Study Bubbly 2020-2021 AP Biology: Course Review
AP BIOLOGY
Table of Contents
UNIT 1 Chemistry of Life
Structure/Properties of Water
Elements of Life
UNIT 2 Cell Structure and Function
Cell Components and their Function
Cell Structure
Membrane Transport
Water Potential
UNIT 3 Cellular Energetics
Enzymes
Photosynthesis
Cellular Respiration
UNIT 4 Cell Communication and Cell Cycle
Cell Communication
Feedback
Cell Cycle
UNIT 5 Heredity
Meiosis
Genetic Diversity
Mendelian Genetics
Non-Mendelian Genetics
Environmental Effects on Phenotype
Chromosomal Inheritance
UNIT 6 Gene Expression and Regulation
DNA and RNA Structure
Replication
Transcription
Translation
Regulation of Gene Expression
Mutations
UNIT 7 Natural Selection
Natural Selection
Population Genetics
Hardy-Weinberg Equilibrium
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Common Ancestry
Continuing Evolution
Phylogeny
Speciation
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UNIT 1 Chemistry of Life
Structure/Properties of Water
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Water is made up of polar H2O molecules that are held together via hydrogen bonding, which is
the attraction of a hydrogen on one molecule to a nonmetal with a high electronegativity on
another molecule (in water’s case, oxygen).
There are 6 characteristics of water that are caused due to its strong covalent bonds and hydrogen
bonding:
○ High specific heat - Specific heat is the amount of heat that must be absorbed in order
for 1 gram of a substance to change its temperature by 1 degree (celsius).
○ High heat capacity - This means that a relatively great amount of heat is needed to
evaporate water.
○ Cohesion and Adhesion - Cohesion is the ability of the molecules in a substance to cling
to other molecules of the same kind. Adhesion is the ability of a substance to cling to
another different molecule/thing, often through opposite charges.
○ Solvent - Water is the universal solvent.
○ Surface tension - Water exhibits strong cohesion tension, so water molecules tend to
stick to each other.
○ Expansion on freezing - Ice is less dense than water, and because of this, floating ice in
deep bodies of water insulates the liquid water below it.
Water has a pH of 7, putting it in between acids (pH < 7) and bases (pH > 7).
Elements of Life
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Organic compounds are molecules containing both carbon and hydrogen (along with other
molecules), and there are 4 key classes of organic compounds:
○ Carbohydrates - They are the starches/sugar/fiber found in foods, and there are 3 main
classes of them:
■ Monosaccharides - They are the simplest sugar and provide energy for cells.
They have a chemical formula of CnH2nOn, and the most common
monosaccharide is glucose (C6H12O6)
■ Disaccharides - They consist of 2 monosaccharides joined together through
dehydration synthesis, which removes water from 2 monomers (ex:
monosaccharides) to form a polymer (ex: disaccharides). They all have a
chemical formula of C12H22O11.
■ Polysaccharides - They are polymers of carbohydrates that form as
monosaccharides are joined together, the 4 key ones are cellulose, starch, chitin,
and glycogen.
○ Lipids - They consist of fats/oils/waxes, and most are made up of 1 glycerol (an alcohol)
and 3 fatty acids (hydrocarbon chains with a carboxyl group on one end). Lipids serve as
energy storage, provide structural support for cell membranes, and some act as hormones.
■ There are two types of lipids: saturated (bad fats, they contain single bonds
between carbon atoms) and unsaturated (good fats, they contain at least one
double bond between carbon atoms.
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Proteins - They are complex polymers/polypeptides responsible for cell growth, repair,
and structure. They function as enzymes, membrane channels, hormones, etc. and their
function is dependent on their shape, which results from 4 levels of structure.. Proteins
consist of the elements S, C, O, H, and N, and they are made up of chains of amino acids.
■ Amino acids are made up of an amino group (NH2), a carboxyl group (COOH),
an R group (varies), and a single H. There are 20 different amino acids, each with
a different R group that varies in elements/polarity/shape.
Nucleic Acids - The two key nucleic acids are DNA and RNA, which have monomers
called nucleotides. Nucleotides consist of a phosphate, a 5-carbon sugar (deoxyribose or
ribose), and a nitrogenous base:
■ In DNA, the bases are adenine, cytosine, guanine, and thymine. In RNA, the
thymine is replaced by uracil.
UNIT 2 Cell Structure and Function
Cell Components and their Function
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There are 14 distinct components that can be found within cells, however not all cells will have
all 14 components.
Plasma Membrane - It is a semipermeable membrane composed of a phospholipid bilayer (made
up of hydrophilic phosphate heads on the outside and hydrophobic fatty acid “tails” on the
inside). Only small, nonpolar molecules moving down their concentration gradient can cross it
easily, but many proteins are attached to it (peripheral/integral/transmembrane) that can help
molecules that don’t fit this criteria cross.
Nucleolus - It is a non-dividing region of the nucleus where r(ribosomal)RNA is synthesized,
subunits of ribosomes are assembled, and proteins from the cytoplasm are combined with rRNA.
Ribosome - It is a site of protein synthesis and is made of rRNA and protein(s). They can be
freely suspended in cells or attached to the endoplasmic reticulum. Free ribosomes are associated
with protein produced for that cell’s use, while attached ribosomes are for export outside the cell.
Peroxisomes - It performs a specialized function of detoxification, as it contains catalase which
converts H2O2 (waste product of respiration) into water with the release of Os.
Nucleus - It is the largest organelle in the cell, and contains chromosomes made of DNA for
reproduction. It is surrounded by its own bilayer membrane that allows the transport of larger
molecules like m(messenger)RNA through its pores.
Endoplasmic Reticulum - It is made up of two different parts, the rough ER and the smooth ER.
The rough ER is studded with ribosomes and produces proteins, while the smooth ER assists in
the synthesis of hormones, stores Ca2+ ions, and detoxifies drugs/poisons from the body.
Golgi Apparatus - It consists of flattened membrane sacs known as cisternae, which are stacked
next to each other. Transport vesicles will carry material from the ER to the cis face of the
cisternae, the material is processed and packaged into vesicles, and then are shipped out via the
trans face of the cisternae and to other parts of the cell.
Lysosome - It is a sac of digestive enzymes surrounded by a single membrane, and it works to
renew cells by recycling and breaking down cell parts in a process known as autophagy. They
also contribute to apoptosis, which is programmed cell death, to break down parts of the cell.
Mitochondria - It consists of an outer double membrane and an inner series of membrane called
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cristae, which ATP production occurs at. It contains its own DNA, and they will divide and fuse
with each other to exchange DNA/compensate for defects, which is necessary for functions such
as respiration, cell development, and apoptosis.
Vacuole - It is a membrane-bound structure used for storage. Plant cells will generally have a
single, large, central vacuole while animal cells will have many smaller vacuoles.
Chloroplast - It contains a double outer membrane and an inner membrane system known as
thylakoids. They contain the green pigment chlorophyll, which is used to absorb light energy to
synthesize sugar in photosynthesis. It is found in plants and algae.
Cytoskeleton - It is a complex mesh of protein filaments that extend through the cytoplasm to
help a cell: maintain shape, position organelles, anchor cells in place, and control cytoplasm flow.
Centriole - A small cylindrical structure that produces microtubules to move/split chromosomes.
Cilia/Flagella - They are threadlike structures that cells use to propel themselves through watery
environments, and they are mostly used by singular-celled organisms.
Cell Structure
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Prokaryotes are smaller and simpler than eukaryotes. They have DNA in a free, circular shape
without the presence of a nucleus, as well as ribosomes, though they lack the many organelles
eukaryotes have.
Eukaryotes are larger and more complex than prokaryotes. They contain DNA bound within a
nucleus, and have many different organelles within their cytosol to carry out different functions.
The plasma membrane of cells contain many different proteins that aid in sending/receiving
signals, bringing particles into/out of the cell, etc:
○ Adhesion Proteins - form junctions between adjacent cells
○ Receptor proteins - serve as places where signals (ligands) can attach to
○ Transport proteins - have pumps that use ATP to transport solutes across the membrane
○ Channel proteins - form channels that allow passive diffusion of particles
○ Cell surface markers - exist on the extracellular matrix surface and play a role in cell
recognition and adhesion.
Animal cells and plant cells have a few key differences. Plant cells have: a cell wall made of
cellulose that provides support for the cell, chloroplasts which contain chlorophyll that can
capture light pigments to give the cell energy, and a large central vacuole (unlike the many, small
vacuoles in animal cells).
Cells need a small volume in order for particles and components to move quickly throughout the
cytoplasm. A large surface area compared to volume allows more particles/components to flow
in/out of a cell, while not having long distances within it to travel, increasing the cell’s efficiency.
Membrane Transport
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Membrane transport can be in the form of: simple diffusion, facilitated diffusion, or active
transport.
○ Simple diffusion involves particles being able to passively move across the plasma
membrane from an area of high concentration to one of low concentration. In order to
move through the membrane bilayer, the particles must be small and/or nonpolar.
○ Facilitated diffusion involves particles passively moving across the plasma membrane
with the help of channel proteins, which provide a channel for them to move through
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without being stopped by the hydrophobic fatty-acid tails. The particles are still moving
from high to low concentration.
Active transport involves particles being moved against their concentration gradient
(from low to high concentration). Particles undergoing active transport are moved by
energy-requiring transport proteins.
Water Potential
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Water Potential (Ψ) is the measure of potential energy in water and how eager the water is to
flow to satisfy the concentration gradient. It is affected by the pressure potential and solute
potential. (Ψ = SΨ + PΨ).
○ SΨ is the solute potential, and PΨ is the pressure potential.
UNIT 3 Cellular Energetics
Enzymes
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Enzymes are proteins that help to speed up chemical reactions without changing the reactions
themselves, and to do so they either bond molecules or split molecules apart. In general, they
lower the activation energy of a reaction so its energy requirement is easier to obtain.
Enzymes are substrate (the reactant molecules that an enzyme works on) specific, and thus will
only have specific substrates bound to them. The substrates will bind to a specific active site of
an enzyme. The property of induced fit means that enzymes won’t fit perfectly with their
substrates, and that they can change shape slightly to better fit.
○ Enzymes also have allosteric sites, which substrates can bind to to “turn off” the enzyme.
○ Competitive inhibition involves enzyme inhibitors binding to the active site of the
enzyme, and blocking the substrate from binding to it.
○ Noncompetitive inhibition involves the inhibitor binding to the allosteric site, causing
the enzyme to distort and lose function.
Enzymatic reactions are influenced by factors such as temperature change and pH change.
Photosynthesis
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Photosynthesis is the process in which light energy is converted into chemical energy, and CO2 +
H2O is converted into C6H12O6 + O2. Two different reactions are a part of photosynthesis, light
reactions and dark reactions.
○ Light reactions (light independent) use light energy directly to produce ATP. Light
reactions occur when photons activate chlorophyll and excite electrons. Activated
chlorophyll will pass excited electrons down a series of electron carries that produce ATP
and NADPH
○ Dark reactions (light dependent) use products of light reactions (ATP and NADPH) to
produce sugar. The carbon used to produce the sugar comes from CO2 via carbon fixation
as the Calvin Cycle.
○ Photosynthetic pigments (such as chlorophyll) absorb light energy and use it to provide
energy for photosynthesis. These pigments are contained inside the thylakoids (disk-like
structures inside the grana of chloroplasts) of chloroplasts, which are structures that
drive photosynthesis.
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The gathered light is able to excite the electrons at the reaction centers,
photosystem I (PSI) and photosystem II (PSII). Each of these reaction centers
have a specific type of chlorophyll that absorbs a particular wavelength of light.
Within chloroplasts is a fluid-filled region called the stroma. Within the stroma are
stacks of thylakoids (referred to as grana), which contain chlorophyll and drive
photosynthesis.
Cellular Respiration
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Cellular Respiration is the process in which chemical energy is converted to ATP, and C6H12O6 +
O2 is converted into CO2 + H2O. There are two types of respiration, aerobic and anaerobic.
○ Aerobic respiration (oxygen included) is the most common and is divided into 4 stages:
glycolysis, formation of Acetyl-CoA, Krebs Cycle, and oxidative phosphorylation.
○ Glycolysis is the splitting of glucose into 2, three carbon molecules called pyruvic acid.
○ The Formation of Acetyl-CoA involves the conversion of the pyruvic acids from
glycolysis into acetyl-coenzyme A (Acetyl-CoA) in the mitochondria and the release of
CO2.
○ Krebs Cycle involves acetyl-CoA combining with oxaloacetate (4 carbon molecules
from citric acid). With each cycle, 3 types of energies are produced: 1 ATP, 3 NADH,
and 1 FADH2.
○ Oxidative phosphorylation involves the carrying of electrons from NADH to O2 via the
electron transport chain to produce H2O. As electrons are passed down the change,
hydrogen ions are pumped across the inner mitochondrial membrane, forming a proton
gradient that acts as potential energy responsible for ATP production.
○ Anaerobic respiration (oxygen not included) functions similar to aerobic respiration,
but lactic acid is produced and oxidative phosphorylation doesn’t occur.
UNIT 4 Cell Communication and Cell Cycle
Cell Communication
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Cells can receive signals through receptors, which are proteins on the surface of the interior of a
cell that grab ligands, which are the molecules that bind to receptors and act as signals.
○ Paracrine and Synaptic signaling are both forms of short-distance signaling. Paracrine
involves local regulator molecules secreted from one cell to others. Synaptic signaling
involves the secretion of neurotransmitter molecules as signals in the nervous system.
○ Endocrine signaling involves hormones traveling through the bloodstream (they move
directly through cells for plants) to target cells throughout the body.
○ Autocrine signaling involves a cell sending signals to itself.
There are three phases of cell communication: reception, transduction, and response:
○ Reception is the target cell’s detection of a ligand, occurring both internally or externally.
There are three major types of transmembrane receptors that receive signals:
■ G protein-coupled receptors are cell-surface transmembrane receptors that
work with the help of a G protein, which is a protein that binds the energy
containing molecule GTP. Their signaling systems are widespread and diverse in
function, and they generally activate a single signal transduction pathway.
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Receptor tyrosine kinases are protein kinases that catalyze the transfer of
phosphate groups from ATP to another protein. The binding of a ligand to an
RTK can activate many different transduction pathways/cellular responses.
■ Ion channel receptors contain a region that acts as a gate that opens/closes when
the receptor changes shape. They play a key role in the nervous system.
Transduction involves the changing of the receptor protein in order to move the signal
into/through the cell. The series of changes of molecules in transduction is called the
signal transduction pathway. After a receptor is activated, it will activate another
molecule, and molecules will keep activating until the final response occurs. At each step,
there is most often a shape change in the next protein to activate it, and this is caused by
phosphorylation (dephosphorylation will deactivate proteins).
■ Second messengers, non-protein/water-soluble parts of signal transduction, can
activate proteins throughout the cell that are affected by their concentration.
Response involves the signal triggering a specific response, which can be any number of
cellular responses, and can occur in the nucleus or cytoplasm. Many responses involve
transcription, and transcription factors will act as the final molecule in the signaling
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pathway to trigger the response in this case. The extent and specificity of response is
regulated in various ways:
■ Signal pathways generally amplify a cell’s response to a signaling event, and the
degree of amplification depends on the function of specific molecules in the
pathway.
■ Many steps of a multi step signal pathway provide control points at which a cell’s
response can be further regulated, allowing coordination with other signal
pathways.
■ Scaffolding proteins enhance the overall efficiency of a response by connecting
relay proteins to each other to pass signals faster.
■ The termination of the signal itself is crucial for the regulation of the response.
Feedback
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Homeostasis is the tendency for something to resist change for the sake of maintaining a stable,
relatively constant internal environment. It is maintained through negative feedback loops,
which are processes that counteract changes of various properties from their target values.
○ There are usually two negative feedback loops per homeostatic circuit: one for if the
level of a certain property rises above the normal amount, and the other for if the level of
a certain property falls below the normal amount.
Positive feedback loops function oppositely from negative feedback loops, as they amplify the
stimulus of the starting signal rather than oppose it.
Cell Cycle
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The cell cycle is the life of a cell from the time it is formed until its division.
The cell cycle for eukaryotes is split into 3 main phases, Interphase, Mitosis, and Cytokinesis:
Interphase is the longest portion of the cell cycle and includes G1 phase, S phase, and G2 phase.
The cell grows by producing proteins and organelles throughout all 3 of these phases, and
chromosomes are duplicated to form 2 sister chromatids in the nucleus.
Mitosis is broken down into prophase, prometaphase, metaphase, anaphase, and telophase.
Each of these phases have specific functions for duplication of the cell.
○ Prophase involves the disappearance of the nucleoli, the start of the formation of the
mitotic spindle, and centrosomes will move away from each other.
○ Prometaphase involves kinetochores, specialized protein structures, forming at the
centromeres of chromatids, and microtubules will attach to them to begin their alignment.
○ Metaphase involves the chromosomes reaching alignment down the middle of the cell,
and the centrosomes reaching opposite ends of the cell.
○ Anaphase involves proteins cleaving the chromatids, and the now split chromosomes
being moved towards opposite ends of the cell as the microtubules holding them shorten.
○ Telophase involves the formation of 2 separate nuclei and the disassembly of the
remaining spindle fibers.
Cytokinesis involves the cytoplasm dividing, which forms the two cells.
Prokaryotes divide through binary fission, where they grow and divide without mitosis.
Three important checkpoints in the cell cycle occur in the G1, G2, and M (mitotic) phases to make
sure that the cell cycle is functioning properly.
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UNIT 5 Heredity
Meiosis
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A life cycle is the generation-to-generation sequence of stages in the reproductive history of an
organism, from its conception to the production of its offspring.
○ Sexual reproduction occurs through gametes, specialized cells in the ovaries and testes of
female and male organisms respectively (egg and sperm)
■ Gametes are haploid, as they contain a single set of chromosomes (23
chromosomes for humans).
■ A zygote is the resulting diploid cell formed from the merging of gametes in
fertilization.
○ Somatic cells are all other cells, which aren’t involved in sexual reproduction. Somatic
cells contain a set amount of chromosomes depending on the organism they belong to.
■ Somatic cells are diploid, as they contain 2 sets of chromosomes (46 total, 23
sets for humans).
■ Two chromosomes of a pair have the same length, centromere position, and
staining pattern, and they are called homologous chromosomes (homologs).
Each homolog has genes controlling the same inherited characteristics.
Meiosis is a special form of cell division that forms haploid gametes, so the resulting offspring
zygote will have the correct amount of chromosomes, with half from each parent. The duplication
of chromosomes in meiosis occurs in two phases, meiosis I and meiosis II.
○ Meiosis I: Prophase I - the mitotic spindle starts to form, centromeres move away from
each other, and crossing over of the chromosomes occurs (when chromosomes of
homologous pairs trade genes)
○ Metaphase I - pairs of homologous chromosomes (tetrads) are arranged down the center
of the cell.
○ Anaphase I - proteins cleave the homologous pairs and the now split homologs are
moved towards opposite ends of the cell as the microtubules holding them shorten
○ Telophase I - Each half of the cell will contain a haploid set of duplicated chromosomes
composed of two sister chromatids.
○ Meiosis II: Prophase II - the mitotic spindle will begin to form again, and chromosomes
will start to move towards the metaphase plate via spindle fibers
○ Metaphase II - the chromosomes get arranged along the metaphase plate, and the
kinetochores of the sister chromatids will be attached to the microtubules
○ Anaphase II - proteins cleave the chromatids and they move to opposite ends of the cell
○ Telophase II - the nuclei will form, the chromosomes will start decondensing, and the
two haploid cells split to form two more haploid cells
Genetic Diversity
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Heredity is the transmission of traits from one generation to the next through inheritance.
Genes are hereditary units that contain coded information, which program specific traits that
emerge as offspring develop. They can come in different variations of a single gene, known as
alleles.
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Independent assortment adds to variation, and it is the process of the first meiotic division
resulting in homologous pairs that sort their homologs into daughter cells independently of other
pairs.
Mendelian Genetics
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A genotype is an organism’s genetic makeup (allele pairing), while a phenotype is the
observable trait from the genotype.
○ If an organism has identical alleles for a gene, that allele will be present in all its gametes,
and the organism is homozygous for that specific gene. If an organism has different
alleles for a gene, half its gametes will receive the dominant allele and the other half will
receive the recessive allele, making the organism heterozygous for that specific gene.
○ Punnett squares are capable of illustrating the genotype combinations of gametes.
Mendel formed three key laws of genetics: the Law of Dominance, Law of Segregation, and
Law of Independent Assortment:
○ Law of Dominance - When a dominant and recessive trait are bred, the dominant allele
will mask the presences of the recessive allele.
○ Law of Segregation - Each gamete receives only one copy of the two copies of a gene.
○ Law of Independent Assortment - Each pair of alleles segregate independently of any
other pair of alleles during gamete formation.
Punnett squares are capable of illustrating the genotype combinations of gametes.
There are two basic probability laws to help predict the outcome of gamete fertilization:
○ The multiplication rule states that to determine the probability of multiple events
occurring, the probability of one event occurring is multiplied by the probability of
another event (and = multiplication).
○ The addition rule states that the probability that any one of two or more mutually
exclusive events will occur is calculated by adding their individual probabilities (or =
multiplication).
Inheritance patterns that are exceptions to the rules of Mendelian Genetics include: polygenic
inheritance, genomic imprinting, and extranuclear genes:
Non-Mendelian Genetics
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Incomplete dominance occurs when neither trait in a cross is dominant, and thus the resulting
offspring will have a blend of the traits.
Codominance occurs when both traits are expressed simultaneously (different from incomplete).
Multiple alleles is a situation in which there are more than two alleles that form a gene, such as
in human blood type.
Linked genes are genes located on the same chromosome. They do not segregate independently.
Environmental Effects on Phenotype
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Phenotypic plasticity is the ability of a genotype to express different phenotypes due to the
environment.
○ Temperature, pH, nutrition, disease, seasonal changes, etc. are all environmental factors
that can affect the phenotype of some organisms/genes.
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Chromosomal Inheritance
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Of the 46 chromosomes in humans, 44 are autosome (22 pairs) and 2 (1 pair) are sex
chromosomes (X and Y).
○ Females (XX) will inherit two copies of the sex-linked genes (X chromosome).
○ Males (XY) inherit only one copy of the sex linked gene.
A pedigree is a family tree that indicates the phenotype of one trait being studied for every
member of a family.
Mutations are any changes in the genome and there are two types of mutations:
○ Gene mutations are caused by a change in the DNA sequence.
○ Chromosome mutations occur during meiosis, such as if homologous chromosomes fail
to separate as they should.
UNIT 6 Gene Expression and Regulation
DNA and RNA Structure
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DNA and RNA are nucleic acids that enable organisms to reproduce/replicate their components
from one generation to the next.
○ DNA and RNA consist of nucleotides, which are composed of : a 5-carbon sugar, a
nitrogenous base, and 1-3 phosphate groups.
○ Each nitrogenous base has one or two rings that include nitrogen atoms, and the number
of rings depends on the category of nitrogenous base:
■ Pyrimidines have one six-membered ring of carbon and nitrogen and include:
cytosine, thymine, and uracil.
■ Purines have a larger, six-membered ring fused to a five-membered ring and
include: adenine and guanine.
Phosphodiester bonds are formed to link the nucleotides themselves, or more specifically the
sugars, while hydrogen bonds link the DNA double-helix strands.
Replication
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Before DNA replication starts, the two strands of a double helix will separate so that each strand
can serve as a template for the formation of a complementary chain, duplicating exactly the
sequence of base pairs on the original helix.
Origins of replication are short stretches of a specific sequence of nucleotides on DNA where
replication starts.
○ A replication fork (Y-shaped region where parental strands of DNA are being unwound)
is at each end of the replication bubble.
○ Helicases are enzymes that untwist the double helix at the replication forks and separate
the two parental DNA strands.
○ Single-strand binding proteins bind to the unpaired DNA strands to prevent them from
re-pairing with each other.
○ Topoisomerase is an enzyme that helps relieve the strain ahead of the replication fork.
○ An RNA primer is set in place by primase to act as the start point for the new strand of
DNA.
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DNA polymerases are enzymes that catalyze the synthesis of new DNA through the
addition of nucleotides to the 3′ end of the new DNA strand. They can only add to the 3′
end of a strand, so two “types” of strands will form:
■ The leading strand is the strand that runs from 5′ to 3′, so DNA polymerase III
can stay in the replication fork and continuously add nucleotides to the strand.
■ The lagging strand is the strand that runs from 3′ to 5′, and since DNA
polymerase III can’t add to the 5′ end, it is synthesized in a series of segments
known as okazaki fragments.
● After a DNA polymerase III forms an okazaki fragment DNA
polymerase I replaces the RNA nucleotides of the adjacent primer with
DNA nucleotides. This allows DNA ligase to join the sugar-phosphate
backbones of the okazaki fragments into a continuous DNA strand.
○ Eukaryotic chromosomal DNA molecules have telomeres at their ends, which are special
nucleotide sequences within genes that postpone the erosion of genes on the end of DNA
molecules.
During replication, DNA polymerases “proofread” each new nucleotide according to its
complementary nucleotide on the template strand and remove incorrectly paired nucleotides upon
finding any.
Transcription
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There are four main types of RNA:
○ Messenger RNA (mRNA) - Temporary RNA version of DNA which gets sent to a
ribosome
○ Ribosomal RNA (rRNA) - Produced in the nucleolus and makes up part of ribosomes
○ Transfer RNA (tRNA) - Transports amino acids to ribosomes, and is responsible for
making the amino acid chain
○ Interfering RNA (RNAi) - Small segments of RNA that are made in the body which can
bind to RNA and mark it for destruction
Transcription involves creating an RNA strand from a section of DNA.
○ Transcription begins at promoters and only one strand needs to be copied as RNA is
single-stranded. The strand that serves as a template is called the template strand
(non-coding strand).
○ The other DNA strand, which the new RNA strand will be a replication of (minus uracil
replacing thymine), is referred to as the coding strand.
○ RNA polymerase builds the RNA, similar to how DNA polymerase builds DNA. Once it
finishes, it separates from the DNA template.
For prokaryotes at this point, mRNA is finished. For eukaryotes, the RNA needs to be processed.
This is done through the removal (splicing) in introns, which are non-protein coding sections of
the RNA (exons are coding sections).
Translation
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Translation is the process of turning mRNA into a protein, which is composed of an amino acid
chain. Translation occurs on ribosomes.
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The flow of information from gene to protein is based on a triplet code, where the
genetic information for the formation of a polypeptide chain is written in the DNA as a
series of sets of three-nucleotides referred to as a codon. All but three codons match an
amino acid, with the three exceptions acting as “stop-signals” in the formation of the
amino acid chain.
The series of codons along an mRNA molecule is translated by separate, transfer RNA (tRNA),
which transfer amino acids from the cytoplasm to a polypeptide chain in a ribosome. Accurate
translation requires two key processes:
○ The tRNA that binds to an mRNA codon specifying a particular amino acid must carry
that amino acid to the ribosome.
○ The tRNA anticodon (a particular nucleotide triplet that base-pairs to a specific mRNA
codon) must pair with the appropriate mRNA codon.
Ribosomes (site of translation) consist of mRNA binding sites, and 3 binding sites for tRNA:
○ The P site holds the tRNA carrying the growing polypeptide chain.
○ The A site holds the tRNA carrying the next amino acid to be added to the chain.
○ The E site serves as the exit site for tRNAs that have added their amino acid to the chain.
Translation can be divided into three stages: initiation, elongation, and termination:
○ Initiation - The start codon (AUG) established the codon reading frame for mRNA, and a
small ribosomal subunit binds to the mRNA and specific initiator tRNA. After the tRNA
binds to the start codon, a large ribosomal subunit gets attached to the smaller one. The
tRNA will sit in the P site of the large ribosomal subunit until a new tRNA fills the A
site, adds its amino acid to the chain, and moves to the P site.
○ Elongation - The amino acid chain will continue to grow, and each addition of an amino
acid involves several proteins (elongation factors). The process of adding an amino acid
occurs in a 3-step cycle:
■ Codon recognition - The anticodon of an incoming tRNA will base-pair with the
complementary mRNA codon in the A site.
■ Peptide bond formation - An rRNA molecule of the large subunit will catalyze
the formation of a peptide bond between the new amino acid and the one on the
chain, shifting the chain from the tRNA in the P site to the tRNA in the A site.
■ Translocation - At the same time the ribosome moves the tRNA in the A site to
the P site, the previous tRNA in the P site is moved to the E site and released.
○ Termination - Elongation continues until a stop codon on the mRNA reaches the A site,
at which point a protein release factor breaks the bond between the tRNA and the amino
acid chain, releasing it.
Regulation of Gene Expression
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Regulation of gene expression allows an organism to express only certain genes.
Operons help with the transcription process by regulating access and expression of genes. They
consist of four parts: structural genes, promoter gene, operator, and regulatory gene.
○ Structural genes code for required enzymes, which will be transcribed to produce
particular enzymes.
○ The promoter gene is the region where RNA polymerase binds to initiate transcription.
○ The operator is the region that controls whether transcription will occur by a repressor.
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○
Regulatory genes code for regulatory proteins called repressors that attach to the
operator and block transcription.
Mutations
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Mutations are errors in genetic code, and there are two types of mutations: point mutations and
gene rearrangements:
○ Point mutations include three separate types of mutations:
■ Nonsense mutations - Cause the original codon to become a stop codon which
results in a preemptive termination of protein synthesis
■ Missense mutations - Cause the original codon to produce a different amino acid
■ Silent mutations - Occur when a codon that codes for an amino acid is replaced
by another codon that also codes for the same amino acid
○ Gene rearrangements involve DNA sequences that have: frameshift mutation,
duplications, inversions, translocations, and transposons.
■ Frameshift mutations - Occur when insertions or deletions of nucleotides
result in the elongation or shortening of a DNA or gene
■ Duplication - Includes an extra copy of genes due to unequal crossing during
meiosis or chromosome rearrangements.
■ Inversions - Result when the orientation of a segment of gene / DNA flips
■ Translocations - Result when different chromosomes break and rejoin that
results in a different chromosome by the amount of DNA sequence that is lost,
repeated or interrupted
■ Transposons - Gene segments that can cut and paste themselves throughout the
genome, they can interrupt a gene
UNIT 7 Natural Selection
Natural Selection
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Charles Darwin based his theory of evolution on three key observations:
○ That individuals in a population vary in their traits, and many of those traits seem to be
heritable.
○ That a population can produce more offspring than can survive to reproduce. The large
amount of offspring a population produces causes inevitable competition, thus many of
the offspring are unable to acquire the resources they need to survive.
○ That species are generally suited to their environments, and thus are adapted to the
circumstances their environment entails.
The theory of natural selection states that individuals with inherited traits that are more
advantageous to the environment are more likely to survive and reproduce than individuals who
lack those traits.
○ Darwin’s “descent with modification” theory proposed that natural selection could cause
an ancestral species to give rise to two or more descendent species over long periods of
time (the idea that all organisms stemmed from one common ancestor).
○ Adaptations are inherited characteristics of organisms that improve their chances
of survival and reproduction in specific environments.
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○ There are three key limits of natural selection:
■ Natural selection doesn’t favor the most ideal phenotype to exist for an
individual in a specific environment, it will only favor the best phenotype
available.
■ Individuals may gain an advantage in one area due to a specific trait, but
that same trait may cause a disadvantage in another area.
■ Chance events, such as natural disasters, storms, etc. can force individuals
to be moved to a new environment, which their traits may not be suitable
for.
Population Genetics
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Natural selection can alter the distribution of heritable traits in three main ways:
○ Directional selection occurs when conditions favor individuals that exhibit one extreme
of a phenotypic range.
○ Disruptive selection occurs when conditions favor individuals exhibiting either of the
two extremes of a phenotypic range.
○ Stabilizing selection occurs when conditions favor individuals with intermediate
phenotypes.
Natural selections influence on allele frequency is related to sexual selection, which is a process
in which individuals with certain inherited traits are more likely to find mates than other
individuals of the same sex. Sexual selection functions in two key ways:
○ Intrasexual selection involves individuals of one sex competing directly for mates.
○ Intersexual selection involves individuals of one sex choosing their mates based off
appearance, behavior, etc.
Balancing selection is also a sub-sect of natural selection that alters allele frequencies, and it is
comprised of two main factors:
○ Frequency-dependent selection involves the ‘fitness’ of a phenotype (how much it helps
an individual survive and reproduce) being dependent on how common that phenotype is
in a population.
○ Heterozygote advantage occurs when individuals who are heterozygous at a particular
locus (portion of a chromosome that a particular gene is located on) have greater fitness
than both kinds of homozygotes.
Genetic drift, a process in which chance events can cause allele frequencies to fluctuate
unpredictably from one generation to the next, can be seen in two key ways:
○ The founder effect is the result of a small number of individuals becoming isolated from
a larger population, and that smaller group establishing a new population whose gene
pool differs from the source population.
○ The bottleneck effect is the result of a sudden change in the environment, such as a
natural disaster, causing a drastic reduction in the size of a population.
Gene flow, the transfer of alleles into or out of a population due to the movement of fertile
individuals (or their gametes), also affects allele frequencies.
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Hardy-Weinberg Equilibrium
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The Hardy-Weinberg Equilibrium (a2 + 2ab + b2 = 1) describes a population where the allele
and genotype frequencies remain constant from generation to generation. It can only be reached if
there are: no mutations, random mating, no natural selection, a large population size, and no gene
flow.
Common Ancestry
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Modern day scientists use a system based on DNA analysis that reflects evolutionary history to
classify organisms, referred to as the three-domain system. It classifies all life into 3 domains:
○ Bacteria - They make up all single-celled prokaryotes with no internal membranes, and
they play a vital role as decomposers, in genetic engineering, and some can carry out
photosynthesis. They also have a thick, rigid cell wall containing peptidoglycan. They
include: blue-green algae, bacteria like E. coli, bacteria necessary in the nitrogen cycle,
and viruses.
○ Archaea - They are unicellular prokaryotes and include extremophiles (organisms that
live in extreme temperatures) such as methanogens (produce methane from hydrogen),
halophiles (thrive in environments with high salt concentrations), and thermophiles
(thrive in high-temperature areas).
○ Eukarya - They have a nucleus and internal organelles, and are made up of four
kingdoms: Protista, Fungi, Plantae, and Animalia
There are a series of speculated evolutionary trends in animals:
○ Specialization of tissues - Animals contain cells, tissues (group of similar cells that
perform a particular function), and organs (group of tissues that work together to perform
related functions).
○ Germ layers - Germ layers are the main layers that form various tissues and organs of
the body, and they are formed early in embryonic development as a result of gastrulation.
Complex animals are triploblastic, meaning they contain an ectoderm (outer layer; skin
and nervous system), mesoderm (middle layer; blood and bones), and endoderm (inner
layer, viscera or digestive system).
○ Bilateral symmetry - Sophisticated animals exhibit bilateral symmetry, where the body
is organized along a longitudinal axis with right and left sides that mirror each other.
○ Cephalization - Animals with bilateral symmetry also have cephalization, where there is
a defined “front end” (anterior) and “rear end” (posterior). The sensory apparatus and
brain are clustered near the anterior, while the digestive, excretory, and reproductive
systems are located at the posterior.
Continuing Evolution
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Evolution is theorized to be constantly occurring, and the evolution of a species is classified into
five patterns:
○ Divergent - Occurs when a population becomes isolated from the rest of the species, and
is exposed to new selective pressures, causing it to evolve into a new species.
○ Convergent - Occurs when unrelated species occupy the same environment, are
subjected to similar selective pressures, and show similar adaptations.
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Parallel - Describes two related species that have made similar evolutionary adaptations
after their divergence from a common ancestor.
○ Coevolution - Describes the reciprocal evolutionary set of adaptations of two interacting
species. (Ex: predator-prey relationships).
○ Adaptive Radiation - Describes the emergence of numerous species from a common
ancestor introduced into an environment (Ex: emergence of 14 separate species of
Galapagos Island finches).
The modern theory of evolution is the Punctuated Equilibrium, proposing that new species appear
suddenly after long periods of stasis (replaced the gradualism theory, which couldn’t be backed
up by fossil records).
Phylogeny
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Phylogeny is the evolutionary history of the theorized descendents of all living organisms from a
common ancestor. A cladogram is a diagrammatic reconstruction of this, and they begin with a
common ancestor, and branch out.
○ Each branch of a cladogram starts with a point referred to as a common ancestor node,
which represents the point when species split into two paths.
Speciation
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Speciation is anything that fragments a population and isolates groups of individuals/genes.
Speciation is separated into two types:
○ Allopatric Speciation - Caused by geographic isolation (separation by landforms that
cause two populations to be unable to interbreed).
○ Sympatric Speciation - Non geographic isolation: polyploidy (a cell has more than two
complete sets of chromosomes), habitat isolation (two organisms live in the same area
but rarely encounter each other), behavioral isolation (mating behaviors/mates are
detected and chosen), temporal isolation (time differences in mating cycles), and
reproductive (closely related species may be unable to mate).
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