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AP Biology Study Guide
I.
Biochemistry
A. Be able to recognize the molecular structure of
1. Cellulose- Complex sugar, polymer, CHO,
2. Glycogen- Polymer of Glucose, energy storage, C24H42O21
3. Phospholipid- Three fatty acid chains attached to phosphate group at the head,
amphipathic, crucial to the phospholipid bilayer/cell membrane
4. Triglycerides- aka Fatty Acids, three fatty acid chains attached to glycerol head, body fat in
animals
5. Steroid- All are cholesterol based, characterized by the 5-Carbon rings with a tail,
examples include Cortisol, Testosterone, and Estrogen
6. Polypeptides- Building blocks of proteins, assembled from long chains of Amino Acids
(polymer), can be a protein alone or quaternary structure will combine many to form a protein
7. Amino Acids- Building blocks of polypeptides, monomer, characterized by Amino Group
(H3N), Carboxyl Group (COOH), and R Group (differs between amino acids), can be polar or
nonpolar, there are twenty amino acids, but nine are essential amino acids (cannot be produced
by the body)
8. ATP- Adenosine Triphosphate, main cellular source of energy
9. Glucose- Simple sugar, monomer, C6H12O6
B. Vocab:
Isomers- Molecules that have the same molecular formula, but different structures. For
example, butane and isobutane.
Monomer- A single molecule that can be binded to other monomers to form polymers. Example:
Amino Acids
Polymers- Chains of more than one monomer. Example: Polypeptides
pH- The acidity or basicity of an aqueous solution. Scale ranges from 1-14 with lower numbers
being acidic, higher being basic, and 7 being neutral.
Amphipathic- A molecule with a non polar and a polar side is described as amphipathic.
Example: Phospholipids (polar, hydrophilic heads and nonpolar, hydrophobic tails).
C. Proteins:
Primary Structure- 2-D chain of amino acids
Secondary Structure- Assembly of the chain of amino acids using Alpha Helix and Beta-Pleated
Sheets (think spiral and accordion), Hydrogen bonds (weak), Heat denatures a protein by
breaking down the secondary structure (hydrogen bonds are broken)
Tertiary Structure- Creation of the polypeptide chain, using stronger bonds (disulfide bridges,
covalent bonds) to fold protein into polypeptide, acids and bases destroy the bonds in the
tertiary structure when denaturing a protein, salts can destroy disulfide bridges in tertiary
structure
Quaternary Structure- Not applicable if protein is only one polypeptide, multiple polypeptides
fold to create a protein
II. Cells
A/B.Organelles:
Mitochondria- The powerhouse of the cell, found in eukaryotic cells, breaks down materials and
nutrients for energy purposes, consists of matrix, inner membrane, and outer membrane, Krebs
Cycle occurs in matrix and ETC occurs in inner membrane
Chloroplasts- Chlorophyll containing organelles that performs photosynthesis, found in plant
cells (and algae), consists of thylakoid membrane, lumen, stroma, inner/outer membrane, and
grana, the light-dependent reactions occur along the Thylakoid Membrane (ETC) , and the
Calvin Cycle occurs in the stroma
Vacuoles- Storage vesicles found in plant and animal cells, have more important role in plant
cells, store vital nutrients for the organism and waste to protect the cell
Ribosomes- Organelles that work closely with the Endoplasmic Reticulum to create proteins,
one of their most important functions is creating mRNA through DNA transcription, found in
eukaryotic and prokaryotic cells
Lipid Bilayers- The phospholipid bilayer is composed of opposing phospholipids with the
hydrophilic, polar heads facing outwards and the hydrophobic, nonpolar tails facing each other.
The bilayer is semipermeable and makes up the plasma (or cell) membrane.
C. Plasma Membrane
The plasma membrane is composed of the phospholipid bilayer with proteins dispersed
throughout. The proteins are used as channels for specific molecules to enter, or leave, the
cell. The plasma membrane is crucial to the success of the cell and is semipermeable to allow
some molecules in and bar others from entering.
D. Saturated vs. Unsaturated vs. Trans Fats
Saturated fats are fats whose carbons are entirely saturated by hydrogen atoms (aka no double
bonds between carbons in the fatty acid chains). These fats are highly stackable, meaning they
clog arteries and increase the risk of atherosclerosis. They are solid at room temperature and
can be found in red meat. Unsaturated fats have a double bond between at least two carbons
in the fatty acid chain, therefore they have a bend in the chain. This bend makes them unable
to stack as easily and are therefore considered healthier fats. They are liquid at room
temperature and can be found in oils. Finally, trans fats are chemically manipulated
unsaturated fats that have been saturated with an additional hydrogen to make them stackable
again. They are not naturally occurring and are very unhealthy.
E. Diffusion/Osmosis, Osmolarity, Solute Concentration, Isotonic, Hypertonic, Hypotonic
Diffusion- The movement of particles from regions where they are in higher concentration to
areas of lower concentration.
Osmolarity- The concentration of a solution.
Solute Potential= -iCRT where i=the ionization constant (1.0 for sugars, 2.0 for NaCl), C=molar
concentration, R= 0.0831 (ALWAYS), T=Temperature in Kelvin (celsius+273).
Isotonic- A solution that is isotonic has an equal balance of water/other solution. Though it is at
equilibrium, molecules still flow across the membrane just at an equal rate.
Hypertonic- Concentration of solutes is greater outside than inside. Example: Celery shrivels in
salt water because the salt water is hypertonic to the celery (higher concentration of fresh water
in the celery than in the salt water).
Hypotonic- Concentration of solutes is greater inside than outside.
F. Transport Across Membranes
1. Active Transport- The movement of ions or molecules across a cell membrane assisted
by enzymes and requiring energy.
2. Osmosis- The diffusion (movement across a semipermeable membrane from an area of
lower to higher concentration) of water.
3. Chemiosmosis- The movement of ions across a semipermeable membrane against their
gradient. Example: the movement of H+ ions across the mitochondrial inner membrane
to generate ATP.
4. Facilitated Diffusion- The spontaneous movement of ions or molecules across a
membrane without using energy (passive transport).
5. Plasmolysis- The process where cells lose water in a hypertonic solution.
G. Surface to Volume Ratios and Relevance
The cell is small because its surface area to volume ratio is the most efficient that way. If the
cell got larger, the ratio would get smaller and the cell would not be able to transport particles
across its membrane efficiently.
III. Cell Metabolism
A. Metabolic Rates in Ectotherms vs. Endotherms
Endotherms generate their heat internally and their body temperature does not rely on the
outside temperature (hypothermia is so deadly because of how it affects the internal
temperature due to outside temperature). Ectotherms, on the other hand, rely on the outside
environment for their internal temperature ie the goldfish slowing their metabolic rate as the
water was cooled.
B. Establishment of Chemical Gradients/ATP Production
In both photosynthesis and cellular respiration, the ETC requires a chemical gradient of H+ ions
in order to function. The NADH/FADH2 and NADPH will drop H+ ions off at the site of the ETC.
These H+ ions will naturally diffuse across the membrane, creating a concentration gradient, to
balance both sides. As these H+ ions flow BACK across the membrane, they go through ATP
Synthase (the enzyme that will produce ATP) and power ATP production. If something (such as
Cyanide) were to block these H+ ions from going back through the membrane, then ATP
production would stop, the difference in pH between the two sides of the membrane would
increase, and the organism would die. Extra Information: Cyanide binds with Oxygen (the final
electron acceptor) and pulls it from ATP Synthase, which is why the H+ cannot flow through
anymore.
C. During which processes of photosynthesis/cellular respiration is ATP produced?
In cellular respiration, ATP is produced in glycolysis, the Krebs Cycle, and in the ETC. In
photosynthesis, ATP is only produced in the light reactions. The Calvin Cycle produces sugars.
D. Anaerobic vs. Aerobic Respiration
The only processes of anaerobic (no oxygen) respiration are glycolysis and fermentation. All
other respiration requires the presence of oxygen to work. Anaerobic respiration is much less
efficient than aerobic respiration, as glycolysis only produces 2 ATP and fermentation produces
just 2 as well. Lactic acid fermentation (the burning in your muscles) is the process of taking the
pyruvate from glycolysis and turning it into lactic acid. The lactic acid then goes to the liver.
Alcohol fermentation (yeast) is where the pyruvate becomes ethanol and carbon dioxide.
E. Terms:
Oxidative Phosphorylation- AKA the Electron Transport Chain
G3P- A 3-Carbon sugar produced in the Calvin Cycle that is the base for the synthesis of other
carbohydrates.
Lactate/Lactic Acid- Produced in lactic acid fermentation from pyruvate. Lactic acid is then
taken to the liver and converted back to glucose.
Acetyl CoA- Delivers the Acetyl group in the Krebs Cycle to be oxidized for energy production.
Citric Acid- The starting and ending point of the Krebs Cycle (also why it is named the Citric
Acid Cycle).
NAD+/NADH- The oxidized and reduced forms (respectively) of the electron carrier used in
cellular respiration to bring the H+ ions to the ETC. It is considered more valuable than FADH2
and is produced in glycolysis and the Krebs Cycle.
NADPH- The reduced form of the electron carrier that is used in photosynthesis to bring H+ ions
to the ETC.
RuBisCo- Enzyme in photosynthesis that converts CO2 into usable carbons.
F. Enzymes!
Enzyme Catalyzed Graph- The graph shows an exergonic reaction because the change in G is
less than 0.
Exergonic/Endergonic- Exergonic reaction are where energy is being released while endergonic
means that energy is being consumed.
Free Energy- The amount of work that a system can perform.
Catabolism/Anabolism- Catabolism means that energy is being released and molecules are
being broken down. Anabolism means energy is consumed to combine smaller molecules and
make more complex ones.
Active Site- The region of the enzyme that binds to a reactant.
Competitive Inhibitors- Something that binds to the active site of an enzyme and prevents the
substrate from doing so.
Allosteric Reactions- The regulation of enzymes by binding a molecule to somewhere other than
the active site.
V. Cell Communication
A. Target Cells and Ligands
Target Cells- A cell that has receptors for a hormone or other signaling molecule ie liver cells for
insulin, sertoli cells for testosterone, etc.
Ligands- A molecule that binds to another larger molecule.
B. Cascade of Events
C. Positive vs. Negative Feedback
Negative Feedback- This occurs when systems need to slow down or stop a process that is
currently taking place. An example of this would be the stopping of the secretion of acid into the
stomach or your body counteracting rising body temperatures.
Positive Feedback- This occurs when physiological processes need to start or be amplified. For
example, the starting of the secretion of acid into the stomach or your body shivering when you
are cold.
D. Pancreas: Insulin vs. Glucagon
Insulin- A hormone produced by the beta cells of the pancreas that helps the body break down
sugars and carbohydrates. It is released when blood sugar levels get too high. Diabetes is a
complication in the production (Type 1) or a built up immunity towards (Type 2) insulin.
Glucagon- A hormone produced in the alpha cells of the pancreas that helps regulate blood
sugar levels when they get too low.
E. Endocrine Organs and Functions
Pancreas- The pancreas produces glucagon and insulin in its alpha and beta cells, respectively.
These hormones help regulate blood sugar levels in the body (above).
Thyroid- The thyroid takes iodine and makes it into thyroid hormones. It is the only part of the
body that can absorb iodine and the hormones that are created help regulate growth,
metabolism, libido, and more.
Hypothalamus- The hypothalamus is the portion of the brain that is the control center of the
endocrine system. It sends signals to the endocrine system via the pituitary glands.
Adrenal Glands- The adrenal glands are located at the top of the kidneys and produce various
hormones that perform a few functions: regulating blood sugar, blood pressure, burning protein
and fat, and reacting to stressors. Most importantly, they produce cortisol (stress hormone) and
aldosterone (osmoregulation hormone).
Reproductive Organs- The ovaries and testes produce various hormones (most notably
testosterone and estrogen) that are crucial to menstruation, reproductive health, and the overall
health of the body.
F. Hormones in Plants and Animals
Oxytocin- The release of oxytocin is controlled by the pituitary gland and the hormone is most
important in breastfeeding and childbirth. During childbirth, oxytocin signals contractions of the
womb.
Ethylene- “One rotten apple ruins the whole bunch” This is true because ripening plants release
the hormone ethylene that leads other plants to ripen as well. Therefore, a rotten apple will
release so much ethylene that those around it will spoil as well.
Epinephrine- Also known as adrenaline, epinephrine is released when the body feels strong
emotions such as anger or fear. Epinephrine is a vasodilator and bronchodilator, making it very
effective in treating severe allergic reactions.
Cortisol- The stress hormone; cortisol is a steroid that causes you to crave carbohydrate-heavy
foods and drains the glycogen stores of the body. It is the reason why chronic stress can lead
to significant weight loss because once the glycogen stores are depleted the body will tap into
its adipose tissue.
VI. Ecology (a little bit)
A. Food webs
Food webs show which organisms consume what and link the lowest on the food chain to the
highest. It is most easily explained through examples.
B. Trophic Levels
Trophic levels are the hierarchy of the food chain in an ecosystem that are comprised of
organisms that share the same function in the food chain and the same nutritional relationship
to the primary sources of energy. A general trophic system would look like the following:
Level 1 (Primary Producers): These are the plants and algae that produce their own food from
the sun.
Level 2 (Primary Consumers): Herbivores that eat plants.
Level 3 (Secondary Consumers): Carnivores that eat herbivores.
Level 4 (Tertiary Consumers): Carnivores that eat other carnivores.
Level 5 (Apex Predators): Have no predators and are the top of the food chain.
C. Sources of Energy
The sun is the ultimate source of energy in all ecosystems as it powers the most basic level of
the chain: the producers. Those who use the sun to create their own food are known as
producers and are the next level in ecosystems. Then, there are the consumers which can
come in any number of levels, but are known as such because they eat other consumers or they
eat the producers. Finally, there is the decomposers, such as fungi, who feed off of the
decomposition of other organisms.
D. Energy Flows and Matter Cycles
The maintenance of an ecosystem relies on the flow and cycle of energy. The energy initially
comes from the sun but is cycled between the producers, the consumers, the decomposers,
and the nutrient pool from which the producers get supply.
All of the organic matter used in an ecosystem is recycled into carbon dioxide, water, and
minerals. That is the cycle of matter.
VII. Evolution
A. Darwin’s Principles of Natural Selection
Darwin’s Theory states that there are variations in a population and that these variations are
inherited from your ancestors. Furthermore, organisms will produce more offspring that are
more likely to survive, considering many offspring will die in nature a parent must produce many
offspring to ensure that some survive. The individuals with the best traits for their environment
will survive and reproduce. This is natural selection in its simplest form: survival of the fittest.
Finally, a population will change over time. As the habitat and environment of certain species
changes, so too will that species.
B. Mutations as a Source of Evolution
Mutations, or the random change in a DNA sequence, are sources of evolution and, despite the
negative connotation, can have positive effects. All mutations are random and the significant
majority of mutations bear no effect on evolution or an organism. However, sometimes
mutations can be highly beneficial. If a population of mice live on white rock, but the ash from a
volcanic eruption makes this environment black, then the white mice will stick out. However, if
one mouse has a mutation that makes its fur black, it is now most likely to survive thanks to a
beneficial mutation. As that mouse reproduces, the mutation evolves to cover the population.
C. Cladograms
A cladogram is a branching diagram that is used to show the relationship between species and
organisms. A cladogram is read from left to right with the oldest species (or least closely
related) being all the way to the left. Any link between two or more species is a common
ancestor. The closer two species are on the central line, the more closely related they are. A
line between two species signifies a homologous structure between the two. Finally, any branch
off of another branch (rabbits from primates) signifies a shared structure between only them and
they are the most closely related to each other.
D. Data Interpretation of Differences in Nucleotide Sequences
In certain genes, a species may have a nucleotide sequence that is 99% similar to another
species, but be completely different. Of course chimpanzees and humans are very different, but
their nucleotide sequences are nearly identical. As nucleotide sequences become more and
more different, species become less and less related.
E. Derived Characters
Derived Characteristics are the traits shared by groups of organisms with a common ancestor
and many similar traits (also known as a clade).
F. Homologous/Analogous Structures, Vestigial Organs, Convergent/Divergent Evolution
Homologous Structures- These are organs, bones, or bone structures that appear in different
species and imply a common ancestor between these species. For example, all four-legged
animals have the same leg/arm pattern of bones, which implies they share a common ancestor.
Analogous Structures- These are structures that can be found in different species that perform
the same function, but have evolved separately and therefore do not imply a common ancestor.
For example, the wings of birds and the fins of fish are similar, but not derived from the same
common ancestor.
Vestigial Organs- A vestigial organ, or structure, is something that is completely rudimentary
(useless) today, but may have been important to ancestors. Examples would be the wisdom
teeth and the appendix.
Convergent Evolution- This is the process where organisms, that are completely unrelated,
independently evolve similar traits as a result of living in similar environments or fulfilling similar
niches. An example would be the evolution of flight in birds and in insects.
Divergent Evolution- This is the process where organisms from a species independently evolve
and form their own, new species. An example of this would be Darwin’s finches whose beaks
evolved on different islands for different food types and all became a new species.
G. Conservation of Vital Genes
Vital genes are genes that are crucial to the survival of an organism. These are genes that will
be preserved through natural selection because they maximize the potential to survive. They
are also known as essential genes.
H. Evidence for Evolution
Evidence for evolution comes through the similarities in living organisms today, the similarities
of embryos, and the fossil layers of the earth. In living organisms, we see many homologous
structures and similar DNA sequences that point us towards the theory of evolution. The fact
that all four-legged animals have homologous structures leads us to understand that they must
all share a common ancestor from whom they evolved. Furthermore, the embryos of many
totally unrelated organisms share a variety of traits, as seen below. Finally, the fossil layers of
the earth show us the variety of species and variation between species in earth’s past. As we
move from layer to layer we see how animals, living in the same areas, changed over time.
I. Stabilizing, Disruptive, and Directional Selection
Disruptive Selection- Type of natural selection where both extremes of a trait are favored over
the average and the population moves towards the extremes.
Stabilizing Selection- Type of natural selection where genetic diversity decreases and the
population stabilizes around one trait.
Directional Selection- Type of natural selection where one extreme of a trait is favored and so
the population strays from the average and leans solely towards the favored extreme.
J. Speciation
Speciation is the formation of new and distinct species (no interbreeding or mingling) through
the course of evolution. This occurs in two ways: allopatric and sympatric speciation.
Allopatric Speciation- This is speciation that occurs where the two new species are entirely
isolated from each other. For example, fish migrate through the Panama Canal and now there
is one species of fish in the Atlantic ocean and the other in the Pacific ocean.
Sympatric Speciation- This is speciation that occurs in the same geographic region. For
example, the fish break off into two new species, but both still live in the Atlantic ocean. Another
example is resident orcas and transient orcas, who both live in the northeast Pacific, but do not
mingle or interbreed.
K. Reproductive Isolation that leads to Speciation
Reproductive Isolation is the collection of evolutionary mechanisms, behaviors, and
physiological processes that are critical for speciation. These include…
Geographic- When species move locations, evolve, and no longer breed with their former
species.
Behavioral- Different behaviors led to the species not interbreeding, for example different mating
calls.
Temporal- The two species have different mating periods so they do not interbreed.
Pre-Reproductive (Zygotic)- Isolation prior to the formation of a zygote (temporal, behavioral,
etc).
Post-Reproductive (Zygotic)- Isolation after a zygote is formed ie through hybrid infertility etc.
L. Polyploidy
Polyploidy is where cells and organisms contain more than two paired sets of chromosomes
(diploid). If an organism is a polyploid it will not reproduce with members of its species--its own
form of speciation.
M. Hardy-Weinberg Equilibrium
The equations for Hardy-Weinberg Equilibrium is p2+2pq+q2=1 and p+q=1
Where p is representative of the dominant allele and q is representative of the recessive allele.
Hardy-Weinberg Equilibrium assumes the following: there are no mutations, there is no
immigration or emigration, it is a large population, there is only random mating, there is no
natural selection (all offspring are equally fit to to survive).
VIII. Experimental Design
A. Independent vs Dependent Variables
The dependent variable is what the experiment is testing and is reliant upon the independent
variable. Typically, experiments will observe the change in the dependent variable and how it
relates to the independent variable. For example, in an experiment where scientists are testing
the impact of a drug on cancer, the independent variables are the dosages used and the
dependent variable is the impact of the drug on cancer.
B. Histograms and Scatter Plot Interpretation
Histogram
Scatter Plot
C. Identifying Controls
Controls are simply a benchmark or baseline test in an experiment that are not being given the
treatment of the experiment. Controls are used as ways for scientists to rule out alternate
results. An example of this would be administering drugs to patients and placebos to patients
as well (with the placebos being the control) to rule out the placebo effect.
IX. Important Vocabulary
A. Biochemistry
Denaturation- The disassembly of the structures protein or polypeptide due to sharp changes in
pH and temperature.
Ion- An atom or molecule with an electric charge.
Macromolecule- A large complex molecule; four big ones are lipids, carbohydrates, proteins,
and nucleic acids.
Monosaccharide- The simplest sugars such as glucose.
Peptide Bond- The bonds between amino acids.
Polysaccharide- A carbohydrate that is composed of multiple sugars bonded together such as
sucrose or starch.
B. Cells/Cell Communication/Cell Metabolism
Aquaporin- Channel proteins in the cell membrane that specifically deal with the flow of water.
Carrier Protein- A protein that carries specific substances into and out of the cell through the cell
membrane.
Channel Protein- A protein in the cell membrane that acts as a tube for certain substances to
move into and out of the cell.
Endocytosis- The process of engulfing and capturing an outside substance with the cell
membrane and bringing it into the cell. This process requires energy.
Exocytosis- Where vesicles fuse with the plasma membrane to release larger molecules. This
process requires energy.
Fluid Mosaic Model- A model of the plasma membrane that describes it as composed of
phospholipids, carbohydrates, and proteins and is semipermeable.
Glycoprotein- These are proteins with a sugar attached to them that give structure to cells,
facilitate digestion, and help form connective tissue.
Phagocytosis- The energy-consuming process of engulfing a small particle that is most
commonly performed by prokaryotes and protists.
Transcription- This is the process of copying a specific segment of DNA into RNA that is
performed by RNA polymerase. This process can be initiated by steroid hormones and protein
hormones.
Transcription Factor- Proteins that are involved in the process of converting DNA into RNA. AN
example would be kinase.
Transmembrane Protein- A protein that spans the entirety of the cell membrane and functions
as a gateway.
Turgor/Turgor Pressure- The rigidity of cells due to the absorption of water. Turgor pressure is
the water pressure inside plant cells.
Water Potential- This is equal to solute potential (above)+pressure potential (0 in an open
container). Water will move from HIGH water potential to LOW water potential and solutes
always lower water potential.
C. Ecology/Evolution
Adaptation- An adaptation is a trait that provides a species an advantage and is evolved through
natural selection.
Bottleneck Effect- This is the idea that if a population were to be squeezed down to very few
organisms and then built back up again, the gene pool of the new population would be highly
concentrated around the traits of the few organisms that did survive. In other words, the
population is squeezed so much that there is significantly less genetic variation in the resulting
larger population.
Endosymbiosis- This is the theory that the mitochondria and chloroplasts were once their own
organisms, but were consumed by eukaryotic cells and became organelles. The theory is
supported by the fact that both have their own DNA, can replicate their own DNA, and can
multiply on their own.
Founder Effect- This is the idea that when a new population is created by a small number of
organisms, the genetic variation is limited to essentially only what traits those original organisms
had.
Gene Flow- The transfer of alleles or genes from one population to another. This can be
caused by migration.
Genetic Drift- Random changes in the frequency of alleles in a gene pool that typically occurs in
small populations. This is closely related to the Founder Effect.
Genotype- The genotype is the genetic makeup of an organism (ie AA, Aa, or aa).
Phenotype- The phenotype is the physical characteristic of the genetic makeup of an organism
(ie red hair, blonde hair, or brown hair).