AP Biology Review Notes

AP Biology Review: One Pagers

Unit 1: Chemistry of Life

Carbohydrates

• Composed of Carbon (C), Hydrogen (H), and Oxygen (O) in a 1:2:1 ratio.
• Monomer: Monosaccharide (e.g., Glucose, Fructose, Galactose).
• Disaccharides: Two monosaccharides linked by a glycosidic linkage (e.g., Sucrose, Lactose, Maltose).
• Structural examples include cellulose (found in plant cell walls) and chitin (found in fungi cell walls and arthropod exoskeletons).
• Storage examples include starch (found in plants) and glycogen (found in animals).
• Starch vs. Cellulose: Both are glucose polymers but have different linkages.
  • Starch: 1-4 linkage of α glucose monomers.
  • Cellulose: 1-4 linkage of β glucose monomers.

Lipids

• Composed of Carbon (C), Hydrogen (H), and Oxygen (O); phospholipids also contain Phosphorus (P).
• Monomer: N/A.
• All lipids are nonpolar.
• Fats: Glycerol + 3 fatty acids.
• Phospholipids: Phosphate + Glycerol + 2 fatty acids; contains a hydrophilic head and hydrophobic tail; amphipathic.
• Steroids: Four fused rings (e.g., cholesterol).
• Saturated fatty acids: All single bonds; each carbon is saturated by hydrogen.
• Unsaturated fatty acids: At least one double bond; not all carbons are saturated by hydrogen.

Proteins

• Composed of Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N), and Sulfur (S).
• Monomer: Amino Acid.
• Bond: Peptide bond (between carboxyl and amino groups).
• Primary Structure:
  • Structure: string of amino acids
• Levels of Protein Structure:
  • Primary: String of amino acids.
  • Secondary: Alpha helix or beta pleated sheet, stabilized by hydrogen bonds between the backbone.
  • Tertiary: Final 3D structure, stabilized by various bonds (hydrogen, covalent, ionic, etc.) between R groups.
  • Quaternary: Association of multiple polypeptides, stabilized by various bonds between R groups of different polypeptides.
  • Hydrophilic Exterior
  • Hydrophobic Interior
  • Charged Exterior
  • N terminus and C terminus

Nucleic Acids

• Composed of Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N), and Phosphorus (P).
• Monomer: Nucleotide.
• Components of a nucleotide: Nitrogenous base, pentose sugar (deoxyribose or ribose), and phosphate group.
• Nitrogenous bases: Purines (Adenine, Guanine) - double ring; Pyrimidines (Cytosine, Thymine, Uracil) - single ring.
• Bond: Phosphodiester linkage (between phosphate and hydroxyl).
• Directionality: 5' → 3'; antiparallel.
• DNA: Nitrogenous bases A, T, C, G; Sugar is deoxyribose; Double-stranded.
• RNA: Nitrogenous bases A, U, C, G; Sugar is ribose; Single-stranded.
• Base Pairing: A & T (2 H bonds); C & G (3 H bonds).

Water

• Polar molecule due to polar covalent bonds between oxygen and hydrogen.
• Hydrogen bonds between water molecules.
• Cohesion: Water molecules attracted to other water molecules.
• Adhesion: Water molecules attracted to other polar substances.
• Capillary Action: Combination of cohesion and adhesion.
• Universal Solvent: Partial negative oxygen binds with positive molecules/ions, and partial positive hydrogen binds with negative molecules/ions.
• Surface Tension: Cohesion develops a "surface" due to hydrogen bonds.
• Less Dense when Solid: Hydrogen bonds inhibit compaction.
• High Specific Heat: Water must absorb or release a large amount of energy to change 1 gram of water by 1°C.
• Evaporative Cooling: Release water to absorb heat energy.
• pH = -log $[H^+]$; as hydronium/hydrogen ion concentration increases, pH decreases.
• Water as a temperature buffer for coastal regions and body temperature.

Unit 2: The Cell

Cellular Organelles

• Nucleus: Double membrane (nuclear envelope) with pores; stores genetic information (DNA); site of RNA synthesis and ribosome subunit assembly.
• Ribosomes: Composed of rRNA and protein; Large & small subunits; Site of protein synthesis; Can be bound (to ER) or free (cytoplasmic).
• Rough ER: Membrane studded with ribosomes; Site of membrane-bound and secreted protein synthesis; Cell compartmentalization; Mechanical support; Involved in intracellular transport.
• Smooth ER: Folded, tubelike structure; Detoxification; Calcium Storage; Lipid synthesis.
• Golgi Complex: Flattened sacs (cisternae); Folding and chemical modification of synthesized proteins; Packaging protein traffic.
• Lysosome: Membrane-enclosed sacs containing hydrolytic enzymes; Intracellular digestion (recycle cell organic materials) & programmed cell death (apoptosis).
• Vacuole: Membrane-bound sac; Storage and release of macromolecules and cellular waste products; Central (water retention - turgor pressure); Contractile (osmoregulation in protists); Food (phagocytosis, fuse with lysosome).
• Mitochondria: Double membrane (outer: smooth; inner: highly folded); Site of oxidative phosphorylation (cristae/inner membrane) and Krebs Cycle (matrix).
• Chloroplast: Double outer membrane (thylakoid sac stacked: grana and fluid: stroma); Site of photosynthesis; Thylakoid (Light Reactions); Stroma (Calvin-Benson Cycle).

Surface Area: Volume

• Smaller cells have a higher surface area-to-volume ratio, allowing for more efficient exchange of materials with the environment.
• Formulas for different shapes:
  • Sphere: Volume V =
    4
    3πr^3, Surface Area $S = 4πr^2$
  • Rectangular Solid: Volume $V = LWH$, Surface Area $S = 2LH + 2LW + 2WH$
  • Cube: Volume $V = s^3$, Surface Area $S = 6s^2$
  • Cylinder: Volume $V = πr^2h$, Surface Area $S = 2πr^2 + 2πrh$

Membrane Transport

• Plasma Membrane Composition: Phospholipids, Membrane Proteins, Glycolipids/Glycoproteins, Cholesterol.
• Passive Transport: No energy required; movement down the concentration gradient.
  • Simple Diffusion: Small, nonpolar molecules; no transport protein needed (e.g., $CO<em>2$, $O</em>2$, $N_2$, steroids).
  • Facilitated Diffusion: Small molecules; requires transport protein (channel vs. carrier protein) (e.g., water, $Na^+$, $K^+$, $Ca^{2+}$).
• Active Transport: Requires input of energy; movement against the concentration gradient; requires transport protein (carrier protein) (e.g., $Na^+$, $K^+$, $Ca^{2+}$, $H^+$).
• Bulk Transport:
  • Endocytosis: Import of materials; Phagocytosis (cellular eating), Pinocytosis (cellular drinking), Receptor-Mediated Endocytosis.
  • Exocytosis: Export of materials; Rough ER (synthesize) → Golgi complex (package/modification) → Plasma Membrane.

Osmosis

• Water moves by osmosis from high to low water potential.
• Hypertonic Solution: High solute concentration, low free water concentration; Gains water from hypotonic solution.
• Isotonic Solution: Equal solute concentration; Equal free water concentration; Equal water movement into and out of solution.
• Hypotonic Solution: Low solute concentration, high free water concentration; Loses water to hypertonic solution.

Unit 3: Cellular Energetics

Gibbs Free Energy & Reactions

• Gibbs Free Energy: Energy available to do work.
• Change in Gibbs Free Energy: $\Delta G = \Delta H - T\Delta S$ or $\Delta G = \Delta G<em>f - \Delta G</em>i$
• Exergonic Reaction: $\Delta G < 0$; Spontaneous; Releases energy.
• Endergonic Reaction: $\Delta G > 0$; Not spontaneous; Absorbs energy.

Enzymes

• Biological catalysts that speed up chemical reactions by reducing the activation energy.
• Enzymes are proteins and are not consumed by the reaction.
• Enzymes have no effect on the change in Gibbs Free Energy.
• Substrate binds to the active site of the enzyme, forming an enzyme/substrate complex. The substrate is converted to products, which leave the active site.
• Inhibitors:
  • Competitive: Bind to the active site.
  • Noncompetitive: Bind to an allosteric site.
• Denaturation: Caused by environmental factors such as temperature, pH, and salinity.

Cellular Respiration

• Glycolysis:
  • Location: Cytosol.
  • Starting Material: Glucose.
  • Products: 2 Pyruvate, 2 NADH, 2 ATP.
• Krebs Cycle:
  • Location: Mitochondrial Matrix.
  • Starting Material: Acetyl CoA.
  • Products: 2 $CO<em>2$, 3 NADH, 1 $FADH</em>2$, 1 ATP.
• Oxidative Phosphorylation:
  • Location: Mitochondrial Cristae.
  • Starting Material: NADH/$FADH_2$ (electrons).
  • Product: ATPs.
  • Two Parts: Electron Transport Chain (protons pumped into IM space, generates proton gradient, final electron acceptor: oxygen) & Chemiosmosis (ATP Synthase uses proton gradient to synthesize ATP).

Photosynthesis

• Light Reactions:
  • Location: Thylakoid Membrane.
  • Starting Material: Water (electrons), Photons (energy).
  • Products: ATP, NADPH.
  • Linear Electron Flow: PS I & PS II; Synthesizes ATP & NADPH.
  • Cyclic Electron Flow: PS I ONLY; Synthesizes ATP ONLY.
• Calvin Cycle:
  • Location: Stroma.
  • Starting Material: 3 $CO_2$, 9 ATP, 6 NADPH.
  • Products: G3P.

Unit 4/5: Cellular Communication & Cell Cycle

Cellular Communication

• Reception: Ligand (signaling molecule) binds to receptor, causing a conformational shape change.
  • Steroid Hormone: Release via simple diffusion; Receptor: Intracellular (e.g., Testosterone, Estrogen).
  • Protein Hormone: Release via exocytosis; Receptor: Extracellular (e.g., Insulin).
• Transduction: Signaling cascades relay signals from receptors to cell targets, amplifying the incoming signals.
  • Phosphorylation Cascade: Protein Kinase phosphorylates relay molecules.
  • Secondary Messengers: $Ca^{2+}$, cAMP.
• Response: Cell growth, secretion of molecules, gene expression, apoptosis.

Mitosis vs. Meiosis

Cell Cycle

• Interphase: G1 (cell grows, duplicates organelles, synthesizes proteins/RNA), S (replication of genetic material), G2 (synthesis of proteins/RNA, makes organelles, reorganizes cellular contents).
• M Phase (Mitosis):
  • Prophase: Chromatin condenses.
  • Metaphase: Sister chromatids line up in the middle.
  • Anaphase: Sister chromatids pulled apart to opposite poles.
  • Telophase: Two new nuclei are formed.
• Cytokinesis: Division of the cytoplasm.
• Checkpoints:
  • G1 Checkpoint: Determines whether to complete the cell cycle; checks for growth factor, adequate reserves, and DNA damage. Enters G0 (nondividing state) if conditions are not met.
  • G2 Checkpoint: Checks all DNA is replicated and not damaged. Halts cell cycle to complete DNA replication or repair damaged DNA.
  • M Checkpoint: Checks sister chromatids attached to the spindle microtubules.
• Cyclin and Cdk:
  • Cyclin-dependent kinases (Cdks) are activated by cyclin.
  • Cdk-cyclin complex phosphorylates target proteins involved in cell cycle progression.
  • APC/C adds ubiquitin, activating separase, which cleaves cohesin.

Meiosis

• Meiosis I: Homologous Chromosomes Separate
  • Prophase I: Chromatin condenses, homologous chromosomes align, crossing over occurs.
  • Metaphase I: Homologous chromosomes align on the metaphase plate; independent assortment occurs.
  • Anaphase I: Homologous chromosomes separate to opposite poles.
  • Telophase I: Nuclear envelope forms around the haploid daughter cells.
• Meiosis II: Sister Chromatids Separate
  • Prophase II: Chromatin condenses.
  • Metaphase II: Sister chromatids align on the metaphase plate.
  • Anaphase II: Sister chromatids separate to opposite poles.
  • Telophase II: Nuclear envelope forms around the haploid daughter cells.

Unit 5/6: Heredity & Molecular Genetics

Inheritance Patterns

• Complete Dominance: Homozygous dominant and heterozygous look the same.
• Codominance: Heterozygous expresses both dominant traits.
• Incomplete Dominance: Heterozygous is a blend between the two dominant traits.
• Monohybrid Cross: Heterozygous for one trait; Complete Dominance (3:1 ratio); Incomplete or Codominance (1:2:1).
• Dihybrid Cross: Heterozygous for two traits; Complete Dominance (9:3:3:1 ratio); Incomplete or Codominance (6:3:3:2:1:1).

Inheritance Types

• Autosomal Inheritance: Allele is located on an autosome (non-sex chromosome).
• Sex-Linked Inheritance: Allele is located on a sex chromosome.
• Maternal Inheritance: Allele is located on the DNA found in a mitochondrial or chloroplast.
• Linked Genes: Genes located on the same chromosome closely together.

Central Dogma

• DNA → RNA → Polypeptide (Transcription then Translation).
• Retroviruses use reverse transcriptase to synthesize DNA from their RNA genome.

Replication

• Location:
  • Eukaryotes: Nucleus.
  • Prokaryotes: Nucleoid.
• Structure:
  • Eukaryotes: Multiple linear chromosomes.
  • Prokaryotes: Single circular chromosome.
    important Enzymes:
• Helicase
• Topoisomerase
• Primase
• DNA polymerase
• ligase

Replication

• Important Enzymes:
  • Helicase unwinds the DNA strands.
  • Topoisomerase relaxes supercoiling in front of the replication fork.
  • Primase synthesizes the RNA primer (DNA polymerase requires RNA primers to initiate DNA synthesis).
  • DNA polymerase synthesizes new strands of DNA continuously on the leading strand and discontinuously on the lagging strand.
  • Ligase joins the fragments on the lagging strand.
• Key Reminders about DNA:
  • Made up of nitrogenous base (A, T, C, G), pentose sugar (deoxyribose), and phosphate group.
  • Purines (A/G) have a double ring structure; Pyrimidines (C/T) have a single ring structure.
  • Base Pair Rules: A & T with 2 H bonds, C & G with 3 H bonds.
  • Directionality: Read 3' to 5', Synthesize 5' to 3' (Antiparallel).

Transcription

• Location:
  • Eukaryotes: Nucleus.
  • Prokaryotes: Nucleoid (cytosol).
• Important Enzyme & Components:
  • RNA polymerase synthesizes mRNA molecules in the 5' to 3' direction by reading the template DNA strand in the 3' to 5' direction.
  • Promoter: Site where RNA polymerase binds to start transcription.
  • Transcription Factors: Activators/inhibitors to turn on/off gene expression.
• Post-Transcriptional Modifications:
  • 5' Guanine Cap: Signals the "start" of the mRNA transcript for ribosome to bind; Facilitates export from nucleus.
  • Poly-A Tail: Inhibits degradation from hydrolytic enzymes in cytosol.
  • Splicing: Removal of introns from pre-mRNA transcript.

Translation

• Location:
  • Eukaryotes: Cytosol/rough ER.
  • Prokaryotes: Cytosol.
• Steps of Translation:
  • Initiation: Start codon (AUG).
  • Elongation: base pair between tRNA/mRNA with amino acid added.
  • Termination: Stop codon (UAG, UAA, UGA).

Mutations

• Point Mutations: Mutation at one nucleotide base pair.
  • Silent: No change in amino acid.
  • Missense: Change from one amino acid to another.
  • Nonsense: Change from amino acid to STOP codon.
  • Frameshift: Insertion/deletion of 1 or 2 nucleotide base pairs; shifts the reading frame for codons.
• Chromosomal Mutations: Rearrangement of chromosome parts or changes in chromosome numbers.
  • Rearrangement: Insertion, Deletion, Duplication, Inversion, Translocation.
  • Changes in Chromosome Number: Nondisjunction, Polyploidy.

Operons

• Gene Regulation found in prokaryotes.
• Repressible Operon (e.g., Trp Operon): Synthesizes tryptophan; Starts ON; Repressor INACTIVE. If Trp is present, Trp binds to repressor to ACTIVATE, repressor binds to operator to turn the operon OFF.
• Inducible Operon (e.g., Lac Operon): Synthesizes enzymes to break down lactose; Starts OFF; Repressor ACTIVE. If lactose is present, lactose binds to repressor to INACTIVATE, repressor no longer binds to operator to turn the operon ON.

Biotechnology

• Gel Electrophoresis: Separates molecules based on size and charge.
• Polymerase Chain Reaction (PCR): Makes multiple copies of DNA fragments.
  • Steps: Denaturing, Annealing, Elongation.
• Bacterial Transformation: Introduce genetic material (plasmid) to bacteria.
• DNA Sequencing: Use radioactive nucleotides to determine the sequence of a DNA strand.

Unit 7: Natural Selection

Natural Selection

• Developed by Charles Darwin.
• Driven by variation in the population and competition for resources.
• Organisms with more favorable traits are more likely to survive and produce more offspring, passing on their traits to the next generation.
• Examples: Peppered Moths, Antibiotic Resistance.
• Types of Selection:
  • Disruptive Selection: Selection for the two extreme phenotypes; selection against the intermediate phenotype.
  • Stabilizing Selection: Selection for the intermediate phenotype; selection against the two extreme phenotypes.
  • Directional Selection: Selection for an extreme phenotype; selection against the other phenotypes.
• Artificial Selection: Organisms with certain traits are bred until population has that trait. Humans affect variation in the population.

Hardy-Weinberg Equilibrium

• Conditions for Equilibrium:
  1. Extremely LARGE population size
  2. Random mating
  3. No mutations
  4. No gene flow (immigration/emigration)
  5. No natural selection
• Equations:
  • p + q = 1
  • $p^2 + 2pq + q^2 = 1$
• Variables:
  • p = frequency of the dominant allele
  • q = frequency of the recessive allele
  • $p^2$ = frequency of homozygous dominant
  • 2pq = frequency of the heterozygous
  • $q^2$ = frequency of the homozygous recessive

Genetic Drift

• Founder's Effect: Small population is isolated from original population.
• Bottleneck Effect: Population is reduced by a natural disaster where there was no selection based on traits.

Evidence of Evolution

• Biochemical: Comparison of DNA or protein sequences.
• Morphological: Homologous structures (similar structures due to common ancestry); Analogous structures (due to convergent evolution).
• Biogeography: Distribution of species and ecosystems in geographic space & through geological time.

Speciation

• Allopatric Speciation: Occurs when biological populations of the same species become isolated due to geographical changes.
• Sympatric Speciation: New species from a surviving ancestral species while both continue to inhabit the same geographic region.
• Prezygotic Isolation: Before zygote is created; Behavioral, Temporal, Geographic, Habitat/Ecological, Mechanical, Gametic.
• Postzygotic Isolation: After zygote is created; Reduced Hybrid Viability, Reduced Hybrid Fertility, Hybrid breakdown.

Unit 8: Ecology

Body Temperature Regulation

• Endotherm: Maintains body temperature through metabolism.
• Ectotherm: Maintains body temperature through behaviors (basking in sunlight, aggregation).

Energy Flow & Trophic Structure

• Autotroph: Capture energy from physical or chemical source.
  • Photosynthetic: Sunlight.
  • Chemosynthetic: Small inorganic molecules in the environment (sometimes without oxygen).
• Heterotroph: Capture energy present in carbon compounds produced by other organisms.
• Organisms use energy to maintain, organize, grow and reproduce.
• Changes in Availability:
  • Change in Energy Resource: Affects number and size of trophic levels.
  • Change in Producer Level: Affects number and size of trophic levels.

Animal Behavior

• Communication: Signaling allows for changes in behaviors of organisms to allow for differential reproductive success.
  • Types of Communication: Visual, Auditory, Electrical, Chemical.
  • Function: Indicate Dominance, Foraging (Finding Food), Establish Territory, Ensure Reproductive Success.
• Altruistic Behaviors: Reduces individual fitness but increases inclusive fitness.
• Intersexual Selection: Reproductive behaviors to attract a mate; individuals of one sex choose members of the opposite sex.
• Intrasexual Selection: Reproductive behaviors to indicate dominance and compete for access to mates.

Population Ecology

• Exponential Growth:
  • Unlimited growth of population; $r = b - d$ (rate of increase = birth rate - death rate).
  • Equation: $\frac{dN}{dt} = r_{max}N$
• Logistic Growth:
  • Population size limited by carrying capacity.
  • Equation: $\frac{dN}{dt} = rN(\frac{K-N}{K})$
• Density Dependent Factors: Factors that intensify as population increases (e.g., competition, predation, disease).
• Density Independent Factors: Factors that affect all individuals regardless of size, population density (e.g., natural disasters, human activity).

Community Ecology

• Species Diversity: Simpson's Index measures biodiversity (species composition and diversity).
  • Simpson Diversity = $1 - \Sigma(\frac{n}{N})^2$
• Interactions: Predator/Prey (+/-), Herbivory (+/-), Competition (-/-), Symbiosis (Parasitism (+/-), Mutualism (+/+), Commensalism (+/0)).
• Keystone Species: Organism with disproportionate effect on the ecosystem.
• Invasive Species: Organism that is not indigenous, or native, to a particular area with no natural predators and unlimited resources.