AP Biology Full Course Exhaustive Study Guide 2023-2024

Unit 1: Chemistry of Life

1.1: Structure of Water and Hydrogen Bonding * Hydrogen Bonding: This is defined as the attraction between a hydrogen atom and another atom that possesses higher electronegativity. * Cohesion: Refers to the specific ability of water molecules to stick to other water molecules. An example of this is water tension. * Adhesion: Refers to the ability of water molecules to stick to molecules that are not water. An example is water moving up the xylem by sticking to the vessel walls. * Heat of Vaporization: The specific amount of heat that water must absorb for $1\,g$ of the substance to be converted into steam. * High Specific Heat: Water's capacity to absorb a significant amount of heat without experiencing a major change in temperature. * Evaporative Cooling: This process is based on water's property of high specific heat, which enables organisms to maintain temperature homeostasis. An example is sweating. * Expansive Freezing: Water expands as it freezes, forming a crystalline structure that makes ice less dense than liquid water. This allows marine ecosystems to survive because only the surface of a lake freezes, acting as an insulator for the liquid water below. * Universal Solvent: Water is capable of dissolving a wide variety of solutes.
1.2: Elements of Life * Carbon: Essential for life due to its ability to form four bonds, allowing for the creation of complex molecular structures. * Hydrogen: Crucial for the formation of water and its associated properties. * Oxygen: Necessary for the survival of all aerobic organisms. * Nitrogen: Required for the formation of nucleic acids. * Phosphorous: Required for the formation of nucleic acids. * Sulfur: Necessary for the formation of proteins.
1.3: Introduction to Biological Macromolecules * Carbohydrates: These always exist in a ratio of $1C:2H:1O$ . The three basic carbohydrates are glucose, fructose, and galactose. * Proteins: These may be polar or nonpolar, a characteristic determined by the presence of nitrogen, oxygen, and sulfur in the R group. * Lipids: Nonpolar molecules that do not possess true monomers; they are composed of subunits. * Nucleic Acids: Composed of DNA and RNA, including subtypes like messenger RNA ( $mRNA$ ), ribosomal RNA ( $rRNA$ ), and transfer RNA ( $tRNA$ ).
1.4 & 1.5: Properties, Structure, and Function of Biological Macromolecules * Carbohydrates: A primary source of energy, categorized into monosaccharides, disaccharides, and polysaccharides. * Proteins: Composed of an amino group, a carboxyl group, and an R group. They have four levels of organization: * Primary: A single chain of amino acids held together by polypeptide (covalent) bonds. * Secondary: Spatial conformation of the chain utilizing hydrogen bonds between R groups, forming structures like the Alpha Helix and Beta Sheet. * Tertiary: A three-dimensional spatial conformation of a single chain held by hydrogen bonds, disulfide bridges, hydrophobic interactions, and ionic bonds. * Quaternary: Spatial conformation involving three or more chains woven together, held by forces similar to those in the tertiary structure. * Lipids: Consist of two to three fatty acid chains featuring a hydrophobic tail and a hydrophilic head. Saturated fats have single bonds, while unsaturated fats contain double bonds. * Nucleic Acids: Crucial for repair, growth, and reproduction (asexual and sexual). They act as a code for organisms, determining genes, traits, enzymes, and proteins.
1.6: Nucleic Acids * Deoxyribose (DNA): Contains deoxyribose sugar and nitrogenous bases Adenine, Thymine, Cytosine, and Guanine. * Ribose (RNA): Contains ribose sugar and nitrogenous bases Adenine, Uracil, Cytosine, and Guanine. * Base Pairing Rules: Adenine and Thymine (or Uracil) are held by two hydrogen bonds; Guanine and Cytosine are held by three hydrogen bonds. * Monomer: Nucleotides: Composed of a Phosphate Group, a $5$ -Carbon Pentose Sugar, and a Nitrogenous Base. * Nitrogenous Base Categories: * Purine (Double ringed): Adenine and Guanine (Mnemonic: "Pure as Gold [AG]"). * Pyrimidine (Single ringed): Thymine, Uracil, and Cytosine.

Unit 2: Cell Structure and Function

2.1 & 2.2: Cell Structure and Function * Prokaryotes: Lack a proper nucleus and membrane-bound organelles. They are generally smaller than eukaryotes. Examples include Bacteria and Archaea. * Eukaryotes: Contain multiple organelles and a nucleus. Examples include Plants, Animals, and some microorganisms. * Organelles and Components: * Cell Membrane (Plasma Membrane): A phospholipid bilayer with embedded proteins. It is fluid and controls the movement of resources. Small nonpolar molecules diffuse passively. Present in ALL CELLS. * Cell Wall: Provides protection and rigid structure. Found in MOSTLY PLANT CELLS. * Chloroplasts: Site of photosynthesis. Found ONLY IN PLANT CELLS. * Smooth ER: Synthesizes, stores, and transports lipids. Found in EUKARYOTES. * Rough ER: Synthesizes and transports proteins; covered in ribosomes. Found in EUKARYOTES. * Flagellum: Long appendage for movement and sensory functions. Found in BACTERIA, ARCHAEA, AND SOME EUKARYOTES. * Golgi Apparatus: Modifies and transports proteins. Found in EUKARYOTES. * Mitochondria: Produces $ATP$ and contains maternal DNA. Found in EUKARYOTES. * Nucleus: Directs cell activity, contains genetic info, transfers $rRNA$ , and is the site of transcription. Found in EUKARYOTES. * Vacuole: Storage organelle. Found in EUKARYOTES. * Pili: Small appendages for surface attachment and interaction. Found in BACTERIA. * Cytoplasm: Fluid volume giving the cell shape; not responsible for specific cellular functions. Found in ALL CELLS. * Microtubule: Intracellular movement and shape retention. Found in PLANT AND ANIMAL CELLS. * Capsule: Outermost layer of BACTERIA. * Ribosomes: Translate genetic code into proteins. Can be bound or free. Found in ALL CELLS. * Centrioles: Barrel-like organelles forming spindle fibers for mitosis/meiosis. Found in MOST EUKARYOTES. * Nuclear Envelope: Bilayer surrounding the nucleus with nuclear pores. Found in EUKARYOTES. * Lysosome: Digestion of macromolecules and waste removal. Found in EUKARYOTES. * Nucleolus: Transfers $rRNA$ to cytoplasm for ribosome production. Found in EUKARYOTES. * Nucleoid Region: Region in PROKARYOTES containing genetic material. * Vesicle: Transport and detoxification. Found in PLANT AND ANIMAL CELLS. * Peroxisome: Detoxification and metabolism. Found in PLANT AND ANIMAL CELLS. * Plastids: Aid in photosynthesis. Found in PLANT CELLS. * Plasmodezmata: Channels for material transfer between plant cells. Found in PLANT CELLS. * Plasmid: Double circular DNA strands for antibacterial resistance. Found in BACTERIA.
2.3: Cell Size * Surface Area to Volume Ratio: A high ratio is better for efficient material transport. A low ratio (high volume) is better for storage. Adding folds to a membrane increases surface area without increasing volume.
2.4 & 2.5: Plasma Membrane and Permeability * Fluid Mosaic Model: Membrane is semipermeable, allowing only certain molecules like small nonpolar $CO_2$ and $O_2$ to pass. * Phospholipid structure: Hydrophilic head and Hydrophobic tail (comprised of saturated or unsaturated fatty acids).
2.6 & 2.7: Membrane Transport * Passive Transport: Movement from high to low concentration without energy. Includes Simple Diffusion and Facilitated Diffusion (utilizing channels like Aquaporins for water). * Active Transport: Movement from low to high concentration requiring energy ( $ATP$ ). Example: Sodium Potassium Pump. * Endocytosis: Phagocytosis (solids), Pinocytosis (liquids), and Receptor-Mediated Endocytosis (ligand binding). * Exocytosis: Fusion of vesicles with the plasma membrane to release contents. * Bulk Flow: One-way movement of fluids due to pressure (e.g., blood in vessels, fluids in xylem/phloem).
2.8: Tonicity and Osmoregulation * Hypotonic: Solute concentration is higher inside the cell than the solution; water enters. * Hypertonic: Solute concentration is lower inside the cell than the solution; water leaves. * Isotonic: Solute concentration is equal indoors and out. * Water Potential ($\Psi$): Water moves toward the more negative value. Calculation helps determine direction of movement.
2.10 & 2.11: Cell Compartmentalization * Compartmentalization increases efficiency by allowing specific metabolic processes and enzymatic reactions to occur spontaneously in controlled environments. * Endosymbiotic Theory: Mitochondria and chloroplasts originated from symbiotic relationships between different prokaryotic cells.

Unit 3: Cellular Energetics

3.1, 3.2 & 3.3: Enzyme Structure, Catalysis, and Regulation * Function: Enzymes act as catalysts to speed up reactions by lowering activation energy. * Active Site: Site where substrate binds. Allosteric sites allow for activation or inhibition. * Induced-fit: Enzymes change shape slightly for substrates. * Specific Factors: Maltase catalyzes the breakdown of maltose. * Environmental Impacts: High/low temperature and pH away from optimum cause denaturation (unfolding). Activity increases with substrate concentration until the saturation point. * Inhibition: * Competitive: Inhibitor blocks the active site. * Noncompetitive: Inhibitor binds to an allosteric site. * Cofactors: Inorganic metal ions (e.g., $Fe^{2+}$ ) or organic coenzymes (Vitamins).
3.4: Cellular Energy * First Law of Thermodynamics: Energy cannot be created or destroyed, only harvested. * Second Law of Thermodynamics: Energy transfer leads to increased entropy (disorder). Input must exceed loss. * Oxidation: Loss of electrons. Reduction: Gain of electrons. * Exergonic: Energy released (e.g., Cellular Respiration). * Endergonic: Energy required (e.g., Photosynthesis). * Reaction Coupling: Utilizing $ATP \rightarrow ADP$ to power endergonic processes.
3.5: Photosynthesis * Equation: $\text{sunlight energy} + 6 CO_2 + 6 H_2O \rightarrow C_6H_{12}O_6 + 6 O_2$ * Light-Dependent Reactions (Thylakoid): Inputs are light and water; outputs are $ATP$ , $NADPH$ , and $O_2$ (from photolysis). Uses PS II ( $P680$ ) and PS I ( $P700$ ). * Cyclic Electron Flow: Occurs at PS I; generates $ATP$ only, no $NADPH$ . * Calvin Cycle (Stroma): Inputs are $CO_2$ , $ATP$ , and $NADPH$ . Outputs sugar (2 turns per glucose). * Photorespiration and Alternatives: Occurs when $O_2$ builds up. CAM plants open stomata at night. C4 plants fix $CO_2$ in different parts of the leaf.
3.6: Cellular Respiration * Equation: $C_6H_{12}O_6 + 6 O_2 \rightarrow 6 CO_2 + 6 H_2O + ATP$ * Glycolysis (Cytoplasm): Glucose splits into $2$ pyruvates. Regulated by $2 ATP$ and $2 NAD^+$ inputs. * Pyruvate Oxidation: $2$ pyruvates converted to $2$ Acetyl-CoA. Catalyst: Pyruvate dehydrogenase complex (PDC). * Krebs Cycle (Matrix): Produces $4 CO_2$ , $6 NADH$ , $2 FADH_2$ , and $2 ATP$ . * Oxidative Phosphorylation: ETC and Chemiosmosis produces $36-38 ATP$ . * Fermentation: Anaerobic; produces Ethanol (yeast) or Lactic Acid (humans).
3.7: Fitness * Defined as the ability to survive and reproduce. Genetic variation increases individual and species fitness.

Unit 4: Cell Communication and Cell Cycle

4.1: Cell Communication Types * Autocrine: Signals to self. * Paracrine: Signals to adjacent cells. * Juxtacrine: Signals through direct contact. * Endocrine: Long-distance signaling.
4.2, 4.3 & 4.4: Signal Transduction * Steps: Reception (ligand binds receptor), Transduction (signal passed, often amplified), and Response.
4.5: Feedback Loops * Negative: Moves toward homeostasis (e.g., thermostat). * Positive: Amplifies stimuli (cascade).
4.6 & 4.7: Cell Cycle and Regulation * Interphase: $G_1$ (growth), $S$ (DNA replication), $G_2$ (mitosis prep). * Mitosis Phases: Prophase (spindle forms), Metaphase (lining up), Anaphase (separation), Telophase (cleavage furrow), Cytokinesis. * Checkpoints: $G_1$ (commitment to divide), $G_2$ (checks for damage), Metaphase/Spindle (checks attachment). * Regulation: Cyclins bind to CDKs. Oncogenes promote growth; tumor suppressor genes inhibit it.

Unit 5: Heredity

5.1: Meiosis * Meiosis I: Homologous pairs separate. Prophase I features Crossing Over. * Meiosis II: Sister chromatids separate. Results in $4$ haploid daughter cells.
5.2: Genetic Diversity Drivers * Crossing Over: Exchange of info between nonsister chromatids in Prophase I. * Independent Assortment: Random alignment of chromosomes in Metaphase I and II. * Law of Segregation: Gametes receive only one allele for each gene. * Random Fertilization: Any sperm can fertilize any egg.
5.3 & 5.4: Genetics Principles * Mendelian Crosses: Heterozygous x Heterozygous results in a $9:3:3:1$ phenotypic ratio for dihybrid crosses. * Non-Mendelian: Codominance, Incomplete dominance. * Sex-Linked: X-linked recessive traits more common in men; X-linked dominant in women. * Mitochondrial: Inherited only from the mother.
5.6: Chromosomal Inheritance * Nondisjunction: Failure to separate correctly. * Examples: Trisomy (Triple X Syndrome), Monosomy (Down Syndrome).

Unit 6: Gene Expression and Regulation

6.2 & 6.3: Replication and Transcription * Replication Enzymes: Helicase (unwinds), Topoisomerase (prevents over-winding), DNA Polymerase III (5’ to 3’ synthesis), DNA Polymerase I, Primase (RNA primers). * Transcription: RNA Polymerase reads DNA $3' \rightarrow 5'$ and synthesizes $mRNA$ . * Processing (Eukaryotes): Introns are removed; Exons are joined. Addition of $5'$ GTP Cap and $3'$ Poly-A Tail.
6.4 & 6.5: Translation and Regulation * Ribosome Sites: A (Arrival), P (Placement/Polypeptide), E (Exit). * Operons: Lac operon is inducible (turned on by lactose). Trp operon is repressible (on by default).
6.7: Mutations * Point mutations: Missense (changes amino acid), Nonsense (early stop), Silent (no change). * Frameshift: Insertion or Deletion of a nucleotide. * Chromosomal: Deletion, Duplication, Inversion, Insertion, Translocation.
6.8: Biotechnology * Gel Electrophoresis: Separates DNA by size using electrical current. * PCR: Amplifies segment copies of DNA/RNA.

Unit 7: Natural Selection

7.1 - 7.4: Mechanisms of Evolution * Evolution: Change in the gene pool over time. * Genetic Drift: Bottleneck Effect (random change). * Gene Flow: Movement between populations.
7.5: Hardy-Weinberg Equilibrium * Allele Frequency: $p + q = 1$ * Genotype Frequency: $p^2 + 2pq + q^2 = 1$ * Criteria: Large population, random mating, no mutations, no gene flow, no natural selection.
7.6 - 7.10: Evidence and Speciation * Structures: Homologous (same structure, different function), Analogous (different structure, same function), Vestigial (no current use). * Speciation: Divergence of species due to geographic isolation or selection.
7.13: Origin of Life * RNA World Hypothesis: RNA was the first genetic material because it can self-assemble.

Unit 8: Ecology

8.1: Animal Behavior * Kinesis: Non-directional change (e.g., woodlice speed). * Taxis: Directional movement (e.g., phototaxis). * Conditioning: Classical (associative sound/food) and Operant (reward/punishment). * Plant Tropisms: Phototropism (light), Gravitropism (gravity), Thigmotropism (touch).
8.2: Energy Flow * Endotherms: Use metabolic heat. Ectotherms: Environment-dependent. * Trophic Levels: $90\%$ energy loss at each level. Producers have the most energy.
8.3 - 8.5: Population and Community Ecology * Growth: Exponential (J-curve) vs Logistic (S-curve, carrying capacity K). * Relationships: Mutualism (+/+), Commensalism (+/neutral), Parasitism (+/-). * Keystone Species: Disproportionately large impact on habitat.
8.7: Disruption * Climate Change: Caused by burning fossil fuels and greenhouse gases like $CO_2$ and methane. * Succession: Primary (no previous life) and Secondary (after disaster, involves pioneer lichens).