AP Biology Notes

UNIT 1

Statistics
● Results will often fall into a bell curve
● Use statistics to describe and quantify differences between data
● 3 measures of central tendency: Mean: (x̄), median: used when there are extreme
values/outliers (to solve: arrange all numbers in order and find the middle one), and
mode: the value that appears the most (only useful when describing distribution of data
where the mean and median would not be appropriate
Variability: the measure of how far a data set diverges from the central tendency
● Measured by range and standard deviation
● Range: difference between the largest and smallest values (larger range=larger
variability)
● Standard deviation: a measure of how spread out the data is from the mean
○ low standard deviation means the data is closer to the mean
■ The independent variable is likely causing the changes
■ Data points are closer to the mean
○ high standard deviation means the data is farther from the mean)
■ Factors other than the independent variable are likely causing changes
■ Data points are spread out all along the graph
○ 1 standard deviation from the mean in either direction on horizontal axis
represents 68% of the data (68% of the data falls within +/- 1s of the mean)
○ 2 standard deviations from the mean will include 95% of the data (95% of the
data falls within +/- 2s of the mean)
○ 3 standard deviations from the mean will include 99% of the data (99% of the
data falls within +/- 3s of the mean)
 ○ How to solve standard deviation:
■ Step 1: find the mean
■ Step 2: determine the deviation from the mean for each data point and
square it
■ Step 3: determine the degrees of freedom (n-1) n: number of samples
■ Step 4: put it all together to determine standard deviation
○ To get 2 standard deviations you +/- the standard deviation on each side of the
bell curve
● Standard error of the mean: used to determine the precision of and confidence in the
mean value
○ How well the mean of a sample represents the true mean of the population
○ Based on standard deviation and the number of data points
○ Low standard error = increase in confidence
○ SEM = standard deviation/square root of sample size
○ Standard error bars are added to graphs to show how much the data differs from
the mean
○ 2 error bars can be drawn and if the error bars overlap, the difference is not
significant, if they do overlap the difference is significant

Properties of Water
● Covalent bonds share electrons
● Electronegativity: an atom’s attraction for the electrons of a covalent bond
● In a water molecule (H2O): Oxygen is one of the most electronegative elements and pulls
the shared electrons towards its nucleus. This leaves the hydrogens with a slightly
positive charge and the oxygen with a slightly negative charge.
● The connections between atoms in a water molecule are polar covalent bonds
● Polar and nonpolar molecules repel each other (like oil and water)
● Hydrogen bonds:
○ The properties of water arise from attraction between oppositely charged atoms
of different water molecules
○ The slightly positive H of one molecule is attracted to the negative O of a different
water molecule
○ The two molecules are therefore held together by a Hydrogen bond. Each bond
only lasts for a few trillionths of a second
○ Water molecules can bond with 4 other water molecules
○ It’s essentially an ionic bond, but since it involves hydrogen magnetically
bonding, it’s called a hydrogen bond
○ The covalent bond in a water molecule is the water molecule’s own hydrogen
bonding with its own oxygen because they’re sharing electrons. The hydrogen
bond in water molecules is between the oxygen and hydrogen in 2 separate
water molecules; they do not share electrons
● Cohesion:
○ water molecules stay close to each other due to hydrogen bonding. (Cohesion -
hydrogen bonds holding the substances together)
 ● Surface tension: a measure of how difficult it is to stretch it break the surface of a liquid
● Transpiration: the water droplets on leaves evaporate and causes the water below it to
move up into the plant
● Water’s high specific heat helps to regulate temperature
● Ice floats, which keeps the temperatures below stable for life

Elements of life
What all life on earth has in common:
● All life is made of the same 5 elements - carbon, hydrogen, oxygen, nitrogen, and
phosphorus (CHONP)
● Carbohydrates: CHO
● Lipids: CHO
○ difference between carbohydrates and lipids is that carbohydrates are rings and
lipids are chains
● Proteins: CHON
● Nucleic acids: CHONP
Difference between “macromolecule” and “organic molecule”:
● Organic molecules are referring to carbon-containing molecules
Monomer vs polymer relationship:
● Monomer is a singular unit of something
● Multiple monomers bond together to form a polymer
Macromolecule monomer polymer

Carbohydrate monosaccharide polysaccharide (starch, cellulose, glycogen)

(glucose)

Protein amino acid polypeptide

Nucleic Acids nucleotide dna

Lipids lipid triglycerides

Carbohydrates
● monosaccharide -> disaccharide -> polysaccharide
● Enzymes remove a water from 2 monosaccharides to make it possible for them to bond
together and from disaccharides (dehydration synthesis)
● A disaccharide can be split apart into 2 monosaccharides by putting the water back in
(hydrolysis)
● Chemical structure/shape determines how molecules act
● Types of bonds that holds 2 sugar molecules together: glycosidic links
● The plant part of a root vegetables sends glucose down to the root (like carrots) which
feeds it
● Carbohydrates can be turned in to cellulose
● Starch: long term energy storage method for plants
● Cellulose: structural, used to build cell walls in plants and is fiber for humans (to humans
it has no nutritional value)
 ● The structure of starch: OH’s pointing down, and in cellulose: OH’s point both up and
down
● Starch - easy to digest / cellulose - hard to digest
● Enzymes in our stomachs can’t attach to cellulose because of the orientation of the
hydroxides
● Homeostasis: equilibrium of levels of different elements in your bloodstream (ex: if blood
sugar is too low, you eat to get the levels of sugar up)

Lipids
● 3 types of lipids:
○ Triglycerides- function as long-term energy storage (glycerol with 3 fatty acid
chains)
■ All chains straight = saturated fat (solid at room temp)
■ 1 bent chain = unsaturated fat (liquid at room temp)
■ Both fats are hydrophobic (nonpolar)
■ Unsaturated fat can be hydrogenated to create trans fats, which can’t be
digested
■ Dehydration synthesis is used 3 times to from a triglyceride (3 times for
the 3 branches)
○ Phospholipids- main component of cell membranes
■ Phosphate group “head” is hydrophilic (polar)
■ Fatty acid tails are hydrophobic (nonpolar)
■ Makes the molecule amphipathic
 ■ The phospholipids sandwich together to make a phospholipid bilayer with
the heads facing out (bread) and the fatty acid tails on the inside (meat)
○ Sterols- steroid based hormones
■ Nonpolar lipids
■ Hormones that regulate gene expression
● Cholesterol is made out of lipids you consume, and it influences the fluidity of cell
membranes
● Lipids are used as…
○ a waxy substance on the outside of plants to protect them
○ steroid hormones and fat-soluble vitamins
○ Insulation for thermoregulation and long-term energy storage
○ Waterproofing in birds
Amino acids/proteins
● Proteins are embedded in the cell membrane and open and close to let select things in
and out of the cell
● Proteins form antibodies
● Enzymes are made out of proteins
● There are 4 steps to folding a protein
1. Primary structure (sequence/order of amino acids)
2. Secondary structure (hydrogen bonding between amino acids at different
locations) - result in alpha helix and beta pleated sheet formations
3. Tertiary structure (the R groups interact with each other)
○ Ionic bonds (salt bridges)
○ Hydrophobic interactions
○ Hydrophilic interactions
○ Disulfide bridges
4. Quaternary structure (multiple tertiary structures covalently bond together)
● 3 ways to disrupt the stabilizing bonds of the quaternary and tertiary structure of proteins
○ Denaturation (to denature) -> shape unfolds -> disastrous to its function
1. Extreme changes in temp (bond-damaging energy)
2. Extreme changes in pH (add H+ or OH- ions, disrupting the existing ionic
interactions)
3. Extreme changes in salt concentration (add Na+ or Cl- ion)
○ Renaturation - ability to “anneal” broken bonds (sometimes happens for proteins
and often happens for DNA/RNA)
● Amino acid structure:
○ Amino group (H-N-H)
○ Carboxyl group (O=C-OH)
○ R groups change depending on which amino acid it is
● Plants obtain nitrogen from the soil
● Dehydration synthesis to form a polypeptide (OH removed from carboxyl group and H
from amino group and then carbon bonds to nitrogen)
○ The carbon-nitrogen bond is called a peptide bond
○ 2 peptide bonds join 3 amino acids together
 ● Most amino acids are nonpolar, but when oxygen or charges are in the side chain (r
group) the amino acid is polar
Nucleic acids
● Function: store and transmit hereditary information
● Examples: RNA (ribonucleic acid) and DNA (deoxyribonucleic acid)
● Nucleic acid monomer: nucleotide
● Every Nucleic acid has a phosphate group and nitrogenous base
● Differences between RNA and DNA
○ Ribose (RNA) has 2 hydroxide groups and deoxyribose (DNA) has 1
○ DNA uses thymine and RNA uses uracil(DNA: ACGT/RNA: ACGU)
○ DNA is a double helix and RNA is a single strand
● RNA assembles in to a copy of DNA and delivers it to ribose to create new proteins
● CHONP
● DNA bonds:
○ T hydrogen bonds with A (2 hydrogen bonds)
○ G hydrogen bonds with C (3 hydrogen bonds)
○ GC bonds are more resilient/harder to break
○ Bonds that are broken can be annealed
○ Bonding together 2 nucleic acids: the oxygen of a sugar, and phosphate group of
another nucleic acid are bonded together by dehydration synthesis with
phosphodiester bonds
○ 2 types of nitrogen bases:
■ Purines (bigger) - 5 sided sugar bonded to a 5 sided and 6 sided A or G
■ Pyrimidines (smaller) - 5 sided sugar bonded to a 6 sided T, C, or U
○ 3’ and 5’ sugars are oriented opposite each other/antiparallel on each side of the
DNA

UNIT 2

Cells and Organelles

● Prokaryotic cells - lack membrane-bound organelles and a nucleus
○ Single-celled organisms (bacteria)
○ Contain one circular chromosome, ribosomes, a cell membrane, a cell wall (dif.
from plant cell wall), and plasmids (extra DNA outside of the chromosome)
○ Produce by binary fission (not mitosis) - the difference is that binary fission is
used to increase the population of cells very fast, while mitosis is used to replace
lost cells
■ Copies of organelles are made in the cell and then it pinches in the middle
and splits off
■ Causes them to evolve faster
○ Quorum sensing - the cells can all act the exact same way at the same time to
release toxins, form slime molds, or form plaque
■ Bacteria
■ Archaea
 ○ Prokaryotic cells can only really create proteins and divide, they can’t form
complex systems like eukaryotic cells can
○ They can only make certain proteins
● Eukaryotic cells - higher level organization and contains a nucleus
○ Produced by mitosis
■ Plants
■ Animals
○ Contain membrane-bound organelles (mitochondria and chloroplasts evolved
from prokaryotic cells)
■ divide by binary fission
■ have two membranes
■ have non-nuclear DNA in the form of plasmids
■ have their own ribosomes that are similar in size to prokaryotic ribosomes
○ Endosymbiotic theory - the mitochondria and chloroplasts evolved from
prokaryotic cells because a larger prokaryote consumed a smaller prokaryote by
endocytosis
● Nucleus - contains linear chromosomes in eukaryotic cells (chromatin). Surrounded by a
nuclear envelope. The first step of protein synthesis (transcription) occurs here.
● Ribosomes (can be free floating or attached to endoplasmic reticulum) - they synthesize
proteins, and are made of 2 parts: a large subunit and a small subunit.
● Endoplasmic reticulum
○ Smooth - synthesizes lipids and contributes to the detoxification of drugs and
harmful chemicals
○ Rough - full of ribosomes and folds proteins
● Golgi apparatus - proteins from the E.R. go to the golgi to be modified, sorted, and
packaged for secretion. It also creates lysosomes
● Endomembrane system - a group of membranes and organelles in eukaryotic cells that
works together to modify, package, and transport lipids and proteins
● Mitochondria - surrounded in a double membrane. Carries out aerobic respiration
through the Krebs cycle in the matrix and oxidative phosphorylation. Generates large
amounts of ATP (energy)
○ Has its own DNA /genetic code different from the nucleus that matches the
mother’s DNA because of endosymbiotic theory
○ Endosymbiotic theory - eukaryotic cells evolved from prokaryotic cells by smaller
bacteria being engulfed by larger bacteria and the small bacteria became
organelles
● Lysosome - involved in digestion and waste removal; digest excess/worn out organelles,
food, particles, and engulfed viruses or bacteria
● Chloroplast - double membrane organelles. Contains pigments within the thylakoid
membranes. Site of photosynthesis.
● Vacuole - in plants, the vacuole stores pigment or poisonous substances
Cell size
● Cells come in different shapes and sizes. Their size and shape evolved in response to
their function.
 ● Cells need to have a high surface area to volume ratio to absorb nutrients
● Microvilli on the cells in intestines have an enormous amount of surface area to volume
ratio to absorb large amounts of nutrients
● Examples of large surface area to volume ratio:
○ Root hairs
○ Nerve cells
○ Blood vessels in lungs
Cell membrane - helps cell keep homeostasis
● Things enter or leave the cell through the cell membrane
● Cell membrane regulates what comes in and out of the cell
● Cell membranes are made of phospholipids (amphipathic)
○ The lipid portion (tail) is made of one saturated fat and one unsaturated fat
● Cell membrane is fluid and flexible
● Cholesterol makes the membrane more rigid, but too much cholesterol can also make it
too rigid
● Molecules that can pass through the nonpolar region with no resistance:
○ Nonpolar molecules
○ Dissolved gases
○ Water (only very small amounts)
● Molecules that can not pass through:
○ Polar molecules
○ Sodium
○ Glucose
● Aquaporins are made of polar and nonpolar amino acids that form proteins that allows
water molecules to enter and leave the cell
● Protein channels allow polar or charged molecules to enter or leave a cell
○ Within membrane: nonpolar amino acids (hydrophobic) anchor the protein into
the membrane
○ Outer surface of membrane: polar amino acids (hydrophilic) attract polar
molecules
● Cell membrane is selectively permeable—it only allows certain molecules to pass
through
Diffusion
● When there is more energy in the system (higher temperature), rate of diffusion happens
faster
● When molecular mass is lower, less energy is required to move them, so the rate of
diffusion happens faster
● The difference between how much of each molecule is on each side influences the rate
of diffusion. When there is a steep concentration gradient, the rate of diffusion increases
because there are less molecules to bounce off of on each side.
● Molecules move from areas with high concentration to areas of low concentration
(concentration gradient)
● When molecules diffuse into or out of the cell through a transport protein it is called
facilitated diffusion
 ○ Every molecule that enters through facilitated diffusion has their own
channel/entry point
○ If the protein channels don’t function properly, the molecules that transport
through them can’t get through
● When water diffuses it’s called osmosis
● There’s simple diffusion (directly through membrane), facilitated diffusion (through
transport protein), and active transport (through transport protein against concentration
gradient)
○ Simple and facilitated diffusion don’t require energy
Active transport
● Cells use active transport when they need to move molecules against their concentration
gradient
○ Molecules move opposite direction: from low concentration to high concentration
● Uses a protein “pump”
● Requires the hydrolysis of ATP (energy)
○ ATP can go anywhere in the cell to deliver energy to proteins that need it (like
transport proteins for active transport)
Endocytosis
● In order to get large molecules like proteins into the cell, the cell membrane reaches
around and encapsulates the molecule and brings it into the cell
● Requires a huge amount of energy
● Example: immune system cells when fighting of a virus or bacteria
Exocytosis
● Cell needs to get rid of a large quantity of waste, so the opposite of endocytosis happens
to discard the waste
● Waste is inside a vesicle, it fuses to the membrane, and the membrane opens up for the
waste to exit
Toxicity and osmoregulation
● Cells are constantly exposed to varying external environments
○ Cells are surrounded in an aqueous environment. Yet, it is not 100% pure water.
There are ions, solutes, amino acids, lipids, proteins, wastes, etc.
○ One challenge organisms face is responding to the changing concentrations of
these solutes
● Molecules within and around cells are constantly moving (usually from high
concentration to low concentration)
● All cells are surrounded by a lipid bilayer that regulates what can move through the cell
membrane
○ Even though water is polar, it can go through the membrane in low
concentrations
○ The most common way for water to move through the membrane is through
aquaporins (protein channels)
● 3 different external environments a cell can be in:
○ Isotonic:
 ■ The concentration of solutes (and water) is equal on both sides of the
membrane
■ Anything other than isotonic means instant death for animal cells
○ Hypotonic:
■ Higher concentration of water (low concentration of solute) outside of the
cell, so water flows into the cell and it bursts (called cell lysis)
○ Hypertonic:
■ Lower concentration of water (high concentration of solute) outside of cell,
so water leaves the cell and the cells shrivel (called plasmolysis)
● Paramecium: single cell organism living in freshwater
Water Potential
● potential - the force responsible for movement of water in a system
○ Has the symbol psi (looks like a trident)
○ Is measured in bars or megapascals
● Pure water has a high water potential because the water molecules are able to move
however and wherever they want
● When solutes are added to water, the water molecules are attracted to the solute, so
they have less free energy (water potential) because the molecules are being restricted
by the solutes they are stuck to
● Has 2 components:
○ Solute potential (will be a negative number)
○ Pressure potential
○ Solute potential + pressure potential = water potential
● The water potential of pure water is given the value of zero
● Hypertonic solutions have a negative water potential
● Water moves from areas of high water potential to areas of low water potential
○ This will occur until the water potential is equal inside and outside the cell
● Flaccid cell: the pressure potential is zero
● If it is hypertonic, the water potential is lower
● Another equation for solute potential:
○ -iCRT
○ i = ionization constant (either 1 or 2 - very rarely 3)
■ 1: sucrose, glucose, fructose, protein…(anything that doesn’t break down
into ions)
■ 2: NaCl, KCl, HCl…(anything that can break down)
■ 3: K2SO4
○ C = molar concentration of sucrose (sometimes given, sometimes obtained from
a graph)
○ R = pressure constant (0.0831)
○ T = temperature in kelvin (273 + C)

UNIT 3

Enzymes
 ● Enzymes speed up metabolic reactions by lowering energy barriers—it is a catalytic
protein (catalyst)
● Catalyst: a chemical agent that speeds up a reaction without being consumed by the
reaction
● How Enzymes work: they catalyze or speed up chemical reactions by lowering the
activation energy
○ Synthesis - active site orients substrates in a correct position for reaction
○ Digestion - active site binds substrate and puts stress on bonds that must be
broken, making it easier to separate molecules
● Enzymes vocabulary:
○ Enzyme - a protein that is a biological catalyst
○ Active site - location on an enzyme where the substrate binds temporarily. Very
specific for the substrate; the active site can be used over and over again
○ Substrate - the reactants in an enzyme-catalyzed reaction that attaches to the
active site
○ Induced fit - enzyme “hugs” the substrate; a complementary substrate can only fit
into a complementary enzyme
○ Products - the end result of the reaction; once the products from, they no longer
fit in the active site and they leave
○ Enzymes substrate complex - when the enzyme and substrate fit together
○ Competitive inhibition - sometimes there are molecules that are shaped (and
charged) just like the substrate and the can attach to the active site, blocking the
substrate and therefore inhibiting the reaction
○ Allosteric site - dent in the enzyme that molecules bind to and allows
non-competitive inhibition
○ Non-competitive inhibition - prevents the complementary substrate from binding
to the active site because of the inhibitor on the allosteric site
● Activation Energy (AE) - The amount of energy required to make a reaction occur
○ Enzymes lower the activation energy by binding one of the substrates and
holding it in a way that lowers the activation energy—the induced fit/the way the
enzyme holds the substrate puts chemical strain on the substrate making it
easier to react
● Environmental factors affecting enzyme function:
1. Temperature
2. pH
3. Concentration
4. Inhibition
Metabolic pathways
● Metabolism - the totality of an organism’s chemical reactions
○ An organism’s metabolism transforms matter and energy
● Metabolic pathway - a series of chemical reactions (catalyzed by enzymes) that starts
with a specific molecule and ends with a product
● 2 kinds of metabolic pathways: catabolic and anabolic -
 ○ Catabolic pathways - release energy by breaking down complex molecules into
simpler compounds
○ Anabolic pathways - consume energy to build complex molecules from simpler
ones
● 2 kinds of reactions: exergonic and endergonic
○ Exergonic reaction - energy released (spontaneous)
○ Endergonic reaction - energy required (not spontaneous)
● ATP - the energy currency of the cell; when cells need energy, ATP is what they use
○ When reactions need energy, the 2nd and 3rd bonds between the phosphate
groups in the ATP break, and that stored potential energy is applied to the
reaction
○ The process of cellular respiration breaks down glucose to produce ATP
○ Glucose has a large amount of potential energy, but it is stored energy that is not
usable by cells. So, the stored energy is used to recharge ATP
Cellular respiration
● 3 steps:
1. Glycolysis
2. Krebs cycle
3. Electron transport
● Glycolysis (only step that’s common in both prokaryotes and eukaryotes):
○ Occurs in the cytoplasm
○ Phosphate bonds to carbon 1 and 6 in the glucose molecule
○ Splits one glucose molecule into 2 (called pyruvates)
■ A 6-carbon glucose is hydrolyzed by an enzyme, and split in half to
become 2 pyruvates that are 3 carbons each
○ Another phosphate bonds to each pyruvate, so there are now 2 phosphate
groups per pyruvate
○ Electrons and hydrogens are stripped off during the chemical reactions to be
carried to the mitochondria by an electron carrier
■ In bacteria, the electrons in the electron carriers are given back to the
pyruvates and produce alcohol
○ 2 ATPs are gained by:
■ Substrate-level phosphorylation -
■ Bond between phosphate and carbon is broken and the phosphorus is
added into ADP to make ATP
■ 4 ATPs are produced, but only 2 ATPs are gained because 2 were
invested in the reaction, so it’s a net gain of 2 ATPs
● Oxidation of Pyruvate:
○ 1 pyruvate (containing 3 carbons) enters the mitochondria and one of the bonds
breaks, releasing a carbon dioxide
○ The 2-carbon molecule that remains is called acetyl
○ When the bond was broken an electron and hydrogen were taken and put in
electron carriers
 ● Krebs cycle: Breaks down carbons from the pyruvates and products are ions/electrons
and 2 ATP
○ 2 carbons bond together with an already existing 4-carbon chain and form citric
acid
○ Oxidation occurs - electrons are taken out and 14 electron carriers are filled up
with electrons
○ 2 CO2 are produced and diffuse out of the cell
○ 2 ATPs are produced through substrate-level phosphorylation
● Electron transport:
○ 2 electrons lead hydrogen into transport proteins and the hydrogen goes inside
the intermembrane space; the cell utilizes magnetic attraction to move the
hydrogen against the concentration gradient
○ The hydrogen ions inside the intermembrane space are extremely unstable
because they are all the same charge, and there is a large amount of kinetic
energy
■ The R-groups in the transport proteins that are facing the intermembrane
space will not denature in low pHs, but the part of the protein facing the
matrix will
○ The hydrogen ions spin the turbine in the ATP synthase enzyme, and ATP is
produced in an endergonic reaction
○ Water is formed as a byproduct because oxygen (which you breathe in) reacts
with hydrogen ions that are discarded
○ Chemiosmosis - the flow of electrons down the electrochemical gradient
○ Oxidative phosphorylation
● Aerobic respiration - requires oxygen
● Anaerobic respiration (fermentation) - does not require oxygen
○ Electrons in electron carriers are given back to the pyruvates
○ The pyruvates turn into lactates, and then into lactic acid
● Moving electrons in respiration:
○ NAD+ is a coenzyme that moves electrons (and hydrogens) inside the cell
○ When electrons fill the vacant spaces in NAD+, it is reduced to become NADH
○ When an electron carrier gains electrons, the charge is reduced, and when
electrons are lost, the charge increases (oxidized)
Fitness
● Plants live rooted in one place throughout different seasons
○ They have the ability to increase the percent of unsaturated fats during the winter
and decrease the percent of unsaturated fats in the summer
● Variation in the number and types of molecules within cells provides organisms a greater
ability to survive and reproduce in different environments
Photosynthesis
● Autotrophs - create their own energy: plants build all of their organic molecules from
CO2, H2O, and sunlight
● Plants collect solar/light energy and transform it into chemical (usable) energy
● Oxygen is a product of photosynthesis, and plants produce so much of it that they can
use it for cellular respiration and also release a lot of oxygen
● Plant’s stomata can open and close; CO2 enters and H2O and O2 leave
○ The stomata closes when it’s too sunny to prevent too much water being lost
through transpiration
● 2 steps of photosynthesis: light reaction (light dependent) and dark reaction (light
independent or calvin cycle)
○ Light-dependent reaction: light energy from the sun is converted into chemical
(usable) energy
■ Water and sunlight are the reactants; energy from sun is invested in water
to break bonds and collect electrons
■ Products: ATP, NADPH, and O2
○ Light-independent reaction/Calvin cycle:
■ ATP, NADPH, and CO2 create glucose
● Inside of chloroplast:
○ Thylakoid (light-dependent reaction occurs here) and stroma (Calvin cycle occurs
here)
Light-dependent reaction:
○ 2 photosystems in the chloroplast where sunlight hits
■ Sunlight/photons excites the electrons in photosystems 1 and 2, which
makes them jump to a higher energy level, and they move through the
electron transport chain
■ In between the photosystems is an electron transport chain
○ Water is split into H2 and O, and the electrons from the water go to the
photosystems
■ Water split = photolysis
○ NADP+ is reduced by the electrons into NADPH after they move through the
ETC
○ hydrogens are accumulated when electrons move through the ETC, and they
create a high hydrogen gradient, so they move into the ATP synthase
(chemiosmosis) and the ATP synthase phosphorylates ADP to become ATP
(called photophosphorylation)
Calvin cycle aka dark reaction aka light independent reaction:
○ The products from the light reaction (NADPH, ATP, and CO2) are used in the
Calvin cycle to create glucose
■ 3 CO2 + 6 ATP + 6 NADPH = 3-carbon sugar (occurs twice to make one
6-carbon sugar)
■ In total 6 CO2, 12 ATP, and 12 NADPH are invested to make a single
glucose molecule
○ carbon fixation:
■ CO2 attaches to RuBP (a chain of 5 carbon) to make a 6-carbon chain;
this happens 3 times, so there are 18 carbons (3 chains of 6 carbons)
■ The 3 6-carbon chains split in half, so there are now 6 3-carbon chains
○ Reduction:
 ■ 6 molecules of ATP phosphorylates the carbon chains, giving them
energy
■ NADPH takes the electrons from each carbon chain and becomes
NADP+
■ 1 of the carbon chains leaves to become a glucose molecule
○ Regeneration:
■ 15 carbons remain, so ATP is invested to arrange the carbons back into
the 3 5-carbon chains of RuBP

UNIT 4

Cell Communication
● Humans are multicellular organisms with independent cells all working together. Almost
all functions of the human body are performed by cells or are started by cells.
● Cells communicate by generating, transmitting, receiving, and responding to chemical
signals
● The two macromolecules that cells use as chemical signals are proteins and lipids
○ Lipid-based chemical signals can cross directly through the cell membrane (ex:
steroid hormones)
○ Protein-based chemical signals cannot cross through the membrane and go
inside the cell (ex: protein-based hormones and polypeptides)
● 3 ways that cells communicate:
○ Direct cell-to-cell contact
■ Ex: plasmodesmata in plants, gap junctions, white blood cells
○ Over short distances with chemical signals
■ Ex: nerve cells, skin cells, quorum sensing
○ Over long distances with chemical signals traveling within the blood
■ Ex: hormones in the endocrine system
● When the ligand attaches to a protein receptor, the signal is received; “signal reception”
● Transmembrane receptor protein
○ Receives signal from outside and changes the shape of the intracellular domain;
conformational change when signal is received, thus different r-groups are
exposed
○ G-protein linked receptors
■ Made up of alpha, beta, and gamma
■ Conformational change makes g-protein move towards the
transmembrane protein, it becomes activated, goes to an enzyme that
converts ATP to cyclic AMP, and returns to its deactivated state
■ Cyclic AMP (secondary messenger) activates protein kinase A
■ ATP phosphorylates protein kinase 1, activating it, and it does this again
to protein kinase 2, and an enzyme that hydrolyzes glycogen
■ The phosphates are removed from the protein kinases and they are
deactivated
○ Receptor tyrosine kinases
 ■ 1 ligand is applied to both receptors to activate the receptor tyrosine
kinases
■ It is phosphorylated by 6 phosphates, and the receptor is now called a
“dimer”
○ Ligand-gated ion channels
■ Is both a receptor and transport protein
■ Neurotransmitter docks to the receptor part of the protein, causing the
gate to open and allowing ions to enter
■ The ligand detaches from the receptor, so the gate closes
Viruses
● Viruses aren’t cells, they’re proteins
○ They aren’t alive, so they can’t be killed, only neutralized
○ Their only goal is to multiply
● When you get a cut, histamine is released and triggers capillary dilation (increased blood
volume), which causes inflammation (heat, swelling, and redness)
○ The capillaries release chemokines, signaling phagocytes to come to the cite of
the cut and get rid of foreign bacteria/viruses
Changes in signal transduction pathways
● The more parts there are to a pathway, the more that can go wrong
● Once an extracellular domain of the pathway is mutated, the rest of the pathway doesn’t
work
Negative Feedback Loops - product inhibits reaction
● Timing and coordination of biological mechanisms involved in growth, reproduction, and
homeostasis depend on organisms responding to environmental cues
● We rely on the endocrine system to help maintain many of our internal conditions
● The endocrine system is composed of organs called glands that produce and release
hormones into our bloodstream
● The hormones will act as ligands or chemical messengers throughout the body to help
maintain homeostasis
● The endocrine system uses negative feedback loops to maintain a steady state within
our bodies
● When there is too much sugar in the bloodstream, insulin is released and signals for the
liver to store excess sugars. When there is too little sugar, glucagon is released and
signals for the liver to release stored sugar.
Positive Feedback Loops - product feeds the reaction
● When a baby breastfeeds, oxytocin is released in the mother and it signals the breast
tissue to produce more milk
○ The more the baby breastfeeds, the more milk is produced — the product makes
more of the product
The Cell Cycle - the life cycle of a cell; the steps a cell goes through in its way to dividing
● Cells divide by mitosis for growth and repair
● Cell spends 90% of its time in interphase - business as usual; cell doing normal jobs
 ○ G0 phase - cells cannot repair themselves or divide (nerve cells and heart cells
are always in this phase because they are too complex and require too much
energy)
○ G1 phase - growth; cell grows larger
○ G1 checkpoint - checks to make sure that the cell has all the resources needed to
divide and that the DNA isn’t mutated
■ Once G1 checkpoint is passed, the cell is irreversibly committed to dividing
○ S phase - cell makes a complete copy of its DNA
■ There are now 2 chromosomes, called identical sister chromatids
■ They are held together by a centromere
○ G2 checkpoint - cell checks that there is no damage in the DNA and that all
chromosomes are lined up correctly
● Cells spend 10% of their time in the M phase - all normal jobs are stopped so the cell
can divide
○ Steps:
1. Prophase -
a. duplicated chromosomes condense
b. the nuclear envelope breaks down
c. Centrosomes (made of 2 centrioles) moves to each end of the cell
2. Metaphase -
a. centrosomes send out spindle fibers, which line up the chromosomes in
the middle of the cell
3. Anaphase -
a. the spindle fibers pull the sister chromatids apart to opposite sides of the
cell
4. Telophase -
a. New nuclear envelopes form
b. DNA uncondenses
5. Cytokinesis -
a. The cytoplasm divides
● The cell knows when to leave each stage because it receives external and internal
signals
● External signals:
○ Growth factors -
■ Epidermal growth factor (local regulator released from nearby cells)
■ Platelet derived growth factor (local regulator released from nearby cells)
■ Growth hormones (released from the anterior pituitary)
Chi Square and the Goodness of Fit Test
● X2 = the sum of (Observed - Expected)2/Expected
● Example: (37-40)2/40 + (43-40)2/40
0.225 + 0.225
= 0.45
observed expected
 tall 37 40

short 43 40
● Null hypothesis: any variation in observed vs expected is due to chance and there is no
significant difference between our observed and expected
● Example: (63-40)2/40 + (17-40)2/40
13.225 + 13.225
= 26.45
observed expected

tall 63 40

short 17 40
● chi square table:
○ degrees of freedom = number of events - 1
○ Where the p value and degrees of freedom intersect is called the critical value
○ If the chi square value is less than the critical value, we fail to reject the null
hypothesis (null hypothesis supported), and if it is greater, the null is rejected and
the alternative hypothesis is supported
Unit terms
● Apoptosis - cell suicide
● Tissue - a group of cells that all perform the same function
● Organ - a distinct structure made of two or more tissues that performs a specific function
● Organ system - a group of organs that all work together to perform a particular function
● Plasmodesmata - channels in between the cell walls of plant cells that allow the cells to
communicate
● Ligands - chemical messengers
● Conformational change - protein changes in shape
● Protein kinases - enzymes that modify the activity of other proteins by chemically adding
phosphate groups to them
● Adipose tissues - store excess sugar
● Mitosis - division of the nucleus
● Cytokinesis - division of cytoplasm

UNIT 5

Meiosis
● Meiosis - creates non-identical daughter cells (sperm cells and egg cells)
● Gametes - reproductive cells
○ Gametes have 23 chromosomes
○ haploid - one set of chromosomes (either from the mom or dad)
○ Haploid cells (n) combine to form a diploid cell (2n)
● Somatic cell - all body cells
 ○ Have 46 chromosomes
○ diploid - two sets of chromosomes (one from each parent)
○ Diploid cells divide to make more diploid cells
● Karyotype - visual representation of chromosomes
● Homologous chromosomes - pair of chromosomes that carry the same genes; they
aren’t identical, they just have the genes for the same thing (ex: each has a gene for eye
color)
● Steps of meiosis:
○ Diploid cell duplicates chromosomes, so there are 92 chromatids
○ It splits into 2 diploids
○ The 2 diploids split into 2 haploids - there are 4 haploids total
● Prophase 1
○ Crossing over - homologous chromosomes exchange parts of the chromosomes
with each other to increase genetic variation - the products are called
recombinant chromatids
● Metaphase 1
○ Homologous chromosomes move to the middle of the cell and the way they line
up (called independent assortment) also increases genetic variation
● Anaphase 1
○ Homologous chromosomes get pulled to opposite sides of the cell
● The process repeats - prophase 2, metaphase 2, anaphase 2, etc.
● In females, 4 non-identical daughter cells are created, but 3 of them are polar bodies,
not eggs, so they disintegrate and 1 egg cell remains.

Nondisjunction
● If homologous chromosomes fail to separate during anaphase 1, then there will be an
unequal distribution of chromosomes in each daughter cell
● When this occurs during anaphase II, one of the sister chromatids fails to separate - this
isn’t as bad as when it happens during meiosis because less of the resulting gametes
are n+1 or n-1 compared to when it happens in anaphase I
● Monosomy: having only one copy of a particular chromosome (n-1)
● Trisomy: an organism has a third copy of a certain chromosome (n+1)

Mendelian Genetics
● The first 22 pairs of chromosomes are called autosomal chromosomes
● The 23rd pair of chromosomes are called sex chromosomes
● Some traits or genes are not inherited on a nuclear chromosome (like in the
mitochondria)
○ Genes located in plasmids in chloroplasts and mitochondria are inherited through
the mother
● Phenotype: the observable characteristics in an individual
● Genotype (also called alleles): complete set of genetic material - the genotype
determines the phenotype
● Locus: the specific location of a gene or other DNA sequence on a chromosome
 ● Homozygous dominant (BB) - true breeding
● heterozygous (Bb) - carrier
● Homozygous recessive (bb) - true breeding
● Wild-type: the phenotype that typically occurs in nature
● Mendel's law of segregation: each individual that is a diploid has a pair of alleles (copy)
for a particular trait. Each parent passes an allele at random to their offspring resulting in
a diploid organism
Non-Mendelian Genetics
● Incomplete dominance
○ The outcomes blend together
○ Black and white chickens come together to make a gray chicken
○ 2 gray chickens can come together and make either black, gray, or which
chickens
● Codominance
○ Both alleles are expressed in the heterozygotes
○ A white and red flower comes together to make a white and red flower
○ Example in humans:
■ Blood type A and B can make type AB
Pedigrees
● Used to determine how traits are inherited through generations - their pattern of
inheritance
● Circles represent females and squares represent males
● The circles or squares that are filled in means that that individual expresses the trait
being discussed
● You have to determine if the traits are…
○ Autosomal dominant
○ Autosomal recessive
○ Sex-linked dominant
○ Sex-linked recessive
Environmental effect on phenotype
● Environmental factors influence gene expression and can lead to phenotypic plasticity
● Phenotypic plasticity occurs when individuals with the same genotype express different
phenotypes in different environments
Linked genes and recombination frequency
● When genes are located on different chromosomes, they assort independently and we
can expect a 1:1:1:1 ratio
● When genes are located on the same chromosome, crossing over occurs
● Crossing over is less likely to occur when genes are too close together - they’re called
linked genes because they often stick together during crossing over
● Recombination frequency = # of recombinant offspring / total offspring x 100
○ If it is more than 50%, then the genes are located on different chromosomes and
are using independent assortment
○ If it’s less than 50%, then the genes are located on the same chromosome
(they’re linked)
 ○ The farther apart two genes are on a chromosome, they higher the recombination
frequency will be
● Wild (+) - normal phenotype
Map Units
● Crossover frequencies can be converted into map units
○ Ex: a 5% crossover frequency equals 5 map units

UNIT 6

Nucleic acids
● Function: store and transmit hereditary information. The primary source of heritable
information
○ Stored in the sequence of nucleotides
● Nucleic acid monomer: nucleotide
○ Made out of a 5-carbon sugar
○ Deoxyribose (DNA) has 1 hydroxide on the 3’ carbon
○ Ribose (RNA) has 2 hydroxides, on on the 3’ and another on the 2’
● Base pairs: Adenine, Cytosine, Guanine, Thymine(DNA), Uracil(RNA)
○ The bonds between base pairs are hydrogen bonds
○ There are 2 hydrogen bonds between A and T
○ There are 3 hydrogen bonds between C and G
● The strands of DNA are antiparallel
● Nucleotides bond together in a phosphodiester bond by dehydration synthesis
○ The new nucleotide is always added to the 3’ end (DNA is built from 5’ to 3’)
○ The nucleotides have 3 phosphate groups, and when the bond between them is
broken, the energy is released and applied to forming a new bond between the 3’
and 5’ carbon
● When and why DNA replicates:
○ During S phase of mitosis
● How DNA replicates:
○ Topoisomerase loosens the hydrogen bonds between base pairs
○ Helicase unzips the 2 strands of DNA
○ The leading strand is continuous, and the lagging strand is synthesized in
segments connected by ligase
Protein synthesis
● How we get the directions about how to make proteins from DNA and bring them to the
ribosome so that it can join amino acids in a specific order to synthesize proteins
● 2 steps: transcription and translation
● All cells, prokaryotes and eukaryotes, perform protein synthesis
○ In prokaryotes, both steps occur in the cytoplasm
○ In eukaryotes, transcription occurs in the nucleus, and translation occurs in the
cytoplasm
● Transcription:
○ How RNA is produced -
 ■ The enzyme RNA polymerase synthesizes messenger RNA by reading
one strand of the DNA and follows base pairing rules to build the mRNA
■ RNA polymerase only unwinds the DNA where transcription occurs. This
is called the transcription bubble
■ The mRNA is synthesized in the 5’ -> 3’ direction and therefore the strand
of DNA that runs in the 3’ -> 5’ is the template strand. The template strand
is the DNA strand that is copied in mRNA
■ As mRNA is synthesized, RNA polymerase continues down the DNA. As
it moves, the double helix winds back up and the mRNA begins to trail off
of the DNA
■ Once the gene has been transcribed, the single stranded mRNA carries
the directions on how to build a protein to a ribosome. (In eukaryotes, the
mRNA will be edited first
○ Promoter region (TATA box) - tells the RNA polymerase where to start
transcription
○ Proteins called transcription factors can attach to the TATA box to increase the
likelihood of RNA polymerase transcribing the protein
Translation
● Initiation -
○ starts with a codon
○ a small ribosomal subunit attaches
○ tRNA attaches, which has the amino acid
○ Large ribosomal subunit attaches
● Elongation -
○ One tRNA attaches and another un attaches
○ The ribosome moves down the RNA and translates it into amino acids
○ There’s a start codon and a stop codon (the stop codon isn’t counted)
Translation in prokaryotes
● They do not undergo RNA splicing
● As soon an mRNA is produced, ribosomes attach and begin translating the mRNA code
into amino acids
Endomembrane system
● Nucleus - transcription and translation
● Rough ER right outside the nucleus
● Ribosomes bound to rough ER
● Transport vesicle brings the protein to the golgi
● Golgi completes protein synthesis
● Transport vesicle brings protein out of the cell membrane by exocytosis
Alternative RNA splicing
● The DNA or RNA between the exons will not be expressed, so they are spliced out by
spliceosomes
● The spliced-out DNA/RNA are called introns
● Sometimes exons are spliced out along with the introns to create a different protein
Mutations
 ● DNA point mutations (aka substitution mutations)
○ When DNA is copied, the matching base pair is incorrect, so there’s a singular
incorrect base pair
○ The consequences could be bad, good, or neutral depending on which amino
acid is translated
○ Silent mutation: the original codon and mutated codon translate to the same
amino acid
○ Missense mutation: the mutation results in a different amino acid (may affect
protein folding and final shape of protein)
○ Nonsense mutation: the mutation translates to be a stop codon and no functional
protein is made
Gel electrophoresis
● Restriction enzymes are used to cut a DNA sample into multiple smaller fragments
● DNA sample placed into a well near the negative electrode, and it moves towards
positive
● Small fragments travel farther than larger fragments
● The size of the band indicates how many DNA fragments exist
● You can also use gel electrophoresis to tell inheritance of alleles
Polymerase Chain Reaction
● A laboratory technique used to rapidly amplify a target sequence of DNA into millions to
billions of copies in a short amount of time
● What is needed to replicate the DNA:
○ Heat the DNA sample to 94°C – 96°C.
■ Denatures the DNA (breaks the hydrogen bonds between the base pairs).
○ Cool the DNA sample to 68°C.
■ Enables DNA primers to anneal and base pair with the target sequence.
○ Warm the DNA sample up to 72°C - the optimum temp for Taq polymerase to
synthesize the complementary strand.
○ Repeat the three steps over and over for exponential growth of the target
sequence
Genetic engineering
● DNA Cloning: when scientists want to work with a gene of interest, they need to make
multiple copies of that gene (gene cloning) and they use bacteria to do this
○ To clone pieces of DNA in the lab, researchers first obtain a plasmid (one that
had been genetically engineered for cloning)
○ Plasmids have a small number of genes
● To join human DNA to a plasmid, a restriction enzyme cuts out the same sequence of
DNA out of the human DNA and the plasmid DNA
○ The plasmid and human dna has “sticky ends” and they fit/bond together
○ The added human DNA is called recombinant DNA
● Making recombinant DNA:
○ Cut DNA with gene of interest with a restriction enzyme
○ Cut plasmid with the SAME restriction enzyme (so sticky ends match)
○ Sticky ends base pair together
 ○ DNA ligase seals the fragments together
● The bacteria cell can now synthesize the protein we want because we gave it the correct
instructions
Plasmid based transformation
● When doing plasmid based transformation, transformation isn’t 100% successful, and
not every plasmid is recombinant
● Some bacteria have a mutation on their plasmid that confers antibiotic resistance, so
they’ll be able to survive if grown on an antibiotic medium.
● When working with plasmids, scientists genetically engineer them to have a gene that
makes them resistant to antibiotics. (Those are the plasmids scientists work with.)
● The bacteria containing the plasmids with antibiotic resistance will be the only ones that
survive to reproduce
Genetic variation in prokaryotes
● Bacteria clone themselves to increase population
○ Called binary fission
● Transformation
○ The bacteria takes something into its genome, so it can now transcribe/translate
a new protein
○ The process of transformation is the alteration of a bacterial cells genotype and
phenotype by the uptake of naked, foreign DNA from the surrounding
environment
● Transduction
● Conjugation
○ Sometimes referred to as bacterial “sex”, conjugation is the direct transfer of
genetic material between two bacterial cells that are temporarily joined. The DNA
transfer is one-way: one cell donates DNA and its “mate” receives the DNA
Operons
● Only in prokaryotic cells
● An operon is a group of related genes in a bacteria
○ Contains the promoter, operator, and the genes they control
○ When these genes are expressed, they are directions for making proteins
○ Each gene in the operon makes a protein; if there are 3 genes, there will be 3
enzymes that function together (they make an enzymatic pathway)
● To turn off the operon (when levels of the wanted protein are high enough):
○ The protein binds to the repressor protein, which then binds to the operator,
which will inhibit the creation of more proteins
○ It will be inhibited until the bacteria has metabolized all of the tryptophan (the
protein)
○ Because the operon is able to be repressed and turned off, we call it a
repressible operon
● There are also inducible operons, which are always off unless they are turned on by
environmental changes
○ An example of this is in intestines, lactase is only produced when there is lactose
present
 ● A TRP OPERON IS A REPRESSIBLE OPERON
Eukaryotic Gene regulation
● Euchromatin is chromatin containing genes that are able to be transcribed and
translated, by heterochromatin is chromatin containing inaccessible genes because it’s
too tightly wound
● Histone acetylation: acetyl group unwinds, making gene binding sites available (turns
heterochromatin into euchromatin)
● DNA methylation: turns euchromatin into heterochromatin
● Epigenetics: DNA methylation does not change the DNA sequence, but can be passed
onto future generations
Viruses
● Contains DNA or RNA or both
● Surrounded by a protein coat
● Some viruses have a membranous envelope
● A virus can have double-stranded DNA, single-stranded DNA, double-stranded RNA, or
single-stranded RNA
● Viral envelope:
○ Some viruses have a membranous envelope
● Viruses can only replicate inside host cells
○ It uses the cell’s replication machinery
● RNA Retroviruses
○ Works backwards—uses the RNA
○ The RNA is used to make viral DNA
● The virus DNA enters the DNA of the cell
○ The cell now creates more viruses and releases it into the body
● Lytic cycle
○ The virus lyses out of a bacteria cell and kills it
● Lysogenic cycle
○ The virus phage inserts its DNA into the genome of the bacteria and doesn’t do
anything for a period of time
■ This is so that when the bacteria replicates, the viral phage DNA is
replicated as well
○ Eventually, every single virus enters the lytic cycle and kills every infected
bacteria
● Not all bacteria has a lysogenic cycle, but they all have the lytic cycle

UNIT 7

Lamarck
● Inheritance of acquired characteristics - stated that these acquired characteristics could
be passed on to offspring
Darwin
● Worked for years testing out his hypothesis and gathering evidence
● His theory was descent with modification by natural selection
Natural selection
● Natural selection: the process whereby organisms better adapted to their environment
tend to survive and produce more offspring
○ It is always happening, but which traits are beneficial depends on the context in
which the species live and mate
○ Natural selection results because of interactions between the individuals and
their environment
○ It can amplify or diminish differing heritable traits, so it needs variation
○ An individual can’t choose to change its phenotype, natural selection is a process
of editing, not a creative mechanism
○ Individuals don’t evolve, they survive or don’t survive—they are only selected for
○ If a population lacks variation and the environment changes, the species risks
extinction
● Adaptation - inherited characteristics of organisms that enhance survival and
reproduction in specific environments
Darwin’s argument
● Observation #1: variation exists in populations. Variation is an inherited trait
● Observation #2: more individuals are born than can survive
● Inference #1: individual with traits better suited to their environment survive and
reproduce
● Inference #2: this unequal ability of individuals to survive and reproduce will lead to an
accumulation of favorable traits in the population over generations
Fitness:
● the ability to survive and reproduce. Or more scientifically—a measure of reproductive
success. An organisms
● Deleterious traits: reduce the chance of survival
● Adaptive traits: Increase the chance of survival
Artificial selection (selective breeding)
● Humans, not the environment, select desirable traits to be passed on to the next
generation
● Through artificial selection, humans affect variation in other species
● Similarities and differences between natural and artificial selection
○ Natural selection:
■ Occurs naturally
■ Adaptive characteristics are selected for
■ Environmental factors exert the selective pressure
■ Produces biological diversity
○ In common:
■ Both result in changes in
Convergent evolution
● Independent development of similar traits or features due to similar environmental
selective pressures
● Descendent of species A has similar traits or features to descendants of species Z
Divergent evolution
 ● Species sharing a common ancestor become more distinct over time
Population genetics
● Different ways a population can evolve:
Non-random occurrences:
○ Natural selection
○ Sexual selection
■ Non-random mating - mates are selected based on who has the most
desirable traits, so those desirable traits have the possibility of being
passed onto offspring
■ Intersexual selection, or often “female choice”, can drive the shift in allele
frequencies over generations
■ Intrasexual selection is when males compete for the females. This also
drives the change in allele frequencies since the mating is not a random
event
■ Sexual selection can lead to sexual dimorphism between males and
females of the same species (they look different)
Random occurrences:
○ Mutations
■ Mutations result in genetic variation, which provides phenotypes on which
natural selection acts
■ The mutations can contribute to higher fitness, so they have a chance of
being passed onto future generations
○ Founder effect
■ Part of a population that has a specific genotype (such as homozygous
recessive) leaves and moves somewhere else, so there is no genetic
variation (no dominant allele) in the new, migrated, population
○ Bottleneck effect
■ A population’s size is reduced due to some event (like a fire), and the
surviving population is only alive due to chance, not necessarily because
they are the fittest
■ This results in a loss of genetic variation, and extinction is a high
probability
○ Gene flow
■ Migration - when individuals move into/out of a population, they bring their
alleles with them
● Evolution: a change in allele frequencies in a population over generations
Hardy Weinberg theorem
● If a population is in hardy weinberg equilibrium, it is not evolving from one generation to
the next
● p (frequency of dominant allele) + q (frequency of recessive allele) = 1
○ Used for allele frequencies
● p2 (homozygous dominant) + 2pq (heterozygous) + q2 (homozygous recessive) = 1
○ Used for genotype frequencies
Evidence for evolution
 ● Evolution is supported by scientific evidence from many disciplines: geographical,
geological, physical, biochemical, and mathematical
● Geographical: how evolution and geography intersect
○ Biogeography - the study of the geographical distribution of organisms. Provides
information about how and when species may have evolved
● Geological: the fossil record provides evidence for when organisms lived on earth, how
species evolved, and how some species have gone extinct
● Physical: homologous structures provide evidence for common ancestry, while
analogous structures show that similar selective pressures can produce similar
adaptations (beneficial features)
○ Homologous structures are similar physical features in organisms that share a
common ancestor, but the features serve completely different functions
○ Analogous structures share a common function, but they were evolved through
divergent evolution
● Biochemical: can be seen in the changes that occur at the molecular level in organisms
over a period of time. These range from deletions, additions, or substitutions of single
nucleotides, through the rearrangement of parts of genes, to the duplication of entire
genes or even whole genomes.
○ Molecular evidence: A comparison of DNA nucleotide sequences and/or protein
amino acid sequences provides evidence for evolution and common ancestry.
Molecular similarities provide evidence for the shared ancestry of life. DNA
sequence comparisons can show how different species are related
● Mathematical: In population genetics, the Hardy–Weinberg principle, also known as the
Hardy–Weinberg equilibrium, model, theorem, or law, states that allele and genotype
frequencies in a population will remain constant from generation to generation in the
absence of other evolutionary influences
● Essential Knowledge: Molecular, morphological, and genetic evidence from extant and
extinct organisms adds to our understanding of evolution
○ Fossils can be dated by a variety of methods
■ The age of the rocks where a fossil is found
■ Carbon dating - the rate of decay of isotopes including carbon-14
■ Geographical data
○ Morphological homologies, including vestigial structures, represent features
shared by common ancestry
Antibiotic resistance
● Bacteria are among the fastest reproducing organisms in the world, doubling every 4 to
20 minutes
○ They reproduce asexually by binary fission
● A mutation can occur that leads to antibiotic resistance
○ When antibiotics are taken, the original bacteria die, but the remaining bacteria
are all resistant to the antibiotics and have high fitness.
○ They will survive and reproduce asexually by binary fission leading to an entire
population that are resistant.
Phylogeny
 ● Phylogenetic trees and cladograms show the evolutionary relationship of species over
lineages
● Phylogenetic trees are calibrated using the fossil record and molecular clocks to show
the amount of change
● Reading the diagram:
○ Time moves from bottom to top from oldest to most recent
○ A point of intersection, called the point of divergence/speciation represents a
different species
○ The lines represent the series of ancestors over time, leading to the present day
species
○ The line that comes before a point of divergence represent the shared
evolutionary history of the different species
● Shared derived traits: traits that indicate common ancestry
● Outgroup: the lineage that is least closely related to the remainder of the organisms in
the phylogenetic tree or cladogram
Punctuated equilibrium vs gradualism
● Gradualism: gradual change; evolution by natural selection as presented by Charles
Darwin
○ Hypothesis that life evolves by small, cumulative changes over long periods of
time
● Punctuated equilibrium: long periods of little/no change (stasis) and followed by rapid
bursts of speciation
○ Hypothesis that evolution occurs by isolated episodes of rapid speciation
between long periods of little or no change. Occurs within a short time period
Adaptive radiation and divergent evolution
● Divergent Evolution: when populations become separated by geographic barriers and
evolve independently into their own species. They evolve in their respective habitats and
become more different from each other over time.
● Adaptive radiation: a type of divergent evolution where a group of organisms quickly
diverge into new species.
○ New species radiate from a common ancestor. This tends to occur when
organisms move into a new environment with a lot of open niches.
Speciation
● What is a species:
○ A species is defined as a group of similar organisms able to interbreed to
produce fertile, viable offspring
○ Reproductive isolation: if a species is defined as its members interbreed and
produce viable, fertile offspring
○ The definition of a species has 2 parts: choose to mate, and have viable, fertile
offspring
■ Choose to mate: things that would prevent mating or prevent a zygote
from forming are called prezygotic barriers
 ● Barriers: geographic isolation, habitat isolation, behavioral
isolation, temporal isolation, mechanical isolation, and gametic
isolation
■ Have viable, fertile offspring: if mating does occur, postzygotic barriers
prevent viable, fertile offspring, keeping them as 2 seperate species
● Barriers: reduced hybrid fertility, reduced hybrid viability, and
hybrid breakdown
● Different isolations:
○ Geographical isolation: a geographical barrier separates 2 groups, so there is no
gene flow between them and they’re different species
○ Habitat isolation: there’s no physical geographical isolation, but their food
sources are in different locations
○ Behavioral isolation: courtship rituals such as dancing or mating calls are
different, and different species aren’t attracted by different rituals
○ Temporal isolation: species that breed during different times of dat, different
seasons, or different years cannot mix gametes; their mating seasons never
overlap
○ Gametic isolation: sperm from one species is unable to fertilize eggs from
another species; it is biologically impossible to fertilize an egg
○ Mechanical isolation: physical differences lead to reproductive isolation/doesn’t
physically allow mating
● Speciation:
○ Allopatric speciation: the 2 populations are living in different geographic regions
which prevent gene flow. Speciation occurs while they are geographically isolated
○ Sympatric speciation: the two populations are living in the same geographic
region and different isolating mechanisms prevent gene flow
● Hybrids:
○ Reduced hybrid viability: parents have incompatible genetics and the hybrid
offspring fail to develop
○ Reduced hybrid fertility: hybrids may be viable (strong, live life as normal) but
they are sterile due to different chromosome numbers from the two parents
○ Hybrid breakdown:
■ P - two different species mate
■ F1 - offspring is viable and fertile
■ F2 - offspring are not viable and fertile
Extinction
● Rock layers hold a record of life on earth - both speciation and extinctions
○ The fossil record also shows how often species go extinct naturally
○ Scientists can calculate the background rate of extinction
○ Background extinction rate refers to the number of species that would be
expected to go extinct over a period of time, based on non-anthropogenic
(non-human) factors.
 ○ A mass extinction event is when species vanish much faster than they are
replaced. This is usually defined as about 75% of the world's species being lost
in a 'short' amount of geological time
■ Usually due to ecological stress or rapid ecological changes, the species
are unable to adapt in a short amount of time.
○ Following a mass extinction, there are open niches that allow for radiation and
divergent evolution.
Variations in populations
● Population dynamics: the portion of ecology that deals with the variation in time and
space of population size and density fit one or more species
● The level of variation in populations affects population dynamics
● A population's ability to respond to changes in the environment is influenced by genetic
diversity
○ Species and populations with little genetic diversity are at risk of decline or
extinction
○ Genetically diverse populations are more resilient to environmental perturbation
because they are more likely to contain individuals who can withstand the
environmental pressure
● Natural selection is always happening, but which traits are beneficial depends on the
context in which the species lives and mates
○ Alleles that are adaptive in one environmental condition may be deleterious in
another because of different selective pressures (ex: peppered moth)
Origins of life on earth
● Most basic unit of life on earth: a cell
● Primordial soup theory: early earth atmospheric conditions were ideal for forming
monomers
● Extraterrestrial theory: life was brought to earth from somewhere else where it already
existed
● The first cells were autotrophic, meaning they could build all of their complex organic
molecules from simple inorganic ones
○ Ex: glucose could be made from formaldehyde in the alkaline conditions that
existed on early earth
● Catalyzing reactions:
● RNA world hypothesis: RNA could have been the earliest genetic molecule
● Cyanobacteria: oxygen was absent from our atmosphere until photosynthesis evolved,
which also then changed life on earth

UNIT 8

Responses to the environment

● Organisms respond to changes in the environment -
● Behavioral mechanisms:
○ Taxis: The movement of an organism in response to a stimulus
■ Positive taxis - movement towards a stimulus
 ■ Negative taxis - movement away from a stimulus
○ Kinesis: The undirected movement of an organism in response to a stimulus
○ Migration: A regular long-distance change in location
■ Environmental stimuli not only trigger behaviors, but also provide cues
that animals use to carry out those behaviors
○ Temperature regulation: Many mammals will alter their behavior depending on
the temperature
■ Nocturnal animals are active during the night while diurnal animals are
active during the day
● Physiological mechanisms:
○ Circadian rhythms: physical, mental, and behavioral changes that follow a
24-hour cycle
■ Plants and animals have circadian rhythms
○ Hibernation/Estivation: state of inactivity and reduced metabolic rate to survive
extreme weather conditions
■ Hibernation - helps animals survive cold weather conditions
■ Estivation - helps animals survive hot/dry weather conditions
○ Phototropism: the growth of an organism in response to a light stimulus
■ Ex: sunflowers turning towards sun
■ The hormone auxin migrates to the shady side of the plant and causes
the cell walls to elongate which causes the stem to curve towards the light
○ Photoperiodism: a plant’s response to changes I. The length of day and night
■ Short day plants - the plant flowers when uninterrupted darkness exceeds
critical night length (shorter days, longer nights)
■ Long day plants - the plant flowers when uninterrupted darkness is less
than the critical night length (longer days, shorter nights)
Communication
● Organisms exchange information with one another in response to internal changes and
external cues which can change behavior
○ Fight or flight response
■ An automatic physiological reaction to an event that is perceived as
stressful or frightening. The perception of threat activates the sympathetic
nervous system and triggers an acute stress response that prepares the
body to fight or flee
■ Biological processes that aren’t essential to survival stop so that energy
can be applied to escaping or fighting
○ Predator warnings: nuthatches vary their alarm cells based upon the source of
eavesdropped signals
○ Plant responses to herbivores
■ Individuals can act on information and communicate it to others
■ Communication occurs through various mechanisms:
■ Organisms have a variety of signaling behaviors that produce changes in
the behavior of other organisms and can result in differential reproductive
success.
 ■ Animals use visual, audible, tactile, electrical, and chemical signals to
indicate dominance, find food, establish territory, and ensure reproductive
success
○ Alarm pheromones: animals that communicate through odors or tastes emit
chemical substances called pheromones
■ Common in mammals and insects and usually involved in reproduction
■ Animals release specific odors into the air when they are stressed, and
these odors increase anxiety in conspecifics. These alarm odors or alarm
pheromones appear to be important signals that are evolutionarily
conserved because they are released by a variety of mammalian species,
including rats, deer, cattle, swine, and humans.
○ The territorial response of male sticklebacks is an example of a fixed action
action pattern - a sequence of unlearned acts directly linked to a simple stimulus
● Innate vs Learned behaviors
● Learning tied to natural selection
○ Parent/offspring interactions offspring survival depends on their ability to learn
from their parents
● Kin selection: a type of natural selection that considers the role relatives play when
evaluating the genetic fitness of a given individual. Kin selection occurs when an animal
engages in self-sacrificial behavior that benefits the genetic fitness of its relatives
Energy flow through ecosystems
● Metabolism - the sum of all chemical reactions within an organism
○ Generates heat (because energy transfer during chemical reactions is not 100%
efficient)
○ That heat can be used to maintain body temperatures (in endotherms)
○ This is related to ecology because the food we eat is the fuel for our chemical
reactions
○ There is a limited amount of available energy in each ecosystem
● Body temperature
○ Every organism on earth needs to regulate their temperature somewhat - if only
to prevent their cells from freezing and bursting open or to prevent proteins
denaturing in hot temperatures
● Endotherms vs ectotherms
○ Endotherms use thermal/heat energy generated by metabolism to maintain
homeostatic body temperatures
■ Have a higher tolerance for a wider range of environments
■ Use the heat generated from metabolism to maintain relatively constant
body temperatures - at least within a narrow range
○ Endotherms’ adaptations:
■ Vasoconstriction and vasodilation: blood vessels dilate to cool body down
or constrict to heat body up
■ Sweating and panting
■ Shivering and goosebumps
■ Countercurrent exchange
 ○ Ectotherms lack efficient internal mechanisms for maintaining body temperature,
though they may regulate their temperature behaviorally by moving into the sun
or shade or by aggregating with other individuals
■ Do not use their metabolism to generate heat (do not thermoregulate)
● Metabolic rate: the number of calories required to perform basic life-sustaining function
○ The smaller the organism, the higher the metabolic rate (think surface area to
volume ratio)
● The highly complex organization of living systems requires constant input of energy and
the exchange of macromolecules
○ A net gain in energy results in energy storage or the growth of an organism
○ A net loss of energy results in loss of mass, and ultimately the death of an
organism
● Food chains
○ A food chain shows the transfer of matter and energy from one organism to the
next
■ The arrows point in the direction that the energy flows
● Food webs
○ Shows how food chains connect and intertwine. A food web is a more realistic
representation of what happens in nature
● Producers: do photosynthesis/get their energy by producing it themselves
○ Autotrophs: capture energy from physical or chemical sources in the environment
○ Photosynthetic organisms: capture energy present in sunlight
○ Chemosynthetic organisms: capture energy from small inorganic molecules
present in their environment
● Consumers
○ Heterotrophs: capture energy present in carbon compounds produced by other
organisms
● Decomposers: break down dead plants or animals into the substances that plants need
for growth
● Ecological components:
○ Abiotic: non-living components; such as water, soil, and atmosphere
○ Biotic: living things within an ecosystem; such as plants, animals, and bacteria
● Plants/autotrophs are the bottom of the food and are the base for determining how much
energy is available in an ecosystem. The amount and quality of sunlight (abiotic) can
influence how much photosynthesis is possible in an area
○ Temperature and rainfall (abiotic) influence the types of plants and animals
(biotic) that grow and live in different ecosystems.
○ The earth’s rotation and wind patterns influence rainfall which then impacts plant
life.
● Biomes
○ Biomes are classified by their climate, which is determined by precipitation and
temperature, and by the community of organisms that live there.
● Trophic levels and energy transfer
○ Changes in energy availability can result in disruptions to an ecosystem.
 ○ A change in energy resources such as sunlight can affect the number and size of
the trophic levels.
○ A change in the producer level can affect the number and size of other trophic
levels
● Energy pyramid
○ An energy pyramid is a model that shows the flow of energy from one trophic
level to the next in an ecosystem
○ A pyramid of energy represents how much energy, initially from the sun, is
retained or stored in the form of new biomass at each trophic level in an
ecosystem
○ Changes in energy availability can result in changes in population size
Intro to ecology
● Population: members of the same species who live in a defined area
○ Members of a population rely on the same resources, are influenced by similar
environmental factors, and are likely to interact and breed together
● Population ecology: explores how biotic (living) and abiotic (non living) factors influence
density, distribution, and size of a population
● Dispersion/distribution
○ Where the individuals of a population are found within a geographic area in
comparison with each other.
○ Can be random, clumped, or uniform.
■ Clumped: when individuals in a population are clustered together, creating
some patches with many individuals and some patches with no
individuals.
■ Random: Individuals are arranged without any apparent pattern.
■ Uniform: individuals are spaced evenly throughout an area
● Factors that affect population growth:
○ Births, immigration, deaths, and emigration
● Population growth: exponential vs logistic -
○ Exponential growth: When a population grows as if there are unlimited resources,
we call that exponential growth.
■ Bacteria reproducing by binary fission is an example of exponential
growth.
■ The per capita growth rate stays the same, making the population grow
faster as it gets larger.
○ Population growth = dN/dt = B - D (change in population size/change in time =
birth rate minus death rate)
○ Populations can’t grow exponentially forever
○ Population density: measurement of how many individuals are in a specific area.
■ As the density changes, it has an impact on competition for food and
resources.
■ As population density increases, each individual has access to fewer
resources.
 ○ There are factors, both biotic and abiotic, that limit how large populations can
grow.
■ Biotic: competition, predators
■ Abiotic: amount of rain, sunlight
■ Called limiting factors
○ Density-independent limiting factors: natural disasters and pollution
■ A factor that affects the size of a population independent or regardless of
the population density
○ Density-dependent limiting factors: predation, disease, and competition
■ A limiting factor of a population wherein large, dense populations are
more strongly affected than small, less crowded ones.
○ Logistic growth:
■ The population will eventually reach a cap (called the carrying capacity) -
the max amount of species that the environment can support
■ The per capita growth rate gets smaller as the population approaches
carrying capacity (k)
■ Equation (takes carrying capacity into account): dN/dt = rmaxN(K - N/K)
○ Limiting factors: low food supply, disease, predators, limited space, nutrient
availability
● Exponential growth: the larger the population gets, the faster it grows. Logistic growth:
the larger the population gets, the slower it grows
Community ecology
● Biological Community: A group of populations of different species living close enough to
interact.
● How an organism interacts with individuals of other species in the community are called
interspecific interactions.
○ Competition
○ Predation
○ Herbivory
○ Symbiosis
○ Facilitation
● Competition:
○ Interspecific competition: Individuals of different species compete for a resource
that limits their growth and survival
● Competitive exclusion
● Ecological niche:
○ In ecology, the term “niche” describes the role an organism plays in a community
○ An ecological niche refers to the interrelationship of a species with all the biotic
and abiotic factors affecting it
○ A species' ecological niche can be defined as the range of resources and
conditions allowing the species to maintain a viable population
○ two species can occupy the same niche. One of them will be outcompeted.
● Resource partitioning: When species divide a niche to avoid competition for resources, it
is called resource partitioning
 ○ Species have evolved to share resources in the wild. Otherwise, one of the
species would die out.
○ Because of resources partitioning, that leads to a realized niche.
○ Fundamental niche is the entire set of conditions under which a species can
survive and reproduce. A Realized niche is the set of conditions actually used by
the species, after interactions with other species (predation and especially
competition) have been taken into account.
● Predation:
○ Predator/prey relationship - high prey population allows over-predation by the
predator, so the prey population decreases. Predators have a harder time finding
prey so their population decreases, and a spike in prey population allows the
predator's population to increase again. The cycle continues

○ Defensive adaptations of prey:

■ Cryptic coloration - blend in
■ Aposematic coloration - they purposely stand out to appear poisonous
■ Mullerian Mimicry is when two or more unpalatable resemble each other
■ Batesian Mimicry is when a harmless or palatable species mimics a
harmful or unpalatable species.
● Symbiosis: two different species interacting in a close relationship
○ Mutualism: Mutualism is a symbiotic relationship in which both species benefit.
■ The bees get to eat and act as pollinators for the flowers.
○ Commensalism: Commensalism is a symbiotic relationship in which one species
benefits while the other species is not affected
■ Barnacles benefit by attaching to the whale and the whale is unaffected.
 ○ Parasitism: Parasitism is a symbiotic relationship in which one species benefits
while the other species is harmed.
■ The tick benefits from the blood while the dog is harmed.
● Facilitation: Species have positive effects (+/+ or 0/+) on the survival and reproduction of
other species without necessarily living in the direct and intimate contact of a symbiosis.
● Species diversity:
○ Species richness: number of a different species in the community
○ Relative abundance: The proportion each species represents of all individuals in
the community
○ Simpson's Diversity Index: a measure of diversity which takes into account the
number of species present, as well as the relative abundance of each species.
As species richness and evenness increase, so diversity increases. n = the total
number of organisms of a particular species.
■ D = 1 - the sum of (n/N)2
■ n = number of specific species
■ N = number of all species
● Species with a large impact
○ Dominant species: the most abundant species
○ Keystone species: Not usually abundant in a community, but exert strong control
on community structure—not by numerical might, but by their pivotal ecological
roles or niches.
● Trophic cascades
○ Trophic cascades are powerful indirect interactions that can control entire
ecosystems. Trophic cascades occur when predators limit the density and/or
behavior of their prey and thereby enhance survival of the next lower trophic level
● Ecological succession:
○ Ecological succession is the process by which the mix of species and habitat in
an area changes over time. Gradually, these communities replace one another
until a climax community is reached, or until a disturbance, like a fire, occurs
○ Primary succession -
■ pioneer species will be the first to arrive and can grow on bare rock
(pioneer species: lichen)
■ Eventually, small grasses and weed type producers will replace the
lichens
■ As time goes by, shrubs will begin to outcompete the grasses and will
begin to replace them
■ Eventually, small trees will begin to grow and they will create shade for
the shrubs growing below. This is an example of plants outcompeting
each other for light.
■ An ecological community in which populations of plants or animals remain
stable and exist in balance with each other and their environment. A
climax community is the final stage of succession, remaining relatively
unchanged until destroyed by an event such as fire or human
interference.
 ○ Secondary succession -
■ Occurs after an ecological disturbance such as a forest fire or humans
clearing land for agriculture.
■ Doesn’t start on bare rock - there’s already soil
Biodiversity
● Biodiversity - diversity within a species (genetic diversity), different types of species
(species diversity), or between ecosystems (ecosystem diversity)
● Natural and artificial ecosystems with fewer component parts and with little diversity
among the parts are often less resilient to changes in the environment.
● Keystone species, producers, and essential abiotic and biotic factors contribute to
maintaining the diversity of an ecosystem.
● The diversity of species within an ecosystem may influence the organization of the
ecosystem.
● The effects of keystone species on the ecosystem are disproportionate relative to their
abundance in the ecosystem, and when they are removed from the ecosystem, the
ecosystem often collapses
Disruption to ecosystems
● There are six major ways that humans are disrupting ecosystems and causing the
extinction of species on earth:
● Habitat loss:
○ Since the dawn of human civilization, we have cut down 46% of the trees on
earth.
○ Currently, the rate of loss due to deforestation is 64 million acres per year and
has been growing rapidly in the last five years.
○ The leading cause of deforestation of the Indonesian rainforest is to plant a
monoculture of palm oil trees.
■ Results in an incredible reduction in biodiversity.
○ A monoculture is a single crop
● Invasive species:
○ Native species: their ecological niche is part of the existing community/ecosystem
○ Non-native species: an introduced species to an area that is not native to the
region. Their presence is not necessarily harmful or destructive
○ Invasive species: an introduced, non native species that undergoes exponential
growth in an area due to the lack of predators or disease in that region and
outcompetes or preys upon native species
■ The intentional or unintentional introduction of an invasive species can
allow the species to exploit a new niche free of predators or competitors
or to outcompete other organisms for resources
■ For invasive species, the availability of resources can result in
uncontrolled population growth and ecological changes.
● Population growth and pollution:
○ Biological magnification: pollutants accumulate and get higher in levels as they
move up the food chain, so the species at the top is more affected by the
pollutants
 ○ Eutrophication: farmers fertilize the soil with nitrogen and phosphorus, which runs
off into the water, and the excess nutrients cause algal blooms.
■ The algae die soon after, leading to an increased decomposer population,
the decomposers consume oxygen, and all life dies
● Over-exploitation:
○ Overfishing
● Climate change:
●