AP Bio Exam Notes

AP Bio Exam Review Plan

Download checklist at apossu.
Use three highlighters: red, green, and yellow.
Stoplight method:
- Green: Know well.
- Yellow: Know a little.
- Red: Don't know at all.
Prioritize studying:
- Red items first.
- Then yellow items.
- Keep green topics fresh.

AP Bio Unit One: Chemistry of Life

Topic 1.1: Water and Hydrogen Bonding

Water is polar and forms hydrogen bonds (weak intermolecular bonds).
Water acts as the universal solvent.
Key properties: cohesion, adhesion, surface tension, and high specific heat.
Hydrogen bonding is present in DNA, RNA, and proteins.

Topics 1.2 to 1.3: Elements of Life, etc.

Molecules of life are built from monomers combining into polymers.
- Dehydration synthesis: combines monomers into polymers.
- Hydrolysis: takes polymers apart.
Carbohydrates:
- Used for energy storage and structure.
- Monosaccharides: energy storage.
- Disaccharides: energy transport.
- Polysaccharides: energy storage (starch) or structure (cellulose in cell walls).
Lipids:
- Non-polar.
- Key unit: fatty acid (saturated or unsaturated).
- Saturated: more solid.
- Unsaturated: bends and kinks, more liquid.
- Functions: energy storage (fats and oils), waterproofing (waxes), membrane formation (phospholipids), signaling (steroids).
Phospholipids:
- Hydrophobic non-polar tail and hydrophilic polar head.
- Form phospholipid bilayer in water (heads bond with water, tails form water-free zone).
Proteins:
- Diverse functions: motion, enzymes, building structures, transport, energy storage, signaling.
- Monomers: amino acids (amino group, carboxy group, R group).
- Four levels of structure:
  - Primary: Linked genetically determined sequence of amino acids.
  - Secondary: Alpha helices and beta-pleated sheets (interactions in polypeptide backbone).
  - Tertiary: Complex turns and loops (R group interactions).
  - Quaternary: Aggregation of multiple polypeptide chains.
Nucleic acids:
- Molecules of heredity.
  - DNA: primary hereditary material in cells.
  - RNA: information transfer (messenger RNA); can catalyze reactions (ribosomes, splices, microRNAs).
- Monomers: nucleotides (five-carbon sugar, nitrogenous base, phosphate group).
- DNA vs. RNA:
  - Different sugar (deoxyribose vs. ribose).
  - Different bases (A, T, C, G in DNA; A, U, C, G in RNA).
DNA structure:
- Double-stranded (double helix).
- Two sugar-phosphate backbones.
- Base pairing rules: adenine with thymine, cytosine with guanine.
- Anti-parallel structure (5' to 3' ends).

AP Bio Unit 2: Cell Structure and Function

Prokaryotic vs. Eukaryotic Cells:
- Differences in size, structure, and DNA packaging.
Cell Biology Focus:
- Knowledge of overall cell geography is important.
- Animal cell parts.
- Plant cell differences marked in bold.

Topic 2.3: Cell Size

Cells are small to maximize surface area to volume ratio.
Increased size reduces surface area relative to volume.
Adaptations to increase surface area: gills, elephant ears, mitochondrial membrane folding, intestine lining.
Adaptations to decrease surface area: whale size (less heat loss).

Topics 2.4 to 2.9: Membrane Structure and Function

Membrane function: selective permeability (controlling entry/exit).
Phospholipids form framework (see Unit One).
Fluid mosaic model: phospholipids, protein, and cholesterol moving in the membrane.
Molecules and their functions:
- Phospholipids: membrane framework.
- Cholesterol: fluidity buffer (stability at high temperatures, fluidity at low temperatures).
- Proteins: transport, cytoskeleton attachment, membrane-embedded enzymes, signal transduction, cell-cell recognition.

Membrane Transport

Diffusion: movement from higher to lower concentration (spontaneous, passive transport).
- Simple diffusion: small, non-polar molecules (oxygen, carbon dioxide), lipids (steroids, fats).
- Facilitated diffusion: polar molecules and ions need channels (protein channels).
Active transport: requires energy (ATP to ADP) to pump molecules up a concentration gradient.
Bulk transport:
- Endocytosis: membrane buckles in, brings fluid/materials into a vesicle.
- Exocytosis: vesicles fuse with membrane, dumping contents outside.
Osmosis: diffusion of water from higher to lower water concentration (hypotonic to hypertonic).
Water potential: formal way to discuss osmosis.
- Equation: $Water Potential = Solute Potential + Pressure Potential$
- Adding solute decreases water potential.
- Adding pressure increases water potential.

Topics 2.10 through 11: Cellular Compartmentalization

Cells have internal compartments with special pH, chemistry.
Endomembrane system: nuclear membrane, rough and smooth ER, vesicles, Golgi, lysosomes.
Mitochondria and chloroplasts:
- Not part of the endomembrane system.
- Endosymbionts (descendants of independent organisms).
- Evolved from free-living bacteria.
- Evidence: own circular DNA, binary fission, bacteria-like ribosomes, protein synthesis, two membranes.

AP Bio Unit 3: Cellular Energetics

Enzymes: protein catalysts that lower the activation energy of reactions.
- Highly specific; bind substrates at active sites.
- Sensitive to pH and temperature (denatured).
- Denaturing: active site shape changes, preventing substrate interaction.
- Competitive inhibition: molecule competes for active site.
- Non-competitive inhibition: molecule binds to allosteric site, changing active site shape.
- Allosteric regulation: modulates enzyme activity.

Topic 3.4: Cell Energy

Metabolic pathways:
- Linked series of reactions controlled by enzymes.
- Linear (glycolysis) or cyclical (Krebs cycle, Calvin cycle).
- Exergonic reactions release energy.
- Endergonic reactions require energy.
ATP:
- Energy coupling.
- Ribose (five-carbon sugar), nitrogenous base, three phosphate groups.
- Adenine (monomer of RNA).
- ATP from ADP + phosphate is endergonic.
- ATP to ADP + phosphate releases energy for cellular work (exergonic).

Topic 3.5: Photosynthesis

Photoautotrophs use light energy to combine carbon dioxide and water to create carbohydrates.
Oxygen is released as a waste product.
Formula: $6CO2 + 6H2O + Light Energy \rightarrow C6H{12}O6 + 6O2$
Two phases:
- Light reactions: light energy converted into chemical energy (ATP and NADPH).
- Calvin cycle: energy in ATP and NADPH converted into carbohydrates (G3P).
Light reactions:
- Light powers electrical current that powers proton pumps.
- Facilitated diffusion through ATP synthase generates ATP.
- Photosystems: proteins packed with chlorophylls; convert light energy into electricity.
- Water molecule splitting: source of oxygen, creates protons.
Calvin cycle:
- Three phases:
  - Carbon fixation: $CO_2$ incorporated into a six-carbon compound, broken into a three-carbon compound.
  - Energy investment: ATP and NADPH used to energize the compound, creating G3P.
  - Regeneration: G3P combined to regenerate RuBP, requiring more ATP.

Topic 3.6: Cellular Respiration

Cells take glucose and convert it into ATP.
Plants do both cellular respiration and photosynthesis; animals only do cellular respiration.
Four stages/phases:
- Glycolysis.
- Link reaction.
- Krebs cycle.
- Electron transport chain.
Oxidizing food (glucose) and creating mobile electron carriers (NADH and $FADH_2$ ).
Glycolysis and the Krebs cycle make little bit of ATP
Most ATP created through oxidative phosphorylation and the electron transport chain.
Electron carriers power an electrical current through an electron transport chain in inner mitochondrial membrane
Oxygen is the final electron acceptor.
Anaerobic respiration: happens without oxygen, creates less ATP, which means that no oxygen is required, it only generates two ATPs, both from glycolysis combined with fermentation
Fermentation:
- Regenerates $NAD^+$
- Pyruvate changed into ethanol or lactic acid.

AP Bio Unit 4: Cell Communication, Feedback, and the Cell Cycle

Cells communicate directly (touching) or through signals (ligands).
Signals are ligands that are complementary to specific receptors. Three phases of cell communication:
- Reception : of the ligand
- Signal transduction: taking the initial signal and making it into another kind of signal
  Often accompanied by amplification of the signal
- Cellular response : of which there can be two kinds
  - Gene activation
  - Enzyme activation
G protein coupled receptors exist
Steroid hormones diffuse through the phospholipid bilayer and bind with cytoplasmic receptors and activate genes.

Topic 4.5: Homeostasis and Feedback

Homeostasis: Maintaining internal conditions at a relatively constant optimal level.
Feedback: When the output of a system is also an input to the system.
Feedback can be positive or negative
Negative feedback: Slows the system
Positive feedback: Accerlerates internal changes and drive a process forward
Glucose homeostasis:
- Involves insulin and glucagon
- Insulin lowers blood sugar back to the set point;
- Glucagon raises it when your blood sugar gets low
- Breakdown results in the disease diabetes.
- Type 1 diabetes:
  - Breakdown in insulin production
- Type 2 diabetes:
  - A problem with cells responding to the insulin signal
One to know about involves oxytocin and childbirth, and it works like this
As the baby grows, it activates stretch receptors in the uterus that cause the release of the hormone oxytocin, which then feeds back to the uterus, increasing contractions and activating the stretch receptors, and that process culminates in childbirth
A similar positive feedback loop works with fruit ripening and the gaseous hormone ethylene.

Topics 4.6 to 4.7: The Cell Cycle

Phases of mitosis: I put my apple in the cart' for interphase, prophase, metaphase, anaphase, and telophase
Mostly Interphase but Interphase can be divided into: growth one (general growth), synthesis of DNA, and then growth two (which is preparation for the M phase), Cells can also enter into this G0 phase when they become highly specialized, essentially leaving the cell cycle
Process is regulated by various checkpoints where the cell checks for various conditions along the way
The cell cycle is regulated both externally and internally, externally by signals coming from outside the cell. There's also internal regulation, and that regulation happens through cyclins and then cyclin-dependent kinases
Cancer: caused by unregulated cell division.
Cancer starts with mutations.
The Cells grow in one location, forming a tumor, mutations in genes called proto-oncogenes increase the rate of cell division, and mutations in tumor suppressor genes remove cell division inhibitors. They undermine the checkpoints that we just talked about. You can think about that with a gas pedal and brakes analogy

AP Bio Unit 5: Heredity

*   Meiosis:

Meiosis produces haploid germ cells, Germ cells that would be in the ovaries and the testes create haploid sperm and egg cells with one chromosome set
Meiosis begins with germ cells again in the testes or the ovaries that start by replicating their DNA, just like at the start of mitosis that creates cells that are diploid with double chromosomes in meiosis I homologous pairs (these pairs that are inherited from the mother and the father) wind up being separated, and in meiosis II, the sister chromatids are pulled apart, meiosis just to put that in context involves the same phases as mitosis, but they're doubled. In prophase I, here's where you see the homologous pairs pairing up, and two important things happen: one is that as they pair up, they wind up exchanging pieces of DNA; that's a process called crossing over. The other thing that happens is that as these homologous pairs are pulled to the cell equator, what every chromosome pair does is independent of every other pair, and that creates tremendous variation in the gametes
resulting meiosis and sexual reproduction generate diversity in three ways. The first is independent assortment; it's how these maternal and paternal homologous chromosomes can be sent to the next generation independently of one another, leading to many combinations of chromosomes. The second is crossing over and genetic recombination. Finally, during fertilization, a gamete from the father winds up fertilizing the gamete from the mother, combining the genomes of two individuals and creating even more variation. That's distinct from mitosis, in which the daughter cells are clones of the parent cell

Topic 5.3 to 5.5: Genetics

Gene:
Unit of heredity passed from parent to offspring
Seen from the viewpoint of molecular genetics, our next topic is a sequence of nucleotides that codes for RNA or protein
know Mendel's principle of
Segregation of alleles
Homozygous and heterozygous
Dominant and recessive
Genotype and phenotype
Monohybrid crosses; cross between two heterozygotes creates a 3:1 ratio in terms of the phenotype and a 1:2:1 ratio in terms of the genotype
Sex-linked genes involve genes that are on the X chromosome, so they're not passed on by the father; they're passed on by the mother, who has the allele on one of her or both of her X chromosomes
males can't be heterozygous; they either have the allele or they don't
Independent assortment;

what every gene pair does is independent of every other gene pair, leading to dihybrid crosses, which result in a 9:3:3:1 phenotypic ratio in the offspring, linked genes, linked genes that are close together usually get inherited together, so B and C, which are very close together, are unlikely to be separated by crossing over. But genes that are further apart, like A and E, are most likely to be separated by crossing over. AS a result fo this you can look at the amount of recombination that happens in various crossing experiments, and you can use those recombination frequencies to generate chromosome maps like this one, which shows the distance in terms of recombination between two alleles that are on the same chromosome

Non-nuclear inheritance
genes that are on mitochondria, not on one of the chromosomes in the nucleus; Incomplete dominance, where there's a blending effect between the two alleles, and there's genotype-environment interaction, where it's the environment that determines the phenotype much more than the genes

AP Bio Unit 6: Gene Expression

DNA replication is semiconservative.
Strand separates and each serves as a template. Daughter strands are half new and half old and is carried out by a team of enzyme. One you should know include helicase, DNA polymerase, primase, ligase and because DNA polymerase can only synthesize in the 5' to 3' direction
*

Topic 6.3: Transcription

Making of RNA from a DNA template
Should be able to use any sequences of RNA and translate into amino acids using a genetic code dictionary, and you should be able to explain the details of protein synthesis itself.

Topic 6.5 to 6.6: Gene Regulation

Important gene regulation system in prokaryotes; eukaryotes don't use operons a key principle in multicellular eukaryotes, like you and me, is that all cells in the same organism are genomically equivalent, this neuron, this epithelial cell, they're quite different phenotypically, but they have the same genes, they're different because they express different genes, Acetylation turns genes on; methylation turns genes off, and that leads to the entire field of changes in DNA expression that involve reversible chemical modifications in DNA or changes in DNA packaging, but not changes in the DNA sequence eukaryotic genes interspersed with introns, which makes phenotypic variation possible because of alternative splicing of exons, exons are expressed sequences; they wind up being translated into protein introns are intervening sequences that get edited out

Topic 6.7: Mutation

Mutation can be a positive, which can make it adaptive; they can be negative or harmful, or they can be neutral, having no effect whatsoever horizontal gene transfer also changes genomes, but by a different mechanism than mutation; it's where one individual transmits genes to another organism of the same generation
techniques that you should be PCR (used for amplifying DNA), restriction enzymes, and gel electrophoresis for analyzing DNA
Finally, DNA sequencing is giving us huge amounts of information that's being used in medical research, evolutionary biology, and every biological field.

AP Bio Unit 7: Evolution

Write the College Board; demand a change, should include natural selection, which brings about adaptations through survival of the fittest, artificial selection, in which humans select favored traits in our domesticated animals and plants, and sexual selection, which is selection for reproductive advantage. Natural Selection is the elimination of the biggest misconception that students have in AP Biology courses, and that is the wrong idea that the dominant allele has to be more common than the recessive allele; somehow, people confuse dominance with frequency, but that is not true
q² = 1 there's an associated Hardy-Weinberg principle in this system. P represents the frequency of the dominant allele; q represents the frequency of the recessive allele , genetic drift (random change in small populations that's caused by things like population bottlenecks or the founder effect), natural selection (some alleles are harmful, some alleles are beneficial), sexual selection (some phenotypes are more attractive than others)
imilarities in amino acid sequences, DNA sequences), or evolution that we continue to observe, such as resistance to pesticides in mosquitoes, antibiotics in bacteria Phylogeny is evolutionary history the concept of a clade, a group of organisms that is derived from a common ancestor. nodes, shared derived features, ancestral features, outgroups, and molecular clocks

Topics 7.10 to 7.12: Speciation, Variation, and Extinction

the biological species concept is that they can naturally interbreed to produce fertile offspring. Prezygotic barriers, that keep a zygote from forming or Postzygotic barriers, where if some confusion arose and these two did mate, then the zygote might not be able to develop Speciation that the two subpopulations become so different they can no longer interbreed, and they might chromosomal changes that happen

Topic 7.13: The Origin of Life

how did life naturally emerge in the absence of life after the Earth became habitable Geological processes and chemical, abiotic synthesis of monomers, eventually combined to form RNA monomers That become combined together to form RNA polymers which we were going to folding into complex shapes that have catalytic ability you have self replication of RNAs. Experiment preformed successful synthesis of amino acids simulated in an early Earth and this apparatus resulted in the production The RNA world and
rganic precursors combine an RNA monomers
RNA molecules turn and form in inorganic folding molecules and is the process 5 steps and RNA's molecules

AP Bio Unit: Ecology

Topic 8.1: Responses to the Environment

These are available on LearnBiology.com include great data sets of explaining monogamy and bees, but on how ants are able to find their way back to their nest after foraging. Main Device on the animal to read or question your best

Topic 8.2: Energy Flow in Individual Organisms and Entire Ecosystems

Animals like shrews have such a higher metabolic rate. The large flow of energy through food webs includes one the idea of the pyramid of energy. How only 10% of the energy gets passed from traffic level to traffic level, from producers to primary consumers and then other ecological pyramids, not limited to but including the pyramid of numbers

Topics 8.3 and 8.4: Population Growth

models which include exponential. How key capacity is a potential fact that population is capable growing and dependent or Independence

Topic 8.5: Species Interactions

evolutionary and definition a chart interactions and the positive or negative influences the interactions
ecological understand and measure biodiversity diversity have a use measure used to the given
human activities wind up reducing variation