Comprehensive Biology Final Exam Review Notes

Chapter 1: Evolution, Themes of Biology, and Scientific Inquiry

Phylogenetic Trees and Common Ancestors

• Phylogenetic Tree: A diagram showing evolutionary relationships among species. The most recent common ancestor is the node where two lineages diverge.

• Application: Identifying the most recent common ancestor helps trace evolutionary history.

Feedback Mechanisms

• Positive Feedback: A process that amplifies a change (e.g., blood clotting).

• Negative Feedback: A process that reduces a change, maintaining homeostasis (e.g., body temperature regulation).

Scientific Method and Data Types

• Hypothesis: A testable explanation for an observation.

• Qualitative Data: Descriptive, non-numerical (e.g., color, texture).

• Quantitative Data: Numerical measurements (e.g., mass, volume).

Genetic Material and Taxonomy

• DNA (Deoxyribonucleic Acid): Hereditary material in all living organisms.

• RNA (Ribonucleic Acid): Involved in protein synthesis and gene regulation.

• Gene: A segment of DNA coding for a protein or RNA molecule.

• Genome: The complete set of genetic material in an organism.

• Domains: The highest taxonomic rank: Bacteria, Archaea, Eukarya.

• Taxonomy: The science of classifying organisms.

Cell Types and Evolution

• Eukaryotic Cells: Have a nucleus and membrane-bound organelles.

• Prokaryotic Cells: Lack a nucleus; DNA is in the nucleoid region.

• Theory of Evolution: Explains the diversity of life through descent with modification.

• Natural Selection: Process where organisms better adapted to their environment tend to survive and reproduce.

Chapter 2: The Chemical Context of Life

Elements and Atomic Structure

• Main Elements in Living Matter: Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N).

• Kinetic Energy: Energy of motion.

• Potential Energy: Stored energy due to position or structure.

• Atomic Number: Number of protons in an atom.

• Atomic Mass: Sum of protons and neutrons.

• Atomic Weight: Average mass of atoms of an element, accounting for isotopes.

• Measuring Atomic Mass: In atomic mass units (amu) or Daltons.

• Isotopes: Atoms of the same element with different numbers of neutrons.

Chemical Bonds

• Nonpolar Covalent Bonds: Electrons shared equally.

• Polar Covalent Bonds: Electrons shared unequally, creating partial charges.

• Hydrogen Bonds: Weak attraction between a hydrogen atom and an electronegative atom.

• Ionic Bonds: Transfer of electrons from one atom to another, forming ions.

Valence Electrons

• Valence Electrons: Electrons in the outermost shell; determine chemical reactivity.

• Calculation: For main group elements, equal to the group number in the periodic table.

Chapter 3: Water and Life

Solutions and Solubility

• Solution: Homogeneous mixture of two or more substances.

• Solvent: The dissolving agent (e.g., water).

• Hydrophilic: Water-loving; substances that dissolve in water.

• Hydrophobic: Water-fearing; substances that do not dissolve in water.

Molecular Mass and Molarity

• Molecular Mass: Sum of atomic masses in a molecule.

• Calculation: Add the atomic masses of all atoms in the molecule.

• 1 M Solution: 1 mole of solute per liter of solution.

pH and Acidity

• pH: Measure of hydrogen ion concentration; scale from 0 (acidic) to 14 (basic).

• Calculation: $pH = -\log_{10}[H^+]$

Chapter 5: The Structure and Function of Large Biological Molecules

Macromolecules

• Biological Molecules: Carbohydrates, lipids, proteins, nucleic acids.

• Functions: Energy storage, structural support, catalysis, genetic information.

• Polymer: Large molecule made of repeating units (monomers).

• Monomer: Single subunit of a polymer.

Reactions and Lipids

• Dehydration Reaction: Joins monomers by removing water.

• Hydrolysis Reaction: Breaks polymers by adding water.

• Phospholipids: Major component of cell membranes; amphipathic nature forms bilayers.

• Saturated Fat: No double bonds; solid at room temperature.

• Unsaturated Fat: One or more double bonds; liquid at room temperature.

• Trans Fats: Unsaturated fats with trans double bonds; associated with health risks.

Proteins and Nucleic Acids

• Peptide Bond: Covalent bond linking amino acids in proteins.

• Protein Structure:

  • Primary: Sequence of amino acids.

  • Secondary: Alpha helices and beta sheets (hydrogen bonding).

  • Tertiary: 3D folding due to side chain interactions.

  • Quaternary: Multiple polypeptide chains.

• DNA Structure: Double helix of nucleotides.

• Nucleotide Structure: Phosphate group, sugar, nitrogenous base.

• Pyrimidines: Cytosine, Thymine, Uracil (single ring).

• Purines: Adenine, Guanine (double ring).

• DNA vs RNA: DNA has deoxyribose and thymine; RNA has ribose and uracil.

Chapter 6: A Tour of the Cell

Cell Organelles and Types

• Major Organelles: Nucleus, mitochondria, endoplasmic reticulum, Golgi apparatus, lysosomes, chloroplasts (plants), vacuoles.

• Prokaryotic vs Eukaryotic Cells: Prokaryotes lack a nucleus and organelles; eukaryotes have both.

• Plant vs Animal Cells: Plant cells have cell walls, chloroplasts, and large central vacuoles; animal cells do not.

• Centrioles: Cylindrical structures involved in cell division in animal cells.

Chapter 7: Membrane Structure and Function

Membrane Properties and Transport

• Selective Permeability: Membranes allow some substances to pass more easily than others.

• Peripheral Proteins: Loosely bound to membrane surface.

• Integral Proteins: Embedded within the membrane.

• Functions of Membrane Proteins: Transport, signal transduction, cell recognition, intercellular joining, attachment to cytoskeleton.

• Substances Passing Through Membrane: Small, nonpolar molecules (e.g., O2, CO2) pass easily; ions and large molecules require transport proteins.

Transport Mechanisms

• Sodium/Potassium Pump: Actively transports Na+ out and K+ into the cell.

• Proton Pump: Moves H+ ions across membranes, creating electrochemical gradients.

• Osmosis: Diffusion of water across a selectively permeable membrane.

• Hypertonic: Higher solute concentration outside; cell loses water.

• Isotonic: Equal solute concentration; no net water movement.

• Hypotonic: Lower solute concentration outside; cell gains water.

• Turgid: Firm (plant cell in hypotonic solution).

• Flaccid: Limp (plant cell in isotonic solution).

• Plasmolysis: Cell membrane pulls away from cell wall (plant cell in hypertonic solution).

• Facilitated Diffusion: Passive transport via proteins; osmosis is water movement, facilitated diffusion is for solutes.

Chapter 8: An Introduction to Metabolism

Thermodynamics and Metabolic Pathways

• First Law of Thermodynamics: Energy cannot be created or destroyed.

• Second Law of Thermodynamics: Every energy transfer increases entropy (disorder).

• Metabolism: All chemical reactions in an organism.

• Anabolism: Building complex molecules from simpler ones (requires energy).

• Catabolism: Breaking down complex molecules (releases energy).

• Dehydration and Hydrolysis: Dehydration builds polymers; hydrolysis breaks them down.

• Types of Energy: Kinetic, chemical, potential, thermal.

• Endergonic Reaction: Requires energy input ($\Delta G > 0$).

• Exergonic Reaction: Releases energy ($\Delta G < 0$).

Enzymes and ATP

• Enzymes: Biological catalysts that lower activation energy.

• Active Site: Region on enzyme where substrate binds.

• Types of Inhibition: Competitive (blocks active site), noncompetitive (binds elsewhere, changes shape).

• ATP Structure: Adenosine triphosphate; energy currency of the cell.

Chapter 9: Cellular Respiration and Fermentation

ATP Production and Pathways

• ATP Yield:

  • Glycolysis: 2 ATP

  • Krebs Cycle: 2 ATP

  • Electron Transport Chain: ~34 ATP

• Aerobic Respiration: Uses oxygen; produces more ATP.

• Anaerobic Respiration: Does not use oxygen; less ATP produced.

• Alcohol Fermentation: Produces ethanol and CO2.

• Lactic Acid Fermentation: Produces lactic acid; occurs in muscles.

• Electron Transport Chain: Series of proteins in mitochondria; produces most ATP.

• Substrate-Level Phosphorylation: Direct transfer of phosphate to ADP; occurs in glycolysis and Krebs cycle.

• Oxidative Phosphorylation: ATP synthesis powered by electron transport chain; occurs in mitochondria.

Chapter 10: Photosynthesis

Light and Dark Reactions

• Light Reactions: Produce ATP and NADPH; occur in thylakoid membranes.

• Dark Reactions (Calvin Cycle): Produce glucose; occur in stroma.

• Photosystem II vs I: PS II comes first, splits water; PS I produces NADPH.

• ATP Synthase Location: Thylakoid membrane.

• Location of Reactions: Light reactions in thylakoid; dark reactions in stroma.

Chapter 12: The Cell Cycle

Mitosis and Cell Division

• Phases of Mitosis: Prophase, metaphase, anaphase, telophase.

• Mitosis vs Meiosis: Mitosis produces identical cells; meiosis produces gametes with half the chromosome number.

• Interphase Stages: G1 (growth), S (DNA synthesis), G2 (preparation for division).

• Cytokinesis: Animals: cleavage furrow; plants: cell plate formation.

• Somatic Cells: Body cells; diploid.

• Gametes: Sex cells; haploid.

• Chromatin: DNA and protein complex.

• Sister Chromatids: Identical copies of a chromosome.

• Chromosomes: DNA molecules with genetic material.

• Centromere: Region where sister chromatids are joined.

Chapter 13: Meiosis and Sexual Life Cycles

Meiosis and Genetic Variation

• Diploid (2n): Two sets of chromosomes.

• Haploid (n): One set of chromosomes.

• Autosomes: Non-sex chromosomes.

• Sex Chromosomes: X and Y chromosomes.

• Homologous Chromosomes: Chromosome pairs with genes for the same traits.

• Phases of Meiosis: Meiosis I (homologs separate), Meiosis II (sister chromatids separate).

• Genetic Variation: Crossing over, independent assortment, random fertilization.

Chapter 14: Mendel and the Gene Idea

Genetics and Probability

• Mendel's Contributions: Laws of segregation and independent assortment.

• Alleles: Different forms of a gene (dominant vs recessive).

• Phenotype: Observable traits.

• Genotype: Genetic makeup.

• Homozygous: Two identical alleles.

• Heterozygous: Two different alleles.

• Punnett Square: Tool to predict genetic crosses.

• Multiplication Rule: Probability of independent events occurring together is the product of their probabilities.

Chapter 16: The Molecular Basis of Inheritance

DNA Experiments and Replication

• Griffith's Experiment: Showed transformation in bacteria.

• Bacteriophages: Viruses that infect bacteria.

• Hershey and Chase: Confirmed DNA is genetic material.

• X-ray Diffraction: Revealed DNA's helical structure.

• Watson and Crick: Discovered double helix structure of DNA.

• Semi-Conservative Model: Each new DNA has one old and one new strand.

• DNA Replication Enzymes: Helicase, primase, DNA polymerase, ligase.

• Leading vs Lagging Strand: Leading synthesized continuously; lagging in Okazaki fragments.

• Chargaff’s Rules: A=T, G=C in DNA.

• Telomeres: Protective ends of chromosomes.

Chapter 17: Gene Expression: From Gene to Protein

Transcription, Translation, and Mutations

• Codon: Three-nucleotide sequence on mRNA coding for an amino acid.

• Anticodon: Complementary three-nucleotide sequence on tRNA.

• Codon Box: Table used to translate mRNA codons into amino acids.

• Wobble Base: Flexibility in third base of codon, allowing some tRNAs to pair with multiple codons.

• Central Dogma: DNA → RNA → Protein.

• Location: Transcription in nucleus; translation in cytoplasm.

• pre-mRNA Processing: Capping, poly-A tail, splicing.

• Mutations:

  • Missense: Changes amino acid.

  • Nonsense: Introduces stop codon.

  • Silent: No change in amino acid.

Chapter 19: Viruses

Viral Structure and Life Cycles

• Viral Composition: Genetic material (DNA or RNA) enclosed in a protein coat (capsid); some have envelopes.

• Lytic Cycle: Virus replicates and lyses host cell.

• Lysogenic Cycle: Viral DNA integrates into host genome; can become lytic later.

• Host Range: Determined by virus's ability to bind to specific host cell receptors.