BIOL 189 Final Exam Study Guide Summary

Unit 1

• Properties of Life
• Emergent Properties
• Three Domains of Life: Bacteria, Archaea, Eukarya
• Four Kingdoms of Eukaryotic Organisms: Protista, Fungi, Plantae, Animalia
• Chemistry
  • Matter: Anything that has mass and takes up space.
  • Elements: A substance that cannot be broken down into other substances by chemical reactions.
  • Atoms: The smallest unit of matter that retains the chemical properties of an element. Includes atomic number (number of protons) and mass number (sum of protons and neutrons).
  • Molecules: Two or more atoms held together by covalent bonds.
  • Compounds: A substance consisting of two or more different elements combined in a fixed ratio.
  • Isotopes: Atoms of the same element with different numbers of neutrons.
  • Electron Distribution Diagrams: Visual representations of electron arrangement in atoms.
  • Chemical Bonding: Forces that hold atoms together.
    • Covalent Bonds: Sharing of electrons between atoms.
    • Ionic Bonds: Transfer of electrons between atoms, resulting in ions.
    • Hydrogen Bonds: Weak attraction between a hydrogen atom and an electronegative atom.
    • Van der Waals Interactions: Weak, short-range attractions between atoms or molecules.
  • Polar vs. Nonpolar Covalent Bonds
    • Polar: Unequal sharing of electrons.
    • Nonpolar: Equal sharing of electrons.
  • Polar vs. Nonpolar Molecules/Compounds: Based on the distribution of charge.
• Water
  • Properties: Cohesion, adhesion, solvent properties, ice formation, heat absorption.
  • Solutes, Solvents, Solutions: Components of a solution.
  • Hydrophobic vs. Hydrophilic: Interactions with water.

Unit 2

• pH
  • Acids vs. Bases: Acids donate hydrogen ions, bases accept hydrogen ions.
  • Calculating pH, [H^+], and [OH^-] of solutions: Using the formula pH = -log[H^+].
  • Buffers: Substances that minimize changes in pH.
• Carbon and Functional Groups
  • Importance of Carbon: Forms the backbone of organic compounds due to its ability to form stable bonds with many elements.
  • Organic vs. Inorganic: Organic compounds contain carbon, while inorganic compounds generally do not.
  • Hydrocarbons: Organic molecules consisting of only carbon and hydrogen.
  • Isomers: Compounds with the same molecular formula but different structures.
  • Functional Groups: Chemical groups attached to carbon skeletons that participate in chemical reactions (hydroxyl, carbonyl, carboxyl, amino, sulfhydryl, methyl, phosphate).
• Macromolecules: Large polymers assembled from small monomer subunits through dehydration synthesis and broken down by hydrolysis.
• Carbohydrates
  • Functions: Energy storage and structural support.
  • Structures and Properties: Monosaccharides, disaccharides, and polysaccharides.
  • Monosaccharides: Simple sugars (e.g., glucose, fructose).
  • Polysaccharides: Complex carbohydrates (e.g., cellulose, chitin, starch, glycogen).
• Lipids
  • Functions: Energy storage, insulation, and cell membrane structure.
  • Structures and Properties: Triglycerides, phospholipids, and steroids.
  • Triglycerides: Fats and oils composed of glycerol and fatty acids.
  • Saturated vs. Unsaturated Fats: Based on the presence of carbon-carbon double bonds.
  • Phospholipids: Major component of cell membranes.
  • Steroids: Lipids with a carbon skeleton consisting of four fused rings.
• Nucleic Acids
  • Functions: Information storage and transfer.
  • Structures and Properties: Nucleotides, DNA, and RNA.
  • Nucleotides: Monomers of nucleic acids (sugar, phosphate, and nitrogenous base).
  • DNA: Deoxyribonucleic acid; stores genetic information.
  • RNA: Ribonucleic acid; involved in gene expression.
  • Base-Pairing: A-T (or A-U in RNA), G-C.
• Proteins
  • Functions: Diverse functions including enzymes, structural components, and signaling molecules.
  • Structures and Properties: Amino acids, polypeptides, and protein folding.
  • Amino Acids: Monomers of proteins (polar, nonpolar, charged).
  • Protein Structure: Primary, secondary, tertiary, and quaternary.
  • Shape Determines Function: The three-dimensional structure of a protein dictates its function.
  • Denaturation: Loss of protein's native structure and function.
• Cells
  • Why are cells so small?: Surface area-to-volume ratio.
  • Prokaryotic vs. Eukaryotic Cells: Structural and functional differences.
  • Organelles and Cellular Structures: Nucleus, endoplasmic reticulum (ER), ribosome, Golgi apparatus, lysosome, vesicle, peroxisome, mitochondria, chloroplast.

Unit 3

• Cell (Plasma) Membrane
  • Structure: Phospholipid bilayer with embedded proteins.
  • Selectively Permeable: Controls movement of substances in and out of the cell.
  • Membrane Proteins: Various functions including transport and signaling.
• Transport
  • Passive Transport vs. Active Transport: Based on energy requirement.
  • Simple Diffusion vs. Facilitated Diffusion: Movement across the membrane.
  • Osmosis: Movement of water across a semipermeable membrane (isotonic, hypotonic, hypertonic).
  • Endocytosis: Uptake of substances into the cell (phagocytosis, pinocytosis, receptor-mediated endocytosis).
  • Exocytosis: Release of substances out of the cell.
• Energy
  • Potential Energy vs. Kinetic Energy: Stored energy vs. energy of motion.
  • Two Laws of Thermodynamics: Conservation of energy and increase in entropy.
  • Exergonic Reactions vs. Endergonic Reactions: Release energy vs. require energy.
  • Activation Energy and Transition State: Energy required to start a reaction.
• Enzymes
  • Catalyze Chemical Reactions: Lower activation energy.
  • Specificity of Substrate to Active Site: Enzymes are specific to their substrates.
  • Induced Fit: Enzyme changes shape upon substrate binding.
  • Steps of Enzyme Catalysis: Substrate binding, catalysis, product release.
  • Effect of Denaturation on Enzyme: Loss of enzyme activity.
  • Effect of Phosphorylation on Enzyme: Can activate or deactivate enzymes.
  • Cofactors vs. Coenzymes: Non-protein helpers for enzymes.
• Metabolism
  • Metabolic Pathways: Series of chemical reactions.
  • Catabolism vs. Anabolism: Breakdown vs. synthesis.
• ATP: Adenosine triphosphate; the main energy currency of the cell.
• Redox
  • Reduction: Gain of electrons.
  • Oxidation: Loss of electrons.
  • Redox Chemical Equations: Identifying oxidized and reduced reactants.
  • Electron Carriers: Molecules that carry electrons (e.g., NAD+, FAD).
• Aerobic Cellular Respiration
  • Glycolysis: Occurs in the cytoplasm; input/output of molecules; does not require oxygen.
  • Pyruvate Oxidation: Occurs in the mitochondrial matrix; input/output of molecules; requires oxygen.
  • Citric Acid/Krebs Cycle: Occurs in the mitochondrial matrix; input/output of molecules; requires oxygen.
  • Oxidative Phosphorylation: Occurs in the inner mitochondrial membrane; input/output of molecules; requires oxygen.
    • Electron Transport Chain: Transfers electrons.
    • Chemiosmosis: Generates ATP.
    • Purpose of Oxygen: Final electron acceptor.
• Fermentation
  • Glycolysis
  • NAD^+ regeneration
  • Lactic Acid vs. Alcohol Fermentation

Unit 4

• Cell Cycle/Mitosis
  • Interphase: G1, S, G2 phases.
  • Mitosis: Prophase, prometaphase, metaphase, anaphase, telophase.
  • Cytokinesis: Cell division.
  • Cell Cycle Checkpoints: During G1, G2, and metaphase.
  • Benign vs. Malignant Tumors: Non-cancerous vs. cancerous.
• Meiosis
  • Ploidy: Haploid vs. diploid.
  • Karyotypes: Homologous chromosomes, autosomes, sex chromosomes.
  • Germ Cell: A cell containing half the number of chromosomes of a somatic cell and able to unite with one from the opposite sex to form a new individual.
  • Gamete: A mature haploid male or female germ cell that is able to unite with another of the opposite sex in sexual reproduction to form a zygote.
  • Meiosis I and Meiosis II: Stages of meiosis.
  • Crossing Over and Independent Assortment: Genetic variation.
  • Nondisjunction: Failure of chromosomes to separate properly.
• DNA Replication
  • Semiconservative Model: Each new DNA molecule consists of one original and one new strand.
  • Replication of Prokaryotic vs. Eukaryotic Chromosomes/Genomes: Differences in replication.
  • Enzymes and Proteins: Helicase, single-strand binding proteins, topoisomerase, primase, DNA polymerase III, DNA polymerase I, DNA ligase.
  • Leading Strand vs. Lagging Strand: Continuous vs. discontinuous replication.
• Gene Expression
  • DNA → RNA → Protein: Central dogma of molecular biology.
  • Types of RNA: mRNA, rRNA, tRNA, snRNA.
  • Transcription: Synthesis of RNA from DNA.
    • Stages: Initiation, elongation, termination.
    • Roles of RNA polymerase, promoter (and TATA box), transcription factors.
  • RNA Processing: 5' cap, 3' poly-A tail, splicing (introns vs. exons).
  • Translation: Synthesis of protein from RNA.
    • Genetic Code and use of codons.
    • mRNA.
    • Roles of tRNA and ribosome.
    • Stages: Initiation, elongation, termination.
  • Mutation: Changes in DNA sequence and their effects on gene expression.