AP Biology Review Notes

Chemistry of Life

Carbohydrates
- Composed of Carbon, Hydrogen, and Oxygen 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).
- Functions:
  - Structural: Cellulose (plant cell walls), Chitin (fungi cell walls & arthropod exoskeletons).
  - Storage: Starch (plants), Glycogen (animals).
- Starch vs. Cellulose: Both are composed of glucose monomers but differ in their linkages (1-4 linkage of $α$ glucose monomers in starch vs. 1-4 linkage of $β$ glucose monomers in cellulose).
Lipids
- Composed of Carbon, Hydrogen, and Oxygen (and Phosphorus in phospholipids).
- Monomer: N/A
- All lipids are nonpolar.
- Types:
  - Fats: Glycerol + 3 fatty acids.
  - Phospholipids: Phosphate + Glycerol + 2 fatty acids; Amphipathic (hydrophilic head, hydrophobic tail).
  - Steroids: Four fused rings (e.g., cholesterol).
- Saturated vs. Unsaturated Fatty Acids:
  - Saturated: All single bonds, each carbon is saturated by hydrogen.
  - Unsaturated: At least one double bond, not all carbons are saturated by hydrogen.
Proteins
- Composed of Carbon, Hydrogen, Oxygen, Nitrogen, and Sulfur.
- Monomer: Amino Acid.
- Bond: Peptide bond (between carboxyl & amino groups).
- 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 bonds between R groups of different polypeptides.
Nucleic Acids
- Composed of Carbon, Hydrogen, Oxygen, Nitrogen, and Phosphorus.
- Monomer: Nucleotide.
- Components of a Nucleotide:
  - Nitrogenous Base: Purine (A, G) or Pyrimidine (C, T, U).
  - Pentose Sugar: Deoxyribose (DNA) or Ribose (RNA).
  - Phosphate Group.
- Bond: Phosphodiester linkage (between phosphate and hydroxyl).
- Directionality: 5' → 3'; antiparallel in DNA.
- DNA vs. RNA:
  - Nitrogenous Bases: A, T, C, G in DNA; A, U, C, G in RNA.
  - Sugar: Deoxyribose in DNA; Ribose in RNA.
  - Strandedness: Double-stranded in DNA; Single-stranded in RNA.
- Base Pairing: A & T (2 H bonds), C & G (3 H bonds).

Water

Polarity
- Polar covalent bonds between oxygen & hydrogen within the water molecule.
- Hydrogen bonds between oxygen & hydrogen between water molecules.
Cohesion/Adhesion
- Cohesion: Water molecules attracted to other water molecules.
- Adhesion: Water molecules attracted to other polar substances.
- Capillary Action: Cohesion and adhesion working together.
Universal Solvent
- Partial negative oxygen binds with other polar molecules (partial positive end) & to positively charged ions (cations).
- Partial positive hydrogen binds with other polar molecules (partial negative end) & to negatively charged ions (anions).
Surface Tension
- Cohesion develops a "surface" based on the interaction of hydrogen bonds.
Less Dense when Solid
- Hydrogen bonds inhibit compaction, Ice floats, temperature buffer.
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 on surface of organism to absorb heat energy from body (and break the bonds cooling down the organism).
pH
- $pH = -log[H^+]$
- As the concentration of hydronium/hydrogen ion increases, the pH decreases.

The Cell

Nucleus
- Structure: Double membrane (nuclear envelope) with pores.
- Functions: Stores genetic information (DNA), Synthesis of RNA, Ribosome subunit assembly.
Ribosomes
- Structure: Composed of rRNA and protein, Large & small subunits.
- Types: Bound (to ER) or free (cytoplasmic).
- Functions: Protein synthesis.
Endoplasmic Reticulum (ER)
- Rough ER:
  - Structure: Membrane studded with ribosomes attached to nuclear envelope.
  - Functions: Site of membrane-bound protein and secreted protein synthesis, Cell compartmentalization, Mechanical support, Role in intracellular transport.
- Smooth ER:
  - Structure: Folded, tubelike structure (cisternae).
  - Functions: Detoxification, Calcium Storage, Lipid synthesis.
Golgi Complex
- Structure: Membrane-bound structure composed on flattened sacs (cisternae).
- Functions: Folding and chemical modification of synthesized proteins, Packaging protein traffic.
Lysosome
- Structure: Membrane-enclosed sacs that contain hydrolytic enzymes.
- Functions: Intracellular digestion (recycle cell organic materials & programmed cell death: apoptosis).
Vacuole
- Structure: Membrane-bound sac.
- Functions: Storage and release of macromolecules and cellular waste products.
  - Central: water retention - turgor pressure.
  - Contractile: osmoregulation (protist).
  - Food: phagocytosis, fuse with lysosome.
Mitochondria
- Structure: Double membrane (outer: smooth; inner: highly folded).
- Functions:
  - Site of oxidative phosphorylation (cristae/inner membrane).
  - Site of Krebs Cycle (matrix).
Chloroplast
- Structure: Double outer membrane (thylakoid sac stacked: grana and fluid: stroma).
- Functions:
  - Site of photosynthesis.
  - Thylakoid: Light Reactions.
  - Stroma: Calvin-Benson Cycle.
Surface Area: Volume
- Volume: $V = \frac{4}{3}πr^3$
- Surface Area: $S = 4πr^2$
- Volume: $V=LWH$
- Surface Area: $S=2LH+2LW+2WH$
- Volume: $V = s^3$
- Surface Area: $S = 6s^2$
- Volume: $V= πr^2h$ or $V=Bh$
- Surface Area: $S = 2πr^2 + 2πrh$
- Smaller cells typically have a higher surface area-to-volume ratio and more efficient exchange of materials with the environment.

Plasma Membrane

Components
- Phospholipids.
- Membrane Proteins (Intrinsic and Extrinsic).
- Glycolipids/Glycoproteins.
- Cholesterol.
Membrane Transport
- Passive Transport (No NRG required)
 - Simple Diffusion: Down concentration gradient, small, nonpolar molecules, no transport protein needed (e.g., $CO2$ , $O2$ , $N_2$ , steroids).
 - Facilitated Diffusion: Down concentration gradient, small molecules, requires transport protein (channel vs. carrier protein) (e.g., water, $Na^+$ , $K^+$ , $Ca^{2+}$ ).
- Active Transport: Requires input of NRG, against 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 (as other solution), EQUAL free water concentration (as other solution), Equal water movement into and out of solution.
- Hypotonic Solution: LOW solute concentration, HIGH free water concentration, LOSES water to hypertonic solution.

Cellular Energetics

Gibbs Free Energy
- Energy available to do work. $ΔG = ΔH - TΔS$
 - $ΔG$ : Change in Gibbs Free Energy
 - $ΔH$ : Change in Enthalpy
 - $T$ : Temperature (K)
 - $ΔS$ : Change in Entropy
- $ΔG = ΔGf - ΔGi$
Endergonic Reaction
- ΔG > 0
- Reaction is not spontaneous.
- Absorbs energy (e.g., $ADP + P_i → ATP$ )
Exergonic Reaction
- ΔG < 0
- Reaction is spontaneous.
- Releases energy (e.g., $ATP → ADP + P_i$ )
Enzymes
- Biological catalyst.
- Speeds up chemical reactions.
- Reduces the activation energy.
- Enzymes are proteins.
- Are NOT consumed by the reaction.
- Have no effect on the change in Gibbs Free Energy.
- Mechanism:
  - Substrate enters active site of enzyme.
  - Enzyme/substrate complex forms.
  - Substrate is converted to products.
  - Products leave the active site of the enzyme.
- Inhibitors
  - Competitive: Binds to active site.
  - Noncompetitive: Binds to allosteric site.
- Denaturation
  - Environmental Temperatures.
  - pH (outside of optimal range).
  - 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 $CO2$ , 3 NADH, 1 $FADH2$ , 1 ATP.
- Oxidative Phosphorylation:
 - Location: Mitochondrial Cristae.
 - Starting Material: NADH/ $FADH_2$ (electrons).
 - Product: ATP.
 - Two Parts:
 - Electron Transport Chain:
 - Protons pumped into IM space.
 - Generates proton gradient.
 - Final electron acceptor: OXYGEN.
 - Chemiosmosis:
 - ATP Synthase uses proton gradient.
 - Synthesizes 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.

Cellular Communication & Cell Cycle

Cellular Communication
- Reception: Ligand (signaling molecule) binds to receptor, Causes confirmational shape change.
  - Steroid Hormone:
    - Release: Simple Diffusion.
    - Receptor: Intracellular.
    - Example: Testosterone, Estrogen.
  - Protein Hormone:
    - Release: Exocytosis.
    - Receptor: Extracellular.
    - Example: Insulin.
- Transduction: Signaling cascades relay signals from receptors to cell targets, often amplifying the incoming signals.
  - Phosphorylation Cascade: Protein Kinase, Phosphorylate relay molecules.
  - Secondary Messengers: $Ca^{2+}$ , cAMP.
- Response: cell growth, secretion of molecules, gene expression, apoptosis.

Mitosis vs. Meiosis

Feature	Mitosis	Meiosis
Parent Cell Ploidy	Diploid	Diploid
DNA Replication	1	1
Nuclear Division	1	2
Daughter Cell Ploidy	Diploid	Haploid
Daughter Cells #	2	4
Compare Parent	Identical	Genetically Distinct
Crossing Over	Does Not Occur	Occurs Prophase I
Independent Assortment	Does Not Occur	Occurs Metaphase I

Cell Cycle
- Interphase (G1, S, G2):
  - G1 (Gap Phase 1): The cell grows, Duplication of cell organelles, Synthesis of proteins, RNA, and building blocks.
  - S (Synthesis): Replication of genetic material.
  - G2 (Gap Phase 2): Synthesis of proteins and RNA, Makes organelles, Reorganizes cellular contents, PREPARE to divide.
- M (Mitotic) Phase: Cell divides.
- Cytokinesis: Division of the cytoplasm.
Checkpoints
- G1: Determines whether to complete the cell cycle, Growth factor, Adequate reserves, Check for DNA damage, If do not pass, enter G0 (nondividing state).
- G2: Check all DNA replicated and not damaged. If detect problems with DNA, the cell cycle is halted, to complete DNA replication or repair the damaged DNA.
- M: Check sister chromatids attached to the spindle microtubules.
Meiosis
- Meiosis I - Homologous Chromosomes.
  - Prophase I: Chromatin condenses, Sister chromatids/homologous chromosomes align, CROSSING OVER, CHIASMATA, HOMOLOGOUS CHROMOSOMES HAVE A DIFFERENT COMBINATION OF ALLELES.
  - Metaphase I: HOMOLOGOUS CHROMOSOMES align on the metaphase plate, INDEPENDENT ASSORTMENT.
  - Anaphase I: HOMOLOGOUS CHROMOSOMES separate to opposite poles.
  - Telophase I: Nuclear envelope forms around the HAPLOID daughter cells.
- Meiosis II - Sister Chromatids.
  - Prophase II: Chromatin condenses, Sister chromatids align.
  - 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.

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 of the two dominant traits.
- Monohybrid: Heterozygous for ONE trait.
- Complete Dominance: 3:1 ratio.
- Incomplete or Codominance: 1:2:1.
- Dihybrid: Heterozygous for TWO traits.
- Complete Dominance: 9:3:3:1 ratio.
- Incomplete or Codominance: 6:3:3:2:1:1.
Allele Location
- Autosomal Inheritance: Allele is located on an autosome (non-sex chromosome).
- Sex-Linked: 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
- $DNA → RNA → Polypeptide$
  - Replication. Transcription. Translation.
- Retroviruses will use reverse transcriptase to synthesize DNA from their RNA genome.
Replication
- Location:
  - Eukaryotes: nucleus.
  - Prokaryotes: nucleoid.
- Structure:
  - Eukaryotes: multiple linear.
  - Prokaryotes: single circular.
- 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.
RNA Synthesis
- 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, 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 (AA).
  - Missense: change from one AA to another AA.
  - Nonsense: change from AA 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.
- Promoter: Site when RNA polymerase binds.
- Operator: Site when repressor binds.
- Repressible Operon: Example: 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: Example: 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: Separate molecules based on size and charge.
- Polymerase Chain Reaction (PCR): Makes multiple copies of DNA fragments, Steps: Heating, Cooling, Annealing.
- Bacterial Transformation: Introduce genetic material (plasmid) to bacteria.
- DNA Sequencing: Use radioactive nucleotides to determine the sequence of a DNA strand.

Natural Selection

Natural Selection
- Developed by Charles Darwin.
- Establish due to variation in the population and competition for resources.
- Organisms with more favorable trait, more likely to survive and produce more offspring to pass on their traits to next generation.
- Examples:
  - Peppered Moths.
  - Antibiotic Resistance.
- Lamarckian statements
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.
Hardy-Weinberg Equilibrium
- Five Fingers of Evolution:
  - Extremely LARGE population size.
  - Random mating.
  - No mutations.
  - No gene flow (immigration/emigration).
  - No natural selection.
- Genetic Drift:
  - Founder's Effect: Small population is isolated from original population.
  - Bottleneck Effect: Population is reduced by a natural disaster (fire, flood, etc) where there was no selection based on traits.
- Equations & 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.
  - p + q = 1. $p^2 + 2pq + q^2 = 1$
Evidence of Evolution:
- Biochemical: DNA or protein Comparison of the number of differences.
- Morphological: Homologous structures: similar structures due to common ancestry Ex: Batwing and Cat arm.
- Ancestral/Derived Traits: characteristics derived from ancestor or from descendants.
- Biogeography: distribution of species and ecosystems in geographic space & through geological time.
- Phylogeny.
Speciation
- Biological Species Concept: two organisms are of the same species if they can INTERBREED and produce FERTILE, VIABLE offspring.
- Prezygotic: Before zygote is created.
  - Behavioral: Two organisms have different mating rituals (dance, song, etc).
  - Temporal: Two organisms mate at different times (day, month, year, etc.).
  - Geographic: Two organisms are separated by a geographical barrier.
  - Habitat/Ecological: Two organisms mate in different ecological environments.
  - Mechanical: Two organisms are incompatible anatomically.
  - Gametic: Two gametes are unable to fuse.
- Postzygotic: After zygote is created.
  - Reduced Hybrid Viability: Hybrid is not healthy/viable.
  - Reduced Hybrid Fertility: Hybrid is not fertile.
  - Hybrid breakdown: First generation hybrid is ok But second and more generations the hybrid starts decreasing viability and fertility.
- Sympatric: New species from a surviving ancestral species while both continue to inhabit the same geographic region Habitat isolation, Behavioral isolation, Sexual Selection, Polyploidy.
- Allopatric: Occurs when biological populations of the same species become isolated due to geographical changes.

Ecology

Body Temperature
- Endotherm: Maintains body temperature through metabolism.
- Ectotherm: Maintains body temperature through behaviors (bask in sunlight, aggregation).
Trophic Structure
- Autotroph: Capture energy from physical or chemical source.
  - Photosynthetic - sunlight.
  - Chemosynthetic - small inorganic molecules in environment (sometimes without oxygen).
- Heterotroph: Capture energy present in carbon compounds produced by other organisms. Metabolize carbohydrates, lipids, and proteins (notice: not nucleic acids) for energy through hydrolysis.
Animal Behavior
- Communication: Signaling allows for changes in behaviors of organisms to allow for differential reproductive success. Visual, Auditory, Electrical, Chemical.
- Altruistic Behaviors: Reduces individual fitness but increases inclusive fitness.
- Intersexual Selection: Reproductive behaviors to attract a mate.
- 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 $dt/dN = rN$
- Logistic Growth: Population size limited by carrying capacity $dt/dN=rN(K-N/K)$
- Density Dependent Factors: Factors that intensifies as population increases Ex: competition, predation, disease
- Density Independent Factors: Factors that affect all individuals regardless of size, population, density Ex: natural disasters, human activity
Community Ecology
- Simpson's Index: measures biodiversity (species composition and diversity)
- Simpson Diversity = 1 - ∑ (n/N)2
  - n = total number of organisms of particular species.
  - N = total of organisms of all species.
- Interactions:
  - Predator/Prey (+/-)
  - Herbivory (+/-)
  - Competition (-/-)
  - Symbiosis: Parasitism (+/-), Mutualism (+/+), Commensalism (+/0)
Invasive Species: Organism that is not indigenous, or native, to a particular area with no natural predators and unlimited resources.