GENERAL BIOLOGY

İÜ Su Bilimleri Fak.
SUBM1003
L1

Doç. Dr. Nur Eda TOPÇU ERYALÇIN Dr. AYAKA AMAHA ÖZTÜRK

ÖNEMLİ UYARI:
Bu sunum İ.Ü. Su Bilimleri Fakültesi Lisans öğrencilerinin eğitimlerine ücretsiz katkı sağlamak amaçlı
hazırlanmış olup, bilimsel kaynak olarak gösterilemez, ücretlendirilemez, izinsiz kaydedilemez,
kullanılamaz, çoğaltılamaz ve ticari bir ürün haline dönüştürülemez.
 No need to take notes, just

You will be given lecture notes

Do tell me when you don’t understand

Try to learn new terms as they are

and not the night before the exam

Study weekly …bbbbbbbbbbbbbbbbbbbb

Don’t simply aim for a good test score and stay curious

When you study:

- Don’t only study from PP slides
- Don’t only study from pdf notes
- Try to synchronize them by chapter
Course Grade Schedule

15 %: Assignments (scheduled during the usual class time)

35 %: Midterm Exam (probably the week of Nov 4)

50 %: Final Exam (probably the first week of Jan 2022)

Assignments

1- Laboratory performance 1 (60p)

2- Laboratory performance 2 (40p)

 This semester…

 Cell and organelles

 Membranes / Energy pathways / Photosynthesis
 Cell division / DNA transmission
 Evolution and Diversity LABs after some lectures

 Origin of life / Hierarchy of life and classification

 a closer look to Archaea and Bacteria
 Diversity of life- «protists»
 Diversity of life- plants
 Diversity of life- animals: an evolutionary look
 Diversity of life- animals
 Adaptations to aquatic life
General Biology Schedule 2022/2023
T: Theoric lecture L: Laboratory session
1. D 21.09: T: Intro to Gen. Biol.
2. D 28.09: T: Cell Structure; Cell membrane No lab
3. D 05.10: T: Energy pathways No lab
4. D 12.10: T: Photosynthesis + L1: Comparison of plant / animal cells + QUIZ 1
5: D 19.10: T: Cell division and genetics No lab
6. D 26.10: T: Cellular basis of inheritance No lab
7. D 02.11: T: Cellular basis of inheritance + L2: cell division + QUIZ 2 (in the lab)
07 – 11 November (to be confirmed): Midterm exams
8. D 16.11: T: Cellular basis of inheritance
9. D 23.11: T: Diversity of life - protists No lab
10. D 30.11: T: Diversity of life - plants L3: Observation of protists
11. D 07.12: T: Diversity of life - animals
12. D 14.12: T: Diversity of life - animals L4: Observation of animal dissections/tissues
13. D 21.12: T: Adaptations to aquatic life L5: Anatomy and reproductive cells in corals
14. D 26.12: T: Finals
 Common and well-defined terms are required for biologists to be

successful and communicate with other biologists

 Most biological terms are derived from Latin words

 Try to learn new terms as they are introduced

 Study weekly
 Do not wait till the night before the test to study
 Study of life and living organisms

structure
evolution

function
distribution
taxonomy
growth
identification

Several branches and subdisciplines

 Cytology - study of cells
 Histology - study of tissues
 Embryology - study of development
 Paleontology - study of fossil
 Ecology - study of populations of organisms as they relate to one another
and to their environment
 Taxonomy - the naming of organisms
 Physiology - study of functions of living organisms
 Botany - study of plants
 Zoology - study of animals
 Bryology - study of mosses
 Bacteriology - study of bacteria
 Ichthyology - study of fishes
 Herpetology - study of amphibians and reptiles
 Ornithology - study of birds
 Mammalogy - study of mammals
 Genetics - study of heredity
 Evolution - study of changes which have occurred in the world over time
 Study of life and living organisms

structure
evolution

function
distribution
taxonomy
growth
identification

Several branches and subdisciplines

But…
 general and unifying concepts in biology:

 Cell: the basic unit of life

 Genes: the basic unit of heredity

 Evolution: the engine that propels the synthesis and creation of

new species

An organism survives by
• consuming and transforming energy
• and by regulating its internal environment to maintain a
stable and vital condition known as homeostasis
 1. Cellular organization

2. Order

3. Sensitivity

4. Growth, development and reproduction

5. Energy utilization

6. Evolutionary adaptation
 A fourth group of biological entities,
the viruses, are not organisms in the same
sense that eukaryotes, archaeans, and
bacteria are. However, they are of
considerable biological importance
 Emergent Properties of Life

single-celled organisms single organism

Rising
complexity:

New
patterns
Multicellular organisms community

Individual Population

born, has a certain natality rate

length of life and dies mortality rate
age distribution
Density….
 Emergent Properties of Life

At its most basic level, the concept of emergent properties states that with rising
levels of complexity in living things, new patterns will emerge. This is the case
whether you move up the chain from simple single-celled organisms to much more
complex multicellular organisms, or whether you move from a single organism to a
population of that organism.

Emergent properties appear at every level of biological organization. At the level of

an organism, the interactions of cells during development would result in an adult
organism which will present much richer properties than the component cells.
Properties of a human, such as fear, hunger or love, result by the interactions of a
great number of cells and connections in a human brain but no brain cell can
present these properties on its own.

Also, groups possess properties that separate individuals do not have. Individuals
are born, have a certain length of life and die. However, we can not define a natality
rate or mortality rate for an individual. These are the emergent properties of a
population like an age distribution of density. Species diversity is an emergent
property of a community…
 Evolution

The definition
Biological evolution, simply put, is descent with modification: change in the
heritable characteristics over successive generations. This definition
encompasses small-scale evolution (changes in gene frequency in a population
from one generation to the next) and large-scale evolution (the descent of
different species from a common ancestor over many generations).

The central idea of biological evolution is that all life on Earth shares a common
ancestor.

Through the process of descent with modification, the common ancestor of life on
Earth gave rise to the biodiversity at every level of biological organisation,
including the levels of species, individual organisms, and molecules.

Mechanisms of change:
• Mutation
• gene flow
• genetic drift
• natural selection

https://evolution.berkeley.edu/
 Which example illustrates descent with
modification — a change in gene
frequency over time?

Imagine a year or two of drought in

which there are few plants that these
beetles can eat.
All the beetles have the same chances
of survival and reproduction, but
because of food restrictions, the beetles
in the population are a little smaller than
the preceding generation of beetles.

Most of the beetles in the population (say

90%) have the genes for bright green
coloration and a few of them (10%) have a
gene that makes them more brown.
Some number of generations later, things
have changed: brown beetles are more
common than they used to be and make up
70% of the population.

https://evolution.berkeley.edu/
 Mechanisms that cause changes in the frequencies of genes in populations
Mutation
A mutation could cause parents with genes for bright green coloration to have
offspring with a gene for brown coloration. That would make genes for brown
coloration more frequent in the population than they were before the mutation.
Migration
Some individuals from a population of brown beetles might have
joined a population of green beetles. That would make genes for
brown coloration more frequent in the green beetle population
than they were before the brown beetles migrated into it.
Genetic drift
Imagine that in one generation, two brown beetles
happened to have four offspring survive to reproduce.
Several green beetles were killed when someone stepped
on them and had no offspring. The next generation would
have a few more brown beetles than the previous
generation — but just by chance. These chance changes
from generation to generation are known as genetic drift.
Natural selection
Imagine that green beetles are easier for birds to spot (and
hence, eat). Brown beetles are a little more likely to survive
to produce offspring. They pass their genes for brown
coloration on to their offspring. So in the next generation,
brown beetles are more common than in the previous
https://evolution.berkeley.edu/ generation.
 changes in the frequencies of genes in populations

mechanisms of evolutionary change

However, natural selection and genetic drift

cannot operate unless there is genetic
variation — that is, unless some individuals
are genetically different from others.

So, what are the

sources of genetic
variation?
 Three primary sources of genetic variation:

1. Mutations are changes in the DNA. A single mutation can have a large effect,
but in many cases, evolutionary change is based on the accumulation of many
mutations. When mutations occur, they may alter the product of a gene, or
prevent the gene from functioning, or have no effect… but mutations do not "try"
to supply what the organism "needs." In this respect, mutations are random —
whether a particular mutation happens or not is unrelated to how useful that
mutation would be. Based on studies in the fly Drosophila melanogaster, it has
been suggested that if a mutation changes a protein produced by a gene, this
will probably be harmful, with about 70% of these mutations having damaging
effects, and the remainder being either neutral or weakly beneficial.
Since all cells in our body contain DNA, there are lots of places for mutations to
occur; however, not all mutations matter for evolution. Somatic mutations occur
in non-reproductive cells and won't be passed onto offspring.

The only mutations that matter to

large-scale evolution are those
that can be passed on to offspring.
These occur in reproductive cells
like eggs and sperm and are
called germ line mutations.
https://evolution.berkeley.edu/
 2. Gene flow is any movement of genes from one population to another. If
genes are carried to a population where previously did not exist, gene
flow can be a very important source of genetic variation.

3. Sexual reproduction can introduce new gene combinations into a

population. This genetic shuffling is another important source of genetic
variation. In asexual organisms, genes are inherited together as they
cannot mix with genes of other organisms during reproduction. In
contrast, the offspring of sexual organisms contain random mixtures of
their parents' chromosomes that are produced through independent
assortment.

https://evolution.berkeley.edu/
 Genetic drift

In each generation, some individuals may, just by chance, leave behind a few
more descendants (therefore genes) than other individuals. The genes of the
next generation will be the genes of the "lucky" individuals, not necessarily the
healthier or "better" individuals. That, very briefly, is genetic drift. It happens to
ALL populations — there's no avoiding the vagaries of chance.

In other words, even if selective forces were absent or relatively weak, allele
frequencies would tend to "drift" upward or downward randomly. This drift ends
when an allele eventually becomes fixed, either by disappearing from the
population, or replacing the other alleles entirely. Genetic drift may therefore
eliminate some alleles from a population due to chance alone. Even in the
absence of selective forces, genetic drift can cause two separate populations
that began with the same genetic structure to drift apart into two divergent
populations with different sets of alleles.

Genetic drift affects the genetic makeup of the population but, unlike natural
selection, through an entirely random process. So although genetic drift is a
mechanism of evolution, it doesn't work to produce adaptations.

https://evolution.berkeley.edu/
 Natural selection

Evolution by means of natural selection is the process by which traits that enhance
survival and reproduction become more common in successive generations of a
population. it necessarily follows three simple facts:

• Variation exists within populations of organisms with respect to morphology,

physiology, and behaviour (phenotypic variation).
• Different traits confer different rates of survival and reproduction (differential fitness).
• These traits can be passed from generation to generation (heritability of fitness).

Remember the population of beetles?

There is variation in traits: For example, some beetles are green and some are brown.

There is differential reproduction:

Since the environment can't support unlimited population growth, not all individuals get
to reproduce to their full potential. In this example, green beetles tend to get eaten by
birds and survive to reproduce less often than brown beetles do.

There is heredity. The surviving brown beetles have brown baby beetles because this
trait has a genetic basis.
End result:
The more advantageous trait, brown coloration, which allows the beetle to have more
offspring, becomes more common in the population. If this process continues,
eventually, all individuals in the population will be brown.
https://evolution.berkeley.edu/
“Bir gencimiz bilim ve inanç konusunda soru
sordu. Ona şu yanıtı verdim: ‘Ben
Müslümanım ve Allah’a inanıyorum. Evrime
inanmak gibi bir şey yoktur, Evrim bir
gerçektir ve inanç meselesi değildir’.”

Aziz Sancar
A short history of Planet Earth
 Planet Earth is between 4.6 and 5 billion years old.

We will take the minimum age of 4.6 billion

(read: 4,600,000,000) years as starting point
for an interesting comparison:

 Imagine the earth to be a 46-year-old person.

 We don’t really know anything about the first 40 years of this person’s life.
 Then at the age of 42 the earth began to awaken.
 Dinosaurs and the great reptiles appeared a year ago, when the planet was 45.
 Mammals arrived on earth only eight months ago.
 Modern humans have been around for four hours.
 During the last hour, humans have discovered agriculture.
 The Industrial Revolution began a minute ago, and during those 60 seconds people have
made a rubbish dump of the earth.
Cell Theory
Scanning Electron Microscope image of SARS-
CoV-2 (gold) emerging from the surface of cells
cultured in lab by National Institute of Allergy and
Infectious Diseases-
https://www.flickr.com/photos/niaid/49557785797,
CC BY 2.0
SEM microscope TEM microscope
https://www.technologynetworks.com/
Cell Theory

• Cells are the fundamental unit of life - nothing less than a cell is alive.

• All organisms are constructed of and by cells.

• All cells arise from preexisting cells. Cells contain the information
necessary for their own reproduction.

• Cells use DNA as the medium of heredity and proteins as catalysts.

• Cells are the functional units of life. All biochemical processes are
carried out by cells.

• Groups of cells can be organized and function as multicellular organisms

• Cells of multicellular organisms can become specialized in form and

function to carry out subprocesses of the multicellular organism.
At 0.1–5.0 µm in diameter, prokaryotic cells are significantly smaller than
eukaryotic cells, which have diameters ranging from 10–100 µm
 2 mm
4 mm
All have the same volume : 64 mm3

BUT
The surface areas are different

For the metabolism of the cell to continue, substances

96 mm2 192 mm2 used in the reactions must be absorbed by the cell and
r=1.5 r=3
waste products must be removed. This is done through
1 mm the membrane at the surface of the cell. The rate at
which substances cross this membrane depends on its
surface area. The surface area to volume ratio is
therefore very important. If the ratio is too small, then
substances will not enter the cell as quickly as they are
required and waste products will accumulate because
they are produced more rapidly than they can be
removed.
As cells increase in size their volume increases more
384 mm2 rapidly than their surface area. As volume increases the
r=6
nucleus is further away from the parts of the cell and
diffusion is less efficient. That’s why some cells are
flattened or folded. More surface area!!!
All cells share four common components:

1) a plasma membrane, an outer covering that separates the cell’s interior from
its surrounding environment;
2) cytoplasm, consisting of a jelly-like region within the cell in which other cellular
components are found;
3) DNA, the genetic material of the cell;
4) ribosomes, particles that synthesize proteins.

prokaryotic cell: a unicellular organism that lacks a nucleus or any other

membrane-bound organelle

eukaryotic cell: a cell that has a membrane-bound nucleus and several other
membrane-bound compartments or sacs
 COMPONENTS OF PROKARYOTIC CELLS
Prokaryotic DNA is found in the central part of the cell: a darkened region called the
nucleoid
Unlike Archaea and eukaryotes, bacteria have a cell wall made of
peptidoglycan, comprised of sugars and amino acids.
Also many have a polysaccharide capsule.
The cell wall acts as an extra layer of protection, helps the cell maintain its
shape, and prevents dehydration.
The capsule enables the cell to attach to surfaces in its environment.
Some prokaryotes have flagella, pili, or fimbriae. Flagella are used for
locomotion, while most pili are used to exchange genetic material during a type
of reproduction called conjugation.
Pseudomonas aeruginosa
 Cyanobacteria

The plasma membrane is highly folded and most of the

cell cytoplasm is filled with layers of light-gathering
membrane
 EUKARYOTIC CELLS
A eukaryotic cell is a cell that has a membrane-bound nucleus
and other membrane-bound compartments or sacs, called
organelles, which have specialized functions.
 Plant cells have
plasmodesmata,
a cell wall,
a large central vacuole,
chloroplasts, and
plastids.

Animal cells have

lysosomes and
centrosomes.
a typical animal
cell
a typical
plant cell
The organelles and other structures of eukaryotic cells can be organized into four
basic functional groups:

1. The nucleus and ribosomes carry out the genetic control of the cell.

2. Organelles involved in the manufacture, distribution, and breakdown of

molecules include the endoplasmic reticulum, Golgi apparatus, lysosomes,
vacuoles, and peroxisomes.

3. Mitochondria in all cells and chloroplasts in plant cells function in energy

processing.

4. Structural support, movement, and communication between cells are the

functions of the cytoskeleton, plasma membrane, and plant cell wall
THE PLASMA MEMBRANE
 The plasma membranes of cells that specialize in absorption are folded
into fingerlike projections called microvilli (singular = microvillus).

Such cells are typically found lining the small intestine, the organ that absorbs
nutrients from digested food.
 THE CYTOPLASM
the entire region between the plasma membrane and the nuclear envelope,
consisting of organelles suspended in the gel-like cytosol, the cytoskeleton, and
various chemicals

70 to 80 percent water

semi-solid consistency, which comes

from the proteins within it

Glucose and other simple sugars,

polysaccharides, amino acids, nucleic
acids, fatty acids, and derivatives of
glycerol are found there too.

Ions of sodium, potassium, calcium, and

many other elements are also dissolved
in the cytoplasm. Many metabolic
reactions, including protein synthesis,
take place in the cytoplasm
THE CYTOSKELETON
Within the cytoplasm, the cytoskeleton is a network of
protein fibers that helps to maintain the shape of the cell,
secures certain organelles in specific positions, allows
cytoplasm and vesicles to move within the cell, and enables
unicellular organisms to move independently.

Collectively, this
network of protein fibers
is known as
the cytoskeleton. There
are three types of fibers
within the cytoskeleton:
microfilaments, also
known as actin
filaments, intermediate
filaments, and
microtubules
Flagella and Cilia
S.N. Characteristics Cilia Flagella
Cilia are short, hair like appendages Flagella are long, threadlike
1 Definition extending from the surface of a appendages on the surface of a
living cell. living cell.
2 Number Numerous Less in Number
3 Length Short and hair like organelle (5-10µ) Long wipe like organelle (150µ)
Presence at one end or two ends or
4 Occurrence Occurs throughout the cell surface.
all over the surface.
5 Cross section Nexin arm present. Nexin arm absent
6 Density Many (hundreds) per cell Few (less than 10) per cell

Cilia beat in a coordinated rhythm

They beat independent of each
7 Beating either simultaneously (synchronous)
other.
or one after the other (metachronic).

Rotational, like a motor, very fast Wave-like, undulating, sinusoidal,

8 Motion
moving slow movement compared to cilia

9 Found in Eukaryotic cells Eukaryotic and prokaryotic cells

Cilia use ‘kinesin’ which has an Flagella are powered by the proton-
10 Energy Production ATPase activity that produces motive force by the plasma
energy to perform the movement. membrane.
Helps in locomotion, feeding
11 Functions Help mainly in locomotion only.
circulation, aeration, etc.
12 Examples Cilia present in Paramecium Flagella present in Salmonella
 THE ENDOMEMBRANE SYSTEM

The endomembrane system (endo = within) is a group of membranes and

organelles in eukaryotic cells that work together to modify, package,
and transport lipids and proteins.
It includes
• the nuclear envelope,
• lysosomes,
• vesicles,
• endoplasmic reticulum and
• the Golgi apparatus

Although not technically within the cell, the plasma membrane is included in
the endomembrane system because it interacts with the other
endomembranous organelles.
 THE NUCLEUS

The nucleus (plural = nuclei) houses the cell’s DNA in the form of chromatin and
directs the synthesis of ribosomes and proteins.
THE ENDOPLASMIC RETICULUM
The Endoplasmic Reticulum and The Golgi Apparatus
LYSOSOMES
VESİCLES AND VACUOLES
RIBOSOMES
MITOCHONDRIA
PEROXISOMES
ANIMAL CELLS VERSUS PLANT CELLS

THE CELL WALL

CHLOROPLASTS
THE CENTRAL VACUOLE