence climate in coastal areas.
 Mountains have a significant effect on the amount of sunlight reaching an area, as well as
on local temperature and rainfall.
 In the Northern Hemisphere, south-facing slopes receive more sunlight than north-
facing slopes, and are therefore warmer and drier.
 These environmental differences affect species distribution.
 At any given latitude, air temperature declines 6°C with every 1,000-m increase in
elevation.
 This temperature change is equivalent to that caused by an 880-km increase in latitude.
 As moist, warm air approaches a mountain, it rises and cools, releasing moisture on the
windward side of the peak.
 On the leeward side of the mountain, cool, dry air descends, absorbing moisture and
producing a rain shadow.
 Deserts commonly occur on the leeward side of mountain ranges.
 The changing angle of the sun over the course of a year affects local environments.
 Belts of wet and dry air on either side of the equator shift with the changing angle of
the sun, producing marked wet and dry seasons around 20° latitude.
 Seasonal changes in wind patterns produce variations in ocean currents, occasionally
causing the upwelling of nutrient-rich, cold water from deep ocean layers.
 Lakes are also sensitive to seasonal temperature changes.
 During the summer and winter, many temperate lakes are thermally stratified or
layered vertically according to temperature.
 These lakes undergo a semiannual mixing, or turnover, of their waters in spring and
fall. Turnover brings oxygenated water to the bottom and nutrient-rich water to the
surface.
 Many features in the environment influence microclimates.
 Forest trees moderate the microclimate beneath them.
 Cleared areas experience greater temperature extremes than the forest interior.
 A log or large stone shelters organisms, buffering them from temperature and moisture
fluctuations.
 Every environment on Earth is characterized by a mosaic of small-scale differences in
abiotic factors that influence the local distribution of organisms.
 Long-term climate changes profoundly affect the biosphere.
 One way to predict possible effects of current climate changes is to consider the changes
that have occurred in temperate regions since the end of the last Ice Age.
 Until about 16,000 years ago, continental glaciers covered much of North America and
Eurasia.
 As the climate warmed and the glaciers melted, tree distribution expanded northward.
 A detailed record of these migrations is captured in fossil pollen in lake and pond
sediments.

Biology Chapter Notes

 If researchers can determine the climatic limits of current geographic distributions for
individual species, they can predict how that species distribution will change with global
warming.
 A major question for tree species is whether seed dispersal is rapid enough to sustain
the migration of the species as climate changes.
 Consider the American beech, Fagus grandifolia.
 Climate models predict that the northern and southern limit of the beech’s range
will move 700–900 km north over the next century.
 The beech will have to migrate 7–9 km per year to maintain its distribution.
 However, since the Ice Age, the beech has migrated into its present rage at a rate of
only 0.2 km per year.
 Without human assistance, the beech will become extinct.

Concept 50.3 Abiotic and biotic factors influence the structure and dynamics of aquatic
biomes
 Varying combinations of biotic and abiotic factors determine the nature of the Earth’s
biomes, major types of ecological associations that occupy broad geographic regions of
land or water.
Aquatic biomes occupy the largest part of the biosphere.
 Ecologists distinguish between freshwater and marine biomes on the basis of physical and
chemical differences.
 Marine biomes generally have salt concentrations that average 3%, while freshwater
biomes have salt concentrations of less than 1%.
 Marine biomes cover approximately 75% of the earth’s surface and have an enormous
effect on the biosphere.
 The evaporation of water from the oceans provides most of the planet’s rainfall.
 Ocean temperatures have a major effect on world climate and wind patterns.
 Photosynthesis by marine algae and photosynthetic bacteria produce a substantial
proportion of the world’s oxygen. Respiration by these organisms consumes huge
amounts of atmospheric carbon dioxide.
 Freshwater biomes are closely linked to the soils and biotic components of the terrestrial
biomes through which they pass.
 The pattern and speed of water flow and the surrounding climate are also important.
 Most aquatic biomes are physically and chemically stratified.
 Light is absorbed by the water and by photosynthetic organisms, so light intensity
decreases rapidly with depth.
 There is sufficient light for photosynthesis in the upper photic zone.
 Very little light penetrates to the lower aphotic zone.
 The substrate at the bottom of an aquatic biome is the benthic zone.
 This zone is made up of sand and sediments and is occupied by communities of
organisms called benthos.
 A major food source for benthos is dead organic material or detritus, which rains
down from the productive surface waters of the photic zone.
 Sunlight warms surface waters, while deeper waters remain cold.
Biology Chapter Notes
  As a result, water temperature in lakes is stratified, especially in summer and winter.
 In the ocean and most lakes, a narrow stratum of rapid temperature change called a
thermocline separates the more uniformly warm upper layer from more uniformly
cold deeper waters.
 In aquatic biomes, community distribution is determined by depth of the water, distance
from shore, and open water versus bottom.
 In marine communities, phytoplankton, zooplankton, and many fish species live in the
relatively shallow photic zone.
 The aphotic zone contains little life, except for microorganisms and relatively sparse
populations of luminescent fishes and invertebrates.
 The major aquatic biomes include lakes, wetlands, streams, rivers, estuaries, intertidal
biomes, oceanic pelagic biomes, coral reefs, and marine benthic biomes.
 Freshwater lakes vary greatly in oxygen and nutrient content.
 Oligotrophic lakes are deep, nutrient poor, oxygen rich, and contain little life.
 Eutrophic lakes are shallow, nutrient rich, and oxygen poor.
 In lakes, the littoral zone is the shallow, well-lit water close to shore.
 The limnetic zone is the open surface water.
 Wetlands are areas covered with sufficient water to support aquatic plants.
 They can be saturated or periodically flooded.
 Wetlands include marshes, bogs, and swamps.
 They are among the most productive biomes on Earth and are home to a diverse
community of invertebrates and birds.
 Because of the high organic production and decomposition in wetlands, their water and
soil are low in dissolved oxygen.
 Wetlands have a high capacity to filter dissolved nutrients and chemical pollutants.
 Humans have destroyed many wetlands, but some are now protected.
 Streams and rivers are bodies of water moving continuously in one direction.
 Headwaters are cold, clear, turbulent, and swift.
 They carry little sediment and relatively few mineral nutrients.
 As water travels downstream, it picks up O2 and nutrients on the way.
 Nutrient content is largely determined by the terrain and vegetation of the area.
 Many streams and rivers have been polluted by humans, degrading water quality
and killing aquatic organisms.
 Damming and flood control impairs the natural functioning of streams and rivers
and threatens migratory species such as salmon.
 Estuaries are areas of transition between river and sea.
 The salinity of these areas can vary greatly.
 Estuaries have complex flow patterns, with networks of tidal channels, islands, levees,
and mudflats.
 They support an abundance of fish and invertebrate species and are crucial feeding
areas for many species of waterfowl.
 An intertidal zone is a marine biome that is periodically submerged and exposed by the
tides.
 The upper intertidal zone experiences longer exposure to air and greater variation in
salinity and temperature than do the lower intertidal areas.
Biology Chapter Notes
  Many organisms live only at a particular stratum in the intertidal.
 The oceanic pelagic biome is the open blue water, mixed by wind-driven oceanic
currents.
 The surface waters of temperate oceans turn over during fall through spring.
 The open ocean has high oxygen levels and low nutrient levels.
 This biome covers 70% of the Earth’s surface and has an average depth of 4,000
meters.
 Coral reefs are limited to the photic zone of stable tropic marine environments with high
water clarity. They are found at temperatures between 18°C and 30°C.
 They are formed by the calcium carbonate skeletons of coral animals.
 Mutualistic dinoflagellate algae live within the tissues of the corals.
 Coral reefs are home to a very diverse assortment of vertebrates and invertebrates.
 Collecting of coral skeletons and overfishing for food and the aquarium trade have
reduced populations of corals and reef fishes.
 Global warming and pollution contribute to large-scale coral mortality.
 The marine benthic zone consists of the seafloor below the surface waters of the coastal
or neritic zone and the offshore pelagic zone.
 Most of the ocean’s benthic zone receives no sunlight.
 Organisms in the very deep abyssal zone are adapted to continuous cold (about 3°C)
and extremely high pressure.
 Unique assemblages of organisms are associated with deep-sea hydrothermal vents
of volcanic origin on mid-ocean ridges.
 The primary producers in these communities are chemoautotrophic prokaryotes that
obtain energy by oxidizing2−H2S formed by a reaction of volcanically heated water
with dissolved sulfate (SO4 ).

Concept 50.4 Climate largely determines the distribution and structure of terrestrial
biomes
 Because there are latitudinal patterns of climate over the Earth’s surface, there are also
latitudinal patterns of biome distribution.
 A climograph denotes the annual mean temperature and precipitation of a region.
 Temperature and rainfall are well correlated with different terrestrial biomes, and each
biome has a characteristic climograph.
 Most terrestrial biomes are named for major physical or climatic features or for their
predominant vegetation.
 Vertical stratification is an important feature of terrestrial biomes.
 The canopy of the tropical rain forest is the top layer, covering the low-tree stratum,
shrub understory, ground layer, litter layer, and root layer.
 Grasslands have a canopy formed by grass, a litter layer, and a root layer.
 Stratification of vegetation provides many different habitats for animals.
 Terrestrial biomes usually grade into each other without sharp boundaries. The area of
intergradation, called the ecotone, may be narrow or wide.
 The species composition of any biome differs from location to location.
 Biomes are dynamic, and natural disturbance rather than stability tends to be the rule.
Biology Chapter Notes
  Hurricanes create openings for new species in tropical and temperate forests.
 In northern coniferous forests, snowfall may break branches and small trees, producing
gaps that allow deciduous species to grow.
 As a result, biomes exhibit patchiness, with several different communities represented
in any particular area.
 In many biomes, the dominant plants depend on periodic disturbance.
 For example, natural wildfires are an integral component of grasslands, savannas,
chaparral, and many coniferous forests.
 Human activity has radically altered the natural patterns of periodic physical disturbance.
 Fires are now controlled for the sake of agricultural land use.
 Humans have altered much of the Earth’s surface, replacing original biomes with urban or
agricultural ones.
 The major terrestrial biomes include tropical forest, desert, savanna, chaparral, temperate
grassland, coniferous forest, temperate broadleaf forest, and tundra.
 Tropical forests are found close to the equator.
 Tropical rain forests receive constant high amounts of rainfall (200 to 400 cm
annually).
 In tropical dry forests, precipitation is highly seasonal.
 In both, air temperatures range between 25°C and 29°C year round.
 Tropical forests are stratified, and competition for light is intense.
 Animal diversity is higher in tropical forests than in any other terrestrial biome.
 Deserts occur in a band near 30° north and south latitudes and in the interior of
continents.
 Deserts have low and highly variable rainfall, generally less than 30 cm per year.
 Temperature varies greatly seasonally and daily.
 Desert vegetation is usually sparse and includes succulents such as cacti and deeply
rooted shrubs.
 Many desert animals are nocturnal, so they can avoid the heat.
 Desert organisms display adaptations to allow them to resist or survive desiccation.
 Savanna is found in equatorial and subequatorial regions.
 Rainfall is seasonal, averaging 30–50 cm per year.
 The savanna is warm year-round, averaging 24–29°C with some seasonal variation.
 Savanna vegetation is grassland with scattered trees.
 Large herbivorous mammals are common inhabitants.
 The dominant herbivores are insects, especially termites.
 Fire is important in maintaining savanna biomes.
 Chaparrals have highly seasonal precipitation with mild, wet winters and dry, hot
summers.
 Annual precipitation ranges from 30 to 50 cm.
 Chaparral is dominated by shrubs and small trees, with a high diversity of grasses and
herbs.
 Plant and animal diversity is high.
 Adaptations to fire and drought are common.

Biology Chapter Notes

 Temperate grasslands exhibit seasonal drought, occasional fires, and seasonal variation
in temperature.
 Large grazers and burrowing mammals are native to temperate grasslands.
 Deep fertile soils make temperate grasslands ideal for agriculture, especially for
growing grain.
 Most grassland in North America and Eurasia has been converted to farmland.
 Coniferous forest, or taiga, is the largest terrestrial biome on Earth.
 Coniferous forests have long, cold winters and short, wet summers.
 The conifers that inhabit these forests are adapted for snow and periodic drought.
 Coniferous forests are home to many birds and mammals.
 These forests are being logged at a very high rate and old-growth stands of conifers
may soon disappear.
 Temperate broadleaf forests have very cold winters, hot summers, and considerable
precipitation.
 A mature temperate broadleaf forest has distinct vertical layers, including a closed
canopy, one or two strata of understory trees, a shrub layer, and an herbaceous layer.
 The dominant deciduous trees in Northern Hemisphere broadleaf forests drop their
leaves and become dormant in winter.
 In the Northern Hemisphere, many mammals in this biome hibernate in the winter,
while many bird species migrate to warmer climates.
 Humans have logged many temperate broadleaf forests around the world.
 Tundra covers large areas of the Arctic, up to 20% of the Earth’s land surface.
 Alpine tundra is found on high mountaintops at all latitudes, including the tropics.
 The plant communities in alpine and Arctic tundra are very similar.
 The Artic tundra winter is long and cold, while the summer is short and mild. The
growing season is very short.
 Tundra vegetation is mostly herbaceous, consisting of a mixture of lichens, mosses,
grasses, forbs, and dwarf shrubs and trees.
 A permanently frozen layer of permafrost prevents water infiltration and restricts root
growth.
 Large grazing musk oxen are resident in Arctic tundra, while caribou and reindeer are
migratory.
 Migratory birds use Arctic tundra extensively during the summer as nesting grounds.
 Arctic tundra is sparsely settled by humans but has recently become the focus of
significant mineral and oil extraction.

Biology Chapter Notes

 Chapter 51 Behavioral Ecology
Chapter Notes

Overview: Studying Behavior

 Humans have studied animal behavior for as long as we have lived on Earth.
 As hunter and hunted, knowledge of animal behavior was essential to human behavior.
 The modern scientific discipline of behavioral ecology studies how behavior develops,
evolves, and contributes to survival and reproductive success.

Concept 51.1 Behavioral ecologists distinguish between proximate and ultimate causes
of behavior
 Scientific questions that can be posed about any behavior can be divided into two classes:
those that focus on the immediate stimulus and mechanism for the behavior and those that
explore how the behavior contributes to survival and reproduction.
 What is behavior?
 Behavioral traits are an important part of an animal’s phenotype.
 Many behaviors result from an animal’s muscular activity, such as a predator chasing a
prey.
 In some behaviors, muscular activity is less obvious, as in bird song.
 Some nonmuscular activities are also behaviors, as when an animal secretes a
pheromone to attract a member of the opposite sex.
 Learning is also a behavioral process.
 Put simply, behavior is everything an animal does and how it does it.
 Proximate questions are mechanistic, concerned with the environmental stimuli that
trigger a behavior, as well as the genetic, physiological, and anatomical mechanisms
underlying a behavioral act.
 Proximate questions are referred to as “how?” questions.
 Ultimate questions address the evolutionary significance of a behavior and why natural
selection favors this behavior.
 Ultimate questions are referred to as “why?” questions.
 Red-crowned cranes breed in spring and early summer.
 A proximate question about the timing of breeding by this species might ask, “How
does day length influence breeding by red-crowned cranes?”
 A reasonable hypothesis for the proximate cause of this behavior is that breeding is
triggered by the effect of increased day length on the crane’s production of and
response to particular hormones.
 An ultimate hypothesis might be that red-crowned cranes reproduce in spring and early
summer because that is when breeding is most productive.
 At that time of year, parent birds can find an ample supply of food for rapidly
growing offspring, providing an advantage in reproductive success compared to
birds that breed in other seasons.
 These two levels of causation are related.
Biology Chapter Notes
  Proximate mechanisms produce behaviors that evolved because they increase fitness in
some way.
 For example, increased day length has little adaptive significance for red-crowned
cranes, but because it corresponds to seasonal conditions that increase reproductive
success, such as the availability of food for feeding young birds, breeding when days
are long is a proximate mechanism that has evolved in cranes.
Classical ethology presaged an evolutionary approach to behavioral biology.
 In the mid-20th century, a number of pioneering behavioral biologists developed the
discipline of ethology, the scientific study of animal behavior.
 In 1963, Niko Tinbergen suggested four questions that must be answered to fully
understand any behavior.
o What is the mechanistic basis of the behavior, including chemical, anatomical, and
physiological mechanisms?
o How does development of the animal, from zygote to mature individual, influence the
behavior?
o What is the evolutionary history of the behavior?
o How does the behavior contribute to survival and reproduction (fitness)?
 Tinbergen’s list includes both proximate and ultimate questions.
 The first two, which concern mechanism and development, are proximate questions,
while the second two are ultimate, or evolutionary, questions.
 A fixed action pattern (FAP) is a sequence of unlearned behavioral acts that is
essentially unchangeable and, once initiated, is usually carried to completion.
 A FAP is triggered by an external sensory stimulus called a sign stimulus.
 In the red-spined stickleback, the male attacks other males that invade his nesting
territory.
 The stimulus for the attack is the red underside of the intruder.
 A male stickleback will attack any model that has some red visible on it.
 A proximate explanation for this aggressive behavior is that the red belly of the intruding
male acts as a sign stimulus that releases aggression in a male stickleback.
 An ultimate explanation is that by chasing away other male sticklebacks, a male decreases
the chance that eggs laid in his nesting territory will be fertilized by another male.
 Imprinting is a type of behavior that includes learning and innate components and is
generally irreversible.
 Imprinting has a sensitive period, a limited phase in an animal’s behavior that is the
only time that certain behaviors can be learned.
 An example of imprinting is young geese following their mother.
 In species that provide parental care, parent-offspring bonding is a critical time in the
life cycle.
 During the period of bonding, the young imprint on their parent and learn the basic
behavior of the species, while the parent learns to recognize its offspring.
 Among gulls, the sensitive period for parental bonding on young lasts one or two days.
 If bonding does not occur, the parent will not initiate care of the infant, leading to
certain death of the offspring and decreasing the parent’s reproductive success.
 How do young gulls know on whom—or what—to imprint?
 The tendency to respond is innate in birds.
Biology Chapter Notes
  The world provides the imprinting stimulus, and young gulls respond to and identify
with the first object they encounter that has certain key characteristics.
 In greylag geese, the key stimulus is movement of the object away from the young.
 A proximate explanation for young geese following and imprinting on their mother is that
during an early, critical developmental stage, the young geese observe their mother
moving away from them and calling.
 An ultimate explanation is that, on average, geese that follow and imprint on their mother
receive more care and learn necessary skills, and thus have a greater chance of surviving,
than those that do not follow.
 Early study of imprinting and fixed action patterns helped make the distinction between
proximate and ultimate causes of behavior.
 They also helped to establish a strong tradition of experimental approaches in
behavioral ecology.

Concept 51.2 Many behaviors have a strong genetic component

Behavior results from both genes and environmental factors.
 Behavioral traits, like other aspects of a phenotype, are the result of complex interactions
between genetic and environmental factors.
 In biology, the nature-versus-nurture issue is not about whether genes or environment
influence behavior, but about how both are involved.
 All behaviors are affected by both genes and environment.
 Behavior can be viewed in terms of the norm of reaction.
 We can measure the behavioral phenotypes for a particular genotype that develop in a
range of environments.
 In some cases, the behavior is variable, depending on environmental experience.
 In other cases, nearly all individuals in the population exhibit identical behavior,
despite internal and external environmental differences during development and
throughout life.
 Behavior that is developmentally fixed is called innate behavior.
 Such behaviors are under strong genetic influence.
 The range of environmental differences among individuals does not appear to alter
innate behavior.
Many animal movements are under substantial genetic influence.
 A kinesis is a simple change in activity or turning rate in response to a stimulus.
 For example, sowbugs are more active in dry areas and less active in humid areas.
 This increases the chance that they will leave a dry area and encounter a moist area.
 A taxis is an automatic, oriented movement toward or away from a stimulus.
 For example, many stream fishes exhibit positive rheotaxis, automatically swimming
or orienting themselves in an upstream direction (toward the current).
 This keeps them from being swept away and keeps them facing in the direction in
which food is coming.
 Ornithologists have found that many features of migratory behavior in birds are
genetically programmed.
Biology Chapter Notes
  Migration is the regular movement of animals over relatively long distances.
 One of the best-studied migratory birds is the blackcap (Sylvia atricapilla), a small
warbler that ranges from the Cape Verde Islands off the coast of West Africa to northern
Europe.
 Migratory behaviors of blackcaps vary greatly among populations.
 During the migration season, captive migratory blackcaps hop restlessly about their
cages all night or rapidly flap their wings while sitting on a perch.
 Peter Berthold studied the genetic basis of this behavior, known as “migratory
restlessness,” in several populations of blackcaps.
 In one study, the researchers crossed migratory blackcaps with nonmigratory ones and
subjected their offspring to environments simulating one location or the other.
 Forty percent of offspring raised in both conditions showed migratory restlessness,
leading Berthold to conclude that migration is under genetic control and follows a
polygenic inheritance pattern.
Animal communication is an essential component of interactions between individuals.
 Much of the social interaction between animals involves transmitting information through
specialized behaviors called signals.
 In behavioral ecology, a signal is a behavior that causes a change in another animal’s
behavior.
 The transmission, reception, and response to signals constitute animal communication.
 Some features of animal communication are under strong genetic control, although the
environment makes a significant contribution to all communication systems.
 Many signals are efficient in energy costs.
 For example, a territorial fish erects its fins when aggressively approaching an
intruder.
 It takes less energy to erect fins that to attack an invading fish.
 Animals communicate using visual, auditory, chemical, tactile, and electrical signals.
 The type of signal is closely related to an animal’s lifestyle and environment.
 For example, nocturnal species use olfactory and auditory signals.
 Birds are diurnal and have a poor olfactory sense.
 They communicate primarily by visual and auditory signals.
 Humans are more attentive to the colors and songs of birds than the rich olfactory
signals of many other animals because of our own senses.
 Many animals secrete chemical substances called pheromones.
 These chemicals are especially common in mammals and insects and often relate to
reproductive behaviors.
 In honeybees, pheromones produced by the queens and her daughters (workers)
maintain the hive’s very complex social order.
 Male drones are attracted to the queen’s pheromone when they are outside the hive.
 Pheromones can also function in nonreproductive behavior.
 When a minnow is injured, an alarm substance is released from glands in the fish’s
skin, inducing a fright response among other fish in the area.
 They become more vigilant and group in tightly packed schools.
 Pheromones are effective at very low concentrations.
Biology Chapter Notes
 The songs of most birds are at least partly learned.
 In contrast, in many species of insect, mating rituals include characteristic songs that are
under direct genetic control.
 In Drosophila, males produce a song by wing vibration.
 A variety of evidence suggests that song structure in Drosophila is controlled
genetically and is under strong selective pressure.
 Females can recognize the songs of males of their own species.
 Males raised in isolation produce a characteristic song with no exposure to other
singing males.
 The male song shows little variation among individuals.
 Some insect species are morphologically identical and can be identified only through
courtship songs or behaviors.
 For example, morphologically identical green lacewings were once thought to belong
to a single species.
 However, studies of their courtship songs revealed the presence of at least 15 different
species, each with a different song.
 Hybrid offspring sing songs that contain elements of the songs of both parental
species, leading researchers to conclude that the songs are genetically controlled.
Prairie vole mating and parental behaviors are under strong genetic influence.
 Mating and parental behavior by male prairie voles (Microtus ochrogaster) are under
strong genetic control.
 Prairie voles and a few other vole species are monogamous, a social trait found in only
3% of mammalian species.
 Male prairie voles help their mates care for young, a relatively uncommon trait among
male mammals.
 Male prairie voles form a strong pair-bond with a single female after they mate,
engaging in grooming and huddling behaviors.
 Mated males are intensely aggressive to strange males or females, while remaining
nonaggressive to their mate and pups.
 Research by Thomas Insel at Emory University suggests that arginine-vasopressin (AVP),
a nine-amino-acid neurotransmitter released in mating, mediates both pair-bond formation
and aggression in male prairie voles.
 In the CNS, AVP binds to a receptor called the V1a receptor.
 The researcher found significant differences in the distribution of V 1a receptors
between the brains of monogamous prairie voles and related promiscuous montane
voles.
 Insel inserted the prairie vole V1a receptor gene into laboratory mice.
 The mice developed the same distribution of V 1a receptors as the prairie voles and also
showed many of the mating behaviors of the voles.
 Thus, a single gene appears to mediate much of the complex mating and parental behavior
of the prairie vole.

Concept 51.3 Environment, interacting with an animal’s genetic makeup, influences the
development of behaviors

Biology Chapter Notes

 Environmental factors modify many behaviors.
 Diet plays an important role in mate selection by Drosophila mojavensis, which mates and
lays its eggs in rotting cactus tissues.
 Two populations of this fruit fly species use different species of cactus for their eggs.
 Flies from each population were raised on artificial media in the lab.
 Females would mate only with males from their own population.
 The food eaten by male flies as larvae strongly influenced mate selection by female
flies.
 The proximate cause in the female mate choices was in the exoskeletons of the
flies, assessed by the sense of taste in female flies.
 When males from the other population were “perfumed” with hydrocarbons
extracted from males of the same population, they were accepted by female flies.
 The California mouse (Peromyscus californicus) is monogamous.
 Like male prairie voles, male California mice are highly aggressive to other mice and
provide considerable parental care.
 Unlike prairie voles, even unmated California mice are aggressive.
 Researchers placed newborn California mice in the nests of white-footed mice (and vice
versa).
 White-footed mice are not monogamous and provide little parental care.
 This cross-fostering changed the behavior of both species.
 Cross-fostered California mice provided less parental care and were less aggressive
toward intruders when they grew up and reared their own young.
 Their brains had reduced levels of AVP, compared with California mice raised by
their own parents.
 White-footed mice reared by California mice were more aggressive as parents than
those raised by their own parents.
 One of the most powerful ways that environmental conditions can influence behavior is
through learning, the modification of behavior based on specific experiences.
 Learned behaviors can be very simple, such as imprinting, or highly complex.
 Habituation involves a loss of responsiveness to unimportant stimuli or stimuli that do
not provide appropriate feedback.
 For example, some animals stop responding to warning signals if signals are not
followed by a predator attack (the “cry wolf” effect).
 In terms of ultimate causation, habituation may increase fitness by allowing an
animal’s nervous system to focus on meaningful stimuli, rather than wasting time on
irrelevant stimuli.
The fitness of an organism may be enhanced by the capacity for spatial learning.
 Every natural environment shows spatial variation.
 As a consequence, it may be advantageous for animals to modify their behavior based on
experience with the spatial structure of their environment, including the locations of nest
sites, hazards, food, and prospective mates.
 The fitness of an animal may be enhanced by the capacity for spatial learning.
 Niko Tinbergen found that digger wasps found their nest entrances by using landmarks,
or location indicators, in their environment.
Biology Chapter Notes
  Landmarks must be stable within the time frame of the activity.
 Because some environments are more stable than others, animals may use different
kinds of information for spatial learning in different environments.
 Sticklebacks from a river learned a maze by learning a pattern of movements.
 Sticklebacks from a more stable pond environment used a combination of
movements and landmarks to learn the maze.
 The degree of environmental variability influences the spatial learning strategies
of animals.
 Some animals form cognitive maps, internal codes of spatial relationships of objects
in their environment.
 It is difficult to distinguish experimentally between the use of landmarks and the
development of a true cognitive map.
 Researchers have obtained good evidence that corvids (a bird family including
ravens, crows, and jays) use cognitive maps.
 Many corvids store food in caches and retrieve it later.
 Pinyon jays may store nuts in as many as a thousand widely dispersed caches,
keeping track of location and food quality (based on time since the food was
stored).
 Birds can learn that caches are halfway between two landmarks.

Many animals can learn to associate one stimulus with another.

 Associative learning is the ability of animals to learn to associate one stimulus with
another.
 For example, a mouse may have an unpleasant experience with a colorful, poisonous
caterpillar and learn to avoid all caterpillars with that coloration.
 Classical conditioning is a type of associative learning.
 Researchers trained Drosophila melanogaster to avoid air carrying a particular scent
by coupling exposure to the odor with an electrical shock.
 Drosophila has a surprising capacity for learning.
 Associative learning may play an important role in helping animals to avoid predators.
 Zebra fish, an Asian minnow, and pike, an American predatory fish, do not occur
together in the wild.
 Researchers exposed zebra fish in an experimental group to an influx of 20 mL of
water containing an alarm substance and then, 5 minutes later, to 20 mL of water with
pike odor.
 Zebra fish had no innate negative reaction to pike odor, but learned to associate pike
odor with the alarm substance.
 The zebra fish were conditioned to associate pike odor with the alarm substance.
 Operant conditioning is also called trial-and-error learning.
 An animal learns to associate one of its own behaviors with a reward or a punishment.
 An example is the mouse eating the poisonous caterpillar and learning to avoid such
caterpillars in the future.
The study of cognition connects behavior with nervous system function.
 The term cognition is variously defined.
 In a narrow sense, it is synonymous with consciousness or awareness.

Biology Chapter Notes

  In a broad sense, animal cognition is the ability of an animal’s nervous system to
perceive, store, process, and use information gathered by sensory receptors.
 The study of animal cognition, called cognitive ethology, examines the connection
between an animal’s nervous system and its behavior.
 One area of research investigates how an animal’s brain represents physical objects in the
environment.
 Cognitive ethnologists have discovered that many animals, including insects, categorize
objects in their environment as “same” or “different.”
 Primates, dolphins, and corvids (crow, ravens, and jays) are capable of novel problem-
solving behavior.
 Individual animals may show great individual variation in the way they attempt to
solve a problem.
 Many animals solve problems by observing the behavior of other individuals.
 Chimpanzees learn to solve problems by copying the behavior of other chimpanzees.
Varying degrees of genetic and environmental factors contribute to the learning of
complex behavior.
 Considerable research on the development of songs by birds has revealed varying degrees
of genetic and environmental influence on the learning of complex behavior.
 In some species, learning plays only a small part in the development of song.
 For instance, New World flycatchers that are reared away from adults of their own
species will sing the song characteristic of their own species without every having
heard it.
 Some songbirds have a sensitive period for developing their songs.
 Individual white-crowned sparrows reared in silence perform abnormal songs, but if
recordings of the proper songs are played early in the life of the bird, normal songs
develop.
 Although the young bird does not sing during the sensitive period, it memorizes the
song of its own species by listening to other white-crowned sparrows sing.
 During the sensitive period, white-crowned sparrows fledging seem to be stimulated
more by songs of their own species than songs of other species, chirping more in
response.
 The young birds learn the songs, but the learning appears to be bounded by genetically
controlled preferences.
 The sensitive period in a white-crowned sparrow’s learning of his song is followed by a
second learning phase, when the juvenile bird sings some tentative notes that researchers
call a subsong.
 The juvenile bird hears its own song and compares it with the song that it memorized
in the sensitive period.
 Once they match, the bird sings that song for the rest of his life.
 Canaries may learn new song “syllables” each year, adding to their song during a yearly
plastic song stage.

Biology Chapter Notes

Concept 51.4 Behavioral traits can evolve by natural selection
 Because of the influence of genes on behavior, natural selection can result in the evolution
of behavioral traits in populations.
Behavior varies in natural populations.
 Behavioral differences between closely related species are common.
 Males of different Drosophila species sing different courtship songs.
 Species of voles differ in paternal care.
 Although less obvious, significant differences in behavior can be found within animal
species.
 When behavioral variation within a species corresponds to variation in environmental
conditions, it may be evidence of past evolution.
 One of the best-known examples of genetically based variation in behavior within a
species is prey selection by the garter snake Thamnophis elegans.
 Coastal garter snakes feed on salamanders, frogs, and toads, but mainly on slugs.
 Inland snakes eat frogs, leeches, and fish, but not slugs.
 Stevan Arnold investigated this variation.
 He offered slugs to snakes from both populations, but only coastal snakes readily
accepted the slugs.
 He tested newborn snakes born in the laboratory and found that 73% of young snakes
from coastal mothers attacked slugs they were offered.
 Only 35% of naïve snakes from inland mothers attacked the slugs.
 Arnold proposed that when inland snakes colonized coastal environments 10,000 years
ago, a small fraction of the population had the ability to recognize slugs by
chemoreception.
 These snakes took advantage of the abundant food source that slugs represented and
had higher fitness than snakes that ignored slugs.
 The capacity to recognize slugs as prey increased in frequency in coastal populations.
 The funnel web spider Agelenopsis aperta lives in riparian zones and the surrounding arid
environment in the western United States.
 The spider’s web is a silken sheet ending in a hidden funnel, where the spider sits and
watches for food while foraging.
 When prey strikes the web, the spider runs out across the web to make its capture.
 Riechert and her colleagues found a striking contrast in the behavior of spiders in riparian
forests and those in arid habitats.
 In arid, food-poor habitats, A. aperta is more aggressive to potential prey and to other
spiders in defense of its web, and it returns to foraging more quickly following
disturbance.
 Hedrick and Riechert reared spiders in the lab and found that the differences in
aggressiveness between desert and riparian spiders are genetic.
 Highly productive riparian sites are rich in prey for spiders, but the density of bird
predators is also high.
 The timid behavior of A. aperta in riparian habitats was selected for by predation risk.
Experiments provide evidence for behavioral evolution.

Biology Chapter Notes

 Researchers are carrying out experiments on organisms with short life spans, looking for
evidence of evolution in laboratory populations.
 Marla Sokolowski studied a polymorphism in a gene for foraging in Drosophila
melanogaster.
 The gene is called for, and it has two alleles.
 One allele, forR, results in a “rover” phenotype in which the fly larva moves more than
usual.
 The other allele, forS, results in a “sitter” phenotype in which the fly larva moves less
than usual.
 Sokolowski reared Drosophila at high and low population densities for 74 generations.
 The forS allele increased in low-density populations, while forR increased in high-
density populations.
 At low densities, short-distance foraging yielded sufficient food.
 At high densities, long-distance foraging helped the larvae to move beyond areas of
food depletion.
 Peter Berthold and his colleagues captured 20 male and 20 female blackcaps wintering in
Britain and transported them to southwest Germany.
 The birds were caged in glass-covered funnel cages lined with carbon paper.
 As the birds moved around the funnels, the marks they made on the paper showed the
direction they were trying to migrate.
 The migratory orientation of wintering adult birds captured in Britain was similar to
their laboratory-reared offspring.
 Young birds originally from Germany had a very different migratory orientation.
 This study indicates a genetic basis for migratory orientation of the young birds.
 Has the behavior evolved over time?
 Berthold’s study suggests that the change in migratory behavior of the blackcaps
is recent and rapid, having taken place over the past 50 years.
 Before 1960, there were no westward-migrating blackcaps in Germany.
 By the 1990s, westward migrants made up 7–11% of the blackcap populations
of Germany.
 Berthold suggested that westward migrants benefited from their new behavior,
due to the milder winter climate and greater abundance of bird feeders in
Britain.

Concept 51.5 Natural selection favors behaviors that increase survival and reproductive
success
 The genetic components of behavior evolve through natural selection favoring traits that
enhance survival and reproductive success in a population.
 Two of the most direct ways that behavior can affect fitness are through influences on
foraging and mate choice.
 Foraging includes not only eating, but also any mechanisms that an animal uses to
recognize, search for, and capture food items.
 Optimal foraging theory views foraging behavior as a compromise between the benefits
of nutrition and the costs of obtaining food, such as the energy expenditure and risk of
predation while foraging.
Biology Chapter Notes
  Natural selection should favor foraging behavior that minimizes the costs of foraging
and maximizes the benefits.
 Behavioral ecologists apply cost-benefit analysis to study the proximate and ultimate
causes of diverse foraging strategies.
 Reta Zach of the University of British Columbia carried out a cost-benefit analysis of
feeding behavior in crows.
 Crows search the tide pools of Mandarte Island, B.C., for snails called whelks.
 A crow flies up and drops the whelk onto the rocks to break its shell.
 If the drop is successful, the crow eats the snail’s soft body.
 If it is not successful, the crow flies higher and tries again.
 Zach predicted—and found—that crows would, on average, fly to a height that would
provide the most food relative to the total amount of energy required to break the
whelk shells.
 Bluegill sunfish feed on small crustaceans called Daphnia, selecting larger individuals
that supply the most energy per unit time.
 Smaller individuals will be selected if larger prey are too far away.
 Optimal foraging theory predicts that the proportion of small to large prey captured will
vary with prey density.
 At high densities, it is efficient for bluegill sunfish to feed only on large crustaceans.
 At low densities, bluegill sunfish should exhibit little size selectivity because all prey
are needed to meet energy requirements.
 In experiments, young bluegill sunfish forage efficiently but not as close to optimum as
older individuals.
 Perhaps younger fish do not judge size and distance as accurately because their vision
is not yet completely developed.
 Learning may also improve the foraging efficiency of bluegill sunfish as they age.
 Risk of predation is one of the most significant potential costs to a forager.
 Mule deer are preyed on by mountain lions throughout their range.
 Researchers studied mule deer populations in Idaho to determine if they forage in a
way that reduces their risk of falling prey to mountain lions.
 The researchers found that food available to mule deer was fairly uniform across the
potential foraging area.
 Risk of predation varied greatly, however.
 Mountain lions killed most mule deer at forest edges.
 Few were killed in open areas and forest interiors.

 How does mule deer feeding behavior respond to the differences in feeding risk?
 Mule deer feed predominantly in open areas, avoiding forest edges and forest interiors.
 When deer are at the forest edge, they spend significantly more time scanning their
surroundings than when they are in other areas.
 Mating behavior, which includes seeking and attracting mates, choosing among potential
mates, and competing for mates, is the product of a form of natural selection called sexual
selection.
 The mating relationship between males and females varies a great deal from species to
species.

Biology Chapter Notes

  In many species, mating is promiscuous, with no strong pair-bond or lasting
relationships.
 In species where the mates remain together for a longer period, the relationship may be
monogamous (one male mating with one female) or polygamous (one individual
mating with several partners).
 Polygamous relationships may involve a single male and many females (polygyny) or
a single female and many males (polyandry).
 Among monogamous species, males and females are often so much alike morphologically
that they are impossible to distinguish based on external characteristics.
 Polygynous species are generally dimorphic, with males being larger and more showy.
 In polyandrous species, females are ornamented and larger than males.
 The needs of young are an important factor constraining the evolution of mating systems.
 Parental investment refers to the time and resources expended for the raising of offspring.
 Most newly hatched birds cannot care for themselves and require a large, continuous food
supply that a single parent cannot provide.
 In such cases, a male will have more successful offspring if he helps his partner to rear
their chicks than if he goes off to seek more mates.
 This is why most birds are monogamous.
 Birds with young that can feed and care for themselves from birth, such as pheasant and
quail, have less need for parents to stay together.
 Males of these species can maximize their reproductive success by seeking other
mates.
 In mammals, the lactating female is often the only food source for the young, and males
play no role in caring for them in most mammal species.
 In some mammal species, males protect many females and their young.
 Certainty of paternity can influence mating systems and parental care.
 If the male is unsure if offspring are his, parental investment is likely to be lower.
 Females can be sure that they contributed to an offspring when they give birth or lay
eggs.
 Males do not have that assurance because the acts of mating and birth are separated
over time.
 Males in many species with internal fertilization engage in behaviors that appear to
increase their certainty of paternity, including guarding females, removing sperm from
the female’s reproductive tract before copulation, and introducing large numbers of
sperm to displace the sperm of other males.
 Certainty of paternity is much higher when egg laying and mating occur together, in
external fertilization.
 Parental care in aquatic invertebrates, fishes, and amphibians, when it occurs, is as
likely to be by males as females.
 Male parental care occurs in only 7% of fish and amphibian families with internal
fertilization and in 69% of families with external fertilization.
 The expression certainty of paternity does not imply conscious awareness of paternity
by the father.
Sexual selection is a form of natural selection.

Biology Chapter Notes

 Sexual dimorphism within a species results from sexual selection, a form of natural
selection in which differences in reproductive success among individuals are a
consequence of differences in mating success.
 Sexual selection can take the form of intersexual selection, in which members of one
sex choose mates on the basis of particular characteristics of the other sex—such as
courtship songs, or intrasexual selection, which involves competition among members
of one sex for mates.
 Mate preferences by females may play a central role in the evolution of male behavior and
anatomy through intersexual selection.
 Witte and Sawka experimented to see whether imprinting by young zebra finches on their
parents influenced their choice of mates when they matured.
 They taped a red feather to the heads of both parents, male parent only, or female
parent only, before the young chicks opened their eyes.
 Control zebra finches were reared by unadorned parents.
 When the chicks matured, they were given a choice of ornamented or unornamented mate
finches.
 Males showed no preference, but females reared by ornamented fathers preferred
ornamented mates.
 These results suggest that females imprint on their fathers and that mate choice by female
zebra finches has played a key role in evolution of ornamentation in male zebra finches.
 Courtship behaviors of stalk-eyed flies are fascinating.
 Males have elongated eyestalks, which they display to females during courtship.
 Females prefer to mate with males with relatively long eyestalks.
 How is this preference adaptive for females?
 Researchers have correlated certain genetic disorders in male flies with an inability
to develop long eyestalks.
 Males with long eyestalks may be demonstrating their genetic quality to females.
 In general, ornaments such as long eyestalks and brightly colored feathers correlate with a
male’s health and vitality.
 A female that chooses a healthy male increases the chance that her offspring will be
healthy.
 Males compete with each other by (often ritualized) agonistic behaviors that determine
which competitors gain access to resources.
 The outcome of such contests may be determined by strength or size.
 In some species, more than one mating behavior can result in successful reproduction.
 In such cases, intrasexual selection has led to the evolution of alternative male mating
behavior and morphology.
 Alternative male mating behaviors have been documented in the marine intertidal isopod
Paracerceis sculpta, which lives in sponges in the Gulf of California.
 This species includes three genetically distinct male types—alpha, beta, and gamma.
 Large alpha males defend harems of females within intertidal sponges, largely against
other alpha males.
 Beta males mimic female morphology and behavior and gain access to guarded
harems.
 Tiny gamma males invade and live within large harems.

Biology Chapter Notes

 The mating success of each type of isopod depends on the relative density of males and
females in the sponges.
 The alpha males sire the majority of young when defending a single female.
 If more than one female is present, beta males father 60% of the offspring.
 The reproductive rate of gamma males increases linearly with harem size.
 Overall, all three types of males have approximately equal mating success, and variation
among males in this species is sustained by natural selection.

Game theory can model behavioral strategies.

 Game theory evaluates alternative strategies in situations where the outcome depends on
each individual’s strategies and the strategies of other individuals.
 Barry Sinervo and Curt Lively used game theory to account for the existence of three
different male phenotypes in populations of side-blotched lizards (Uta stansburiana).
 Males have three genetically controlled colors: orange throats, blue throats, and yellow
throats.
 Orange-throat males are the most aggressive and defend large territories with many
females.
 Blue-throat males are also aggressive but defend smaller territories with fewer females.
 Yellow-throat males are nonterritorial and use sneaky tactics to mimic females and
sneak copulations.
 Frequency of the three types of males varies from year to year.
 Modeling showed that the relative success of different males varies with the abundance
of other types of males.
 When blue-throat males are abundant, they can defend their few females from the
sneaky yellow-throat males.
 However, they cannot defend their territories against the aggressive orange-throat
males.
 Orange-throat males take over large territories but cannot defend large numbers of
females against the sneaky yellow-throat males.
 Yellow-throat males then increase in numbers but are defeated by the blue-throat
males.
 The cycle continues.

Concept 51.6 The concept of inclusive fitness can account for most altruistic social
behavior
 Most social behaviors are selfish, meaning that they benefit the individual at the expense
of others, especially competitors.
 Behavior that maximizes an individual’s survival and reproductive success is favored by
selection, regardless of its effect on other individuals.
 How do we account for behaviors that help others?
 Altruism is defined as behavior that appears to decrease individual fitness but
increases the fitness of others.
 Belding’s ground squirrel lives in some mountainous regions of the western United States.
 The squirrel is vulnerable to predators such as coyotes and hawks.
Biology Chapter Notes
  If a squirrel sees a predator approach, it often gives a high-pitched alarm call, which
alerts unaware individuals.
 The alerted squirrels then retreat to their burrows.
 This conspicuous alarm behavior calls attention to the caller, who has a greater risk of
being killed.
 In honeybees, workers are sterile but labor on behalf of a single fertile queen.
 Workers will sacrifice themselves to sting intruders in defense of the hive.
 Naked mole rats are highly social rodents that live in underground chambers and tunnels
in Africa.
 These rodents are hairless and nearly blind and live in colonies of 75–250 individuals.
 Each colony has only one reproducing female, the queen, who mates with one to three
males, called kings.
 The rest of the colony consists of nonreproductive females and males who forage for
underground roots and tubers and care for the kings, queen, and young rats.
 How can a naked mole rat (or a honeybee or a ground squirrel) enhance its fitness by
helping other members of the population?
 How is altruistic behavior maintained by evolution?
 If related individuals help each other, they are, in effect, helping keep their own genes
in the population.
 Inclusive fitness is defined as the effect an individual has on proliferating its own genes
by reproducing and by helping relatives raise offspring.
 William Hamilton proposed a quantitative measure for predicting when natural selection
should favor altruistic acts.
 Hamilton’s rule states the conditions under which altruistic acts will be favored by
natural selection.
 The three key variables are as follows:
o The benefit to the recipient is B.
o The cost to the altruist is C.
o The coefficient of relatedness is r, which equals the probability that a particular gene
present in one individual will also be inherited from a common parent or ancestor in a
second individual.
 The rule is as follows:
 rB > C
 The more closely related two individuals are, the greater the value of altruism.
 Kin selection is the mechanism of inclusive fitness, where individuals help relatives raise
young.
 Some animals behave altruistically toward others who are not close relatives.
 Such behavior can be adaptive if the aided individual can be counted on to return the
favor in the future.
 This exchange of aid is called reciprocal altruism and is commonly used to explain
altruism between unrelated humans.
 Reciprocal altruism is limited to species with stable social groups in which individuals
have many opportunities to exchange aid and where there would be negative social
consequences for those who “cheat” and refuse to return favors to those who have helped
them in the past.
Biology Chapter Notes
 However, because cheating may provide a large benefit to cheaters, behavioral ecologists
have questioned how reciprocal altruism could arise.
 To answer this question, behavioral ecologists have turned to game theory.
 Axelrod and Hamilton found that reciprocal altruism can evolve and persist in a
population where individuals adopt a behavioral strategy called tit for tat.
 In this strategy, an individual treats another individual the same way it was treated the
last time they met.
 Individuals are always altruistic, or cooperative, on the first encounter, and will remain
so as long as their altruism is reciprocated.
 When it is not, they will retaliate immediately but will return to cooperative
behavior as soon as the other individual becomes cooperative.
Animals learn by observing others.
 Social learning is learning through observing others.
 Social learning forms the roots of culture, which can be defined as a system of
information transfer through social learning or teaching.
 Cultural transfer of information has the potential to alter behavioral phenotypes and
influence the fitness of individuals.
 Social learning is not restricted to humans.
 In many species, mate choice is strongly influenced by social learning.
 Mate choice copying, a behavior in which individuals in a population copy the mate
choices of others, has been extensively studied in the guppy Poecilia reticulata.
 Female guppies prefer to mate with males having a high percentage of orange coloration.
 However, if a female sees another female engaging in courtship with a male with
relatively little orange, she will choose a male with little orange herself.
 Below a certain threshold of difference in mate color, mate choice copying by female
guppies can mask genetically controlled female preference for orange males.
 What is the advantage for females?
 A female that mates with males that are attractive to other females may increase the
probability that her male offspring will also be attractive and have high reproductive
success.
 In their studies of vervet monkeys in Amboseli National Park, Kenya, Dorothy Cheny and
Richard Seyfarth found that performance of a behavior can improve through learning.
 Vervet monkeys (Cercopithecus aethiops) produce a complex set of alarm calls.
 Distinct alarm calls warn of leopards, eagles, or snakes, all of which prey on the small
vervets.
 Vervets react to each alarm differently, depending on the threat.
 Infant vervets give alarm calls but in an undiscriminating way.
 For example, they call “eagle” for any bird.
 With age, they improve their accuracy.
 Vervets learn how to give the right call by observing other members of the group
and by receiving social confirmation for accurate calls.
Sociobiology places social behavior in an evolutionary context.

Biology Chapter Notes

 Human culture is related to evolutionary theory in the discipline of sociobiology, whose
main premise is that certain behavioral characteristics exist because they are expressions
of genes that have been perpetuated by natural selection.
 In his seminal 1975 book Sociobiology: The New Synthesis, E. O. Wilson speculated
about the evolutionary basis of certain kinds of social behavior in nonhuman animals, but
he also included human culture, sparking a heated debate.
 The spectrum of possible human social behaviors may be influenced by our genetic
makeup, but that is very different from saying that genes are rigid determinants of
behavior.
 This distinction is at the core of the debate about evolutionary perspectives on human
behavior.
 Evolutionary explanations of human behavior do not reduce us to robots stamped out
of rigid genetic molds.
 Just as individuals vary extensively in anatomy, so we should expect variation in
behavior.
 Because of our capacity for learning, human behavior is probably more plastic than that of
any other animal.
 Over our recent evolutionary history, we have built up a diversity of structured societies
with governments, laws, religions, and cultural values that define acceptable and
unacceptable behavior, even when unacceptable behavior might enhance an individual’s
Darwinian fitness.
 In human behavior, as in other animals, genes and environmental factors build on each
other.
 What is unique about our species?
 Perhaps it is our social and cultural institutions that provide us with the only uniquely
human feature.

Biology Chapter Notes

 Chapter 52 Population Ecology
Chapter Notes

Overview: Earth’s Fluctuating Populations

 To understand human population growth, we must consider the general principles of

population ecology.
 Population ecology is the study of populations in relation to the environment, including
environmental influences on population density and distribution, age structure, and
population size.

Concept 52.1 Dynamic biological processes influence population density, dispersion,

and demography
 A population is a group of individuals of a single species that live in the same general
area.
 Members of a population rely on the same resources, are influenced by similar
environmental factors, and have a high likelihood of interacting with and breeding with
one another.
 Populations can evolve through natural selection acting on heritable variations among
individuals and changing the frequencies of various traits over time.
Two important characteristics of any population are density and the spacing of
individuals.
 Every population has a specific size and specific geographical boundaries.
 The density of a population is measured as the number of individuals per unit area or
volume.
 The dispersion of a population is the pattern of spacing among individuals within the
geographic boundaries.
 Measuring density of populations is a difficult task.
 We can count individuals, but we usually estimate population numbers.
 It is almost always impractical to count all individuals in a population.
 Instead, ecologists use a variety of sampling techniques to estimate densities and total
population sizes.
 For example, they might count the number of individuals in a series of randomly
located plots, calculate the average density in the samples, and extrapolate to
estimate the population size in the entire area.
 Such estimates are accurate when there are many sample plots and a homogeneous
habitat.
 A sampling technique that researchers commonly use to estimate wildlife populations
is the mark-recapture method.
 Individuals are trapped and captured, marked with a tag, recorded, and then
released.
 After a period of time has elapsed, traps are set again, and individuals are captured
and identified.
 The second capture yields both marked and unmarked individuals.
Biology Chapter Notes
  From these data, researchers estimate the total number of individuals in the
population.
 The mark-recapture method assumes that each marked individual has the same
probability of being trapped as each unmarked individual.
 This may not be a safe assumption, as trapped individuals may be more or less
likely to be trapped a second time.
 Density results from dynamic interplay between processes that add individuals to a
population and those that remove individuals from it.
 Additions to a population occur through birth (including all forms of reproduction) and
immigration (the influx of new individuals from other areas).
 The factors that remove individuals from a population are death (mortality) and
emigration (the movement of individuals out of a population).
 Immigration and emigration may represent biologically significant exchanges between
populations.
 Within a population’s geographic range, local densities may vary substantially.
 Variations in local density are important population characteristics, providing insight
into the environmental and social interactions of individuals within a population.
 Some habitat patches are more suitable that others.
 Social interactions between members of a population may maintain patterns of
spacing.
 Dispersion is clumped when individuals aggregate in patches.
 Plants and fungi are often clumped where soil conditions favor germination and
growth.
 Animals may clump in favorable microenvironments (such as isopods under a fallen
log) or to facilitate mating interactions.
 Group living may increase the effectiveness of certain predators, such as a wolf pack.
 Dispersion is uniform when individuals are evenly spaced.
 For example, some plants secrete chemicals that inhibit the germination and growth of
nearby competitors.
 Animals often exhibit uniform dispersion as a result of territoriality, the defense of a
bounded space against encroachment by others.
 In random dispersion, the position of each individual is independent of the others, and
spacing is unpredictable.
 Random dispersion occurs in the absence of strong attraction or repulsion among
individuals in a population, or when key physical or chemical factors are relatively
homogeneously distributed.
 For example, plants may grow where windblown seeds land.
 Random patterns are not common in nature.
Demography is the study of factors that affect population density and dispersion patterns.
 Demography is the study of the vital statistics of populations and how they change over
time.
 Of particular interest are birth rates and how they vary among individuals (specifically
females), and death rates.
 A life table is an age-specific summary of the survival pattern of a population.

Biology Chapter Notes

 The best way to construct a life table is to follow the fate of a cohort, a group of
individuals of the same age, from birth throughout their lifetimes until all are dead.
 To build a life table, we need to determine the number of individuals that die in each age
group and calculate the proportion of the cohort surviving from one age to the next.
 A graphic way of representing the data in a life table is a survivorship curve.
 This is a plot of the numbers or proportion of individuals in a cohort of 1,000
individuals still alive at each age.
 There are several patterns of survivorship exhibited by natural populations.
 A Type I curve is relatively flat at the start, reflecting a low death rate in early and
middle life, and drops steeply as death rates increase among older age groups.
 Humans and many other large mammals exhibit Type I survivorship curves.
 The Type II curve is intermediate, with constant mortality over an organism’s life
span.
 Many species of rodent, various invertebrates, and some annual plants show Type II
survivorship curves.
 A Type III curve drops slowly at the start, reflecting very high death rates early in life,
then flattens out as death rates decline for the few individuals that survive to a critical
age.
 Type III survivorship curves are associated with organisms that produce large
numbers of offspring but provide little or no parental care.
 Examples are many fishes, long-lived plants, and marine invertebrates.
 Many species fall somewhere between these basic types of survivorship curves or show
more complex curves.
 Some invertebrates, such as crabs, show a “stair-stepped” curve, with increased
mortality during molts.
 Reproductive rates are key to population size in populations without immigration or
emigration.
 Demographers who study sexually reproducing populations usually ignore males and
focus on females because only females give birth to offspring.
 A reproductive table is an age-specific summary of the reproductive rates in a
population.
 The best way to construct a reproductive table is to measure the reproductive output
of a cohort from birth until death.
 For sexual species, the table tallies the number of female offspring produced by
each age group.
 Reproductive output for sexual species is the product of the proportion of females
of a given age that are breeding and the number of female offspring of those
breeding females.
 Reproductive tables vary greatly from species to species.
 Squirrels have a litter of two to six young once a year for less than a decade, while
mussels may release hundreds of thousands of eggs in a spawning cycle.

Concept 52.2 Life history traits are products of natural selection

 Natural selection favors traits that improve an organism’s chances of survival and
reproductive success.

Biology Chapter Notes

 In every species, there are trade-offs between survival and traits such as frequency of
reproduction, number of offspring produced, and investment in parental care.
 The traits that affect an organism’s schedule of reproduction and survival make up its life
history.
Life histories are highly diverse, but they exhibit patterns in their variability.
 Life histories entail three basic variables: when reproduction begins, how often the
organism reproduces, and how many offspring are produced during each reproductive
episode.
 Life history traits are evolutionary outcomes reflected in the development, physiology,
and behavior of an organism.
 Some organisms, such as the agave plant, exhibit what is known as big-bang
reproduction, in which an individual produces a large number of offspring and then dies.
 This is known as semelparity.
 By contrast, some organisms produce only a few offspring during repeated reproductive
episodes.
 This is known as iteroparity.
 What factors contribute to the evolution of semelparity versus iteroparity?
 In other words, how much does an individual gain in reproductive success through one
pattern versus the other?
 The critical factor is survival rate of the offspring.
 When the survival of offspring is low, as in highly variable or unpredictable
environments, big-bang reproduction (semelparity) is favored.
 Repeated reproduction (iteroparity) is favored in dependable environments where
competition for resources is intense.
 In such environments, a few, well-provisioned offspring have a better chance of
surviving to reproductive age.
Limited resources mandate trade-offs between investment in reproduction and survival.
 Organisms have finite resources, and limited resources mean trade-offs.
 Life histories represent an evolutionary resolution of several conflicting demands.
 Sometimes we see trade-offs between survival and reproduction when resources are
limited.
 For example, red deer females have a higher mortality rate in winters following
summers in which they reproduce.
 Selective pressures also influence the trade-off between number and size of offspring.
 Plants and animals whose young are subject to high mortality rates often produce large
numbers of relatively small offspring.
 Plants that colonize disturbed environments usually produce many small seeds,
only a few of which reach suitable habitat.
 Smaller seed size may increase the chance of seedling establishment by enabling
seeds to be carried longer distances to a broader range of habitats.
 In other organisms, extra investment on the part of the parent greatly increases the
offspring’s chances of survival.
 Oak, walnut, and coconut trees all have large seeds with a large store of energy and
nutrients to help the seedlings become established.
 In animals, parental care does not always end after incubation or gestation.
Biology Chapter Notes
  Primates provide an extended period of parental care.

Concept 52.3 The exponential model describes population growth in an idealized,

unlimited environment
 All populations have a tremendous capacity for growth.
 However, unlimited population increase does not occur indefinitely for any species, either
in the laboratory or in nature.
 The study of population growth in an idealized, unlimited environment reveals the
capacity of species for increase and the conditions in which that capacity may be
expressed.
 Imagine a hypothetical population living in an ideal, unlimited environment.
 For simplicity’s sake, we will ignore immigration and emigration and define a change in
population size during a fixed time interval based on the following verbal equation.
Change in population size = Births during − Deaths during
during time interval time interval time interval
 Using mathematical notation, we can express this relationship more concisely:
 If N represents population size, and t represents time, then N is the change is
population size and t is the time interval.
 We can rewrite the verbal equation as:
N/t = B − D where B is the number of births and D is the number of deaths.
 We can convert this simple model into one in which births and deaths are expressed as the
average number of births and deaths per individual during the specified time period.
 The per capita birth rate is the number of offspring produced per unit time by an average
member of the population.
 If there are 34 births per year in a population of 1,000 individuals, the annual per
capita birth rate is 34/1000, or 0.034.
 If we know the annual per capita birth rate (expressed as b), we can use the formula B =
bN to calculate the expected number of births per year in a population of any size.
 Similarly, the per capita death rate (symbolized by m for mortality) allows us to calculate
the expected number of deaths per unit time for a population of any size.
 Now we will revise the population growth equation, using per capita birth and death rates:
N/t = bN − mN
 Population ecologists are most interested in the differences between the per capita birth
rate and the per capita death rate.
 This difference is the per capita rate of increase or r, which equals b − m.
 The value of r indicates whether a population is growing (r > 0) or declining (r < 0).
 If r = 0, then there is zero population growth (ZPG).
 Births and deaths still occur, but they balance exactly.
 Using the per capita rate of increase, we rewrite the equation for change in population size
as:
N/t = rN

Biology Chapter Notes

 Ecologist use differential calculus to express population growth as growth rate at a
particular instant in time:
dN/dt = rN
 Population growth under ideal conditions is called exponential population growth.
 Under these conditions, we may assume the maximum growth rate for the population
(rmax), called the intrinsic rate of increase.
 The equation for exponential population growth is:
dN/dt = rmaxN
 The size of a population that is growing exponentially increases at a constant rate,
resulting in a J-shaped growth curve when the population size is plotted over time.
 Although the intrinsic rate of increase is constant, the population accumulates more
new individuals per unit of time when it is large.
 As a result, the curve gets steeper over time.
 A population with a high intrinsic rate of increase grows faster than one with a lower rate
of increase.
 J-shaped curves are characteristic of populations that are introduced into a new or unfilled
environment or whose numbers have been drastically reduced by a catastrophic event and
are rebounding.

Concept 52.4 The logistic growth model includes the concept of carrying capacity
 Typically, resources are limited.
 As population density increases, each individual has access to an increasingly smaller
share of available resources.
 Ultimately, there is a limit to the number of individuals that can occupy a habitat.
 Ecologists define carrying capacity (K) as the maximum stable population size that a
particular environment can support.
 Carrying capacity is not fixed but varies over space and time with the abundance of
limiting resources.
 Energy limitation often determines carrying capacity, although other factors, such as
shelters, refuges from predators, soil nutrients, water, and suitable nesting sites can be
limiting.
 If individuals cannot obtain sufficient resources to reproduce, the per capita birth rate b
will decline.
 If they cannot find and consume enough energy to maintain themselves, the per capita
death rate m may increase.
 A decrease in b or an increase in m results in a lower per capita rate of increase r.
 We can modify our mathematical model to incorporate changes in growth rate as the
population size nears the carrying capacity.
 In the logistic population growth model, the per capita rate of increase declines as
carrying capacity is reached.
 Mathematically, we start with the equation for exponential growth, adding an expression
that reduces the rate of increase as N increases.

Biology Chapter Notes

 If the maximum sustainable population size (carrying capacity) is K, then K − N is the
number of additional individuals the environment can accommodate and (K − N)/K is the
fraction of K that is still available for population growth.
 By multiplying the intrinsic rate of increase rmax by (K − N)/K, we modify the growth rate
of the population as N increases.
 dN/dt = rmaxN((K − N)/K)
 When N is small compared to K, the term (K − N)/K is large and the per capita rate of
increase is close to the intrinsic rate of increase.
 When N is large and approaches K, resources are limiting.
 In this case, the term (K − N)/K is small and so is the rate of population growth.
 Population growth is greatest when the population is approximately half of the carrying
capacity.
 At this population size, there are many reproducing individuals, and the per capita rate
of increase remains relatively high.
 The logistic model of population growth produces a sigmoid (S-shaped) growth curve
when N is plotted over time.
 New individuals are added to the population most rapidly at intermediate population
sizes, when there is not only a breeding population of substantial size, but also lots of
available space and other resources in the population.
 Population growth rate slows dramatically as N approaches K.
 How well does the logistic model fit the growth of real populations?
 The growth of laboratory populations of some organisms fits an S-shaped curve fairly
well.
 These populations are grown in a constant environment without predators or
competitors.
 Some of the assumptions built into the logistic model do not apply to all populations.
 The logistic model assumes that populations adjust instantaneously and approach the
carrying capacity smoothly.
 In most natural populations, there is a lag time before the negative effects of increasing
population are realized.
 Populations may overshoot their carrying capacity before settling down to a relatively
stable density.
 Some populations fluctuate greatly, making it difficult to define the carrying capacity.
 The logistic model assumes that regardless of population density, an individual added to
the population has the same negative effect on population growth rate.
 Some populations show an Allee effect, in which individuals may have a more difficult
time surviving or reproducing if the population is too small.
 Animals may not be able to find mates in the breeding season at small population
sizes.
 A plant may be protected in a clump of individuals but vulnerable to excessive wind if
it stands alone.
 The logistic population growth model provides a basis from which we can consider how
real populations grow and can construct more complex models.
 The model is useful in conservation biology for estimating how rapidly a particular
population might increase in numbers after it has been reduced to a small size, or for
estimating sustainable harvest rates for fish or wildlife populations.
Biology Chapter Notes
 The logistic model predicts different per capita growth rates for populations of low or
high density relative to carrying capacity of the environment.
 At high densities, each individual has few resources available, and the population
grows slowly.
 At low densities, per capita resources are abundant, and the population can grow
rapidly.
 Different life history features are favored under each condition.
 At high population density, selection favors adaptations that enable organisms to
survive and reproduce with few resources.
 Competitive ability and efficient use of resources should be favored in populations
that are at or near their carrying capacity.
 These are traits associated with iteroparity.
 At low population density, adaptations that promote rapid reproduction, such as the
production of numerous, small offspring, should be favored.
 These are traits associated with semelparity.
 Ecologists have attempted to connect these differences in favored traits at different
population densities with the logistic model of population growth.
 Selection for life history traits that are sensitive to population density is known as
K-selection, or density-dependent selection.
 K-selection tends to maximize population size and operates in populations living
at a density near K.
 Selection for life history traits that maximize reproductive success at low densities
is known as r-selection, or density-independent selection.
 r-selection tends to maximize r, the rate of increase, and occurs in environments
in which population densities fluctuate well below K, or when individuals face
little competition.
 Laboratory experiments suggest that different populations of the same species may
show a different balance of K-selected and r-selected traits, depending on conditions.
 Many ecologists claim that the concepts of r- and K-selection oversimplify the
variation seen in natural populations.

Concept 52.5 Populations are regulated by a complex interaction of biotic and abiotic
influences
 Why do all populations eventually strop growing?
 What environmental factors stop a population from growing?
 Why do some populations show radical fluctuations in size over time, while others remain
relatively stable?
 These questions have practical applications at the core of management programs for
agricultural pests or endangered species.
 The first step to answering these questions is to examine the effects of increased
population density on rates of birth, death, immigration, and emigration.
 Density-dependent factors have an increased effect on a population as population density
increases.
 This is a type of negative feedback.
 Density-independent factors are unrelated to population density.
Biology Chapter Notes
 Negative feedback prevents unlimited population growth.
 A variety of factors can cause negative feedback on population growth.
 Resource limitation in crowded populations can reduce population growth by reducing
reproductive output.
 Intraspecific competition for food can lead to declining birth rates.
 In animal populations, territoriality may limit density.
 In this case, territory space becomes the resource for which individuals compete.
 The presence of nonbreeding individuals in a population is an indication that
territoriality is restricting population growth.
 Population density can also influence the health and thus the survival of organisms.
 As crowding increases, the transmission rate of a disease may increase.
 Tuberculosis, caused by bacteria that spread through the air when an infected person
coughs or sneezes, affects a higher percentage of people living in high-density cities
than in rural areas.
 Predation may be an important cause of density-dependent mortality for a prey species if a
predator encounters and captures more food as the population density of the prey
increases.
 As a prey population builds up, predators may feed preferentially on that species,
consuming a higher percentage of individuals.
 The accumulation of toxic wastes can contribute to density-dependent regulation of
population size.
 In wine, as yeast population increases, they accumulate alcohol during fermentation.
 However, yeast can only withstand an alcohol percentage of approximately 13%
before they begin to die.
 For some animal species, intrinsic factors appear to regulate population size.
 White-footed mice individuals become more aggressive as population size increases,
even when food and shelter are provided in abundance.
 Eventually the population ceases to grow.
 These behavioral changes may be due to hormonal changes, which delay sexual
maturation and depress the immune system.
 All populations for which we have data show some fluctuation in numbers.
 The study of population dynamics focuses on the complex interactions between biotic
and abiotic factors that cause variation in population size.
 Populations of large mammals, such as deer and moose, were once thought to remain
relatively stable over time.
 A long-term population study of a moose population on Isle Royale has challenged that
view.
 The population has had two major increases and collapses over the past 40 years.
 Large mammal populations do show much more stability than other populations.
 Dungeness crab populations fluctuated hugely over a 40-year period.
 One key factor causing these fluctuations is cannibalism.
 Large numbers of juveniles are eaten by older juveniles and older crabs.
 In addition, successful settlement of crabs is dependent on water temperatures and
ocean currents.

Biology Chapter Notes

  Small changes in these variables cause large fluctuations in crab population
numbers.
 Immigration and emigration can also influence populations.
 This is particularly true when a group of populations is linked together to form a
metapopulation.
 Some populations undergo regular boom-and-bust cycles, fluctuating in density with
regularity.
 For example, voles and lemmings tend to have 3- to 4-year cycles.
 Ruffled grouse and ptarmigan have 9- to 11-year cycles.
 A striking example of population cycles is the 10-year cycles of lynx and snowshoe hare
in northern Canada and Alaska.
 Three main hypotheses have been proposed to explain the lynx/hare cycles.
o The cycles may be caused by food shortage during winter.
o The cycles may be due to predator-prey interactions.
o The cycles may be affected by a combination of food resource limitation and excessive
predation.
 If hare cycles are due to winter food shortage, they should stop if extra food is added to a
field population.
 Researchers conducted such an experiment over 20 years.
 They found that hare populations increased, but that populations of lynx and hares
continued to cycle.
 The first hypothesis can be discarded.
 Field ecologists have placed radio collars on hares, to find them as they die and determine
the cause of death.
 90% of dead hares were killed by predators; none appear to have died of starvation.
 These data support the second or third hypothesis.
 Ecologists tested these hypotheses by excluding predators from one area and by both
excluding predators and adding food to another area.
 The results support the hypothesis that the hare cycle is driven largely by predation but
that food availability also plays an important role, especially in winter.
 Perhaps better-fed hares are more likely to escape from predators.
 Many different predators contribute to these cycles, not only lynx.
 Long-term experimental studies continue to be conducted to help unravel the complex
causes of these population cycles.

Concept 52.6 Human population growth has slowed after centuries of exponential
increase
 The concepts of population dynamics can be applied to the specific case of the human
population.
 It is unlikely that any other population of large animals has ever sustained so much
population growth for so long.

Biology Chapter Notes

 The human population increased relatively slowly until about 1650 when approximately
500 million people inhabited Earth.
 The Plague took a large number of lives.
 Since then, human population numbers have doubled three times.
 The global population now numbers more than 6 billion people, and is increasing by about
73 million each year, or 201,000 people each day.
 Population ecologists predict a population of 7.3–8.4 billion people on Earth by the year
2025.
 Although the global population is still growing, the rate of growth began to slow
approximately 40 years ago.
 The rate of increase in the global population peaked at 2.19% in 1962.
 By 2003, it had declined to 1.16%.
 Current models project a decline in overall growth rate to just over 0.4% by 2050.
 Human population growth has departed from true exponential growth, which assumes a
constant rate.
 The declines are the result of fundamental changes in population dynamics due to diseases
and voluntary population control.
 To maintain population stability, a regional human population can exist in one of 2
configurations:
Zero population growth= High birth rates − High death rates.
Zero population growth= Low birth rates − Low death rates.
 The movement from the first toward the second state is called the demographic
transition.
 After 1950, mortality rates declined rapidly in most developing countries.
 Birth rates have declined in a more variable manner.
 In the developed nations, populations are near equilibrium, with reproductive rates near
the replacement level.
 In many developed nations, the reproductive rates are in fact below replacement level.
 These populations will eventually decline if there is no immigration and no change in
birth rate.
 Most population growth is concentrated in developing countries, where 80% of the
world’s people live.
 A unique feature of human population growth is the ability to control it with family
planning and voluntary contraception.
 Reduced family size is the key to the demographic transition.
 Delayed marriage and reproduction help to decrease population growth rates and move
a society toward zero population growth.
 However, there is disagreement among world leaders as to how much support should be
provided for global family planning efforts.
 One important demographic variable is a country’s age structure.
 Age structure is shown as a pyramid showing the percentage of the population at each
age.
 Age structure differs greatly from nation to nation.
Biology Chapter Notes
  Age structure diagrams can predict a population’s growth trends and can point to
future social conditions.
 Infant mortality, the number of infant deaths per 1,000 live births, and life expectancy
at birth, the predicted average length of life at birth, also vary widely among different
human populations.
 These differences reflect the quality of life faced by children at birth.
Estimating Earth’s carrying capacity for humans is a complex problem.
 Predictions of future human population vary from 7.3 to 10.3 billion people by the year
2050.
 Will Earth be overpopulated by this time?
 Is it already overpopulated?
 What is the carrying capacity of Earth for humans?
 This question is difficult to answer.
 Estimates of the answer have ranged from less than 1 billion to more than 1 trillion.
 Carrying capacity is difficult to estimate, and scientists have used different methods to
obtain their answers.
 Some use curves like those produced by the logistic equation to predict the future
maximum human population size.
 Others generalize from existing “maximum” population density and multiply by the
area of habitable land.
 Other estimates are based on a single limiting factor, usually food.
 Humans have multiple constraints. We need food, water, fuel, building materials, and
other amenities.
 The concept of an ecological footprint summarizes the aggregate land and water area
appropriated by each nation to produce all the resources it consumes and to absorb all the
waste it generates.
 Six types of ecologically productive areas are distinguished in calculating the ecological
footprint:
o Arable land (suitable for crops)
o Pasture
o Forest
o Ocean
o Built-up land
o Fossil energy land (land required for vegetation to absorb the carbon dioxide absorbed
by burning fossil fuels)
 Countries vary greatly in their individual footprint size and in their available ecological
capacity (the actual resource base of each country).
 The overall analysis of human impact via ecological footprints suggests that the world is
at or slightly above its carrying capacity.
 We can only speculate about Earth’s ultimate carrying capacity for humans, or about the
factors that will eventually limit our growth.
 Perhaps food will be the main factor.
 Malnutrition and famine result mainly from unequal distribution, rather than
inadequate production, of food.

Biology Chapter Notes

  So far, technological improvements in agriculture have allowed food supplies to keep
up with global population growth.
 Environments can support a larger number of herbivores than carnivores.
 Perhaps we will eventually be limited by suitable space.
 Humans may run out of nonrenewable resources, such as certain metals or fossil fuels.
 The demands of many populations have already far exceeded the local and regional
supplies of water.
 More than one billion people lack access to sufficient water for basic sanitation.
 It is possible that the human population will eventually be limited by the capacity of
the environment to absorb its wastes.
 Some optimists suggest that there is no practical limit to human population growth, due to
our ability to develop technology.
 Exactly what the world’s carrying capacity is, and when and how we will approach it, are
topics of great concern and debate.
 Unlike other organisms, we can decide whether zero population growth will be attained
through social changes based on human choices or increased mortality due to resource
limitation, war, or environmental degradation.

Biology Chapter Notes

 Chapter 53 Community Ecology
Chapter Notes

Overview: What Is a Community?

 A community is defined as an assemblage of species living close enough together for

potential interaction.
 Communities differ in their species richness, the number of species they contain, and the
relative abundance of different species.

Concept 53.1 A community’s interactions include competition, predation, herbivory,

symbiosis, and disease
 There are a number of possible interspecific interactions that link the species of a
community.
 Interspecific interactions can be symbolized by the positive (+) or negative (−) effects of
the interaction on the individual populations.
 0 indicates that a population is not affected by the interaction.
 The effect of an interaction between two species may change as circumstances change.
 Interspecific competition can occur when species compete for a specific limiting
resource.
 When two species compete for a resource, the result is detrimental to one or both
species (−/−)
 Strong competition can lead to the local elimination of one of the two competing species,
a process called competitive exclusion.
 The competitive exclusion principle states that two species with similar needs for the
same limiting resources cannot coexist in the same place.
 The ecological niche is the sum total of a species’ use of abiotic and biotic resources in
the environment.
 In the analogy stated by ecologist Eugene Odum, an organism’s habitat is its
“address,” and the niche is the organism’s “profession.”
 For example, the niche of a tropical tree lizard includes the temperature range it
tolerates, the size of branches it perches on, the time of day when it is active, and the
kind of insects it eats.
 The competitive exclusion principle can be restated to say that two species cannot
coexist in a community if their niches are identical.
 However, ecologically similar species can coexist in a community if their niches differ
in one or more significant ways.
 A species’ fundamental niche is the niche potentially occupied by that species.
 The fundamental niche may differ from the realized niche, the niche a species actually
occupies in a particular environment.
 When competition between two species with identical niches does not lead to the local
extinction of either species, it is generally because evolution by natural selection results in
modification of the resources used by one of the species.
Biology Chapter Notes
  Resource partitioning is the differentiation of niches that enables two similar species
to coexist in a community.
 Character displacement is the tendency for characteristics to be more divergent in
sympatric populations of two species than in allopatric populations of the same two
species.
 Predation is a +/− interaction between species in which one species, the predator, kills
and eats the other, the prey.
 The term predation elicits images such as a lion attacking and eating an antelope.
 This interaction also includes interactions such as seed predation, in which seed-eating
weevils eat plant seeds.
 Natural selection favors adaptations of predators and prey.
 Predators have many feeding adaptations, including acute senses and weaponry such as
claws, fangs, stingers, or poison to help catch and subdue prey.
 Predators that pursue prey are generally fast and agile; those who lie in ambush are
often camouflaged.
 Prey animals have evolved adaptations that help them avoid being eaten.
 Behavioral defenses include fleeing, hiding, and self-defense.
 Alarm calls may summon many individuals of the prey species to mob the predator.
 Adaptive coloration has evolved repeatedly in animals.
 Camouflage or cryptic coloration makes prey difficult to spot against the
background.
 Some animals have mechanical or chemical defenses.
 Chemical defenses include odors and toxins.
 Animals with effecting chemical defenses often exhibit bright warning aposematic
coloration.
 Predators are cautious in approaching potential prey with bright coloration.

 One prey species may gain protection by mimicking the appearance of another prey
species.
 In Batesian mimicry a harmless, palatable species mimics a harmful, unpalatable
model.
 In Müllerian mimicry, two or more unpalatable species resemble each other.
 Each species gains an additional advantage because predators are more likely to
encounter an unpalatable prey and learn to avoid prey with that appearance.
 Predators may also use mimicry.
 Some snapping turtles have tongues resembling wiggling worms to lure small fish.
 Herbivory is a +/− interaction in which an herbivore eats parts of a plant or alga.
 Herbivores include large mammals and small invertebrates.
 Herbivores have specialized adaptations.
 Many herbivorous insects have chemical sensors on their feet to recognize
appropriate food plants.
 Mammalian herbivores have specialized dentition and digestive systems to process
vegetation.
 Plants may produce chemical toxins, which may act in combination with spines and
thorns to prevent herbivory.

Biology Chapter Notes

 Parasitism is a +/− symbiotic interaction in which a parasite derives its nourishment
from a host, which is harmed in the process.
 Endoparasites live within the body of the host; ectoparasites live and feed on the
external surface of the host.
 Parasitoidism is a special type of parasitism in which an insect (usually a wasp) lays
eggs on or in living hosts.
 The larvae feed on the body of the host, eventually killing it.
 Many parasites have complex life cycles involving a number of hosts.
 Some parasites change the behavior of their hosts in ways that increase the probability
of the parasite being transferred from one host to another.
 Parasites can have significant direct and indirect effects on the survival, reproduction,
and density of their host populations.
 Pathogens are disease-causing agents that have deleterious effects on their hosts (+/−)
 Pathogens are typically bacteria, viruses, or protists.
 Fungi and prions can also be pathogenic.
 Parasites are generally large, multicellular organisms, while most pathogens are
microscopic.
 Many pathogens are lethal.
 Mutualism is an interspecific symbiosis in which two species benefit from their
interaction (+/+).
 Examples of mutualism include nitrogen fixation by bacteria in the root nodules of
legumes; digestion of cellulose by microorganisms in the guts of ruminant mammals;
and the exchange of nutrients in mycorrhizae, the association of fungi and plant roots.
 Mutualistic interactions may result in the evolution of related adaptations in both species.
 Commensalism is an interaction that benefits one species but neither harms nor helps the
other (+/0).
 Commensal interactions are difficult to document in nature because any close
association between species likely affects both species, if only slightly.
 For example, “hitchhiking” species, such as the barnacles that attach to whales, are
sometimes considered commensal.
 The hitchhiking barnacles gain access to a substrate and seem to have little effect
on the whale.
 However, the barnacles may slightly reduce the host’s efficiency of movement.
 Conversely, they may provide some camouflage.
 Coevolution refers to reciprocal evolutionary adaptations of two interacting species.
 A change in one species acts as a selective force on another species, whose adaptation
in turn acts as a selective force on the first species.
 The linkage of adaptations requires that genetic change in one of the interacting
populations of the two species be tied to genetic change in the other population.
 An example is the gene-for-gene recognition between a plant species and a species
of virulent pathogen.
 In contrast, the aposematic coloration of various tree frog species and the aversion
reactions of various predators are not examples of coevolution.
 These are adaptations to other organisms in the community rather than coupled
genetic changes in two interacting species.

Biology Chapter Notes

Concept 53.2 Dominant and keystone species exert strong controls on community
structure
Species diversity is a fundamental aspect of community structure.
 A small number of species in the community exert strong control on that community’s
structure, especially on the composition, relative abundance, and diversity of species.
 The species diversity of a community is the variety of different kinds of organisms that
make up the community.
 Species diversity has two components.
 Species richness is the total number of different species in the community.
 The relative abundance of the different species is the proportion each species
represents of the total individuals in the community.
 Species diversity is dependent on both species richness and relative abundance.
 Measuring species diversity may be difficult, but is essential for understanding
community structure and for conserving biodiversity.
Trophic structure is a key factor in community dynamics.
 The trophic structure of a community is determined by the feeding relationships
between organisms.
 The transfer of food energy up the trophic levels from its source in autotrophs (usually
photosynthetic organisms) through herbivores (primary consumers) and carnivores
(secondary and tertiary consumers) and eventually to decomposers is called a food chain.
 In the 1920s, Oxford University biologist Charles Elton recognized that food chains are
not isolated units but are linked together into food webs.
 A food web uses arrows to link species according to who eats whom in a community.
 How are food chains linked into food webs?
 A given species may weave into the web at more than one trophic level.
 Food webs can be simplified in two ways.
 We can group species in a given community into broad functional groups.
 For example, phytoplankton can be grouped as primary producers in an aquatic
food web.
 A second way to simplify a food web is to isolate a portion of the web that interacts
little with the rest of the community.
 Each food chain within a food web is usually only a few links long.
 Charles Elton pointed out that the length of most food chains is only four or five links.
 Why are food chains relatively short?
 The energetic hypothesis suggests that the length of a food chain is limited by the
inefficiency of energy transfer along the chain.
 Only about 10% of the energy stored in the organic matter of each trophic level is
converted to organic matter at the next trophic level.
 The energetic hypothesis predicts that food chains should be relatively longer in
habitats with higher photosynthetic productivity.

Biology Chapter Notes

  The dynamic stability hypothesis suggests that long food chains are less stable than
short chains.
 Population fluctuations at lower trophic levels are magnified at higher levels,
making top predators vulnerable to extinction.
 In a variable environment, top predators must be able to recover from
environmental shocks that can reduce the food supply all the way up the food
chain.
 The dynamic stability hypothesis predicts that food chains should be shorter in
unpredictable environments.
 Most of the available data supports the energetic hypothesis.
 Another factor that may limit the length of food chains is that, with the exception of
parasites, animals tend to be larger at successive trophic levels.
 Certain species have an especially large impact on community structure because they are
highly abundant or because they play a pivotal role in community dynamics.
 The exaggerated impact of these species may occur through their trophic interactions
or through their influences on the physical environment.
 Dominant species are those species in a community that are most abundant or have the
highest biomass (the sum weight of all individuals in a population).
 There is no single explanation for why a species becomes dominant in a community.
 One hypothesis suggests that dominant species are competitively successful at
exploiting limiting resources.
 Another hypothesis suggests that dominant species are most successful at avoiding
predation or disease.
 This could explain why invasive species can achieve such high biomass in their
new environments, in the absence of their natural predators and pathogens.
 One way to investigate the impact of a dominant species is to remove it from the
community.
 Keystone species are not necessarily abundant in a community.
 They influence community structure by their key ecological niches.
 If keystone species are removed, community structure is greatly affected.
 Ecologist Robert Paine of the University of Washington first developed the concept of
keystone species.
 Paine removed the sea star Pisaster ochraceous from rocky intertidal communities.
 Pisaster is a predator on mussels such as Mytilus californianus, a superior
competitor for space in the intertidal areas.
 After Paine removed Pisaster, the mussels were able to monopolize space and
exclude other invertebrates and algae from attachment sites.
 When sea stars were present, 15 to 20 species of invertebrates and algae occurred in
the intertidal zone.
 After experimental removal of Pisaster, species diversity declined to fewer than 5
species.
 Pisaster thus acts as a keystone species, exerting an influence on community
structure that is disproportionate to its abundance.
 Some organisms exert their influence by causing physical changes in the environment
that affect community structure.

Biology Chapter Notes

  An example of such a species is the beaver, which transforms landscapes by felling
trees and building dams.
 Such species are called ecosystem “engineers” or “foundation species.”
 These influential species act as facilitators, with positive effects on the survival
and reproduction of other species.
The structure of a community may be controlled from the bottom up by nutrients or from
the top down by predators.
 Simplified models based on relationships between adjacent trophic levels are useful for
discussing how communities might be organized.
 Consider three possible relationships between plants (V for vegetation) and herbivores
(H).
 VH VH V  H
 Arrows indicate that a change in biomass at one trophic level causes a change in
biomass at in the other trophic level.
 We can define two models of community organization.
 The bottom-up model postulates V  H linkages, in which the presence or absence of
mineral nutrients (N) controls plant (V) numbers, which control herbivore (H)
numbers, which control predator (P) numbers.
 A simplified bottom-up model is N  V  H  P.
 The top-down model postulates that it is mainly predation that controls community
organization.
 Predators limit herbivores, which limit plants, which limit nutrient levels through
the uptake of nutrients during growth and reproduction.
 A simplified top-down model is thus N  V  H  P.
 The top-down control of community structure is also called the trophic cascade
model.
 The effect of any manipulation thus moves down the trophic structure as a series of
+/− effects.
 Many intermediate models are between extreme bottom-up and top-down models.
 For example, all interactions between trophic levels may be reciprocal ( ).
 The direction of interaction may alternate over time.
 Communities vary in their relative degree of bottom-up and top-down control.
 Simplified models are valuable as a starting point for the analysis of communities.
 Pollution has degraded freshwater lakes in many countries.
 Because many freshwater lakes seem to be structured according to the top-down
model, ecologists have a potential means of improving water quality.
 This strategy is called biomanipulation.
 In lakes with three trophic levels, removing fish may improve water quality by
increasing zooplankton and thus decreasing algal populations.
 In lakes with four trophic levels, adding top predators will have the same effect.

Concept 53.3 Disturbance influences species diversity and composition

 Stability is the tendency of a community to reach and maintain a relatively constant
composition of species despite disturbance.
Biology Chapter Notes
  Many communities seem to be characterized by change rather than stability.
 The nonequilibrium model proposes that communities constantly change following a
disturbance.
 A disturbance is an event that changes a community by removing organisms or altering
resource availability.
 Storms, fires, floods, droughts, frosts, human activities, or overgrazing can be
disturbances.
 A disturbance can have a beneficial effect on a community.
 Disturbances can create opportunities for species that have not previously occupied
habitat in a community.
 Small-scale disturbances can enhance environmental patchiness and thus maintain
species diversity in a community.
 The intermediate disturbance hypothesis suggest that moderate levels of disturbance
can create conditions that foster greater species diversity than low or high levels of
disturbance.
 Frequent small-scale disturbances may prevent a large-scale disturbance.
 Increasing evidence suggests that some amount of nonequilibrium resulting from
disturbance is the norm for communities.
Humans are the most widespread agents of disturbance.
 Human activities cause more disturbances than natural events do.
 Agricultural development has disrupted the vast grasslands of the North American
prairie.
 Logging and clearing for urban development have reduced large tracts of forest to
small patches of disconnected woodlots throughout North America and Europe.
 Tropical rain forests are disappearing due to clear-cutting.
 Human-caused disturbances usually reduce species diversity in communities.
Ecological succession is the sequence of community changes after a disturbance.
 Ecological succession is the transition in species composition in disturbed areas over
ecological time.
 Primary succession begins in a lifeless area where soil has not yet formed, such as a
volcanic island or the moraine left behind as a glacier retreats.
 Initially, only autotrophic prokaryotes may be present.
 Next, mosses and lichens colonize and cause the development of soil.
 Once soil is present, grasses, shrubs, and trees sprout from seeds blown or carried in
from nearby areas.
 Secondary succession occurs where an existing community has been removed by a
disturbance such as a clear-cut or fire, while the soil is left intact.
 Herbaceous species grow first, from wind-blown or animal-borne seeds.
 Woody shrubs replace the herbaceous species, and they in turn are replaced by forest
trees.
 Early arrivals and later-arriving species are linked in one of three key processes.
o Early arrivals may facilitate the appearance of later species by changing the
environment.
 For example, early herbaceous species may increase soil fertility.
Biology Chapter Notes
 o Early species may inhibit establishment of later species.
o Early species may tolerate later species but neither hinder nor help their colonization.

Concept 53.4 Biogeographic factors affect community biodiversity

 Two key factors correlated with a community’s biodiversity (species diversity) are its
geographic location and its size.
 In the 1850s, both Charles Darwin and Alfred Wallace pointed out that plant and animal
life were more abundant and varied in the tropics.
 They also noted that small or remote islands have fewer species than large islands or
those near continents.
 Such observations suggest that biogeographic patterns in biodiversity conform to a set of
basic principles.
Species richness generally declines along an equatorial-polar gradient.
 Tropical habitats support much larger numbers of species of organisms than do temperate
and polar regions.
 What causes these gradients?
 The two key factors are probably evolutionary history and climate.
 Over the course of evolutionary time, species diversity may increase in a community as
more speciation events occur.
 Tropical communities are generally older than temperate or polar communities.
 The growing season in the tropics is about five times longer than that in a tundra
community.
 Biological time thus runs five times faster in the tropics.
 Repeated glaciation events have eliminated many temperate and polar communities.
 Climate is likely the primary cause of latitudinal gradients in biodiversity.
 Solar energy input and water availability can be combined as a measure of
evapotranspiration, the evaporation of water from soil plus the transpiration of water
from plans.
 Actual evapotranspiration, determined by the amount of solar radiation,
temperature, and water availability, is much higher in hot areas with abundant
rainfall than in areas with low temperatures or precipitation.
 Potential evapotranspiration, a measure of energy availability, is determined by the
amount of solar radiation and temperature.
 The species richness of plants and animals correlates with both measures of
evapotranspiration.
Species richness is related to a community’s geographic size.
 The species-area curve quantifies what may seem obvious: the larger the geographic area
of a community, the greater the number of species.
 Larger areas offer a greater diversity of habitats and microhabitats than smaller areas.
 In conservation biology, developing species-area curves for the key taxa in a community
allows ecologists to predict how loss of habitat is likely to affect biodiversity.
Species richness on islands depends on island size and distance from the mainland.

Biology Chapter Notes

 Because of their size and isolation, islands provide excellent opportunities for studying
some of the biogeographic factors that affect the species diversity of communities.
 “Islands” include oceanic islands as well as habitat islands on land, such as lakes,
mountain peaks, or natural woodland fragments.
 An island is thus any patch surrounded by an environment unsuitable for the “island”
species.
 Robert MacArthur and E. O. Wilson developed a general hypothesis of island
biogeography to identify the key determinants of species diversity on an island with a
given set of physical characteristics.
 Imagine a newly formed oceanic island that receives colonizing species from a distant
mainland.
 Two factors will determine the number of species that eventually inhabit the island:
o The rate at which new species immigrate to the island.
o The rate at which species become extinct on the island.
 Two physical features of the island affect immigration and extinction rates:
o Its size.
o Its distance from the mainland.
 Small islands have lower immigration rates because potential colonizers are less likely to
happen upon them.
 Small islands have higher extinction rates because they have fewer resources and less
diverse habitats for colonizing species to partition.
 Islands closer to the mainland will have a higher immigration rate than islands that are
farther away.
 Arriving colonists of a particular species will reduce the chance that the species will go
extinct.
 At any given time, an island’s immigration and extinction rates are also affected by the
number of species already present.
 As the number of species increases, any individual reaching the island is less likely to
represent a new species.
 As more species are present, extinction rates increase because of the greater likelihood
of competitive exclusion.
 The hypothesis of island biogeography predicts that a dynamic equilibrium will eventually
be reached where the rate of species immigration equals the rate of species extinction.
 The number of species at this equilibrium point is correlated with the island’s size and
distance from the mainland.
 Studies of plants and animals on many island chains, including the Galapagos, support
these predictions.
 The island equilibrium model has been attacked as an oversimplification.
 Over longer periods, abiotic disturbances such as storms, adaptive evolutionary
changes, and speciation may alter species composition and community structure on
islands.

Concept 53.5 Contrasting views of community structure are the subject of continuing
debate
Biology Chapter Notes
 The integrated hypothesis of community structure depicts a community as an
assemblage of closely linked species locked into association by mandatory biotic
interactions.
 The community functions as an integrated unit, as a superorganism.
 The individualistic hypothesis of community structure depicts a community as a chance
assemblage of species found in the same area because they happen to have similar abiotic
requirements for rainfall, temperature, or soil type.
 These two very different hypotheses suggest different priorities in studying biological
communities.
 The integrated hypothesis emphasizes assemblages of species as the essential units for
understanding the interactions and distributions of species.
 The individualistic hypothesis emphasizes single species.
 The hypotheses make contrasting predictions about how plant species should be
distributed along an environmental gradient.
 The integrated hypothesis predicts that species should be clustered into discrete
communities with noticeable boundaries because the presence or absence of a
particular species is largely governed by the presence or absence of other species.
 The individualistic hypothesis predicts that communities should generally lack discrete
geographic boundaries because each species has an independent, individualistic,
distribution along the environmental gradient.
 In most cases where there are broad regions characterized by gradients of environmental
variation, the composition of plant communities does seem to change continuously, with
each species more or less independently distributed.
The debate continues with the rivet and redundancy models.
 The individualistic hypothesis is generally accepted by plant ecologists.
 Further debate arises when these ideas are applied to animals.
 American ecologists Anne and Paul Ehrlich proposed the rivet model of communities.
 This hypothesis is a reincarnation of the interactive model and suggests that most animal
species are associated with particular other species in the community.
 Reducing or increasing the abundance of one species in a community will affect many
other species.
 Australian ecologist Brian Walker’s redundancy model proposes that most animal
species in a community are not closely associated with one another.
 Species operate independently, and an increase or decrease in one species in a
community has little effect on other species.
 In this sense, species in a community are redundant.
 If a predator disappears, another predatory species will take its place as a consumer of
specific prey.
 The rivet and redundancy models represent extremes; most communities have some
features of each model.
 We still do not have enough information to answer the fundamental questions raised by
these models: Are communities loose associations of species or highly integrated
units?
 To fully assess these models, we need to study how species interact in communities
and how tight these interactions are.

Biology Chapter Notes

 Chapter 54 Ecosystems
Chapter Notes

Overview: Ecosystems, Energy, and Matter

 An ecosystem consists of all the organisms living in a community as well as all the
abiotic factors with which they interact.
 The dynamics of an ecosystem involve two processes that cannot be fully described by
population or community processes and phenomena: energy flow and chemical cycling.
 Energy enters most ecosystems in the form of sunlight.
 It is converted to chemical energy by autotrophs, passed to heterotrophs in the organic
compounds of food, and dissipated as heat.
 Chemical elements are cycled among abiotic and biotic components of the ecosystem.
 Energy, unlike matter, cannot be recycled.
 An ecosystem must be powered by a continuous influx of energy from an external
source, usually the sun.
 Energy flows through ecosystems, while matter cycles within them.

Concept 54.1 Ecosystem ecology emphasizes energy flow and chemical cycling
 Ecosystem ecologists view ecosystems as transformers of energy and processors of
matter.
 We can follow the transformation of energy by grouping the species in a community into
trophic levels of feeding relationships.
Ecosystems obey physical laws.
 The law of conservation of energy states that energy cannot be created or destroyed but
only transformed.
 Plants and other photosynthetic organisms convert solar energy to chemical energy,
but the total amount of energy does not change.
 The total amount of energy stored in organic molecules plus the amounts reflected and
dissipated as heat must equal the total solar energy intercepted by the plant.
 The second law of thermodynamics states that some energy is lost as heat in any
conversion process.
 We can measure the efficiency of ecological energy conversions.
 Chemical elements are continually recycled.
 A carbon or nitrogen atom moves from one trophic level to another and eventually to
the decomposers and back again.
Trophic relationships determine the routes of energy flow and chemical cycling in
ecosystems.
 Autotrophs, the primary producers of the ecosystem, ultimately support all other
organisms.

Biology Chapter Notes

  Most autotrophs are photosynthetic plants, algae or bacteria that use light energy to
synthesize sugars and other organic compounds.
 Chemosynthetic prokaryotes are the primary producers in deep-sea hydrothermal
vents.
 Heterotrophs are at trophic levels above the primary producers and depend on their
photosynthetic output.
 Herbivores that eat primary producers are called primary consumers.
 Carnivores that eat herbivores are called secondary consumers.
 Carnivores that eat secondary producers are called tertiary consumers.
 Another important group of heterotrophs is the detritivores, or decomposers.
 They get energy from detritus, nonliving organic material such as the remains of dead
organisms, feces, fallen leaves, and wood.
 Detritivores play an important role in material cycling.
Decomposition connects all trophic levels.
 The organisms that feed as detritivores form a major link between the primary producers
and the consumers in an ecosystem.
 Detritivores play an important role in making chemical elements available to producers.
 Detritivores decompose organic material and transfer chemical elements in inorganic
forms to abiotic reservoirs such as soil, water, and air.
 Producers then recycle these elements into organic compounds.
 An ecosystem’s main decomposers are fungi and prokaryotes.

Concept 54.2 Physical and chemical factors limit primary production in ecosystems
 The amount of light energy converted to chemical energy by an ecosystem’s autotrophs in
a given time period is an ecosystem’s primary production.
An ecosystem’s energy budget depends on primary production.
 Most primary producers use light energy to synthesize organic molecules, which can be
broken down to produce ATP.
 The amount of photosynthetic production sets the spending limit of the entire ecosystem.
 A global energy budget can be analyzed.
 Every day, Earth is bombarded by approximately 10 23 joules of solar radiation.
 The intensity of solar energy striking Earth varies with latitude, with the tropics
receiving the greatest input.
 Most of this radiation is scattered, absorbed, or reflected by the atmosphere.
 Much of the solar radiation that reaches Earth’s surface lands on bare ground or
bodies of water that either absorb or reflect the energy.
 Only a small fraction actually strikes algae, photosynthetic prokaryotes, or plants,
and only some of this is of wavelengths suitable for photosynthesis.
 Of the visible light that reaches photosynthetic organisms, only about 1% is
converted to chemical energy.

Biology Chapter Notes

  Although this is a small amount, primary producers produce about 170 billion tons of
organic material per year.
 Total primary production in an ecosystem is known as gross primary production (GPP).
 This is the amount of light energy that is converted into chemical energy per unit time.
 Plants use some of these molecules as fuel in their own cellular respiration.
 Net primary production (NPP) is equal to gross primary production minus the energy
used by the primary producers for respiration (R):
 NPP = GPP − R
 To ecologists, net primary production is the key measurement, because it represents the
storage of chemical energy that is available to consumers in the ecosystem.
 Primary production can be expressed as energy per unit area per unit time, or as biomass
of vegetation added to the ecosystem per unit area per unit time.
 This should not be confused with the total biomass of photosynthetic autotrophs
present in a given time, which is called the standing crop.
 Primary production is the amount of new biomass added in a given period of time.
 Although a forest has a large standing cross biomass, its primary production may
actually be less than that of some grasslands, which do not accumulate vegetation
because animals consume the plants rapidly.
 Different ecosystems differ greatly in their production as well as in their contribution to
the total production of the Earth.
 Tropical rain forests are among the most productive terrestrial ecosystems.
 Estuaries and coral reefs also are very productive, but they cover only a small area
compared to that covered by tropical rain forests.
 The open ocean has a relatively low production per unit area but contributes more net
primary production than any other single ecosystem because of its very large size.
 Overall, terrestrial ecosystems contribute two-thirds of global net primary production, and
marine ecosystems contribute approximately one-third.
In aquatic ecosystems, light and nutrients limit primary production.
 Light is a key variable controlling primary production in oceans, since solar radiation can
only penetrate to a certain depth known as the photic zone.
 The first meter of water absorbs more than half of the solar radiation.
 If light were the main variable limiting primary production in the ocean, we would expect
production to increase along a gradient from the poles toward the equator, which receives
the greatest intensity of light.
 There is no such gradient.
 There are parts of the ocean in the tropics and subtropics that exhibit low primary
production, while some high-latitude ocean regions are relatively productive.
 More than light, nutrients limit primary production in aquatic ecosystems.
 A limiting nutrient is an element that must be added for production to increase in a
particular area.
 The nutrient most often limiting marine production is either nitrogen or phosphorus.
 In the open ocean, nitrogen and phosphorous levels are very low in the photic zone but
are higher in deeper water where light does not penetrate.
 Nitrogen is the nutrient that limits phytoplankton growth in many parts of the ocean.
Biology Chapter Notes
  This knowledge can be used to prevent algal blooms by limiting pollution that
fertilizes phytoplankton.
 Some areas of the ocean have low phytoplankton density despite their relatively high
nitrogen concentrations.
 For example, the Sargasso Sea has a very low density of phytoplankton.
 Nutrient-enrichment experiments showed that iron availability limits primary
production in this area.
 Marine ecologists carried out large-scale field experiments in the Pacific Ocean, spreading
low concentrations of dissolved iron over 72 km2 of ocean.
 A massive phytoplankton bloom occurred, with a 27-fold increase in chlorophyll
concentration in water samples from test sites.
 Why are iron concentrations naturally low in certain oceanic areas?
 Windblown dust from the land delivers iron to the ocean, and relatively little dust
reaches the central Pacific and Atlantic Oceans.
 The iron factor in marine ecosystems is related to the nitrogen factor.
 When iron is limiting, adding iron stimulates the growth of cyanobacteria that fix
nitrogen.
 Phytoplankton proliferate, once released from nitrogen limitation.
 Iron  cyanobacteria  nitrogen fixation phytoplankton production
 In areas of upwelling, nutrient-rich deep waters circulate to the ocean surface.
 These areas have exceptionally high primary production, supporting the hypothesis
that nutrient availability determines marine primary production.
 Areas of upwelling are prime fishing locations.
 Nutrient limitation is also common in freshwater lakes.
 Sewage and fertilizer pollution can add nutrients to lakes.
 Additional nutrients shifted many lakes from phytoplankton communities dominated by
diatoms and green algae to communities dominated by cyanobacteria.
 This process is called eutrophication and has a wide range of ecological impacts,
including the loss of most fish species.
 David Schindler of the University of Alberta conducted a series of whole lake
experiments that identified phosphorus as the nutrient that limited cyanobacteria growth.
 His research led to the use of phosphate-free detergents and other water quality
reforms.
In terrestrial ecosystems, temperature and moisture are the key factors limiting primary
production.
 Tropical rain forests, with their warm, wet conditions, are the most productive of all
terrestrial ecosystems.
 By contrast, low-productivity ecosystems are generally dry (deserts) or dry and cold
(arctic tundra).
 Between these extremes lie temperate forest and grassland ecosystems with moderate
climates and intermediate productivity.
 These contrasts in climate can be represented by a measure called actual
evapotranspiration, which is the amount of water annually transpired by plants and
evaporated from a landscape.
Biology Chapter Notes
  Actual evapotranspiration increases with precipitation and with the amount of solar
energy available to drive evaporation and transpiration.
 On a more local scale, mineral nutrients in the soil can play a key role in limiting primary
production in terrestrial ecosystems.
 Primary production removes soil nutrients.
 A single nutrient deficiency may cause plant growth to slow and cease.
 Nitrogen and phosphorus are the soil nutrients that most commonly limit terrestrial
production.
 Scientific studies relating nutrients to terrestrial primary production have practical
applications in agriculture.
 Farmers can maximize crop yields with the right balance of nutrients for the local soil
and type of crop.

Concept 54.3 Energy transfer between trophic levels is usually less than 20% efficient
 The amount of chemical energy in consumers’ food that is converted to their own new
biomass during a given time period is called the secondary production of an ecosystem.
 We can measure the efficiency of animals as energy transformers using the following
equation:
 production efficiency = net secondary production / assimilation of primary production
 Net secondary production is the energy stored in biomass represented by growth and
reproduction.
 Assimilation consists of the total energy taken in and used for growth, reproduction, and
respiration.
 Production efficiency is thus the fraction of food energy that is not used for respiration.
 This differs among organisms.
 Birds and mammals generally have low production efficiencies of between 1% and
3% because they use so much energy to maintain a constant body temperature.
 Fishes have production efficiencies of around 10%.
 Insects are even more efficient, with production efficiencies averaging 40%.
 Trophic efficiency is the percentage of production transferred from one trophic level to
the next.
 Trophic efficiencies must always be less than production efficiencies because they take
into account not only the energy lost through respiration and contained in feces, but
also the energy in organic material at lower trophic levels that is not consumed.
 Trophic efficiencies usually range from 5% to 20%.
 In other words, 80–95% of the energy available at one trophic level is not transferred
to the next.
 This loss is multiplied over the length of a food chain.
 If 10% of energy is transferred from primary producers to primary consumers, and
10% of that energy is transferred to secondary consumers, then only 1% of net primary
production is available to secondary consumers.
 Pyramids of net production represent the multiplicative loss of energy in a food chain.

Biology Chapter Notes

  The size of each block in the pyramid is proportional to the new production of each
trophic level, expressed in energy units.
 Biomass pyramids represent the ecological consequences of low trophic efficiencies.
 Most biomass pyramids narrow sharply from primary producers to top-level carnivores
because energy transfers are so inefficient.
 In some aquatic ecosystems, the pyramid is inverted and primary consumers outweigh
producers.
 Such inverted biomass pyramids occur because the producers—phytoplankton—grow,
reproduce, and are consumed by zooplankton so rapidly that they never develop a large
standing crop.
 They have a short turnover time, which means they have a small standing crop
biomass compared to their production.
 turnover time = standing crop biomass (mg/m2) / production (mg/m2/day)
 Because the phytoplankton replace their biomass at such a rapid rate, they can support
a biomass of zooplankton much greater than their own biomass.
 Because of the progressive loss of energy along a food chain, any ecosystem cannot
support a large biomass of top-level carnivores.
 With some exceptions, predators are usually larger than the prey they eat.
 Top-level predators tend to be fairly large animals.
 As a result, the limited biomass at the top of an ecological pyramid is concentrated in a
small number of large individuals.
 In a pyramid of numbers, the size of each block is proportional to the number of
individuals present in each trophic level.
 The dynamics of energy through ecosystems have important implications for the human
population.
 Eating meat is an inefficient way of tapping photosynthetic production.
 Worldwide agriculture could feed many more people if humans all fed as primary
consumers, eating only plant material.
Herbivores consume a small percentage of vegetation: the green world hypothesis.
 According to the green world hypothesis, herbivores consume relatively little plant
biomass because they are held in check by a variety of factors, including predators,
parasites, and disease.
 How green is our world?
 83 × 1010 metric tons of carbon are stored in the plant biomass of terrestrial
ecosystems.
 Herbivores annually consume less than 17% of the total net primary production.
 The green world hypothesis proposes several factors that keep herbivores in check:
 Plants have defenses against herbivores.
 Nutrients, not energy supply, usually limit herbivores.
 Animals need certain nutrients that plants tend to supply in relatively small
amounts.
 The growth and reproduction of many herbivores are limited by availability of
essential nutrients.
 Abiotic factors limit herbivores.
 Temperature and moisture may restrict carrying capacities for herbivores below the
level that would strip vegetation.
Biology Chapter Notes
  Intraspecific competition can limit herbivore numbers.
 Territorial behavior and competitive behaviors may reduce herbivore population
density.
 Interspecific interactions check herbivore densities.
 Parasites, predators, and disease limit the growth of herbivore populations.
 This applies the top-down model of community structure.

Concept 54.4 Biological and geochemical processes move nutrients between organic and
inorganic parts of the ecosystem
 Chemical elements are available to ecosystems only in limited amounts.
 Life on Earth depends on the recycling of essential chemical elements.
 Nutrient circuits involve both biotic and abiotic components of ecosystems and are called
biogeochemical cycles.
 There are two general categories of biogeochemical cycles: global and regional.
 Gaseous forms of carbon, oxygen, sulfur, and nitrogen occur in the atmosphere, and
cycles of these elements are global.
 Elements that are less mobile in the environment, such as phosphorus, potassium,
calcium, and trace elements generally cycle on a more localized scale in the short term.
 Soil is the main abiotic reservoir for these elements.
 We will consider a general model of chemical cycling that includes the main reservoirs of
elements and the processes that transfer elements between reservoirs.
 Each reservoir is defined by two characteristics: whether it contains organic or
inorganic materials and whether or not the materials are directly available for use by
organisms.
 Reservoir a. The nutrients in living organisms and in detritus are available to other
organisms when consumers feed and when detritivores consume nonliving organic
material.
 Reservoir b. Some materials move to the fossilized organic reservoir as dead organisms
and are buried by sedimentation over millions of years. Nutrients in fossilized deposits
cannot be assimilated directly.
 Reservoir c. Inorganic elements and compounds that are dissolved in water or present in
soil or air are available for use by organisms.
 Reservoir d. Inorganic elements present in rocks are not directly available for use by
organisms. These nutrients may gradually become available through erosion and
weathering.
 Describing biogeochemical cycles in general terms is much simpler than trying to trace
elements through these cycles.
 Ecologists study chemical cycling by adding tiny amounts of radioactive isotopes to
the elements they are tracing.
There are a number of important biogeochemical cycles.
 We will consider the cycling of water, carbon, nitrogen, and phosphorus.
The water cycle
 Biological importance
Biology Chapter Notes
  Water is essential to all organisms and its availability influences rates of ecosystem
processes.
 Biologically available forms
 Liquid water is the primary form in which water is used.
 Reservoirs
 The oceans contain 97% of the water in the biosphere.
 2% is bound as ice, and 1% is in lakes, rivers, and groundwater.
 A negligible amount is in the atmosphere.
 Key processes
 The main processes driving the water cycle are evaporation of liquid water by solar
energy, condensation of water vapor into clouds, and precipitation.
 Transpiration by terrestrial plants moves significant amounts of water.
 Surface and groundwater flow returns water to the oceans.
The carbon cycle
 Biological importance
 Organic molecules have a carbon framework.
 Biologically available forms
 Autotrophs convert carbon dioxide to organic molecules that are used by heterotrophs.
 Reservoirs
 The major reservoirs of carbon include fossil fuels, soils, aquatic sediments, the
oceans, plant and animal biomass, and the atmosphere (CO2).
 Key processes
 Photosynthesis by plants and phytoplankton fixes atmospheric CO 2.
 CO2 is added to the atmosphere by cellular respiration of producers and consumers.
 Volcanoes and the burning of fossil fuels add CO2 to the atmosphere.
The nitrogen cycle
 Biological importance
 Nitrogen is a component of amino acids, proteins, and nucleic acids.
 It may be a limiting plant nutrient.
 Biologically available forms
 Plants and algae can use ammonium (NH4+) or nitrate (NO3−).
 Various bacteria can also use NH4+, NO3−, or NO2.
 Animals can use only organic forms of nitrogen.
 Reservoirs
 The major reservoir of nitrogen is the atmosphere, which is 80% nitrogen gas (N2).
 Nitrogen is also bound in soils and the sediments of lakes, rivers, and oceans.
 Some nitrogen is dissolved in surface water and groundwater.
 Nitrogen is stored in living biomass.
 Key processes
 Nitrogen enters ecosystems primarily through bacterial nitrogen fixation.
 Some nitrogen is fixed by lightning and industrial fertilizer production.
Biology Chapter Notes
  Ammonification by bacteria decomposes organic nitrogen.
 In nitrification, bacteria convert NH4+ to NO3−.
 In denitrification, bacteria use NO3− for metabolism instead of O2, releasing N2.
The phosphorus cycle
 Biological importance
 Phosphorus is a component of nucleic acids, phospholipids, and ATP and other
energy-storing molecules.
 It is a mineral constituent of bones and teeth.
 Biologically available forms
 The only biologically important inorganic form of phosphorus is phosphate (PO 43−),
which plants absorb and use to synthesize organic compounds.
 Reservoirs
 The major reservoir of phosphorus is sedimentary rocks of marine origin.
 There are also large quantities of phosphorus in soils, dissolved in the oceans, and in
organisms.
 Key processes
 Weathering of rocks gradually adds phosphate to soil.
 Some phosphate leaches into groundwater and surface water and moves to the sea.
 Phosphate may be taken up by producers and incorporated into organic material.
 It is returned to soil or water through decomposition of biomass or excretion by
consumers.
Decomposition rates largely determine the rates of nutrient cycling.
 The rates at which nutrients cycle in different ecosystems are extremely variable as a
result of variable rates of decomposition.
 Decomposition takes an average of four to six years in temperate forests, while in a
tropical rain forest, most organic material decomposes in a few months to a few years.
 The difference is largely the result of warmer temperatures and more abundant
precipitation in tropical rain forests.
 Like net primary production, the rate of decomposition increases with actual
evapotranspiration.
 In tropical rain forests, relatively little organic material accumulates as leaf litter on the
forest floor.
 75% of the nutrients in the ecosystem are present in the woody trunks of trees.
 10% of the nutrients are concentrated in the soil.
 In temperate forests, where decomposition is slower, the soil may contain 50% of the
organic material.
 In aquatic ecosystems, decomposition in anaerobic mud of bottom sediments can take 50
years or more.
 However, algae and aquatic plants usually assimilate nutrients directly from the water.
 Aquatic sediments may constitute a nutrient sink.
Nutrient cycling is strongly regulated by vegetation.
 Long-term ecological research (LTER) monitors the dynamics of ecosystems over long
periods of time.
Biology Chapter Notes
  The Hubbard Brook Experimental Forest has been studied since 1963.
 The study site is a deciduous forest with several valleys, each drained by a small creek
that is a tributary of Hubbard Brook.
 Preliminary studies confirmed that internal cycling within a terrestrial ecosystem
conserves most of the mineral nutrients.
 Some areas were completely logged and then sprayed with herbicides for three years to
prevent regrowth of plants.
 All the original plant material was left in place to decompose.
 Water runoff from the altered watershed increased by 30–40%, apparently because there
were no plants to absorb and transpire water from the soil.
 The concentration of Ca2+ in the creek increased four-fold, while concentration of K+
increased by a factor of 15.
 Nitrate loss was increased by a factor of 60.
 This study demonstrates that the amount of nutrients leaving an intact forest ecosystem is
controlled by the plants.
 Results of the Hubbard Brook studies assess natural ecosystem dynamics and provide
insight into the mechanisms by which human activities affect ecosystem processes.

Concept 54.5 The human population is disrupting chemical cycles throughout the
biosphere
 Human activities and technologies have disrupted the trophic structure, energy flow, and
chemical cycling of ecosystems worldwide.
The human population moves nutrients from one part of the biosphere to another.
 Human activity intrudes in nutrient cycles.
 Nutrients from farm soil may run off into streams and lakes, depleting nutrients in one
area, causing excesses in another, and disrupting chemical cycles in both places.
 Humans also add entirely new materials—many toxic—to ecosystems.
 In agricultural ecosystems, a large amount of nutrients are removed from the area as crop
biomass.
 After a while, the natural store of nutrients can become exhausted.
 The soil cannot be used to grow crops without nutrient supplementation.
 Nitrogen is the main nutrient lost through agriculture.
 Plowing and mixing the soil increase the decomposition rate of organic matter,
releasing usable nitrogen that is then removed from the ecosystem when crops are
harvested.
 Recent studies indicate that human activities have approximately doubled the worldwide
supply of fixed nitrogen, due to the use of fertilizers, cultivation of legumes, and burning.
 This may increase the amount of nitrogen oxides in the atmosphere and contribute to
atmospheric warming, depletion of ozone, and possibly acid precipitation.
 The key problem with excess nitrogen seems to be critical load, the amount of added
nitrogen that can be absorbed by plants without damaging the ecosystem.
 Nitrogenous minerals in the soil that exceed the critical load eventually leach into
groundwater or run off into freshwater and marine ecosystems, contaminating water
supplies, choking waterways, and killing fish.
Biology Chapter Notes
 Lakes are classified by nutrient availability as oligotrophic or eutrophic.
 In an oligotrophic lake, primary productivity is relatively low because the mineral
nutrients required by phytoplankton are scarce.
 Overall productivity is higher in eutrophic lakes.
 Human intrusion has disrupted freshwater ecosystems by cultural eutrophication.
 Sewage and factory wastes and runoff of animal wastes from pastures and stockyards
have overloaded many freshwater streams and lakes with nitrogen.
 This results in an explosive increase in the density of photosynthetic organisms,
released from nutrient limitation.
 Shallow areas become choked with weeds and algae.
 As photosynthetic organisms die and organic materials accumulate at the lake bottom,
detritivores use all the available oxygen in the deeper waters.
 This can eliminate fish species.
Combustion of fossil fuels is the main cause of acid precipitation.
 The burning of fossil fuels releases oxides of sulfur and nitrogen that react with water in
the atmosphere to produce sulfuric and nitric acids.
 These acids fall back to earth as acid precipitation—rain, snow, sleet or fog with a pH less
than 5.6.
 Acid precipitation is a regional or global problem, rather than a local one.
 The tall exhaust stacks built for smelters and generating plans export the problem far
downwind.
 Acid precipitation lowers the pH of soil and water and affects the soil chemistry of
terrestrial ecosystems.
 With decreased pH, calcium and other nutrients leach from the soil.
 The resulting nutrient deficiencies affect the health of plants and limit their growth.
 Freshwater ecosystems are very sensitive to acid precipitation.
 Lakes underlain by granite bedrock have poor buffering capacity because of low
bicarbonate levels.
 Fish populations have declined in many lakes in Norway, Sweden, and Canada as pH
levels fall.
 Lake trout are keystone predators in many Canadian lakes.
 When they are replaced by acid-tolerant species, the dynamics of food webs in the
lakes change dramatically.
 Environmental regulations and new industrial technologies have led to reduced sulfur
dioxide emissions in many developed countries.
 The water chemistry of many streams and freshwater lakes is slowly improving as a
result.
 Ecologists estimate that it will take another 10 to 20 years for these ecosystems to
recover, even if emissions continue to decline.
 Massive emissions of sulfur dioxide and acid precipitation continue in parts of central and
eastern Europe.
Toxins can become concentrated in successive trophic levels of food webs.
 Humans introduce many toxic chemicals into ecosystems.

Biology Chapter Notes

  These substances are ingested and metabolized by organisms and can accumulate in
the fatty tissues of animals.
 These toxins become more concentrated in successive trophic levels of a food web, a
process called biological magnification.
 Magnification occurs because the biomass at any given trophic level is produced
from a much larger biomass ingested from the level below.
 Thus, top-level carnivores tend to be the organisms most severely affected by toxic
compounds in the environment.
 Many toxins cannot be degraded by microbes and persist in the environment for years
or decades.
 Other chemicals may be converted to more toxic products by reaction with other
substances or by the metabolism of microbes.
 For example, mercury was routinely expelled into rivers and oceans in an insoluble
form.
 Bacteria in the bottom mud converted it to methyl mercury, an extremely toxic
soluble compound that accumulated in the tissues of organisms, including humans
who fished in contaminated waters.
Human activities may be causing climate change by increasing atmospheric carbon
dioxide.
 Since the Industrial Revolution, the concentration of CO 2 in the atmosphere has increased
greatly as a result of burning fossil fuels and wood removed by deforestation.
 The average CO2 concentration in the environment was 274 ppm before 1850.
 Measurements in 1958 read 316 ppm and have increased to 370 ppm today.
 If CO2 emissions continue to increase at the present rate, the atmospheric concentration of
this gas will be double what it was at the start of the Industrial Revolution by the year
2075.
 Increased productivity by vegetation is one consequence of increasing CO 2 levels.
 Because C3 plants are more limited than C4 plants by CO2 availability, one effect of
increasing CO2 levels may be the spread of C3 species into terrestrial habitats previously
favoring C4 plants.
 For example, corn may be replaced on farms by wheat and soybeans.
 To assess the effect of rising levels of atmospheric CO 2 on temperate forests, scientists at
Duke University began the Forest-Atmosphere Carbon Transfer and Storage (FACTS-1)
experiment.
 The FACTS-1 study is testing how elevated CO2 influences tree growth, carbon
concentration in soils, insect populations, soil moisture, understory plant growth, and
other factors over a ten-year period.
 Rising atmospheric CO2 levels may have an impact on Earth’s heat budget.
 When light energy hits the Earth, much of it is reflected off the surface.
 CO2 causes the Earth to retain some of the energy that would ordinarily escape the
atmosphere.
 This phenomenon is called the greenhouse effect.
 If it were not for this effect, the average air temperature on Earth would be
−18°C.
 A number of studies predict that by the end of the 21st century, atmospheric CO2
concentration will have doubled and average global temperature will rise by
2°C.
Biology Chapter Notes
 An increase of only 1.3°C would make the world warmer than at any time in the past
100,000 years.
 If increased temperatures caused the polar ice caps to melt, sea levels would rise by an
estimated 100 m, flooding coastal areas 150 km inland from current coastlines.
 A warming trend would also alter geographic distribution of precipitation, making
major U.S. agricultural areas much drier.
 Scientists continue to construct models to predict how increasing levels of CO 2 in the
atmosphere will affect Earth.
 Global warming is a problem of uncertain consequences and no certain solutions.
 Stabilizing CO2 emissions will require concerted international effort and the acceptance of
dramatic changes in personal lifestyles and industrial processes.
 Many ecologists think that this effort suffered a major setback in 2001, when the United
States pulled out of the Kyoto Protocol, a 1997 pledge by industrialized nations to reduce
their CO2 output by 5% over a ten-year period.
Human activities are depleting atmospheric ozone.
 Life on earth is protected from the damaging affects of ultraviolet radiation (UV) by a
layer of O3, or ozone, that is present in the lower stratosphere.
 Studies suggest that the ozone layer has been gradually “thinning” since 1975.
 The destruction of ozone probably results from the accumulation of CFCs, or
chlorofluorocarbons—chemicals used in refrigeration, as propellant in aerosol cans, and
for certain manufacturing processes.
 The breakdown products from these chemicals rise to the stratosphere, where the
chlorine they contain reacts with ozone to reduce it to O2.
 Subsequent reactions liberate the chlorine, allowing it to react with other ozone
molecules in a catalytic chain reaction.
 At middle latitudes, ozone levels have decreased by 2–10% during the past 20
years.
 The result of a reduction in the ozone layer may be increased levels of UV radiation
that reach the surface of the Earth.
 Some scientists expect increases in skin cancer and cataracts, as well as
unpredictable effects on crops and natural communities.
 Even if all chlorofluorocarbons were banned globally today, chlorine molecules
already present in the atmosphere will continue to reduce ozone levels for at least a
century.
 The impact of human activity on the ozone layer is one more example of how much we
are able to disrupt ecosystems and the entire biosphere.

Biology Chapter Notes

 Chapter 55 Conservation Biology and Restoration
Ecology
Chapter Notes

Overview: The Biodiversity Crisis

 Conservation biology integrates ecology, evolutionary biology, physiology, molecular

biology, genetics, and behavioral ecology to conserve biological diversity at all levels.
 Restoration ecology applies ecological principles in an effort to return degraded
ecosystems to conditions as similar as possible to their natural, predegraded state.
 Scientists have described and formally named about 1.8 million species of organisms.
 Some biologists think that about 10 million more species currently exist.
 Others estimate the number to be as high as 200 million.
 Throughout the biosphere, human activities are altering trophic structures, energy flow,
chemical cycling, and natural disturbance.
 The amount of human-altered land surface is approaching 50%, and we use more than
half of the accessible surface fresh water.
 In the oceans, we have depleted fish stocks by overfishing.
 Some of the most productive aquatic areas, such as coral reefs and estuaries, are
severely stressed.
 Globally, the rate of species loss may be as much as 1,000 times higher than at any time in
the past 100,000 years.

Concept 55.1 Human activities threaten Earth’s biodiversity

 Extinction is a natural phenomenon that has been occurring since life evolved on Earth.
 The current rate of extinction is what underlies the biodiversity crisis.
 Humans are threatening Earth’s biodiversity.
The three levels of biodiversity are genetic diversity, species diversity, and ecosystem
diversity.
 Biodiversity has three main components: genetic diversity, species diversity, and
ecosystem diversity.
 Genetic diversity comprises the individual genetic variation within a population but also
the genetic variation among populations that is often associated with adaptations to local
conditions.
 If a local population becomes extinct, then the entire population of that species has lost
some genetic diversity.
 The loss of this diversity is detrimental to the overall adaptive prospects of the
species.
 The loss of wild populations of plants also means the loss of genetic resources that
could potentially be used to improve crop qualities, such as disease resistance.

Biology Chapter Notes

 Species diversity, or species richness, is the variety of species in an ecosystem or
throughout the entire biosphere.
 Much of the discussion of the biodiversity crisis centers on species.
 The U.S. Endangered Species Act (ESA) defines an endangered species as one in
danger of extinction throughout its range, and a threatened species as one likely to
become endangered in the foreseeable future.
 Here are a few examples of why conservation biologists are concerned about species loss.
 The International Union for Conservation of Natural Resources (IUCN) reports that
12% of the 9,946 known bird species and 24% of the 4,763 known mammal species
are threatened with extinction.
 The Center for Plant Conservation estimates that 200 of the 20,000 known plant
species in the United States have become extinct since records have been kept, and
another 730 are endangered or threatened.
 About 20% of the known freshwater species of fish in the world have become extinct
or are seriously threatened.
 One of the largest rapid extinctions is the ongoing loss of freshwater fishes in East
Africa’s Lake Victoria. About 200 of the more than 500 species of cichlids in the lake
have been lost, mainly as a result of the introduction of the Nile perch in the 1960s.
 Since 1900, 123 freshwater vertebrate and invertebrate species have become extinct in
North America, and hundreds more are threatened.
 Harvard biologist Edward O. Wilson has compiled the Hundred Heartbeats Club, a list
of species that number fewer than one hundred and are only that many heartbeats away
from extinction.
 Several researchers estimate that at the current rate of destruction, more than half of all
plant and animal species will be gone by the end of this new century.
 Extinction of species may be local, when a species is lost in one area but survives in an
adjacent one.
 Global extinction means that a species is lost from all its locales.
 We do not know enough about many species to assess their situation.
 The variety of the biosphere’s ecosystems is the third level of biological diversity.
 The local extinction of one species, especially a keystone predator, can affect an entire
community.
 Each ecosystem has characteristic patterns of energy flow and chemical cycling that
can affect the whole biosphere.
 For example, the productive “pastures” of phytoplankton in the oceans may help
moderate the greenhouse effect by consuming massive quantities of CO 2 for
photosynthesis and for building bicarbonate shells.
 Some ecosystems are being erased from the Earth at an astonishing pace.
 For example, within the contiguous United States, wetland and riparian ecosystems
have been altered drastically in the past few centuries.
 More than 50% of wetlands have been drained and converted to other
ecosystems, primarily agricultural.
Biodiversity at all three levels is vital to human welfare.
 Why should we care about biodiversity?
 Perhaps the purest reason is what E. O. Wilson calls biophilia, our sense of connection to
nature.

Biology Chapter Notes

  The belief that other species are entitled to life is a pervasive theme of many religions
and the basis of a moral argument for the preservation of biodiversity.
 Future human generations may be deprived of Earth’s species richness.
 Biodiversity is a crucial natural resource.
 Species that are threatened could provide crops, fibers, and medicines for human use.
 In the United States, 25% of all prescriptions dispensed from pharmacies contain
substances originally derived from plants.
 The loss of species also means the loss of genes.
 Each species has certain unique genes, and biodiversity represents the sum of all the
genomes of all organisms on Earth.
 Such enormous genetic diversity has the potential for great human benefit.
 The polymerase chain reaction is based on an enzyme extracted from thermophilic
prokaryotes from hot springs.
 Because millions of species may become extinct before we even know about them, we
will lose the valuable genetic potential held in their unique libraries of genes.
 Humans evolved in Earth’s ecosystems, and we are finely adjusted to these systems.
 Ecosystem services encompass all the processes through which natural ecosystems and
the species they contain help sustain human life on Earth.
 A few of these services include:
 Purification of air and water.
 Reduction of the severity of droughts and floods.
 Generation and preservation of fertile soils.
 Detoxification and decomposition of wastes.
 Pollination of crops and natural vegetation.
 Dispersal of seeds.
 Cycling of nutrients.
 Control of many agricultural pests by natural enemies.
 Protection of shorelines from erosion.
 Protection from ultraviolet rays.
 Moderation of weather extremes.
 Provision of beauty and recreational opportunities.
 The functioning of ecosystems and, hence, their capacity to perform particular services is
linked to biodiversity.
The four major threats to biodiversity are habitat destruction, introduced species,
overexploitation, and disruption of interaction networks.
 Human alteration of habitat is the single greatest threat to biodiversity throughout the
biosphere.
 The IUCN states that destruction of physical habitat is responsible for the 73% of
species designated extinct, endangered, vulnerable, or rare.
 Habitat destruction may occur over immense regions.
 For instance, approximately 98% of the tropical dry forests of Central America and
Mexico have been cut down.
 Many natural landscapes have been broken up, fragmenting habitats into small patches.
 Forest fragmentation is occurring at a rapid rate in tropical forests.
Biology Chapter Notes
  In almost all cases, habitat fragmentation leads to species loss, since the smaller
populations in habitat fragments have a higher probability of local extinction.
 The prairies of southern Wisconsin now occupy less than 0.1% of the 800,000
hectares they covered when the Europeans arrived in North America.
 Habitat loss is also a major threat to marine biodiversity, especially on continental
coasts and coral reefs.
 About 93% of the world’s coral reefs have been damaged by humans.
 At the present rate of destruction, 40–50% of the reefs, home to one-third of marine
fish species, will be lost in the next 30–40 years.
 Aquatic habitat destruction and species loss also result from dams, reservoirs,
channel modification, and flow regulation affecting most of the world’s rivers.
 Habitat destruction has caused fragmentation of many natural landscapes.
 Introduced species, also called invasive species, are those that humans move from native
locations to new geographic regions.
 The modern ease of travel by ship and airplane has accelerated the transplant of
species.
 Free from the predators, parasites, and pathogens that limit their populations in their
native habitats, such transplanted species may spread through a new region at
exponential rates.
 Introduced species usually disrupt their adopted community, often by preying on
native organisms or outcompeting native species for resources.
 For example, the brown tree snake was accidentally introduced to the island of Guam
after WWII.
 Since then, 12 species of birds and 6 species of lizards have become extinct due to
predation by the brown tree snake.
 Humans have introduced many species deliberately, often with disastrous results.
 The European starling was introduced intentionally to New York’s Central Park by
a citizen’s group intent on introducing all the plants and animals mentioned in
Shakespeare’s plays.
 Starling populations in North America now exceed 100 million.
 They have displaced many native songbirds.

 Overexploitation refers to the human harvesting of wild plants and animals at rates that
exceed the ability of those populations to rebound.
 It is possible for overexploitation to endanger certain plant species, such as rare trees
that are harvested for their wood.
 However, the term usually applies to commercially hunted or fished animal species.
 Large organisms with low intrinsic reproductive rates are especially susceptible to
overexploitation.
 The African elephant has been overhunted largely due to the ivory trade.
 Elephant populations have declined dramatically over the past 50 years.
 Despite a ban on the sale of new ivory, poaching continues in central and east
Africa.
 The great auk was overhunted for its feathers, eggs, and meat.
 It became extinct in the 1840s.
 The bluefin tuna is another example of an overharvested species.
 This big tuna brings $100 per pound in Japan, where it is used for sushi and
sashimi.
Biology Chapter Notes
  With this demand, it took just ten years to reduce North American bluefin
populations to 20% of their 1980 levels.
 The collapse of the northern cod fishery off Newfoundland in the 1990s shows that it is
possible to overharvest what had been a very common species.
 Ecosystem dynamics depend on networks of interspecific interactions within biological
communities.
 The extinction of one species can doom others, especially if the extinction involves a
keystone species, an ecosystem engineer, or a species with a highly specialized
relationship with other species.
 Sea otters are a keystone species whose elimination over most of their historic range
led to major changes in the structure of shallow-water benthic communities along the
west coast of North America.
 The extermination of beavers, one of the best-known ecosystem engineers, resulted in
a large reduction in wetland and pond habitats across much of North America.

Concept 55.2 Population conservation focuses on population size, genetic diversity, and
critical habitat
 Biologists focusing on conservation at the population and species levels follow two main
approaches—the small-population approach and the declining-population approach.
 The small-population approach studies the processes that can cause very small
populations to become extinct.
 The extinction vortex is a downward spiral unique to small populations.
 A small population is prone to positive-feedback loops of inbreeding and genetic drift
that draw it into a vortex toward smaller and smaller numbers until extinction is
inevitable.
 The key factor driving the vortex is the loss of genetic diversity necessary to enable
evolutionary responses to environmental change, such as new strains of pathogens.
 Not all populations are doomed by low genetic diversity.
 Overhunting of northern elephant seals in the 1890s reduced the species to only 20
individuals—clearly a bottleneck that reduced genetic variation.
 Since that time, northern elephant seal populations have rebounded to 150,000
individuals, although the genetic variation of the species remains low.
 A number of plant species have inherently low genetic variation.
 Species of cord grass, which thrive in salt marshes, are genetically uniform at many
loci.
 Having spread by cloning, this species dominates large areas of tidal mudflats in
Europe and Asia.
 How small is too small for a population? How small does a population have to be before it
starts down the extinction vortex?
 The answer depends on the type of organism and its environment, and must be
determined case by case.
 The greater prairie chicken (Tympanuchus cupido) was common in large areas of North
America a century ago.
 Agriculture fragmented the population of the greater prairie chicken in the central and
western states and provinces.

Biology Chapter Notes

  In Illinois, greater prairie chickens numbered in the millions in the 19th century,
declined to 25,000 birds by 1933, and were down to 50 by 1993 (although large
populations remained in other states).
 The Illinois population of greater prairie chickens has since rebounded, but it was on
its way down into an extinction vortex until rescued by a transfusion of genetic
variation.
 The minimal population size at which a species is able to sustain its numbers and survive
is the minimum viable population size (MVP).
 Population viability analysis (PVA) is a method of predicting whether or not a
species will survive over time.
 Modeling approaches such as PVA allow conservation biologists to explore the
potential consequences of alternative management plans.
 A combination of theoretical modeling and field studies of the managed populations
are most effective.
 The effective population size (Ne) is based on the breeding potential of a population,
incorporating information about the sex ratio of breeding individuals.
 Ne = 4NfNm/(Nf + Nm)
 Nf and Nm are the numbers of females and males that successfully breed.
 The goal of sustaining Ne stems from concern that populations retain enough genetic
diversity.
 Numerous life history traits can influence Ne.
 Formulas for estimating Ne take into account family size, maturation age, genetic
relatedness among population members, the effects of gene flow between
geographically separated populations, and population fluctuations.
 In actual populations, Ne is always some fraction of the total population.
 One of the first population viability analyses was conducted in 1978 by Mark Shaffer of
Duke University as part of a long-term study of grizzly bears in Yellowstone National
Park and surrounding areas.
 Grizzly bear (Ursus arctos horribilis) populations had been drastically reduced and
fragmented.
 In 1800, an estimated 100,000 grizzlies ranged over more than 500 million hectares
of contiguous habitat, while today 1,000 individuals live in six isolated populations
with a total range of less than 5 million hectares.
 Shaffer attempted to determine viable sizes for U.S. grizzly populations.
 Using life history data obtained for individual bears over a 12-year period, he
simulated the effects of environmental factors on survival and reproduction.
 His models predicted that, given a suitable habitat, a total grizzly bear population of
70 to 90 individuals would have a 95% chance of surviving for 100 years.
 How does the actual size of the Yellowstone grizzly population compare with
Shaffer’s estimates of minimum viable population size?
 Several sources of information indicate that the grizzly population of Yellowstone
is growing.
 The relationship of estimates of total grizzly population to effective population size,
Ne, is dependent on several factors.
 Usually, only a few dominant males breed. It may be difficult for them to locate
females, since individuals inhabit such large areas.
 As a result, Ne is about 25% of total population size.

Biology Chapter Notes

  Because small populations tend to lose genetic variation over time, a number of
research teams have used protein, mitochondrial DNA, and nuclear microsatellite
DNA to assess the genetic variability in the Yellowstone grizzly population.
 These analyses show that the Yellowstone population has lower levels of genetic
variability than other grizzly bear populations in North America.
 However, the isolation and decline in genetic variability in the population appears
to have been gradual and not as severe as feared.
 The studies also show that the effective size of the Yellowstone grizzly population
is larger than formerly thought—approximately 100 individuals.
 How might conservation biologists increase the effective size and genetic variation of
the Yellowstone grizzly bear population?
 Migration between isolated populations of grizzlies could increase both effective
and total population sizes.
 Computer modeling predicts that introducing only two unrelated bears into a
population of unrelated bears would reduce the loss of genetic variation in the
population by about half.
 For small populations, finding ways to promote dispersal among populations
may be one of the most urgent conservation needs.
The declining-population approach is a proactive conservation strategy for detecting,
diagnosing, and halting population declines.
 The small-population approach emphasizes MVP size, and interventions include
introducing genetic variation from one population into another.
 The declining-population approach is more action oriented, focusing on threatened and
endangered species even when the populations are larger than the MVP.
 This approach emphasizes the environmental factors that caused a population to
decline and requires that population declines be evaluated on a case-by-case basis.
 The declining-population approach takes a number of steps in the diagnosis and treatment
of declining populations.
o Assess population trends and distribution to confirm that the species is in decline or
that it was formerly more abundant.
o Study the species’ natural history to determine its environmental requirements.
o Develop hypotheses for all the possible causes of the decline, including human
activities and natural events, and list the predictions for further decline of each
hypothesis.
o Test the most likely hypothesis first to determine if this factor is the main cause of the
decline. For example, remove the suspected agent of decline to see if the experimental
population rebounds relative to a control population.
o Apply the results of this diagnosis to the management of the threatened species and
monitor recovery.
 The red-cockaded woodpecker (Picoides borealis) is an endangered species endemic to
the southeastern United States.
 To take the declining-population approach, we must understand the habitat
requirements of an endangered species.
 This species requires mature pine forest, preferably dominated by longleaf pine, for its
habitat.
 The red-cockaded woodpecker drills its nest holes in mature, living pine trees.
 Red-cockaded woodpeckers drill small holes around the entrance to their nest
cavities, which causes resin from the tree to ooze down the trunk.
Biology Chapter Notes
  The resin repels certain predators that eat bird eggs and nestlings.
 The understory of plants around the pine trunks must be low profile so the
woodpeckers have a clear flight path into their nests.
 Historically, periodic fires swept through longleaf pine forests, keeping the
understory low.
 One factor leading to the decline of the red-cockaded woodpecker is the destruction or
fragmentation of suitable habitat by logging and agriculture.
 Recognition of the key habitat factors, protection of some longleaf pine forests, and the
use of controlled fires to reduce forest undergrowth have helped restore habitat that can
support viable populations.
 However, designing a recovery program was complicated by the birds’ social
organization.
 Red-cockaded woodpeckers live in groups of one breeding pair and up to four male
helpers.
 Helpers are offspring who do not disperse and breed but remain behind and
assist in incubating eggs and feeding nestlings.
 They may wait years before attaining breeding status.
 Young birds that disperse usually occupy abandoned territories or excavate
nesting cavities, which can take several years.
 Individuals have a better chance of reproducing by remaining as helpers than by
dispersing and excavating homes in new territories.
 Ecologists tested the hypothesis that social behavior restricts the ability of the red-
cockaded woodpecker to rebound.
 They constructed new cavities in pine trees and found that 18 of the 20 sites were
colonized by red-cockaded woodpeckers.
 This experiment supported the hypothesis that red-cockaded woodpeckers had
been leaving suitable habitats unoccupied because of an absence of breeding
cavities.
 This is a good example of how understanding habitat can lead to a successful
conservation effort.
Conserving species involves weighing conflicting demands.
 Conservation biology often highlights the relationship between science, technology, and
society.
 For example, programs to restock wolves in Yellowstone Park are opposed by many
ranchers concerned with potential loss of livestock.
 Large, high-profile vertebrates are not always the focal point in such conflicts, but habitat
use is almost always an issue.
 Should a highway bridge be built if it destroys the only remaining habitat of a species
of freshwater mussel?
 Another important consideration is the ecological roles of species.
 We cannot save every endangered species, so we must determine which are most
important for conserving biodiversity as a whole.
 Species do not exert equal influence on community and ecosystem processes.
 Identifying keystone species and finding ways to sustain their populations can be
central to the survival of whole communities.
 Management aimed at conserving a single species carries with it the possibility of
negatively affecting populations of other species.
Biology Chapter Notes
  For example, management of pine forests for the red-cockaded woodpecker might
impact migratory birds associated with broadleaf temperate forests.
 To test for such impacts, ecologists compared bird communities near clusters of nest
cavities in managed pine forests with communities in forests not managed for
woodpeckers.
 The managed sites actually supported higher numbers and diversity of other birds than
the control forests.

Concept 55.3 Landscape and regional conservation aim to sustain entire biotas
 On a broad scale, the principles of community, ecosystem, and landscape ecology can be
brought to bear on studies of the biodiversity of entire landscapes.
 Human population dynamics and economics are also considered.
 Landscape ecology is the application of ecological principles to the study of human land-
use patterns.
 A landscape is a regional assemblage of interacting ecosystems.
 This type of ecology is important in conservation biology because many species use
more than one type of ecosystem and many live on the borders between ecosystems.
Edges and corridors can strongly influence landscape biodiversity.
 Boundaries, or edges, between ecosystems and within ecosystems are defining features of
landscapes.
 An edge has its own set of physical conditions, which differ from those on either side
of it.
 Edges have their own communities of organisms.
 Some organisms thrive in edge communities because they have access to the resources of
both adjacent areas.
 For example, the ruffled grouse (Bonasa umbellatus) requires forest habitat for nesting,
winter food, and shelter.
 It also needs forest openings with dense shrubs and herbs for summer food.
 The proliferation of edge species can have positive or negative effects on a community’s
biodiversity.
 For example, a 1997 study in Cameroon suggested that forest edges may be important
sites of speciation.
 On the other hand, communities in which edges have resulted from human alterations
often have reduced biodiversity because of domination by edge-adapted species.
 Cowbirds flourish in areas where forests are heavily cut and fragmented, creating
more edge habitat and open land.
 Increasing cowbird parasitism and loss of habitat are correlated with declining
populations of cowbird’s host species.
 The influence of fragmentation on the structure of communities has been explored for two
decades in the long-term Biological Dynamics of Forest Fragments Project in the Amazon
River basin.
 Researchers are clearly documenting the physical and biological effects of forest
fragmentation in taxa ranging from bryophytes to beetles to birds.

Biology Chapter Notes

  Species adapted to forest interiors show the greatest declines in the smallest fragments,
suggesting that landscapes dominated by small fragments will support fewer species,
mainly due to loss of interior-adapted species.
 A movement corridor is a narrow strip or series of small clumps of good habitat
connecting otherwise isolated patches.
 Such corridors can be deciding factors in conserving biodiversity.
 Streamside habitats often serve as corridors. Some nations prohibit destruction of these
riparian areas.
 In areas of heavy human use, artificial corridors have been constructed.
 For example, a bridge in Banff National Park helps animals cross a major highway.
 Movement corridors can promote dispersal and reduce inbreeding in declining
populations.
 They are especially important to species that migrate between different habitats
seasonally.
 However, corridors can also be harmful, aiding in the spread of disease.
 Habitat corridors facilitated the movement of disease-carrying ticks among forest
patches in northern Spain.
Conservation biologists face many challenges in setting up protected areas.
 Conservation biologists apply ecological research in setting up reserves or protected areas
to slow the loss of biodiversity.
 Governments have set aside about 7% of the world’s land in various types of reserves.
 Choosing locations for protection and designing nature reserves pose many challenges.
 If a community is subject to fire, grazing, and predation, should the reserve be
managed to reduce these processes? Or should the reserve be left as natural as
possible?
 Much of the focus has been on biodiversity hot spots, areas with exceptional
concentrations of endemic species and a large number of threatened or endangered
species.
 Nearly 30% of all bird species are confined to only 2% of the Earth’s land area.
 About 50,000 plant species (17% of those known) inhabit 178 hot spots that comprise
only 0.5% of the global land species.
 Hot spots also include aquatic ecosystems, such as coral reefs and certain river
systems.
 Biodiversity hot spots are obvious choices for reserves, but recognizing them can be
difficult.
 A hot spot for one taxonomic group may not be a hot spot for another taxonomic
group.
 Designating an area as a biodiversity hot spot is often biased toward vertebrates and
plants, with less attention paid to invertebrates and microorganisms.
Nature reserves must be functional parts of landscapes.
 It is important that nature reserves are not isolated from the natural environment.
 Disturbance is a functional component of all ecosystems, and management policies that
ignore natural disturbances or attempt to prevent them are generally self-defeating.
 For instance, setting aside an area of a fire-dependent community, such as tallgrass
prairie or dry pine forest, without periodic burning is unrealistic.
Biology Chapter Notes
  Without the dominant disturbance, fire-adapted species are usually outcompeted by
other species, and biodiversity is reduced.
 A major conservation question is whether it is better to create one large reserve or a group
of smaller ones.
 Extensive reserves are beneficial for large, far-ranging animals with low-density
populations, such as the grizzly bear.
 As conservation biologists learn more about the requirements for achieving minimum
viable population sizes for endangered species, it is clear that most national parks and
other reserves are far too small.
 The biotic boundary, the area needed to sustain the grizzly, is more than ten times
as large as the legal boundary, the actual area of the parks.
 In some cases, when reserve land is surrounded by commercially viable property, the
use of land for agriculture or forestry must be integrated into conservation strategies.
 Several nations have adopted an approach to landscape management called zoned reserve
systems.
 A zoned reserve is a large region of land that includes one or more areas undisturbed
by humans surrounded by lands that are used for economic gain and have been
changed by humans.
 The key challenge of the zoned reserve approach is to develop a social and economic
climate in the surrounding lands that is compatible with the long-term viability of the
protected core area.
 The surrounding areas continue to be used to support the human population, but with
regulations to prevent the types of extensive alterations that will impact the protected
area.
 The surrounding tracts of land serve as buffer zones against intrusion into the
undisturbed areas.
 The small Central American nation of Costa Rica has become a world leader in
establishing zoned reserves.
 Costa Rica has eight zoned reserves, called “conservation areas,” which contain
national park land.
 The buffer zones provide a steady, lasting supply of forest products, water, and
hydroelectric power, as well as support sustainable agriculture and tourism.
 Costa Rica hopes to maintain at least 80% of its native species in its zoned reserves.
 A 2003 analysis of land cover change between 1960 and 1997 showed negligible
deforestation in Costa Rica’s national parks and a gain in forest cover in the 1-km
buffer around the parks.
 However, significant losses in forest cover were discovered in the 10-km buffer zone
around all national parks, which threatens to turn the parks into isolated habitat islands.
 The continued high rate of human exploitation of ecosystems leads to the prediction that
less than 10% of the biosphere will ever be protected as nature reserves.
 Sustaining biodiversity often means working in landscapes that are almost entirely
human dominated.
 For example, commercially important fish populations around the world have
collapsed in the face of mounting fishing pressure from increasingly sophisticated
fishing equipment.
 It has been proposed that marine reserves be established around the world that are
off limits for fishing.

Biology Chapter Notes

  Such reserves would increase fish populations within the reserves and improve
fishing success in nearby areas.

Concept 55.4 Restoration ecology attempts to restore degraded ecosystems to a more

natural state
 Restoration ecology applies ecological principles in developing ways to return degraded
areas to natural conditions.
 Biological communities can recover from many types of disturbances through a series
of restoration mechanisms that occur during ecological succession.
 The amount of time required for such natural recovery is more closely related to the
spatial scale of the disturbance than the type of disturbance.
 The larger the area disturbed, the longer the time required for recovery.
 However, communities are not infinitely resilient.
 Restoration ecologists work to identify and manipulate the processes that most limit the
speed of recovery, in order to reduce the time it takes for a community to bounce back
from disturbance.
 Natural disturbances such as periodic fires or floods are part of the dynamics of many
ecosystems and need to be considered in restoration strategies.
 Bioremediation is the use of living organisms, usually prokaryotes, fungi, or plants, to
detoxify polluted ecosystems.
 Restoration ecologists use various types of organisms to remove many different types
of toxins from ecosystems.
 For example, some plants adapted to soils containing heavy metals are capable of
accumulating high concentrations of potentially toxic metals.
 Restoration ecologists can use these plants to revegetate sites polluted by mining
and then harvest the plants to remove the metals from the ecosystem.
 The bacterium Pseudomonas has been used to clean up oil spills on beaches.
 Genetic engineering may become increasingly important as a tool for improving the
performance of certain species as bioremediators.
 In contrast to bioremediation, which is a strategy for removing harmful substances,
biological augmentation uses organisms to add essential materials to a degraded
ecosystem.
 Augmenting ecosystem processes requires determining what factors, such as chemical
nutrients, have been removed from an area and are limiting its rate of recovery.
 Encouraging the growth of plants that thrive in nutrient-poor soils often speeds up the
rate of successional changes that can lead to recovery of damaged sites.
 An example is the rapid regrowth of indigenous plants alongside roads in Puerto
Rico after colonization of the areas by a nonnative plant that thrives on nitrogen-
poor soils.
 The rapid buildup of organic material from the nonnative plant enabled the
indigenous plants to recolonize the area and overgrow the introduced species.
 Because restoration ecology is a new discipline, there is still much to learn.
 Many restoration ecologists advocate adaptive management—experimenting with
several types of management to learn what works best.

Biology Chapter Notes

  The key to adaptive management (and the key to restoration ecology) is to consider
alternative ways of accomplishing goals and to learn from mistakes as well as
successes.
 The long-term goal of restoration is to speed the reestablishment of an ecosystem as close
as possible to the predisturbance ecosystem.

Concept 55.5 Sustainable development seeks to improve the human condition while
conserving biodiversity
 Many have embraced the concept of sustainable development, the long-term prosperity
of human societies and the ecosystems that support them.
 The Sustainable Biosphere Initiative is a research agenda endorsed by the Ecological
Society of America.
 The goal is to obtain the basic ecological information necessary for responsible
development, management, and conservation of Earth’s resources.
 The research agenda includes studies of global change, including interactions between
climate and ecological processes, biological diversity and its role in maintaining
ecological processes, and the ways in which the productivity of natural and artificial
ecosystems can be sustained.
 This initiative requires a strong commitment of human and economic resources.
 Sustainable development is not just about science.
 It must include life sciences, social sciences, economics, and humanities.
 Equally important, it requires a reassessment of our values.
 The success of conservation in Costa Rica has involved leadership by the national
government as well as an essential partnership with nongovernmental organizations and
private citizens.
 How have living conditions of Costa Ricans fared as the country pursued conservation
goals?
 Infant mortality rate in Costa Rica declined sharply during the 20th century, and life
expectancy at birth increased.
 The 2003 literacy rate in Costa Rica was 96%.
 Such statistics show that living conditions in Costa Rica improved greatly over the period
in which the country dedicated itself to conservation and restoration.
 One of the challenges the country faces is maintaining its commitment to conservation in
the face of a growing population.
 Costa Rica’s population, currently 4 million, is predicted to grow to 6 million people
over the next 50 years.
 It is likely that the Costa Rican people will confront the remaining challenges of
sustainable development with success.
The future of the biosphere may depend on our biophilia.
 Not many people live in truly wild environments or even visit such places.
 Biophilia includes our sense of connection to diverse organisms and our attachment to
pristine landscapes.
 Most biologists have embraced this idea.

Biology Chapter Notes

 We should be motivated to preserve biodiversity because we depend on it for many
resources.
 Maybe we can also work to prevent the extinction of other forms of life because it is the
ethical thing to do.
 Biology is a scientific expression of our desire to know nature.
 We are most likely to protect what we appreciate, and we are most likely to
appreciate what we understand.
 By learning about the processes and diversity of life, we become more aware of ourselves
and our place in the biosphere.

Biology Chapter Notes