AP Biology

Unit 1 - Chemistry of Life

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Key Terms:
● Solvent: able to dissolve other substances.
● Solute: the minor component in a solution, dissolved in the solvent.
● Polar: when electrons are not evenly distributed in a covalent bond
● Non-Polar: when electrons are evenly distributed in a covalent bond
● Cohesion: attraction that occurs between identical molecules
● Adhesion: attraction that occurs between molecules of different substances.
● Specific heat: the heat needed in order to raise the temperature of the unit mass of
a given substance by a given amount (usually one degree).
● Density: calculated by dividing the mass of a substance by its volume
● Heat of Vaporization: The amount of energy needed to change one gram of a
liquid substance to a gas at constant temperature.
● Macromolecules: A large molecule composed of many smaller molecules

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1. Structure of water and hydrogen bonding:
● Water: a “universal solvent” due to its ability to dissolve many solutes
● Properties of water:
o cohesion, ability of adhesion, being a “universal solvent”, the solid being
less dense than the liquid, having a high specific heat, and having a high
boiling point (212 degrees Fahrenheit, 100 degrees Celsius), and surface
tension.
● Hydrogen bond: weak chemical bond
o Formed when partial charges resulting from polar molecules attract/are
attracted to each other
o Example: cohesion between water molecules are a result of hydrogen
bonds
● Water has a high vaporization temperature.
o Evaporative Cooling: when humans sweat, the water absorbs the body’s
excess heat and then evaporates, cooling the body
● Water molecules form hydrogen bonds between each other, forming a strong
lattice structure. The result is high surface tension.
● Water has a bent or V-Shaped figure because of its polarity.

2. Elements of life:
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● Living system: Open systems that take in raw materials, use certain parts of the
system, and then proceed to release waste
● Energy: The ability to do work or cause change
● Constant input of energy: necessary to maintain the complicated organization of a
system.
● Matter: Anything that has mass and takes up space.
● Examples of Macromolecules: Carbohydrates, Lipids, Proteins, and Nucleic acids.
● Atoms: matters building blocks or basic units
● Exchange of matter between the environment and organisms allows organisms to
grow, reproduce, and retain organization.
● Carbon: backbone of most, but not all, biological macromolecules.
● Nitrogen: A necessary atom in proteins and nucleic Acids, but not in
carbohydrates and lipids.
● Taxonomy:
o biological branch of study that classifies species, establishes the ordering
of species into groups based on the characteristics they share.
● Levels of Taxonomy (most to least inclusive):
1. Domain -- Dear
2. Kingdom -- King
3. Phylum -- Phillip
4. Class – Came
5. Order – Over
6. Family -- For
7. Genus -- Good
8. Species -- Soup
● Bacteria, Archaea, and Eukarya: Differences
o Bacteria: Prokaryotic
o Archaea: Prokaryotic
o Eukarya: Eukaryotic, 3 groups (Animalia, Fungi, Plantae), includes
protists
● Darwin’s two main ideas:

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 o "Descent with modification"
o "Natural Selection" - Those who are the most fit and apt have a higher
chance of survival and passing on the good genes to their offspring.
● Darwin’s Observations
o Individuals have a variety of traits in themselves and between themselves,
with many passed on through offspring
o Competition is unavoidable because offspring are constantly being created
and are in need for resources
o Species adapt to have advantage within the population and to have better
access to the limited resource pool
● “Edits:
o "Edit”: metaphor for natural selection; natural selection cuts out or edits
out the unnecessary or disadvantageous traits, as beings with those traits
are less likely to survive and reproduce
● Common ancestry and natural selection:
o First common ancestor or "prototype”is marked as the beginning of all
life. All life began from an ancestor, so we are united, but natural selection
has changed life throughout time through adaptation and “edits”

3. Introduction to Biological Macromolecules:

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 ● Hierarchy: organizes interacting biological levels of structures
● Monomer: simple compound or molecule that is joined with other molecules to
produce polymers.
● Polymer: large and complex compound that is composed of combined smaller
compounds, or monomers.
● Hydrolysis: process where a molecule is split through the addition of water
● Dehydration synthesis: Condensation reaction where molecules are joined
together by the removal of water

4. Properties of Biological Molecules:

● Protein: A three-dimensional polymer made of conjoined amino acids.
● Amino Acids: Building blocks of proteins.
● Carbohydrate: composed of carbon, hydrogen, and oxygen atoms
o Acts as a major source of short term energy for the body
o Monosaccharides: Building blocks of carbohydrates.
● Lipids (fats):Composed of long carbon chains
o Often used in the body through insulation and long term energy (energy
storage)
o Fatty acids: chains of carbon that build most lipids.
o Glycerol: A three- carbon alcohol that covalently bonds to fatty acids,
forming oils and fats (lipids)
● Nucleic acids: contain hydrogen, oxygen, nitrogen, carbon, and phosphorus
o Nucleotides: Building blocks of nucleic acids.
o Five-Carbon Sugar: part of nucleotides
▪ Deoxyribose: A Five-Carbon sugar that is a component of DNA
nucleotides.
▪ Ribose: A Five-Carbon sugar present in RNA.
o Phosphate: part of of nucleotides, connected to the five-carbon-sugar’s 5’
end
o Nitrogen base: part of a nucleotide. Includes adenine, guanine, cytosine,
thymine, or uracil; attached to the five-carbon-sugar’s 1’ end

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 ● Polypeptide: a large protein macromolecule whose conjoined amino acids are held
together by peptide bonds.
● Primary structure: The first level of a protein structure; linear sequence of amino
acids
o Amino (or N-) terminus: The end of the protein chain that has an exposed
amino group (-NH2).
o Carboxyl (or C-) terminus: The end of the protein chain that has an
exposed carboxylic acid group (-COOH).
o R group (side chain): Part of amino acid that determines the molecule’s
physical and chemical properties.
▪ R group properties: Non-polar, polar, acidic, basic, or ionic.
● Polysaccharides: complex carbohydrates made of sugar monomers.
o Examples: Starch, glycogen, cellulose
● Lipid properties:
-Do not form polymers,
-Water fearing or hydrophobic
-Fatty acids are long non polar hydrocarbon chains with an acid group at the
end
● Saturated fats: A fat that is solid at room temperature; hydrogens are saturated, or
the carbons are all connected with single bonds
o Examples: animal fats, lards, and dairy products.
● Unsaturated fats: contain at least one double bond resulting in a kink in structure.
o Cannot pack in an organized manner, and thus they are liquid at room
temperature. these are often found in plants and fish
● Phospholipids: composed of two fatty acids, plus hydrophilic phosphate, and
glycerol.
o They play a role in cell membranes

5. Structure and Function of Biological Macromolecules:

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 ● Structure: The directionality and order of subcomponents (monomers) in a
macromolecule (polymer)
o Form = function
● 5’ end and 3’ end: 5’ end – has a 5’ carbon attached to a phosphate. 3’ end – has a
3’ carbon attached to the next nucleotide in the linear chain of DNA or RNA.
● Anti-parallel: Separate strands that run in opposite directions.
● Adenine: The nucleotide that is bonded by hydrogen bonds to the nucleotide
thymine in DNA using (two hydrogen bonds).
● Thymine: The nucleotide that is bonded by hydrogen bonds to the nucleotide
adenine in DNA (using two hydrogen bonds).
● Cytosine: The nucleotide that is bonded by hydrogen bonds to the nucleotide
guanine in DNA (using three hydrogen bonds).
● Guanine: The nucleotide that is bonded by hydrogen bonds to the nucleotide
cytosine in DNA (using three hydrogen bonds).
● Growing polypeptide chain: Linear chains of amino acids formed by creating
covalent bonds at the carboxyl terminus.
● Primary structure of protein: The amino acid sequence.
● Secondary structure of protein: local folding and twisting of amino acid chains
into elements such as alpha-helices and beta-sheets.
o Alpha-helix: spiral shape
o Beta-sheet: side by side folding of amino acids with each other through
hydrogen bonds
● Tertiary structure of proteins: 3-D structure; formed through hydrophobic and
hydrophilic interactions between far off regions in the polypeptide (not local).
Shape aims to minimize the free energy
o Hydrogen bonds, disulfide bonds, ionic bonds, other interactions
● Quaternary structure of proteins: conjoining of multiple polypeptides.
● Carbohydrate structure: made of linear chains of monomers, connected through
covalent bonds

6. Nucleic Acids:

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● Nucleic acids: formed through the conjoin of nucleotide monomers
● Nucleotides: a nucleic acid monomer, contains 3 parts
o Nitrogenous base, pentose sugar, phosphate group.
▪ Pentose: Ribose (ribonucleotides) or 2-prime-deoxyribose
(deoxyribonucleotides).
▪ Phosphate: Phosphorous attaches to the nitrogenous base.
● Nucleic acids hold genetic info
● Nitrogenous bases: A, C, T, G, U.
● Complementary bases: A and T, C and G
o These will always pair together in DNA structure
● Purines: large nitrogenous bases A and G.
● Pyrimidines: small nitrogenous bases T, C (U replaces T for RNA)

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 AP Biology
Unit 2 - Cell Structure and Function
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1. Cell Structure: SubCellular Components:

● Cell: Smallest unit of living organism.
● Membrane: fluid phospholipid bilayer with integrated proteins.
o The rate at which a molecule diffuses across a lipid bilayer depends on its
electric charge and size.
o Membrane works as a selectively permeable barrier, cel subdivision and
compartmentalization
● Chemistry of the membrane: consists of lipids, protein and carbohydrate
● Membrane Structure: Asymmetric and fluid
● Nucleus: eukaryotic membrane-enclosed organelle, acts as the control center for
cells
o Nuclear envelope: envelopes the nucleus, and is continuous with the
membrane of the RER; dotted with ribosomes.
o Nuclear Pores: responsible for molecular transport through nuclear
envelope
o Fibrous Lamina: inner surface of nuclear membrane.
● Fibrous Lamina Function: Maintain nuclear stability, organize chromatin, bind
nuclear pore, complexes and important cellular vents like DNA replication & cell
division
● Nucleus: DNA and histones.
o Euchromatin
o Heterochromatin
● Free ribosomes: synthesize or make cytoplasmic proteins
● Smooth Endoplasmic Reticulum: Endoplasmic reticulum without attached
ribosomes. Differs from RER both structurally and functionally, in the form of
tubes arranged neatly in parallel rows or in a tangle.

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● Functions of SER: Biosynthesis of steroids (testis), Drug Detox (liver), Ca
pumping ( muscle ), Sequestration
● Golgi Apparatus: Attaches sugar to the protein= glycoproteins. Condenses the
protein and packages them into membrane bound secretion granules. Has 2 faces-
concave and forming.
● Lysosomes: Digests waste inside the cell by digesting internal cellular debris
(autophagy). Created in ER and packaged in Golgi apparatus
o Lysosomal Enzyme Deficiencies: Pompe, Tay-Sach, & Danon.
● Peroxisomes: Bounded by a single permeable membrane with a crystalline core.
Catalase. Breakdown of H2O2 (hydrogen peroxide). Involved in cholesterol
biosynthesis.
● Mitochondria: Production of ATP, Cell signaling, Cell differentiation, Apoptosis.
● Mitochondria Structure: 2 concentric membrane-bounded spaces.
● Intermediate filaments: Provide mechanical support & strength. Ex: lamina,
keratin, desmin, vimentin, neurofilaments.
o Microfilaments (Actin filaments): 2 stranded helical polymers.
▪ Relate to cell mobility, organelle transport and contraction.
o Myosin filaments: Differ in cell distribution & function: contraction,
vesicular transport.
o Microtubules: Widest filaments in the cell. Found in most cells, especially
near the cell center.
● Microtubules (Flagella & cilia): Central pair & 9 outer doublet microtubules.
Interaction with ATPase dynein & ATP in the transduction of chemical energy.
● Microtubules (Mitotic Apparatus): Mitotic spindle/ spindle fibers.
● Microtubules: Cytoskeletal. Microtubules are positioned in a way that stiffens or
supports the cytoplasm.
● Microtubules (Saltatory Movements): They make these movements that start
abruptly. The mechanism seems to be along microtubules tracts.
● Centriole: Non Membrane organelle which exists in pairs in each cell.
Play a role in establishing cell polarity and the spindle during cell division.
● Glycogen: Highly branched polymer of D-glucose.

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 o Function of glycogen: Carbohydrate energy store
● Function of lipid droplets: Storage of triglycerides
● Distribution of lipid droplets: Adipose (Fat cells), quantity varies with metabolic
state.
● Mitosis & Meiosis Cell Cycle: process of cell division, has stages:
○ G1: Rapidly synthesize RNA & protein, enlarging their nuclei and
cytoplasm from the last cell division.
○ G2: Cells with polytene chromosomes & polyploid cells (mammalian liver
cells), remain in this period indefinitely.
● Chromosome: Highly condensed chromatin.
○ Humans have 46
● Mitosis Stages
○ Prophase: Nucleolus disappears as centrioles begin to divide and move to
opposite sides of the cell
○ Metaphase: Chromosomes align themselves in a plane called metaphase
plate. Homologous chromosomes do not line up side by side.
○ Anaphase: The centromeres holding the sister chromatids split in half, and
each one is now called a daughter chromosome.
○ Telophase: Process of uncoiling all chromosomes and reforming nuclear
envelopes.
● Meiosis: going from diploid to haploid
○ Synaptonemal complexes: Sites in pairing between 2 homologous
chromosomes.
○ Metaphase 1/Anaphase 1: Same as in mitosis, except that the homologous
chromosomes pair up side by side
○ Metaphase II/ Anaphase II: Each bivalent splits producing 2 sister
chromatids. None of the daughter cells have identical sets of
chromosomes.
○ Down Syndrome: common condition that results from meiotic
abnormalities in humans, trisomy 21
● Genetic diversity:

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 ○ crossing over (recombination) between homologous chromosomes
○ random separation of homologous chromosomes
● Structure of the biological membrane:
○ Globular proteins are suspended and laterally mobile (fluid-mosaic model)
The membrane is asymmetric with carbohydrates located exclusively
outside of cells.
● Lysosome and disease:
○ When the cells are lysed or lysosomes fuse with plasma membrane, or
lysosomal leak out during phagocytosis, released enzymes harm
surrounding environment
○ Defective lysosomal genes: The substrate of this particular enzyme
accumulates in the cells, which causes lysis or dysfunction of the cells or
organs. When lysosomal fusion with phagosome is impaired, the
individual becomes very susceptible to various infectious diseases.

2. Cell Structure and Function:

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● Cell: basic unit of all living things
● Cell theory:
o All living organisms are composed of one or more cells.
o Cells are the basic unit of structure and organization of all living
organisms.
o Cells come from other living cells, passing down their genetic information
to their daughter cells.
● Compound light microscope: microscope composed of two or more lenses and
uses light to produce a magnified image; can magnify to a maximum of 1000x
● SEM: produces a 3-D image of the surface of the specimen
● TEM: electron microscope; uses electrons to show contrast of structures
● STM: scanning tunnel microscope; used to scan molecules such as DNA
● Components of the Cell
o Plasma membrane: boundary of the cell, controls entrance of molecules
o Organelles: specialized structures with specific functions
o Transport proteins: proteins tunnels that allow substances to get pass the
plasma membrane
o Cytoskeleton: network of fibers that maintain cell shape and provide an
anchor for the organelles; composed of microfilaments and microtubules
o Cytoplasm: a semi-fluid environment outside the nucleus
o Ribosome: organelle; manufactures proteins; made of protein and RNA
o Nucleolus: within the nucleus where ribosomes are made
o Endoplasmic reticulum (ER): system of folded sacs and conjoined
channels; where proteins and lipids are synthesized
o Golgi apparatus: flattened stack of membranes that modifies and packages
proteins into vesicles
o Vesicles: sacs that fuse with the plasma membrane to release proteins to
the environment outside the cell
o Vacuoles: organelle that acts as a storage center
o Lysosomes: digest excess or worn-out organelles and food particles
o Centrioles: groups of microtubules that function during cell division;

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 located in the cytoplasm of animal and protist cells
o Mitochondrion: converts food particles (mainly sugars) into usable
energy..
o Chloroplast: organelle that captures light energy and converts it to
chemical energy through photosynthesis
o Cell wall: thick, rigid, mesh of fibers that surrounds the outside of the
plasma membrane, protects and give support to the plant cell
o Cilia: short, hair-like projections that help in the movement of some cells
o Flagellum: long projection that helps in the movement of some cells
● Diffusion: net movement of particles from an area of high concentration to area of
lower concentration
● Brownian movement: random movement of particles
● Facilitated diffusion: transport proteins allow substances to move across the
plasma membrane without using any energy
● Osmosis: diffusion of water; important in maintaining homeostasis
o Isotonic solution: concentration of cell environment the same as on the
inside of the cell
o Hypotonic solution: solution that has a lower concentration of solutes than
inside the cell; cell will swell
o Hypertonic solution: solution that has a higher concentration of solutes
than inside the cell; cell will shrink
● Passive transport: cell transport that does not require a cell to use energy such as
diffusion or osmosis
● Active transport: cell transport that requires a cell to use energy such as
endocytosis or exocytosis
o Endocytosis: process where the cell surrounds a substance and pinches off
inside the cell; requires energy
o Exocytosis: secretion of materials at the plasma membrane and removes
substances from the cell; requires energy

3. Cell Size:

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 ● Small cells are more efficient
○ The surface area to volume ratio limits the size of a cell.
○ Cell size is limited because you need a rapid exchange of materials
between the environment and the cell for the cell to survive.
● The plasma/cell membrane is responsible for maintaining homeostasis
○ Regulates exchange of all materials
● The greater the distance materials must travel to reach their destinations
(organelles or exit the cell), the slower the rate.
○ The volume of a cell slows the rate of exchange
○ For the cell to be most efficient, a large surface area compared to the
volume is needed.
4. Plasma Membranes:
● Phospholipids are amphipathic which means they have a hydrophilic and a
hydrophobic region.
○ As temperature decreases, phospholipids pack together and solidify.
membranes can be fluid at a lower temp if they have phospholipids with
unsaturated hydrocarbon tails.
● Steroid cholesterol helps resist changes in fluidity
● Integral proteins penetrate the lipid bilayer
● Peripheral proteins are loosely bound to membrane
● Proteins are attached to cytoskeleton and fibers of ECM
● Transport protein provides a hydrophilic channel and shuttles substances, or
hydrolyzes (chemical breakdown) ATP
● Signal transduction: part of cellular communication
○ Cell to cell recognition: glycoproteins recognize other membrane proteins
○ Intercellular joining: membrane proteins that bind together in gap/tight
junctions
○ Cytoskeleton attaches to ECM: microfilaments non covalently bond to
membrane proteins for cell shape

● Permeability of lipid bilayer: nonpolar molecules cross easily, polar molecules

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 (who love water) pass slowly, ex ions
● Aquaporins: facilitate passage of water molecules
○ Involved in osmosis
● Channel proteins: holds onto passengers and changes shape to take them across
● Concentration gradient: substance diffuse from its higher concentration to lower
concentration areas
● Tonicity: ability of a solution to cause cells to lose or gain water.
● Osmoregulation: cells with no cell walls need this which is the control of solute
concentration and water balance
○ Turgid/flaccid: healthy state of plants where water intake by osmosis has
cell wall opposing further intake.
limp
○ Plasmolysis: when plant cell shrivels up and the plant wilts and the
membrane pulls away from cell wall
● ATP: energy molecules often involved in active transport of signal transduction
○ Sodium potassium pump: exchange of Na for K
○ Membrane potential: voltage (electrical potential energy) across the
membrane. cytoplasmic is neg to ECM
○ Electrochemical gradient: passive transport. chemical and electrical forces
push ions in and out of the cell. ions diffuse down its electrochemical
gradient
○ Electrogenic pump: a transport protein that makes voltage across the
membrane. It helps store energy.
● Proton pump: for plants, fungi, bacteria that transports proteins (H+)
● Cotransport: transport protein that does the downward diffusion of a solute and
upward of a 2nd substance against its concentration. H+ helps transport sucrose
● Bulk Transport: transport of large molecules
○ Exocytosis: fusion of vesicles with the plasma membrane. vesicle
membrane and membrane fuse. It’s used to export carbohydrates and
proteins
○ Endocytosis: cell takes in molecules to form vesicles from plasma

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 membrane
○ Phagocytosis: cell engulfs particle to be digested in food vacuoles
○ Pinocytosis: cell gulps extracellular fluid to form infoldings in plasma
membrane
○ Receptor mediated endocytosis: cell acquires bulk quantities of fluid
where proteins are exposed to it

5. Membrane permeability:

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 ● Small Hydrophobic Molecules: Pass through the membrane through simple
diffusion (Ex: O2, CO2, N2)
● Small Uncharged Polar Molecules: Small enough to slip through the membrane
(Ex: H2O, glycerol, ethanol)
● Large Uncharged Polar Molecules: Do not go through the Membrane!! (Ex:
Amino Acids, glucose, nucleotides)
● Ions: Do not go through the Membrane!! (Ex: H+, Na+, K+, Cl-, etc.)
6. Mechanisms of Transport:
● Energy in diffusion: does not require energy
○ The rate of diffusion is affected by: presence of a gradient membrane
electrical potential, and pressure difference. It is also affected by the
amount of substance available, and its lipid solubility
● Simple Diffusion (no channel): Occurs FREELY through "openings" of the lipids
of the bilayer.
○ Substances with high lipid solubility
7. Cell Compartmentalization (terms previously covered):
● ER: where proteins, lipids, and molecules are modified.
o Smooth ER: synthesis of lipids, metabolism or carbs. storage for calcium
ions.
o Rough ER: site for translation, processes proteins. send them to be
secreted.
● Golgi apparatus: proteins, lipids and molecules are further modified in the golgi.
material enters the cis side and exits the trans side via vesicles.
● Vesicles: organelles that shuttle between other organelles and the plasma
membrane.
● Free ribosome: ribosomes that are free within the cell.
● Bound ribosomes are attached to the ER. (rough ER)
● Plasma membrane. delivers stuff from outside of the cell to the inside.
● Mitochondria: generate chemical energy needed to power the cell's biochemical
reactions, produced energy is stored in adenosine triphosphate (ATP).
o Cristea: Folds inside the mitochondria.

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 o Matrix: Gel-like space in the mitochondria. Where the citric acid cycle
takes place.
● Chloroplasts: a plastid that contains chlorophyll and in which photosynthesis
takes place.

8. Origins of Cell Compartmentalization:

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 ● Endosymbiotic theory: mitochondria and chloroplasts were once free-living
prokaryotic cells that entered a large host cell through endocytosis. Overtime, the
prokaryotes and their hosts evolved together
● Prokaryotes:
o Free floating DNA takes a circular form; it does not contain membrane
bound organelles. Includes bacteria and archaea, and are usually small and
always unicellular
● Eukaryotes:
o Linear DNA inside the membrane bound nucleus, has membrane bound
organelles. Include animal, plant, fungi, and protist cells and can be either
multicellular or unicellular

Sources
● www.khanacdemy.org

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 AP Biology
Unit 4 - Communication and Cell Cycle
From Simple Studies, https://simplestudies.edublogs.org & @simplestudiesinc on
Instagram

1. Cell Communication:
● Amplification: An effect that occurs when the original signal is strengthened by
many domino-effect reactions within signal transduction.
● Apoptosis: can be termed as “cell suicide”, occurs as a result of cell signals
● Epinephrine: water soluble ligand molecule; signals the cell to convert glycogen
into usable sugar/energy
o responsible for the onset of the fight or flight reaction
o also referred to as adrenaline
● G protein: Binds with GTP and works with a G-protein coupled receptor to relays
signals from the outside to the inside of the cell
● Gap junction: intercellular junction common between animal cells, allows
materials to pass through
● Glycogen: polysaccharide that acts as a storage for glucose; it is common in
muscle and liver cells
● Ligand: a molecule that binds to a very specific receptor in the cell membrane; it’s
binding to the receptor is the onset of signal transduction
o Water soluble ligands require an external receptor, while hydrophobic
ligands usually have intracellular receptors
o Ligand-gated ion channel: channel in the plasma membrane that opens
in response to the binding of a specific ligand
● Local regulator: type of cell signal that acts locally
o Common in short distance cell signaling
● Protein kinase: Enzyme that removes the phosphate from ATP and attaches it to
the next protein kinase in a reaction cascade
o encourages the cascade of reaction during signal transduction
● Protein phosphatase: enzyme the removes the phosphate group from proteins

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 kinases in signal transduction
o Often used to halt a certain signal that has been cascading
● Receptor tyrosine kinase: Another plasma membrane receptor that functions in cell
signaling
o helps cells in their regulation of cell cycle and cell reproductive
signals, as it is able to trigger numerous signal pathways at the same
time
● Signal transduction: the processes that include how the cell responds an
extracellular (or intracellular) signal
● Testosterone: steroid hormone that works as a ligand for multiple signals that aid
in the process of male reproductive system development.
● Transcription factor: A regulatory protein that binds to DNA and affects
transcription of specific genes.
● Stages of Cell Communication:
o reception - ligand binds to receptor
o transduction - original signal from ligand is amplified through a
cascade of reactions
o response - cell responds when the end of the cascade is reached

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2. Introduction to Signal Transduction:
● Hormone: chemical substance that acts as a ligand in signal transduction;
common in long-distance communication
● Endocrine function: produces and sends hormones
● Neurocrine function: Hormones transmit the molecular signal from neuron to its
axon and then into bloodstream to the distant target cells
● Paracrine function: hormonal signals that act on local cells
● Autocrine function: hormone acts back on the cells of their origin to modulate
their own secretion or intracellular processes
● Steroid hormones are made from cholesterol
o , aldosterone, progestins, vitamin D, estrogens
● Major classes of hormone receptors:
o Extracellular/membrane receptors: binding of hormonal ligand to an
extracellular receptor causes a conformational change, which in turn
activates more enzymes that continue the cascade effect of signal
transduction. Some common ones are:
▪ Adenylyl cyclase
▪ cGMP phosphodiesterase
▪ Ca2+ and K+ channels
▪ Phospholipase-C, -A2 or D
o Nuclear receptors: water-fearing hormones bind to intracellular receptors,
and their effect is dependent on the number of hormones/ligands present to
kickstart the cell response

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3. Signal Transduction:
● Intracellular Signals: protein kinases or signal receptors inside the cell that bind to
hydrophobic ligands
o Steroids, hormones
● Transduction: cascades of interactions between protein kinases and ATP that
amplify the signal received by the binding of ligand
o Amplification occurs when a single kinase activates multiple kinases in
the next level of the cascade reaction
o The multiple kinases allow places for control and regulation
o Signals are constantly transduced (translated) into a different form until
another signal is sent to prevent phosphorylation of ATP.
▪ Kinases stimulate pathways
▪ Phosphatase shuts off pathways
● Dephosphorylation: Occurs when phosphatase enzymes remove the phosphates
from the protein.
● Secondary Messengers: Small, non-protein, water-soluble molecules or ions that
pass a signal; spread via diffusion.
o cyclic-AMP: responsible for activating the protein kinase cascade. Often
works with adenylyl cyclase
o Calcium Ions: a common messenger and relays signals in G-Protein and
Tyrosine Kinase Receptor pathways.
● Cell signaling leads to a cytoplasmic response or a change in the nucleus that
leads to protein production, inciting a cellular response.
● Gene Expression: gene information is used to produce proteins through translation
and transcription
o Transcription: copies DNA into RNA
o Translation: RNA used to make proteins
● Signal Termination: Signal response is terminated quickly by the reversal of the
ligand binding.

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4. Other Signal Involved in Signal Transduction
● Quorum sensing: cellular communication method common in bacteria where
bacteria inform each other of the excess of products in their environment
● Pheromone: chemical signal released externally by animals of the same species
● Antigen-presenting cell (APC): immune system cells that help in regulation
● Helper T lymphocyte (TH): CD4+ cells help in the adaptive characteristic of the
immune system
● Plasmodesma: allow small molecules (including signaling molecules) to flow
between neighboring cells
● Neurotransmitters: ligand for nerve cells
● Insulin: hormone produced to help the body use sugar

5. Feedback:
● Negative Feedback Loop: similar to homeostasis in which a system aims to stay at
or close to a set point
● Positive Feedback Loop: signal pathways that move away from a set point; a
signal in one direction activates and amplifies in that direction
● Feedback Mechanism: a system in which the products formed by a signal pathway
help regulate and inhibit that pathway

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6. Cell Cycle:
● Purpose of Cell Division:
o Unicellular: to reproduce and have their kind continue on
o Multi-Cellular: growth, repair, replace dying/dead cells
● Parent and daughter cells are identical: DNA, organelles, etc.
● DNA in Cell Division
o Chromatin: coiled DNA
o Chromosomes: DNA that is wrapped tightly
o Mitotic chromosome: a chromosome that has duplicated, often referred to as
sister chromatids
● Stages of Cell Cycle
o Interphase: cells are often in this phase; the longest phase
▪ NO division happens here
o 3 phases of interphase: G1 phase, S phase, G2 phase
▪ G0 phase of interphase: optional part of interphase where cells exit the
cell cycle and no longer divide
▪ G1 of interphase: cells grow after they are "born"
▪ S phase of interphase: DNA replicates in preparation for division
● DNA replicates prior to cell division so each daughter cell gets
a full set of DNA
▪ G2 phase of interphase: cell finishes growth; prepares to divide by
making organelles, proteins, and membranes
● Mitosis: cell division of somatic cells that produces identical daughter cells
o Prophase: Chromosomes become visible, nuclear envelope dissolves,
centrosomes form and spindle fibers attach to chromosomes
o Metaphase: Chromosomes line up in the middle of the cell; centrosomes move
to opposite poles of cell
o Anaphase: sister chromatids are pulled to opposite sides of cell by spindle
fibers and centrosome
o Telophase: centrosomes disassemble, nuclei reform, chromosomes start to
uncoil back into chromatin

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 o Cytokinesis in animal cells: cleavage furrow
o Cytokinesis in plant cells: cell plate, which then becomes a cell wall that
separates the resulting daughter cells

7. Regulation of the Cell Cycle:

● Cancer: cell division that is uncontrolled and unregulated
● Benign: form of cancer that produces tumors, but does not metastasize
● Malignant: cancerous tumor that metastasizes
● Chemotherapy: chemical therapy used to treat cancer
● Radiation: another cancer therapy that targets cancer cells with radiation
● Regulatory Proteins: "signals that help the cell know when to duplicate, when to
progress through the cell cycle, etc.

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 AP Biology
Unit 5- Heredity
From Simple Studies, https://simplestudies.edublogs.org & @simplestudiesinc on
Instagram
1. Meiosis:
● Crossing over: homologous chromosomes exchange parts of their chromatids with
each other
● Gene: unit of DNA that codes for RNA, proteins, and polypeptides
● Synapsis: the pairing of homologous chromosomes
o Line up gene by gene
● X chromosome: sex xhromosome; occurs twice in females, and once inmales.
● Y chromosome: sex chromosome present only in males
● Genetic recombination: the resulting regrouping of genes in an offspring that
results from meiosis
● Haploid: cell containing only one set of chromosome (n)
● Diploid: cell containing two set of chromosomes (2n)
● Karyotype: display of a cell’s chromosomes, with homologues paired up and in
order
● Genome: all of the cell’s DNA
● somatic cell: diploid cells that undergo mitosis; also referred to as bodily cells
● Gamete: haploid cells that have already undergone meiosis; also referred to as sex
cells
● Homologous chromosomes: chromosomes with the same length, shape, and genes
(can have different alleles however in the same genes)
● Fertilization: when two haploid gametes contain to form a diploid cell
o Ex: the union between egg and sperm
● Zygote: result of fertilization; diploid cell
produces somatic cells by mitosis
● Prophase I: occupies more than 90% of the time required for meiosis
-chromosomes condense

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 -synapse and crossing over
-tetrads and chiasmata
● Sexual reproduction: the fusion of gametes
● Asexual reproduction: not involving the fusion of gametes.
● Chiasmata: point of crossover in homologous chromosomes
● Variation: difference of expressed alleles in gene pool
● Random fertilization: cause of genetic variation; refers to random process of
fertilization between a random egg and random sperm

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2. Meiosis and Genetic Diversity:
● Purpose
○ Produce gametes for sexual reproduction
○ Women: happens in ovaries
○ Men: happens in tests
● Nuclear division splits the amount of chromosomes in the parent cell into half
○ 2n → n
● Cellular division (Meiosis):
● Meiosis 1
○ prophase
○ Metaphase
○ Anaphase
○ Telophase
○ Cytokinesis
● Meiosis11
○ prophase
○ Metaphase
○ Anaphase
○ Telophase
○ Cytokines
● Meiosis ends with four gametes each containing half the genetic complement of
the parent
● Comparing Mitosis and Meiosis: MITOSIS: results in the production of 2
daughter cells IDENTICAL to the parent cell to make somatic cells(2n)
-growth and repair of cell organisms
-23 pairs of chromosomes in identical daughter cells
-DNA replicated 1 time
-creates 2 diploid cells
-1 nuclear division
MEIOSIS: results in the reproduction of chromosomes number by half in the 4
new cells(used only in fertilization)

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 -To make sex cells(n)
-Production of sex cells for sexual reproduction
-23 chromosomes in each 4 genetically different daughter cells
-DNA replicates 1 time
-Creates 4 haploid cells
-2 nuclear division

Mitosis Meiosis

● results in the production of 2 daughter ● results in the reproduction of

cells IDENTICAL to the parent cell to chromosomes number by half in the 4
make somatic cells(2n) new cells(used only in fertilization)

● growth and repair of cell organisms ● To make sex cells(n)

● DNA replicated 1 time ● Production of sex cells for sexual

reproduction
● creates 2 diploid cells
● 1 nuclear division ● DNA replicates 1 time

● Creates 4 haploid cells

● 2 nuclear division

● Genetic Diversity:
○ Crossing Over
○ Randomization

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3. Mendelian Genetics:
● Allele: Different forms of a gene
● Dominant: dominating allele
● Recessive: inferior allele; masked in the presence of a dominant allele
● Homozygous: two identical alleles for a trait
● Heterozygous: two different alleles for a trait
● Genotype: genetic makeup
● Phenotype: An organism's physical appearance
● Sex-linked: genes locatd on sec chromsomes
● Carrier: A person who has one recessive allele for a trait but does not have the
trait.
● Pedigree: A diagram that shows the occurrence of a genetic trait in several
generations of a family.
● Mendelian traits are traits that are passed down by dominant and recessive alleles
of one gene.

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4. Non-Mendelian Genetics:
● Not determined by the simplicity of dominant versus recessive
● Recombination Frequency: average amount of crossovers
● X Inactivation: Condensation of X chromosomes into Barr bodies
● Codominance: where both dominant, differing alleles are equally expressed in the
phenotype
● Epistasis: when a gene also control the expression of other, independent genes
● Incomplete Dominance: where both dominate, differing alleles are blended;
neither are expressed fully
● Linkage: Occurs when different traits are inherited together more often that they
would have been by chance along
● Mitochondrial Inheritance: genes passed through the mother’s side
● Pleiotropy: The ability of a single gene to have an effect on multiple expressions
in the phenotype
● Polygenic Traits: Characteristics that are influenced by more than one pair of
genes
● Multiple Alleles: A gene that has more than two alleles

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5. Chromosomal inheritance:
● Chromosome theory of inheritance:chromosomes contain genes, and the behavior
of those genes during the process of meiosis affects the phenotype of the resulting
offspring
● Genes close enough to each other on the chromosome that result in their constant
inheritance as a pair
● Recombinant: new combination of inherited gene
● Linkage map: a map of genes on a chromosome depending on the genes’
recombination frequency
o Map units: a unit of measurement of the distance between genes. one map
unit is equivalent to a 1% recombination frequency
● Nondisjunction: error that occurs in cell division in which homologous
chromosomes do not detach from each other
o Aneuploidy: cell genome is missing a chromosome
o Polyploidy: cell genome contains an extra chromosome
● Genetic Mutations
o Deletion: one or more nucleotides are deleted or lost
o Duplication: portion of a chromosome is duplicated
o Inversion: fragment during crossover is moved in a reverse orientation to
the chromosome
o Translocation: a chromosomal fragment is removed from a chromosome
and attached to a different chromosome
● Disorders that result from GeneAbnormalities
o klinefelter syndrome: XXY
o turner syndrome: XO
o SRY gene: Y linked gene that triggers the male sexual development
pathway in animals.
▪ A disorder occurs if this gene is deleted from the Y chromosome of a
male; THe individual is genetically male, but has female reproductive
organs
o Trisomy X Syndrome: female has an extra X, resulting in XXX

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 AP Biology
Unit 7 - Natural Selection
From Simple Studies, https://simplestudies.edublogs.org & @simplestudiesinc on
Instagram

1. Introduction to Natural Selection:

● Frequency dependent selection: a phenotype’s fitness is dependent on how
common it is in the population
○ Negative frequency dependent selection:selection favors the less common
trait
○ Positive frequency dependent selection: selection favors the more common
trait.
● Oscillating selection: where at one time, selection favors one phenotype, and then
another time, selection favors the other (happens often with changing seasons)
● Industrial melanism: event where selection favors darker individuals over lighter
individuals. (Ex: peppered moths due to pollution)
● Heterozygote advantage: more chances of reproductive success for heterozygotes
● Types of Selection
○ Directional selection: one extreme of a variation is favored
○ Disruptive selection: both extremes of a variation are favored
○ Stabilizing selection: where extremes are not favored, but rather
intermediates have the selection advantage.
● Relative fitness:how likely an organism is to reproduce in comparison to other
organisms
● Natural selection: where the environment favors certain traits, allowing organisms
with these traits to have a selective advantage
● Adaptation: characteristic that a species overtime develops as natural selection
wipes out a less favorable trait

1
2. Natural Selection:
● Results in a group of organisms that have traits the environment favors; the most
fit individuals survive
● Variation of Traits: the varied alleles and traits that parents have and that they
pass on to their offspring
● Over-reproduction: too much offspring
● Competition:
○ Survival of the fittest: natural process that leaves the most fit individuals
in the population, and wipes out individuals with unfavorable traits
● Evolutionary Trends/Changes
○ Adaptive radiation: An evolutionary pattern in which many species evolve
from a single ancestral species
○ Genetic Drift: gene pool of a population changes due to chance
○ Bottleneck Effect: gene pool of a population changes due to the dramatic
decrease in population; often a result of disaster or disturbance to the
ecosystem
○ Founder's Effect: genetic drift, but in the case where a certain group of
organisms migrate to an uninhabited area, and thus change the proportions
of alleles in the gene pool
○ Gene Flow: Mixture of genes between populations
○ Mutation: changes that occur in a gene’s DNA sequence

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3. Artificial Selection:
● Artificial Selection: Selection brought about by humans (ex: breeding)
● Genetic Engineering: intention and direct manipulation traits in DNA
● Selective Breeding: artificial selection; breeding is done deliberately and
selectively to produce desired traits.
● GMOs: Genetically modified organisms
● Convergent evolution:unrelated, independent organisms in the same environment
evolve similar traits in relation one another, only because of the environment and
not because of evolutionary origin
○ Analogous structures: structures in unrelated species that are similar in
function and appearance; result of undergoing similar environmental
pressures, not a result of evolutionary origin
● Divergent evolution: when species of a common ancestor evolve in different
directions, becoming even more distinguishable from each other overtime
○ Adaptive radiation: a single species or a small group of species evolve in
different directions

3
4. Population Genetics:
● Charles Darwin
○ The differential survival and reproduction of individuals in a population based
on variations in their traits
○ Adaptation was a product of natural selection
○ Divergent species have a common ancestor, from which they evolved due to
descent with modification
● Jean Baptiste Lamarck
○ Use and Disuse (Lamarckism): in a single organism’s lifetime, its less utilized
body parts will shrink and disappear. More utilized body parts will be
maintained and will change to become more beneficial. These traits are then
passed down
○ Very different from Darwin’s theory
● Natural selection occurs between individuals and their environment, but
individuals do not evolve. Evolution occurs in a species or group of organisms
where individuals with less favorable traits die off, while those with a specific
favorable trait survive and reproduce. Thus, the species evolves to have favorable
traits, not the individual itself.
● Hardy Weinberg Theorem: shuffling of alleles due to meiosis and random
fertilization have no effect on overall gene pool. (ex: Just mixing marbles in a
sack)
○ For a population to be considered in Hardy-Weinberg equilibrium there
can be NO "outside factors" that affect allele frequencies. But this
equilibrium is hardly ever achieved in reality. These five factors are
1. No genetic drift: must have very large population
2. No gene flow: no migration or transfer of alleles with other populations
3. No net mutations: no changing alleles in another
4. Random mating
5. No natural selection: differential survival and reproduction will alter
genotypic frequency
What is the Hardy Weinberg equation?

4
 p = dominant
q = recessive
p² + 2pq + q² = 1
p+q = 1 (1 = 100%)
p = freq of dominant allele = 1 - q
q = freq of recessive allele
● heterozygous individuals: 2pq.
● Microevolution refers to specific changes in gene pool on the small scale e.g.
changes in frequency of allele in the population from generation to generation.
Change occurs constantly through mutation, natural selection, genetic drift, gene
flow. If one allele at specific locus is changing from gen to gen, then pop is said
to be evolving even if in H-W eq for all other loci
○ Caused often by genetic drift and natural selection
● Genetic drift cannot increase genetic diversity, but will actually decrease genetic
diversity as alleles disappear and reappear overtime in smaller populations. The
only way to truly increase genetic diversity is by introducing new traits and alleles
e.g. via mutation.
● Genetic drift is a direct result of independent assortment. The chromosomes that
align randomly during meiosis create great variations in resulting offspring, and
even more variation hidden behind carrier organisms (heterozygous). IN smaller
populations, it is clear to see how there would be fluctuations in alleles, and then
sudden surges in allele frequencies. The drift is a result of this.
● Geographic variations are differences in variation between population subgroups
in different areas. A graded change in a trait along a geographic axis: cline
In contrast to cline, geographic variation between isolated pops often consist of
discrete differences
● Balanced polymorphism is when 2 or more phenotypes of the same locus
maintain stable frequency in the population. Two mechanisms for preserving this
are heterozygous advantage e.g. sickle cell anemia AND frequency dependent
selection.

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● What does macroevolution refer to?
- evolution above species level; such as appearance of a pelvis in tetrapods
- think of it as "the big picture", which includes patterns of macroevolution i.e.
gradualism vs. punctuated equilibrium...how speciation occurs, etc.
● Prezygotic Barriers = factors that prevent mating between organisms
● Postzygotic barriers = advance past prezygotic barriers; prevents the proper fusion
of gametes and the proper development of viable zygotes.
● Allopatric Speciation (means "other - homeland") occurs when gene flow is
disturbed when population is divided into geographically (physical barrier)
isolated subpopulations?
● Sympatric Speciation - speciate even without a physical barrier
● Parapatric speciation is when ranges do not significantly overlap but are
immediately adjacent to each other e.g. "ring species" in which populations that
overlap interbreed but end populations are too distantly related to breed
● Punctuated equilibrium: Pattern of evolutionary change over time; describes
periods of apparent stasis punctuated by sudden change in species caused by shift
in gene pool.
● Allometric Growth: Proportional growth that helps the body get its specific form.

e.g. fetal skulls of human & chimp are similar, but allometric growth

transforms rounded skull of newborn chimp into ape skull with ↑ jaw growth

and downward sloping brow

● Evolution of morphology that arises by modification of allometric growth is an
example of heterochrony = evolution of morphology that arises by modification
of allometric growth. e.g. salamanders evolved to vertical climbing developed
larger, webbed feet
● Homeotic Genes: Genes that control how body parts are organized and placed in
the phenotypic expression
○ Hox Genes = class of homeotic genes that provide positional information in
animal embryo. Prompts structures to develop into structures appropriate for a
particular location.

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5. Evidence of Evolution:
● Fossil Record: Can show the changes that occurred over time for a specific type
of creature. Older fossils are found deeper than more recent fossils.
● Biogeography: the study of the past and present geological distribution of species
and the patterns that emerge from such analysis
● Embryo: a developing, unborn offspring
● Embryology: scientific branch that compares/studies embryos and various
developmental stages
● Molecular Homology: Comparing DNA molecules or protein sequence between
organisms to show how closely related they are

6. Common Ancestry:
● Proven by the observation that organisms have similar life processes: glycolysis,
DNA/RNA, cells with membranes, membrane bound organelles.

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7. Continuing Evolution:
● Proven with genetic changes and changes in fossils overtime
● Evolution is constant in this never-ending cycle, along with that of pesticides,
herbicides, and even chemotherapy drugs that drive that cycle
● Speciation: The formation of a new, distinct species through evolution
● Morphology: The study of the forms of living organisms and the relationships
between their structures
● Fossils: The remains of a prehistoric organism in stone or amber
● Monophyletic: descended from a common ancestor or ancestral group that is not
shared with any other group
● Phylogenetics: The study of evolutionary relationships between groups of
organisms
● Phylogenetic tree: A diagram showing the hypothesized evolutionary
relationships between species
● Analogous structures: Structures that have the same use but have different
evolutionary history
● Cladogram: A diagram showing the cladistic relationship between different
species

● DNA sequence alignment: A way of arranging the DNA sequences to identify

similarities that may be a result of evolutionary relationships
● Homologous Structures: Structures that have anatomical similarities
demonstrating descent from a common ancestor

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8. Speciation:
● Speciation: the origin of new species is at the focal point of evolutionary theory
○ New species occur due to many of the following factors
● Barriers: Mechanisms preventing interbreeding (gene flow) are central to
speciation
● Extrinsic Barriers: Physical barriers (mountains, rivers) are isolating mechanisms
● Intrinsic barriers are isolating mechanisms
○ Habitat Isolation
■ two species occupy different habitats and meet rarely
■ Not isolated by physical barriers
■ Differentiation of niches
○ Temporal Isolation: Species that breed at different times
○ Behavioral Isolation: Courtship rituals and other behaviors unique to a
species are effective barriers to mating
○ Mechanical Isolation: reproductive organs are not compatible for mating
○ Gametic Isolation: sperm and egg cannot fuse due to their incompatibility
● Hybrid: Offspring from an interspecific cross, normally of parents from the same
genus
○ Reduced hybrid viability: Genes of the different parent species may
interact and impair the hybrid's development or survival in its environment
○ Reduced hybrid fertility
○ Even if hybrids are vigorous, they may be sterile

9. Extinction:
● Extinction: When an entire species dies out
● Mass Extinction: Many species going extinct at once
● Background Extinction: The "normal" extinction rate
● Biodiversity: extinction leaves empty niches that many species are free to

9
 takeover, giving space for biodiversity and speciation

10. Variations in Populations:

● Essential for survival. If all individuals in a population had the same set of genes,
the entire population is vulnerable to complete wipeout by a single disastrous
event. Variation is like a safeguard that allows for some individual to survive and
pass on their genes in the case of a disaster.

11. Origin of Life on Earth:

● LUCA: Last Universal Common Ancestor
● Stromatolites: Fossilized mats of cyanobacteria
● All living things have Right-handed spiral DNA (double helix), Universal genetic
code, DNA, RNA, Protein. 400 genes that code for same proteins
● Miller-Urey Experiment: Experiment that replicated conditions from early earth
● RNA was most likely the first genetic model

Sources: www.khanacademy.org

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