AP Biology: Chemistry of Life

• AP Biology encompasses various units that cover a wide range of biological concepts, from molecular biology to ecosystems.

Unit 1: Chemistry of Life

• Living organisms are composed of matter, which is made up of elements.
• Essential elements for life include carbon, hydrogen, oxygen, nitrogen, phosphorus, and sulfur (CHNOPS).
• Atoms are the smallest units of matter that retain the chemical properties of an element.
• Atoms consist of protons, neutrons, and electrons.
• Protons have a positive charge, neutrons are neutral, and electrons have a negative charge.
• The number of protons determines the element's atomic number.
• Isotopes are variants of an element with different numbers of neutrons.
• Chemical bonds include:
  • Covalent bonds: sharing of electrons between atoms.
  • Ionic bonds: transfer of electrons between atoms, creating ions.
  • Hydrogen bonds: weak bonds between hydrogen and electronegative atoms.
  • Van der Waals interactions: weak attractions between molecules.
• Water is essential for life due to its properties:
  • Cohesion: water molecules stick together.
  • Adhesion: water molecules stick to other substances.
  • High specific heat: water resists temperature changes.
  • Universal solvent: water dissolves polar and ionic substances.
• pH is a measure of hydrogen ion concentration; acids have a high concentration of H+ ions while bases have a low concentration.
• Organic molecules contain carbon.
• Carbon can form diverse molecules by bonding with four other atoms.
• Functional groups attached to carbon skeletons determine the properties of organic molecules.
• Important classes of organic molecules:
  • Carbohydrates: sugars and polymers of sugars providing energy and structure.
  • Lipids: fats, oils, and steroids, which are hydrophobic and used for energy storage, insulation, and hormones.
  • Proteins: polymers of amino acids, used for structural support, enzymes, transport, and defense.
  • Nucleic acids: DNA and RNA, which store and transmit genetic information.
• Polymers are large molecules made of repeating monomer subunits.
• Dehydration reactions link monomers by removing water, while hydrolysis breaks polymers by adding water.
• Proteins have four levels of structure:
  • Primary: amino acid sequence.
  • Secondary: local folding (alpha helix, beta sheet).
  • Tertiary: overall 3D shape.
  • Quaternary: multiple polypeptide chains.
• Enzymes are biological catalysts that speed up chemical reactions by lowering activation energy.

Unit 2: Cell Structure and Function

• The cell is the basic unit of life.
• Prokaryotic cells (bacteria and archaea) lack a nucleus and membrane-bound organelles.
• Eukaryotic cells (protists, fungi, plants, and animals) have a nucleus and membrane-bound organelles.
• Key organelles and their functions:
  • Nucleus: contains DNA and controls cell activities.
  • Ribosomes: synthesize proteins.
  • Endoplasmic reticulum (ER): synthesizes and transports proteins and lipids.
    • Rough ER: contains ribosomes.
    • Smooth ER: synthesizes lipids and detoxifies drugs.
  • Golgi apparatus: modifies, sorts, and packages proteins and lipids.
  • Lysosomes: contain enzymes for intracellular digestion.
  • Mitochondria: generate ATP through cellular respiration.
  • Chloroplasts (in plants): carry out photosynthesis.
  • Vacuoles: store water, ions, and other molecules.
• The plasma membrane is a selectively permeable barrier made of a phospholipid bilayer.
• Membrane proteins have various functions: transport, enzymatic activity, signal transduction, cell-cell recognition, intercellular joining, and attachment to the cytoskeleton and ECM.
• Transport across the membrane:
  • Passive transport: diffusion, osmosis, and facilitated diffusion (no energy required).
  • Active transport: requires energy (ATP) to move substances against their concentration gradients.
  • Endocytosis: cell takes in substances by forming vesicles.
  • Exocytosis: cell releases substances by fusing vesicles with the plasma membrane.
• Cell communication:
  • Direct contact: gap junctions and plasmodesmata.
  • Local signaling: paracrine and synaptic signaling.
  • Long-distance signaling: endocrine signaling (hormones).
• Signal transduction pathways: reception, transduction, and response.

Unit 3: Cellular Energetics

• Metabolism is the sum of all chemical reactions in an organism.
• Catabolic pathways break down complex molecules into simpler ones, releasing energy.
• Anabolic pathways build complex molecules from simpler ones, requiring energy.
• ATP (adenosine triphosphate) is the primary energy currency of the cell.
• Enzymes lower the activation energy of reactions.
• Factors affecting enzyme activity: temperature, pH, substrate concentration, and inhibitors.
• Cellular respiration converts glucose into ATP:
  • Glycolysis: glucose is broken down into pyruvate.
  • Pyruvate oxidation: pyruvate is converted to acetyl CoA.
  • Krebs cycle (citric acid cycle): acetyl CoA is oxidized, releasing CO2 and generating ATP, NADH, and FADH2.
  • Electron transport chain (ETC) and oxidative phosphorylation: electrons from NADH and FADH2 are passed through the ETC, creating a proton gradient that drives ATP synthesis.
• Fermentation occurs in the absence of oxygen:
  • Lactic acid fermentation (in animals).
  • Alcohol fermentation (in yeast).
• Photosynthesis converts light energy into chemical energy (glucose):
  • Light-dependent reactions: light energy is used to split water, releasing oxygen and generating ATP and NADPH.
  • Calvin cycle: CO2 is fixed and reduced to form glucose, using ATP and NADPH.

Unit 4: Cell Communication and Cell Cycle

• Cell communication involves reception, transduction, and response.
• Types of signaling: paracrine, endocrine, autocrine, and direct contact.
• Signal receptors:
  • Intracellular receptors: located inside the cell.
  • Plasma membrane receptors: located on the cell surface.
• Signal transduction pathways involve cascades of protein interactions.
• Second messengers (e.g., cAMP, calcium ions) amplify the signal.
• Cellular responses include changes in gene expression or enzyme activity.
• The cell cycle is the series of events that lead to cell growth and division.
• Phases of the cell cycle:
  • Interphase (G1, S, G2): cell grows and replicates DNA.
  • Mitotic phase (M phase): cell divides.
• Mitosis: division of the nucleus:
  • Prophase: chromosomes condense, spindle forms.
  • Metaphase: chromosomes align at the metaphase plate.
  • Anaphase: sister chromatids separate.
  • Telophase: nuclear envelope reforms, chromosomes decondense.
• Cytokinesis: division of the cytoplasm.
• Cell cycle checkpoints ensure proper division:
  • G1 checkpoint: checks for DNA damage.
  • G2 checkpoint: checks for complete DNA replication.
  • M checkpoint: checks for chromosome alignment.
• Apoptosis: programmed cell death.
• Cancer results from uncontrolled cell division due to mutations in genes that regulate the cell cycle.

Unit 5: Heredity

• Heredity is the transmission of traits from parents to offspring.
• Genes are units of heredity made of DNA.
• Chromosomes are structures containing DNA.
• Asexual reproduction: single parent produces genetically identical offspring.
• Sexual reproduction: two parents produce offspring with unique combinations of genes.
• Meiosis: cell division that produces gametes (sperm and egg) with half the number of chromosomes.
• Fertilization: fusion of sperm and egg to form a zygote.
• Mendelian genetics:
  • Law of segregation: alleles for each gene separate during gamete formation.
  • Law of independent assortment: alleles of different genes assort independently during gamete formation.
• Genotype: genetic makeup of an organism.
• Phenotype: physical traits of an organism.
• Dominant allele: masks the effect of the recessive allele.
• Punnett squares: used to predict the genotypes and phenotypes of offspring.
• Non-Mendelian genetics:
  • Incomplete dominance: heterozygous phenotype is intermediate between the two homozygous phenotypes.
  • Codominance: both alleles are expressed in the heterozygous phenotype.
  • Multiple alleles: more than two alleles for a gene in the population.
  • Polygenic inheritance: trait controlled by multiple genes.
  • Sex-linked traits: genes located on sex chromosomes (X and Y).
• Chromosomal mutations:
  • Deletion: loss of a chromosome segment.
  • Duplication: repetition of a chromosome segment.
  • Inversion: reversal of a chromosome segment.
  • Translocation: movement of a chromosome segment to a non-homologous chromosome.

Unit 6: Gene Expression and Regulation

• DNA structure: double helix made of nucleotides (sugar, phosphate, and nitrogenous base).
• DNA replication: DNA is copied, producing two identical DNA molecules.
• Transcription: DNA is transcribed into RNA.
• Translation: RNA is translated into protein.
• Gene expression: the process by which DNA directs the synthesis of proteins.
• Central dogma of molecular biology: DNA -> RNA -> Protein.
• RNA types:
  • mRNA: carries genetic information from DNA to ribosomes.
  • tRNA: transfers amino acids to ribosomes during translation.
  • rRNA: component of ribosomes.
• Genetic code: set of rules by which information encoded in genetic material (DNA or RNA) is translated into proteins (amino acid sequences) by living cells.
• Mutations: changes in DNA sequence:
  • Point mutations: single base change.
    • Silent: no effect on amino acid sequence.
    • Missense: changes amino acid.
    • Nonsense: creates a stop codon.
  • Frameshift mutations: insertion or deletion of bases that alter the reading frame.
• Gene regulation: control of gene expression:
  • Prokaryotes: operons (e.g., lac operon).
  • Eukaryotes: transcriptional control, RNA processing, translational control, and post-translational modifications.
• Biotechnology:
  • DNA sequencing.
  • Polymerase chain reaction (PCR): amplifies DNA.
  • Gel electrophoresis: separates DNA fragments.
  • Genetic engineering: modifying genes.
  • CRISPR-Cas9: gene editing technology.

Unit 7: Natural Selection

• Evolution is the change in the genetic makeup of a population over time.
• Natural selection: differential survival and reproduction based on heritable traits.
• Evidence for evolution:
  • Fossil record.
  • Homologous structures.
  • Vestigial structures.
  • Biogeography
  • Molecular biology.
• Mechanisms of evolution:
  • Mutation: creates new alleles.
  • Gene flow: movement of alleles between populations.
  • Genetic drift: random changes in allele frequencies.
    • Bottleneck effect: drastic reduction in population size.
    • Founder effect: small group establishes a new population.
  • Natural selection: differential survival and reproduction.
• Adaptation: trait that enhances survival and reproduction.
• Types of natural selection:
  • Directional selection: favors one extreme phenotype.
  • Disruptive selection: favors both extreme phenotypes.
  • Stabilizing selection: favors intermediate phenotypes.
• Speciation: the process by which new species arise:
  • Allopatric speciation: geographic isolation.
  • Sympatric speciation: reproductive isolation within the same geographic area.
• Phylogeny: evolutionary history of a species or group of species.
• Phylogenetic tree: diagram that represents evolutionary relationships.

Unit 8: Ecology

• Ecology is the study of interactions between organisms and their environment.
• Levels of ecological study:
  • Organismal ecology: individual organisms.
  • Population ecology: groups of individuals of the same species.
  • Community ecology: interactions between different species.
  • Ecosystem ecology: interactions between organisms and their physical environment.
  • Global ecology: interactions on a global scale.
• Population ecology:
  • Population size: number of individuals.
  • Population density: number of individuals per unit area.
  • Population dispersion: pattern of spacing among individuals.
  • Population growth: influenced by birth rate, death rate, immigration, and emigration.
• Community ecology:
  • Interspecific interactions: competition, predation, herbivory, symbiosis (mutualism, commensalism, parasitism).
  • Ecological niche: the sum of a species' use of biotic and abiotic resources.
  • Trophic structure: feeding relationships in a community.
  • Food chain: transfer of energy from producers to consumers.
  • Food web: interconnected food chains.
  • Keystone species: species that have a disproportionately large impact on the community.
• Ecosystem ecology:
  • Energy flow: energy enters ecosystems as sunlight and is converted to chemical energy by autotrophs.
  • Primary production: the amount of light energy converted to chemical energy by autotrophs.
  • Trophic efficiency: the percentage of energy transferred from one trophic level to the next.
  • Biogeochemical cycles: cycling of nutrients (e.g., water, carbon, nitrogen).
• Conservation biology: efforts to protect biodiversity.
• Threats to biodiversity: habitat loss, invasive species, pollution, overexploitation, and climate change.