1: Evolution, the themes of biology, and scientific unity

Evolution: the process on earth by which organisms have been

transformed from its earliest beginnings into the complexity and
diversity of life found on earth today
Biology: the scientific study of life; an ongoing inquiry about the
nature of life
4 themes: organization, information, energy and matter, interactions
The study of life reveals common themes
Many levels of life
Biosphere: all life on earth and all places where life exists
Ecosystem: the biotic and abiotic factors in a particular area
Communities: all the organisms of different species living
within one ecosystem, interacting with each other
Populations: All the individuals of a certain species within an
ecosystem
Organism: One living thing
Organs/organ systems
Tissues
Cells
Organelles
Molecules
Emergent properties: more complexity at each higher level of life
Systems biology: studying a biological system by analyzing the
interaction of its parts
Lifes processes involve the expression and transmission of genetic
information
Genome: all the DNA that an organism inherits
Genomics: the process by which a scientist studies whole sets
of genes in one or more species
Proteomics: the study of sets of proteins and their properties
Life requires the transfer and transformation of energy and matter
Energy flows into a system and out of the system
Molecules are recycled within a system
Interactions super important in biology
Feedback regulation: the output of a system regulates that
process
Negative feedback, positive feedback (blood clotting,
giving birth, etc.)
Evolution super important
Domains: Eukarya, Bacteria, Archaea
3 kingdoms in eukarya: Animalia, Plantae, Fungi- distinguished in
part by modes of nutrition
Plantae: produce their own food by photosynthesis

 Fungi: absorb nutrients from its surroundings

Animalia: Eat and digest other organisms
In studying nature, scientists make observations and form and test
hypotheses
Inductive reasoning: conclusion formed from a lot of
data/specific observations
WATER IS WEIRD
Cohesion: contributes to transport of water and dissolved
nutrients against gravity in plants
Adhesion: the clinging of water to other surfaces
Surface tension: there is an ordered arrangement between
water molecules which are hydrogen bonded to each other so
there is a high surface tension
Kinetic energy: the energy of motion
Thermal energy: kinetic energy associate with the RANDOM
MOTION OF ATOMS
Temperature: measures the average kinetic energy of
molecules in a body of matter, REGARDLESS OF VOLUME
Total thermal energy: does depend on volume
Heat: thermal energy in transfer from one body of matter to
another
4: Carbon and the Molecular Diversity of Life
Hydrocarbon: organic molecules consisting of only carbon and
hydrogen
Nonpolar
Release a relatively large amount of energy (ooh like
gasoline)
Isomers: have the same elements but have a different structure
and thus different properties
Structural isomers: have different COVALENT
arrangement of their atoms aka different carbon skeletons
(pentane vs 2-methyl butane)
Cis-trans isomers: carbons have covalent bonds to the
same atoms, but the atoms have differing SPATIAL
ARRANGEMENTS because of the double bond
Enantiomers: left handed and right handed versions of the
molecule
FUNCTIONAL GROUPS SUPES IMPORTANT. MEMORIZE
THEM!
5: The Structure and Function of Large Biological Molecules
Macromolecules: proteins, nucleic acids, carbohydrates
Dehydration reaction: water out, MOLECULES ATTACH
Hydrolysis: water in, molecules break apart

Carbs, nucleic acids, and proteins are chain-like molecules called

polymers
LIPIDS DONT FORM POLYMERS
Monosaccharide: molecular formulas that are of some unit
CH2O
Disaccharide: two monosaccharides joined by a glycosidic
linkage (covalent bond between 2 monosaccharides formed by
a dehydration reaction)
Polysaccharide: huge long chains of monosaccharides joined
by glycosidic linkage
Plants store starch: a polymer made of GLUCOSE monomers.
Most are joined by 1-4 linkages (1 carbon attaches to the 4
carbon of another glucose molecule). Basically a carb bank,
glucose can be withdrawn through glycolysis
Animals store glycogen: kinda like amylopectin (type of starch
with 1-6 linkage) but MORE BRANCHED. Stored in LIVER AND
MUSCLE. Humans need to eat regularly because glycogen stores
are usually depleted in about a day
Cellulose: a structural polysaccharide. Most abundant organic
compound on earth
Starch uses alpha configuration (OH group is BELOW the plane of
glucose), cellulose uses beta configuration (OH group is ABOVE
the plane of glucose)
Cellulose never branched, the molecule is straight (starch
molecules largely helical)
Chitin: used by arthropods to build their exoskeletons. Structure
like cellulose except with a nitrogen-containing appendage
Yay lipids
Fat: consists of glycerol and a fatty acid
Three fatty acids are joined to the glycerol by an ESTER LINKAGE
Another name is triacylglycerol (since there are three fatty
acids)
Phospholipids: two fatty acids (one has a cis bond so it bends)
attached to a glycerol with a phosphate group attached to it
Nuclear envelope, plasma membrane, mitochondrial
membrane, chloroplasts all have phospholipid membrane
Steroids: lipids characterized by a carbon skeleton with four
fused rings
Proteins
There are TWENTY amino acids
Primary structure: sequence of amino acids

Secondary structure: alpha helix or beta pleated sheet. CAUSED

BY HYDROGEN BONDS BETWEEN The POLYPEPTIDE BACKBONE
(not side chains)
Tertiary structure: overall shape of the protein. Caused by the
interactions of the side chains
Quaternary structure: multiple polypeptide subunits are brought
together
Chaperonins: proteins that assist the folding of other proteins.
Keeps the protein isolated from disruptive chemical conditions in
the cytoplasmic environment
Pyrimidines: ONE RING, T C
Purines: TWO RINGS, A, G
A tour of the cell
Yay microscopes
Transmission electron microscope: used to study internal
structure of cells
Cell fractionation: takes cells apart and separates the major
organelles from one another so you can see how each organelle
functions
Yay organelles
Organelle
Function
Smooth ER
Diverse metabolic processes. Includes synthesis of
lipids, detox of drugs and poisons, metabolism of carbs,
storage of CALCIUM. Synthesizes sex hormones and
various steroids that are secreted by the adrenal
glands.
So therefore very common in sex cells, muscle cells,
and liver cells
Rough ER
Produces secretory proteins from the ribosomes
attached to it.
Membrane keeps them separate from the proteins
produced by ribosomes in the cytosol
Makes lots of membranes- grows in place by adding
membrane phospholipids to its own membrane.
Flagellum
For motility
Centrosome
Contains centrioles, responsible for microtubule
manufacturing
Cytoskeleton Includes microfilaments, intermediate filaments,
microtubules, provides support for the cell and allows
cell movement
Microvilli
Projections that increase the cells surface area
Peroxisome
Moves H from various substances and transfers them to
water, forming H2O2 aka hydrogen peroxide, and then
converts that to water
Can break fatty acids down into smaller components

Mitochondrio
n
Lysosome

Golgi
apparatus

Ribosomes
Nuclear
envelope
Nucleus
Nucleolus
Chromatin
Central
vacuole

Plasmodesm
ata
Chloroplast
Other
vacuoles

Can detox alcohol

Glyoxysomes: found in plant seeds. Converts fatty
acids to sugar, which the seedling can use as a source
of sugar
Where cellular respiration occurs
Digestive organelle where macromolecules are
hydrolyzed
Can do this by phagocytosis: where the cell engulfs a
particle, and then the food vacuole fuses with a
lysosome
Autophagy: a process by which lysosomes digest
damaged organelles. A double membrane forms around
the organelle/cytosol
Synthesis, modification, sorting, and secretion of cell
products. Especially extensive in cells specialized for
secretion, because it deals with a lot of proteins from
the ER.
Proteins enter the cis face and leave from the trans face
Also makes macromolecules like polysaccharides
Protein synthesis
Double membrane enclosing the nucleus, joined to ER
Where DNA is stored
Lined by nuclear lamina: proteins that help the
nuclear envelope maintain its shape
Contains rRNA. Also makes large and small subunits of
ribosomes (the actual ribosome is synthesized OUTSIDE
of the nucleolus)
Material consisting of DNA and proteins
In plants, used to store nutrients and water, also
breakdown of waste products, hydrolysis of
macromolecules. The enlargement of vacuole is a major
way for plants to grow
main repository of inorganic ions
Channels through cell walls that connect neighboring
cells
Photosynthetic organelle; converts energy
Food vacuoles: form through phagocytosis
Contractile vacuoles: pump excess water out of the
cell
Some carry out enzymatic hydrolysis (in plants and
fungi)
In plants and fungi, some also carry pigments and

stockpile organic compounds

Endomembrane system: nuclear envelope, ER, Golgi apparatus,
lysosomes, various kinds of vesicles and vacuoles, and the plasma
membrane
Glycoproteins: proteins with a carbohydrate covalently bonded to
them
Microtubule assembly of a cilium or flagellum anchored in the cell by a
basal body
Outer cytoplasmic layer of the cell called the cortex: surrounded by
microfilaments and therefore has a more gel-like consistency
Actin: for bearing tension in the cell
Actin and myosin contribute to cytoplasmic streaming: a circular
flow of cytoplasm within cells. Speeds the distribution of materials
within cell.
Intermediate filaments: only found in the cells of some animals (so
not all eukaryotic cells)
Diverse class of cytoskeletal elements
Pretty much just stay there, dont really assemble/disassemble
that easily
Cell wall stuff
First excretes primary cell wall
Between adjacent primary cell walls lies the middle lamella:
sticky and filled with sticky polysaccharides aka pectins.
Some have a secondary wall which has a strong and durable
matrix that protects the cell
Animal membrane
They have an extracellular matrix: made of glycoproteins and
other carbohydrate-containing molecules that are secreted by
the cells
Collagen: most abundant glycoprotein, forms strong fibers
outside the cells
Collagen fibers embedded in a network of proteoglycans
secreted by cells. Protein molecule+ many carbohydrate chains
covalently attached
Fibronectin: bind to cell-surface receptor proteins called
integrins that are built into the plasma membrane
Yay cell junctions
Plasmodesmata: channels that connect plant cells. Unify plant
cells into one living continuum, since the cytoplasm can flow
through it.
Tight junctions: plasma membrane very tightly pressed against
each other, bound together by specific proteins. Establishes a
barrier that prevents the leakage of extracellular fluid (ex:
epithelial cells)

Desmosomes: like rivets, fastening cells together into strong

sheets. KERATIN anchors the desmosomes in the cytoplasm. Ex:
muscle cell to muscle cell
Gap junctions: cytoplasmic channels from one cell to an
adjacent cell
Membrane structure and function
Amphipathic: both a hydrophilic region and a hydrophobic
region
Membrane held together by hydrophobic interactions, which are
weaker than covalent bonds
Yay fluid mosaic model=lateral movement of phospholipids. Can
switch positions 107 times per second
Cholesterol: makes the membrane less fluid at high
temperatures, also lowers temp required for the membrane to
solidify
Lots of proteins embedded in membrane; determine its functions
Integral proteins: penetrate the hydrophobic part of the lipid
bilayer. Most are transmembrane: goes through the entire
plasma membrane
Peripheral proteins: loosely bound to the surface of the
membrane, often attached to integral proteins
Membrane carbohydrates super important in cell-cell recognition
Cells recognize other cells by binding onto molecules, usually
containing carbohydrates. Some glycolipids, some glycoproteins
Vesicles from the Golgi apparatus fuse with the plasma
membrane to form new membrane. So all the proteins on the
membrane are formed in the ER and Golgi.
Nonpolar molecules (like CO2 and O2) can cross the lipid bilayer.
Everything else is a bit trickier.
Two types of transport proteins: channel proteins (like a channel),
allows certain molecules to pass through. Aquaporins: a
channel for water. Then there are carrier proteins, which change
shape, allowing the molecule to pass through. SUPER SELECTIVE
Passive transport: the cell doesnt have to expend energy to
make it happen
Tonicity: the ability of a surrounding solution to cause a cell to
gain or lose water
Hypertonic= shriveling
Hypotonic= exploding
Osmoregulation: a way to maintain solute concentrations and
water balance
Channel proteins that transport ions are called ion channels,
and normally they function as gated channels. (so ion gated

channels???). Open or close in response to a STIMULUS. In some,

the stimulus is electrical
There are also carrier proteins, the one that are like doors that
change their shape. Those involved in facilitated diffusion DONT
EXPEND ENERGY because it moves down the conc. Gradient
ALL ACTIVE TRANSPORT PROTEINS ARE CARRIER PROTEINS
Membrane potential: difference of the voltage across a
membrane (OUTSIDE-INSIDE) If its negative, that means the
inside of the membrane has more anions. Therefore favors the
passage of cations into the cell and anions out of the cell
Electrochemical gradient: the combination of the chemical
and electrical forces acting on an ion.
Electrogenic pump: a transport protein that generates voltage
across a membrane. Helps store energy that can be tapped for
cellular work (OH LIKE ATP GENERATION!!!)
Proton pump: very common example of an electrogenic pump
COTRANSPORT SUPER IMPORTANT UNDERSTAND CONCEPT
Exocytosis: where the cell secretes stuff by binding vesicles to
the plasma membrane
Endocytosis: the cell takes in molecules and particulate matter
by forming new vesicles from the plasma membrane
Phagocytosis: where it engulfs a food particle
Pinocytosis: cellular drinking aka when vesicles form
around droplets and take in all the molecules. Non specific
Receptor-mediated endocytosis: where there are
receptors on the plasma membrane that bind to
ligands, and thus the substances that are in the
vesicle that forms are more specific
Ligand: a molecule that binds to a receptor on another molecule
Energy, enzymes, metabolism
Endosymbiont theory: an early eukaryotic cell engulfed an
oxygen using non photosynthetic prokaryotic cell, and eventually
the engulfed cell became an endosymbiont. Eventually they
merged into a single organism: a eukaryotic cell with a
mitochondrion
THERE ARE RIBOSOMES AND DNA IN MITOCHONDRIA AND
CHLOROPLASTS
Metabolism: the totality of an organisms chemical reactions
Metabolic pathway: begins with a specific molecule, then
altered in a series of defined steps, which is catalyzed by a
specific enzyme
Bioenergetics: the study of how energy flows through living
organisms
Energy: the capacity to cause change

Kinetic energy: energy associated with motion

Thermal energy: energy associated with the random motion of
ATOMS
Heat: thermal energy in transfer from one object to another
Thermodynamics: the study of energy transformation that
occur in a collection of matter
First law: energy can be transferred and transformed, but it
cant be created or destroyed
Second law: every energy transformation increases the entropy
of the universe
Free energy: the portion of a systems energy that can perform
work when temperature and pressure are uniform throughout the
system. SPONTANEOUS WHEN NEGATIVE
Exergonic reaction: energy released, spontaneous
Endergonic reaction: energy required, nonspontaneous
3 types of cellular work: transport (pumping of substances across
a membrane), mechanical work (contraction of muscle cells,
movement of chromosomes, etc.), and chemical work (the
building of polymers from monomers, etc.)
G= -7.3kcal/mol ATP
THE ATP CYCLE IS A REVOLVING DOOR THROUGH WHICH ENERGY
PASSES DURING ITS TRANSFER FROM CATABOLIC TO ANABOLIC
PATHWAYS
Competitive inhibitors: inhibitors that directly block the active
site
Noncompetitive inhibitors: bind on not the active site,
causing the enzyme to change shape
Cellular Respiration and Fermentation
BLAH BLAH GLYCOLYSIS AND CITRIC ACID CYCLE AND BLAH
Photosynthesis
Chlorophyll a: the primary pigment that captures light
Chlorophyll b: the accessory pigment
Carotenoids: absorb and dissipate excessive light energy that
would otherwise damage chlorophyll or interact with oxygen
Energy released by the electrons during the light reactions are
used to pump H+ across a membrane, which generates ATP
because of the ATP synthase. This ATP is used to reduce CO2 to
H2O
G3P: product produced directly by the Calvin Cycle
The cell cycle
A typical human cell has 2m of DNA

While the mitotic spindle assembles, parts of the cytoskeleton

disassemble, which provides the material to construct the
spindle
Mitotic spindle comes from centrosome. Centrioles are in the
middle of centrosomes, though NOT NECESSARY FOR CELL
DIVISION. (not even present in plants)
Anaphase begins when the enzyme separase cleaves the
cohesions holding the sister chromatids of each chromosome
During metaphase, the nonkinetochore microtubules overlap
significantly. During anaphase, motor proteins attached to these
microtubules walk them away from each other
Kinases that drive cell cycle have to be present at a constant
concentration in the cell, but usually they are inactive unless
they are attached to cyclin, whose levels constantly fluctuate
UNDERSTAND REGULATION
Growth factor: a protein released by certain cells that
stimulates other cells to divide
Transformation: the process that enables normal cells to
behave like cancer cells
Meiosis
Autosomes: all the chromosomes that arent sex chromosomes
after interphase, sister chromatids attached to each other by
proteins called cohesions
DNA of two nonsister chromatids (but homologous
chromosomes) broken at precisely the same point
Then the synaptonemal complex holds both homologous
chromosomes together
Synapsis: where the DNA breaks are closed up by joining the
broken end to the corresponding segment of the nonsister
chromatid
AT LEAST ONE CROSSOVER PER CHROMOSOME MUST
OCCUR IN ORDER FOR HOMOLOGOUS PAIR TO STAY
TOGETHER
Cell cycle and cancer
Proto-oncogenes: code for proteins that stimulate normal cell
growth and division
Oncogenes: cancer-causing genes
tumor-suppressor genes: proteins help prevent uncontrolled
cell growth
protein products repair damaged, NA, they control the
adhesion of cells to each other (cell anchorage usually
absent in cancers), some are components of cell-signaling
pathways that inhibit cell cycle

ras gene: codes for the ras protein. This protein relays a signal
from a growth factor receptor protein on the plasma membrane
to a set of protein kinases. Cellular response at the end of this
signaling pathway stimulates the cell cycle. In a mutation, the g
protein will be activated no matter if the growth factor is bound
to the receptor or not. Mutations occur in about 30% of human
cancers
p53 gene: a tumor suppressor gene that accounts for ~50% of
human cancers. Promotes synthesis of cell cycle-inhibiting
proteins. Usually activates the p21 gene, product halts cell cycle
by binding to cdks, which allows time for cell to repair DNA. Also
activates expression of miRNAs, which inhibits cell cycle. Also
activates suicide genes. Basically, p53 is good because it
prevents the rereplication of damaged DNA??
Since mutant tumor-suppressor alleles are usually recessive,
mutations must knock out BOTH alleles in a cells genome
Cell communication
Signaling mechanisms first evolved in ancient prokaryotes and
single-celled eukaryotes, then adopted for new uses by their
molecular descendants.
Cells can communicate with direct contact via cell-cell
recognition or gap junctions/Plasmodesmata
In other cases of local signaling, messenger molecules secreted
by the signaling cell. Some of these travel short distances, and
influence cells in the vicinity. Ex: growth factors, that stimulate
nearby cells to grow and divide.
Paracrine signaling: a secreting cell acts on nearby target cells
by secreting molecules of a local regulator
Synaptic signaling: a nerve cell releases neurotransmitter
molecules into a synapse, stimulating a target cell
Long distance signaling: uses circulatory system
3 stages: reception, transduction, response
Reception: the target cells detection of a signaling
molecule coming from outside the cell. Signal detected
when signaling molecule binds to a receptor protein
located at the cells surface
Transduction: the receptor protein changes in some way. It
converts the signal to a form that can bring about a
specific cellular response. Normally a sequence of changes
in a series of specific molecules: signal transduction
pathway
Response: transduced signal triggers a specific cellular
response
Ligand: a molecule that specifically binds to another molecule

G-protein coupled receptor: cell-surface transmembrane

receptor that works with the help of a G protein, which binds GTP
Receptor tyrosine kinases: kinase: an enzyme that catalyzes
the transfer of phosphate groups. They are membrane receptors
that attach phosphates to tyrosines. One RTK can activate ten or
more different transduction pathways and cellular responses at
once. Which is what makes it different from GPCRs
Ligand-gated ion channel: ion channel stays closed until a
ligand binds to it, then it changes shape and then opens the ion
channel. Hooray Super important in the nervous system
Abnormal functioning of RTKs associated with many types of
cancers
Protein kinase: an enzyme that transfers phosphate groups
from ATP to a protein
Protein phosphatases: enzymes that can rapidly remove
phosphate groups from proteins, allows the signal transduction
pathway to be turned off when the initial signal is no longer
present
Second messengers: small, non-protein, water-soluble
molecules used in signal-transduction pathways
Cyclic AMP: kinda like AMP (Adenosine monophosphate).
Adenylyl cyclase converts ATP to cyclic AMP in response to an
extracellular signal
cAMP converted back to AMP because of phosphodiesterase
inositol triphosphate and diacylglycerol are produced by a
cleavage of a certain kind of phospholipid in the plasma
membrane, and lead to the release of calcium from the cells ER
Many signaling pathways ultimately regulate protein synthesis
Scaffolding proteins: large relay proteins to which several
other relay proteins are simultaneously attached
Mendelian Genetics
Character: a heritable feature that varies among individuals. Ex:
flower color
Trait: each variant for a character
True-breeding: where the offspring, after many generations,
are still the same variety as the parent plant
Law of segregation: the two alleles for a heritable character
segregate during gamete formation and end up in different
gametes
Testcross: breeding an organism of unknown genotype with a
recessive homozygote, because it can reveal the genotype of
that organism
Monohybrids: organisms heterozygous for one particular
character being followed in the cross (Rr)

Dihybrids: organisms heterozygous for two traits (RrSs)

Law of independent assortment: two or more genes assort
independently. Each pair of alleles segregates independently of
each other pair of alleles during gamete formation. Only works if
genes are on different chromosomes/far away on the same one.
Cystic fibrosis: most common lethal genetic disease
Anatomical signs of sex begin to emerge when the embryo is
about 2 months old in humans
Sex-linked gene: a gene located on either sex chromosome
If an x-linked trait is recessive, females will display this trait only
if they are homologous for the trait. Males, however, will display
this trait regardless.
Duchenne muscular dystrophy: an x-linked trait.
Characterized by a progressive weakening of the muscles and
loss of coordination
Hemophilia also x-linked disorder
Almost all of one x-chromosome in each cell in female mammals
condenses into a Barr body and becomes inactive. In the
ovaries, the Barr-body chromosomes become reactivated, so
every egg has an active x
The x-inactive specific transcript becomes active on the
chromosome that will become the Barr body
Linked genes: genes that are close together on a chromosome
and are thus inherited together
Recombinant type: the offspring have different combinations
of traits than the parents
The farther apart two genes are, the higher the probability that a
crossover will occur between them and therefore the higher the
recombination frequency.
Linkage map: a genetic map based on recombination
frequencies
Map units: a way to express distances between genes, one map
unit being 1% recombination frequency
Nondisjunction: members of a pair of homologous
chromosome/sister chromatids dont separate during meiosis
Aneuploidy: where the zygote will have an abnormal number of
a particular chromosome
Deletion: part of the chromosome is deleted. Duplication:
where a segment is repeated. Inversion: where a segment is
reversed. Translocation: where nonhomologous chromosomes
switch genes (reciprocal) or where a fragment transfers to
another chromosome (nonreciprocal)
Genomic imprinting: variation in phenotype depending oh
whether an allele is inherited from the male or female parent.

 Maternal inheritance in chromosomal and mitochondrial genes

The molecular basis of inheritance
Origin of replication: where the DNA begins to duplicate
DNA helicase: unwinds the DNA
Single-strand binding protein: binds to the unwound DNA,
keeps the DNA from pairing up together again
Topoisomerase: relieves the strain put onto the unwound DNA
by breaking and rejoining the DNA strands
Initial nucleotide sequence is a short stretch of RNA
DNA polymerase: catalyze the synthesis of new DNA, attach
nucleotides to pre-existing chain
DNA polymerase I: replaces the RNA primers in the Okazaki
fragments with DNA
DNA ligase: joins okazaki fragments together
Mismatch repair: other enzymes remove and replace
incorrectly paired nucleotides that have resulted from replication
errors
Telomeres: special nucleotide sequences at the end of DNA
molecules. No genes, just lots of sequences. They prevent the
staggered ends of the daughter molecule from activating the
cells systems for monitoring DNA damage. It provides protection
against the genes shorting
Gene expression
RNA polymerase: transcribes RNA
Starts transcription at promoter (a set of genes on DNA), ends
transcription on terminator. Promoter contains a start point
where transcription actually occurs.
Transcription factors: bind onto the DNA and allow RNA
polymerase to bind onto it
Transcription-initiation complex: RNA polymerase+
transcription factors
5 cap added to the 5 end, a poly-A tail added to the 3 end.
Help facilitate export of mature mRNA from the nucleus, help
protect the mRNA from degradation by hydrolytic enzymes, help
ribosomes attach to the 5 end of the mRNA once the mRNA
reaches the cytoplasm
spliceosome: an enzyme that cuts out the introns
Ribozymes: RNA molecules that act like enzymes, splicing their
own segments
Alternative RNA splicing: RNA is spliced in different ways to
manifest different traits
Domains: discrete structural and functional regions of proteins

Aminoacyl-tRNA synthetases: binds the amino acid to its

proper tRNA molecule
Ribosomes are made up of proteins and rRNAs.
rRNAs largely responsible for the function of the chromosome
Viruses and their genetics
Viruses NOT LIVING because they cant reproduce or carry
out metabolism outside a host cell
Martinus Beijerinck: discovered the virus
Virus: nucleic acid surrounded by protein coat
Genomes consist of either single/double stranded DNA, or
single/double stranded RNA
Capsid: the protein shell that encloses the viral genome
Viral envelopes: sometimes surround viruses, made from the
membranes of the HOST CELL and contain phospholipids and
membrane proteins
Host range: the limited types of cell that a specific virus can
invade
Lytic cycle: where the bacteria breaks open and releases the
phages that were produced in the cell.
Virulent phage: a phase that replicates only by a lyric cycle
Restriction enzymes: enzymes in the bacterium that
recognizes that the phage DNA is foreign, and thus cuts it up
Parasite-host relationship in evolutionary flux because natural
selection favors both bacteria with restriction enzymes and
surface proteins that arent recognized by phages, but also
favors phages that can bind the altered receptors and are
resistant to the restriction enzymes
Lysogenic cycle: allows replication of the host genomes DNA
without destroying the host
Temperate phages: phages that can both lytic and lysogenic
cycle
Prophage: the viral DNA thats incorporated into the bacterial
DNA
So the lysogenic cycle causes a bunch of viral DNA to produce.
However, nothing happens until a signal occurs (environmental,
high energy radiation, etc.) and then the bacterial lyses (so lytic
cycle) and produces more phages
Most RNA viruses infect ANIMALS.
Retroviruses: (class VI). They have an enzyme called reverse
transcriptase, translates RNA template into DNA.
RNA gets transcribed into DNA, which gets incorporated into the
bacterial chromosome (called a provirus), which never leaves

the hosts genome, then RNA polymerase transcribes the

provirus into RNA, and proteins get made.
Example of retrovirus: HIV
Viruses can suddenly be a problem because of the high rate of
RNA mutations (viral RNA polymerases dont proofread and
correct errors in replicating)
Viroids: circular RNA molecules that infect plants. Dont encode
proteins but can replicate in host plants. Cause errors in
regulatory systems that control plant growth.
Prions: infectious proteins
Gene Regulation in Prokaryotes
Operator: a segment of DNA that controls access of RNA
polymerase to genes
Operon: the operator, the promoter, and the genes that they
control
Corepressor: a small molecule that cooperates with a repressor
protein to switch an operon off (tryptophan)
REGULATORY GENE CODES FOR THE REPRESSOR
Inducer: something that can bind to the repressor protein to
cause the repressor to change shape and to turn the operon on
(lactose)
cAMP accumulates when glucose is scarce. When theres lots of
cAMP, it can activate the regulatory protein (catabolite activator
protein), aka an activator, which binds to DNA and stimulates
transcription of a gene. Attachment increases affinity of RNA
polymerase for the promoter
So RNA polymerase will still bind to the lac operon (as long as the
repressor isnt bound to it aka there is lactose). But because
there is glucose and thus there is no activator, the RNA
polymerase has less affinity for it
So the repressor controls whether the lac operon is transcribed at
all, the presence of CAP controls the rate
Bacteria and Archaea
Capsule: a sticky layer of polysaccharide or protein that covers
the bacteria wall
Fimbriae: hairlike appendages on the cell walls of bacterium
that are used to attach themselves to other surfaces/one another
Pili: appendages that pull two cells together for DNA TRANSFER
Bacteria are small, they reproduce by binary fission, and they
often have short generation times.
Transformation: uptake of DNA from its foreign surroundings
Transduction: PHAGES carry prokaryotic genes from one host
cell to another

Gene

Conjugation: aka bacterial sex. Aka DNA is transferred between

two prokaryotic cells that join together with a sex pilus.
F factor: the ability for form pili and donate DNA during
conjugation
regulation in eukaryotes
Differential gene expression: the expression of different
genes by cells with the same genome
Histone acetylation: adds an acetyl group to the tails of
histone proteins, which causes the chromatin structure to
UNWIND, which PROMOTES transcription
DNA methylation: methyl groups bind DIRECTLY TO THE DNA,
which causes the genes to NOT be expressed. Methylation
patterns passed on during cell division
Epigenetic inheritance: inheritance of traits transmitted by
mechanisms not involving the nucleotide sequence. Aka
modifications to the chromatin. Which can be reversed.
Control elements: segments of noncoding DNA that serve as
binding sites for transcription factors
Most transcription factors bind to PROTEINS, which include other
transcription factors and RNA polymerase II
PROMOTERS AND ENHANCERS ARE GENES
proximal control elements: located close to the promoter
enhancers: groupings of genes that are located far away from
the gene or even an intron. Made up of DISTAL CONTROL
ELEMENTS (sequences of genes)
Best way to repress genes is to have proteins affect
chromatin structure
Lots of different enhancers, due to the different combinations of
distal control elements
Many signaling molecules can bind to the surface of the cell,
triggering a signal transduction response that promotes
transcription
Alternative RNA splicing: where different mRNA molecules are
produced from the same primary transcript
Life of bacterial mRNAs is super short, which is why they can
change their patterns of protein synthesis super quickly
microRNAs: small, single stranded RNA molecules that bind to
complementary sequences of mRNA, which blocks
translation/degrades the mRNA
small interfering RNAs: similar in structure and function to
miRNAs. Theyre different because of subtle differences in the
structure of their precursors
RNA interference (RNAi): the blocking of gene expression by
siRNAs

 CHROMATIN REMODELING BY NCRNAS????

DNA tools and biotechnology
Nucleic acid hybridization: the base pairing of one strand of a
nucleic acid to the complementary sequence on a strand from
another nucleic acid molecule
DNA sequencing: uses the principle of complementary base
pairing to determine complete nucleotide sequence of DNA
molecule. DNA first cut into fragments, and then each fragment
is sequenced.
Cloning vector: a DNA molecule that can carry foreign DNA into
a host cell and replicate there.
Restriction enzymes: enzymes that cut up DNA molecules at
precise points
Restriction site: a precise point in the DNA that restriction
enzymes cut up
Sticky end: one single stranded end from a restriction fragment
(because its cut in a staggered manner)
Gel electrophoresis: uses a gel made of a polymer as a
molecular sieve to separate out a mixture of nucleic acids
PCR uses a heat stable polymerase called Taq polymerase.
Cannot substitute for gene cloning in cells because there are
occasional errors in PCR replication limit. Used to provide a
supply of DNA for cloning
Expression vector: a cloning vector containing a highly active
bacterial promoter just upstream of a restriction site where the
eukaryotic gene can be inserted in the correct reading frame. So
in short highly active promoter= highly expressed gene and so if
you stick a gene after the promoter a lot of proteins will be
made?
Better to use eukaryotic host cells, because many eukaryotic
proteins will not function unless they are modified after
translation
Electroporation: brief electrical pulse creates temporary holes
in plasma membranes, so DNA can be inserted into eukaryotic
cells
In situ hybridization: a method of identifying which cells
express genes by using nucleic acid probe, allowing us to see the
mRNA in place
Reverse transcriptase-polymerase chain reaction: allows
one to compare amounts of a specific mRNA in several samples
at the same time, like in different cell types or in embryos at
different stages of development.
Reverse transcriptase turns mRNA into double-stranded
DNAs.

Resulting double stranded DNA called complementary

DNA (cDNA) because it lacks introns and can be used for
protein expression in bacteria
Then gel electrophoresis will reveal amplified DNA products
only in samples that contain the mRNA transcribed from the
specific gene (after PCR is used to amplify the gene)
DNA microarray assays: consists of a large number of singlestranded DNA fragments that represent different genes fixed to a
glass slide in a tightly-spaced grid (kinda like a DNA chip). cDNAs
made, then made to fluoresce and allowed to hybridize into a
DNA microarray.
In vitro mutagenesis: specific mutations introduced into a
cloned gene, mutated gene returned to the cell so that it knocks
out original gene, in order to the study the role of the gene by
observing the phenotype
Genome-wide association studies: studies of a large
population with similar phenotypic conditions (heart disease,
diabetes, etc.) to try to see if there are genetic differences
between them and people without that condition. Test for
genetic markers: DNA sequences that vary in the population.
Single nucleotide polymorphism: a single base-pair site
where variation is found in at least 1% of the population
Totipotent; any differentiated cell with the potential to
dedifferentiate and become a different cell (aka taking a bunch
of differentiated root cells, putting them in culture, and seeing
them grow into a plant)
Embryonic stem cells reproduce indefinitely, can be made to
differentiate into a wide variety of specialized cells
Adult stem cells can give rise to multiple cell types
Pluripotent: cells that can differentiate into many different cell
types
Gene therapy: the introduction of genes into an afflicted
individual for therapeutic purposes
Transgenic: an organism with a gene from another organism.
Remove eggs from a female of recipient species, fertilize them in
vitro, clone desired gene and then inject it directly into the nuclei
of the fertilized eggs. Some integrate the foreign DNA into their
genome.
Short tandem repeats: tandemly repeated units of two- to
five- nucleotide sequences in the specific regions of the genome.
Number present highly variable, so we can use it to identify
individuals. PCR used to amplify particular STRs
Embryogenesis and development

Differentiation: the process by which cells become specialized

in structure and function
Morphogenesis: the physical process that gives an organism its
shape. Aka development of the form of an organism and its
structures
Cytoplasmic determinants: maternal substances in the egg
that influence the course of early development. There is an
unequal distribution of RNA/proteins etc. in the cytoplasm, so
when it divides there are now different cytoplasmic
determinants, which can influence gene expression
Also influential is the environment around a cell: signal
transduction, contact with cell-cell surface receptors, and the
binding of growth factors from other cells can affect gene
expression
Induction: a process by which such signals cause a change in
the target cell
Determination: the point in which an embryonic cell is
irreversibly determined to be a specific type of cell
Pattern formation: the spatial organization in which tissues
and organs of an organism are all in their characteristic places.
Begins early in the embryo, where the major axes are
established.
Positional information: molecular cues that control pattern
formation, provided by cytoplasmic determinants and inductive
signals.
Scientists studied Drosophilia to determine pattern formation and
how that all works
Homeotic genes: genes that control pattern formation
Embryonic lethals: mutations with phenotypes causing death
at the embryonic or larval stage. Cant reproduce and therefore
cant be bred for study
Exposed flied to a mutagenic chemical that affected the flies
gametes. Mated mutagenized flies, scanned descendants for
dead embryos/other defects. Ex: to find genes that would set up
anterior-posterior axis, they looked for flies with weird ends
Maternal effect gene: gene that, when mutant in the mother,
results in a mutant PHENOTYPE in the offspring regardless of the
offsprings gene. Woo cytoplasmic determinants. Also called
egg-polarity genes
Biocid: gene that determines body axes of the offspring.
Produces a protein product called Bicoid. Concentrated around
the tail end, which causes it to differentiate properly?? A TYPE OF
MATERNAL EFFECT GENE

Morphogens: gradients of this substance would establish an

embryos axes and other features of its form
Bicoid mRNA highly concentrated at anterior end of mature egg,
then bicoid protein diffuses towards the posterior end, so it forms
a conc. Gradient with the highest being at the anterior end.
Led to identification of specific proteins
Helped us understand how different regions of the egg can
give rise to cells that go down different developmental
pathways
Gradient of morphogens can determine polarity and
position
Animal development
Model organisms: species chosen for the ease with which they
can be studied in the laboratory
Fertilization: the formation of a diploid zygote from a haploid
egg and sperm (below is sea urchin fertilization)
Acrosomal reaction: begins with discharge of hydrolytic
enzymes from the acrosome aka a specialized vesicle at
the tip of the sperm. Enzymes partially digest jelly coat of
egg, Allows acrosomal process to elongate and penetrate
the coat. Triggers fusion of plasma membranes
Sperm nucleus enters egg cytoplasm, sodium ions diffuse
into the egg and cause depolarization, which acts as a fast
block to polyspermy
Slow block to polyspermy: established by vesicles that lie
just beneath the egg plasma membrane, in the cortex.
Cortical granules fuse with the egg plasma membrane
Rise in Ca2+ also results in egg activation
Zona pellucida: the extracellular matrix of the egg. Binding of
the sperm to a sperm receptor induces an acrosomal reaction
Cleavage: consists primarily of S and M phages. G1 and G2
phases essentially skipped, and little or no protein synthesis
happens. NO INCREASE IN MASS, INCREASE IN CELL NUMBER
Cleavage partitions the cytoplasm of the large egg into many
smaller cells called blastomeres
First five to seven divisions produce a hollow ball of cells called
the blastula, which surround a fluid-filled cavity called the
blastocoel
In some animals like sea urchins, cleavage is symmetric. In
other, like frogs, cleavage is asymmetric, reflecting the
distribution of yolk (stored nutrients) across the egg.
Vegetal pole: where the majority of yolk is concentrated
Animal pole: where there is less yolk
Holoblastic: cleavage furrow passes entirely through the egg

Meroblastic: only the region of the egg that doesnt have yolk
undergoes cleavage (fish, birds, reptiles, insects)
In a newly fertilized egg, a crap ton of proteins are needed and
the single nucleus cant produce them all. So development is
carried out by RNA and proteins that are deposited in the egg
during oogenesis.
After cleavage, there are a crap ton of nuclei and the cells are
small, so the nucleus can take over. Hooray
Morphogenesis: the cellular and tissue-based processes by
which the animal takes shape
Gastrulation: cells at/near the surface of the body moves to an
interior location, cell layers established, primitive digestive tube
formed. Reorganization from a hollow blastula into a gastrula
Organogenesis: the formation of organs
Gastrula: a two or three-layered embryo
Germ layers: cell layers produced by gastrulation
Ectoderm: forms the outer layer
Mesoderm: forms the middle layer
Endoderm: forms the inner layer
Archenteron: after invagination, the infolding of sheet cells
forms this deeper, narrower, blind-ended tube
Blastopore: open end of the archenteron
Human gastrulation
After cleavage, the human has about 100 cells arranged
around the central cavity. This has reached the uterus. This
embryo is called a blastocyst, aka a mammalian version
of the blastula.
At one end, there is a group of cells called the inner cell
mass, which develops into the actual embryo. Source of
embryonic stem cell lines
Trophoblast: epithelial lining of the blastocyst. Used for
implantation into the uterus. Enzymes secreted by the
trophoblast break down molecules of the endometrium
(lining of uterus)
Trophoblast also extends finger-like projections into the
endometrium, causing the capillaries to break and blood to
spill out, which is captured by the trophoblast
During implantation, inner cell mass forms an epiblast and
a hypoblast.
Human embryo develops almost entirely from
epiblast cells
After implantation, trophoblast continues to implant into
the cell, and four new membranes appear.

These extraembryonic membranes are from the

embryo, but they enclose structures that are outside the
embryo.
Once implantation is complete, gastrulation begins.
Some epiblast cells remain as ectoderm, others move
through a primitive streak and form mesoderm and
endoderm,
Extraembryonic membranes
For reptiles, birds and mammals only
Mammals, reptiles, and birds surrounded by a fluid-filled
sac called an amnion, and therefore they are called
amniotes
Chorion: site of gas exchange. Forms placenta?
Allantois: disposes of wastes. In mammals, it is
incorporated into the umbilical cord. Forms blood vessels,
transports oxygen and nutrients from the placenta to the
embryo and rid the embryo of carbon dioxide and
nitrogenous wastes
Amnion: cushions and protects the embryo
Yolk sac: site of early formation of blood cells in
mammals, and encloses yolk in the eggs of mammals.
Organogenesis
Organogenesis involves the development of organs
Neuralation begins as cells from dorsal (back) mesoderm
form the notochord (disappears before birth. Some
remain as inner portions of disks in adult spine. As in
herniated disks)
The signaling molecules that are secreted by these
mesodermal cells get the ectoderm above the notochord to
become the neural plate
This is an example of induction: process by which a group
of cells or tissues influences the development of another
group through close-range interactions
Then, neural plate rolls itself into a neural tube, which will
become the brain and the spinal cord
Neural crest: a group of cells that form above the neural
tube, which then migrates to other parts of the body to
form other cells, like peripheral nerves/teeth and skull
bones
Somites: blocks of cells that are on both sides of the
notochord. Plays a significant role in organizing the
segmented structure of the vertebrate body.
Parts of somites will dissociate into mesenchyme cells,
which migrate individually to new locations. Some form

vertebrae, some form muscles associated with the

vertebral column and the rubs
Organogenesis in Chicks and Insects
In insects, tissues from the nervous system form on the
ventral side of the insect embryo rather than the dorsal
side
Mechanisms of morphogenesis
Morphogenesis is the process by which the organs take
shape
Reorganization of cytoskeleton is really important part of
human development
Convergent extension: a rearrangement that causes a
sheet of cells to become narrower while it becomes longer
Cell adhesion molecules play a key role in cell migration by
promoting interaction between pairs of cells. Also involves
the ECM
Cytoplasmic determinants and inductive signals contribute to cell
fate specification
Determination: the process by which a cell or group of
cells becomes committed to a particular fate
Differentiation: the resulting specialization in structure
and function
Fate maps: diagrams showing the structure arising from
each region of an embryo.
In Frogs: Cortical rotation happens towards the site of
sperm entry. So ventral side is sperm entry aka where the
animal (top) and vegetal (bottom, lots of yolk) interact,
while the dorsal side has the gray crescent
In chicks, gravity establishes anterior-posterior axis (egg
travels down the hens oviduct before being laid), and the
pH difference between 2 sides of the blastoderm establish
dorsal-ventral axis
First two blastomeres of the frog embryo are totipotent:
can each develop into all the different types of that species
Twinningness: if the separation occur before the
trophoblast and inner cell mass have been determined,
then two identical embryos will form
In other cases, two embryos that form will share a chorion,
and sometimes (when separation is particularly late), an
aminon
Pattern formation: the process governing the
arrangement of organs and tissues in their characteristic
places in three-dimensional space. Controlled by inductive
signals

Positional information: molecular cues that control

pattern formation. They cell a cell where it is with respect
to the animals body axes and help to determine how the
cell and its descendants will respond to molecular signaling
Apical ectodermal ridge: secretes the fibroblast growth
factor that promotes limb bud outgrowth. Surgically
removing this prevents outgrowth of the limb on the
proximal-distal axis. Abnormality: cleft hand
Zone of polarizing activity: a specialized block of
mesodermal tissue that regulates development along the
anterior-posterior axis. Abnormality: triphalangeal thumb
Cilia and cell fate
Monocilia act as antennae on the cell surface, receiving
signals form multiple signaling proteins, which affect
development
Biology and integration?
Amniocentesis: physician inserts needle into uterus,
extracts amniotic fluid, detects genetic disorders
Chorionic villus sampling: takes tissue from the
placenta. You can get the karyotype a lot faster, and you
can do it earlier
Things I need to review for my final
Functional groups
Things I need to remember/not screw up
Proton pumps pump H+ OUT of the mitochondrial matrix during
oxidative phosphorylation
Sucrose= Glucose+ Fructose
Maltose= Glucose+ Glucose
Lactose= Glucose+ Galactose
YES ENERGY FOR BULK TRANSPORT
Ras stimulates cell cycle, p53 inhibits cell cycle
Ubiquitin attaches to the protein, which goes into the
proteasome, which is then degraded