Comprehensive Biology University Study Guide

BIOLOGY: THE STUDY OF LIFE
  • Biology: The scientific study of life, spanning from microscopic molecules to the global ecosystem.
  • Properties of Life: Life is defined by a set of shared characteristics:
    • Order: Highly ordered structures (e.g., sunflower seeds).
    • Evolutionary Adaptation: Heritable traits that enhance survival.
    • Response to the Environment: Reaction to external stimuli.
    • Regulation: Maintenance of internal homeostasis (e.g., blood flow/pH).
    • Energy Processing: Converting fuel into chemical energy (e.g., cellular respiration).
    • Growth and Development: Inherited information (DNA) controls growth patterns.
    • Reproduction: Producing offspring of the same species.
  • Hierarchy of Life: Atoms $\rightarrow$ Molecules $\rightarrow$ Organelles $\rightarrow$ Cells $\rightarrow$ Tissues $\rightarrow$ Organs/Organ Systems $\rightarrow$ Organisms $\rightarrow$ Populations $\rightarrow$ Communities $\rightarrow$ Ecosystems $\rightarrow$ Biosphere.
  • Reductionism vs. Systems Biology: Reductionism simplifies systems to parts; systems biology examines the interactions of those parts to understand emergent properties.
CELLULAR ORGANIZATION AND GENETICS
  • Cell Types:
    • Eukaryotic Cell: Contains membrane-bound organelles; the nucleus is the largest organelle. Size is typically 10−100 μm10-100 \, \mu m.
    • Prokaryotic Cell: Lacks a nucleus and membrane-bound organelles; DNA is in the nucleoid. Size is typically 1−5 μm1-5 \, \mu m.
  • The Genetic Code: DNA molecules are made of two long chains arranged in a double helix. Each chain is made of four nucleotides (A, G, C, T).
    • Gene Expression: The process by which information in a gene directs the manufacture of a cellular product (DNA $\rightarrow$ RNA $\rightarrow$ Protein).
  • Feedback Mechanisms:
    • Negative Feedback: The most common form; the response reduces the initial stimulus (e.g., insulin signaling to lower blood sugar).
    • Positive Feedback: The response reinforces the stimulus (e.g., blood clotting or labor contractions).
THE CORE THEME: EVOLUTION
  • Evolution: Organisms are modified descendants of common ancestors.
  • Taxonomy: Diversity is classified into three domains:
    • Domain Bacteria: Diverse and widespread prokaryotes.
    • Domain Archaea: Prokaryotes often found in extreme environments (extremophiles).
    • Domain Eukarya: Includes kingdoms Plantae (producers), Fungi (absorptive decomposers), Animalia (ingestive consumers), and Protista (mostly unicellular eukaryotes).
  • Natural Selection: Darwin's observation that individuals with inherited traits better suited to the environment are more likely to survive and reproduce.
THE PROCESS OF SCIENTIFIC INQUIRY
  • Scientific Method: A formalized process involving:
    1. Observations: Gathering data.
    2. Hypothesis: A tentative answer; must be testable through experimentation.
    3. Prediction: Often an "If… then" statement.
    4. Experimentation: Testing variables.
  • Reasoning:
    • Inductive: Specific observations $\rightarrow$ Broad generalizations.
    • Deductive: General premises $\rightarrow$ Specific results.
  • Variables: Independent variable (manipulated by the researcher) and Dependent variable (measured response).
THE CHEMICAL CONTEXT OF LIFE
  • Atomic Composition: Matter is made of elements. Elements vary by the number of Protons (atomic number).
  • Isotopes: Atoms of the same element with different numbers of neutrons. Radioactive isotopes decay spontaneously, releasing energy; used in medical imaging and dating fossils.
  • Electron Shells: Electrons are found in shells with specific energy levels:
    • First shell: Max 2 electrons.
    • Second/Third shells: Max 8 electrons (Octet Rule).
    • Valence Electrons: Outermost electrons that determine chemical behavior.
CHEMICAL BONDING
  • Strong Bonds:
    • Covalent: Sharing electrons. Single (H−HH-H) vs. Double (O=OO=O).
    • Electronegativity: An atom's attraction for the electrons in a covalent bond. Polar covalent bonds result in partial charges (δ+\delta^{+} and δ−\delta^{-}).
    • Ionic: Transfer of electrons. The attraction between an Anion (negative) and Cation (positive) creates an ionic bond.
  • Weak Bonds: Allow for temporary interactions between molecules.
    • Hydrogen Bonds: H atom bonded to an electronegative atom is attracted to another electronegative atom.
    • Van der Waals: Fluctuations in electron distribution create "hot spots" of charge.
WATER AND THE FITNESS OF THE ENVIRONMENT
  • Water Polarity: Hydrogen bonds form between water molecules because oxygen is highly electronegative.
  • Specific Heat: Water resists temperature change because heat must first break hydrogen bonds before the molecules can move faster. Water's specific heat is 1 cal/(g⋅∘C)1 \, \text{cal}/(\text{g} \cdot ^{\circ}C).
  • Evaporative Cooling: High heat of vaporization allows organisms to cool down (sweating).
  • Solvent Properties: Water is a versatile solvent because of its polarity, forming a hydration shell around solutes.
  • Acids and Bases:
    • pHpH scale range: 0 (acidic) to 14 (basic).
    • Calculation: pH=−log⁡[H+]pH = -\log[H^{+}].
    • A change of 1 unit on the pH scale represents a 10-fold change in concentration.
CARBON AND MOLECULAR DIVERSITY
  • Carbon Diversity: Carbon can form 4 bonds, allowing for complex skeletons (rings, branches, chains).
  • Hydrocarbons: Molecules consisting only of carbon and hydrogen (nonpolar, high energy storage).
  • Functional Groups:
    • Hydroxyl (-OH): Alcohols; polar.
    • Carbonyl (>C=O): Ketones and aldehydes.
    • Carboxyl (-COOH): Organic acids (can donate H+H^{+}).
    • Amino (-NH2): Bases (can pick up H+H^{+}).
    • Sulfhydryl (-SH): Forms disulfide bridges in proteins.
    • Phosphate (-OPO3^2-): High energy (ATP); acidic.
    • Methyl (-CH3): Affects gene expression when on DNA.
MACROMOLECULES: POLYMERS OF LIFE
  • Carbohydrates:
    • Glycosidic Linkage: Covalent bond joining two monosaccharides.
    • Storage: Starch (plants) and Glycogen (animals).
    • Structure: Cellulose (unbranched eta glucose polymers) and Chitin (contains nitrogen).
  • Lipids: Do not form true polymers.
    • Fats (Triglycerides): Three fatty acids linked to one glycerol.
    • Saturated: All single bonds, straight tails (solid at room temperature).
    • Unsaturated: One or more double bonds, kinked tails (liquid at room temperature).
  • Proteins:
    • Amino Acids: Carboxyl group + Amino group + R group.
    • peptide bond: Linkage between amino acids via dehydration.
    • Protein Folding: Assisted by chaperonins (protein molecules that provide a safe environment for folding).
  • Nucleic Acids:
    • Nucleotide: Pentose sugar + Nitrogenous base + Phosphate group.
    • DNA vs RNA: DNA uses deoxyribose and Thymine; RNA uses ribose and Uracil.
A TOUR OF THE CELL
  • Endomembrane System: Regulates protein traffic and performs metabolic functions.
    • Smooth ER: Detoxification and calcium storage.
    • Rough ER: Secretory protein synthesis.
    • Golgi: Modifies products of the ER.
  • Endosymbiont Theory: Mitochondria and chloroplasts were once small prokaryotes that began living within larger cells. Evidence: double membranes, own DNA, independent ribosomes.
  • The Cytoskeleton:
    • Microtubules: Hollow tubes (tubulin); maintain shape, chromosome movement.
    • Microfilaments: Two intertwined strands (actin); muscle contraction, cytoplasmic streaming.
    • Intermediate Filaments: Fibrous proteins (keratin); anchor nucleus.
MEMBRANE STRUCTURE AND FUNCTION
  • Fluidity: Membranes remain fluid as temperature decreases until phospholipids settle into a closely packed arrangement. Cholesterol prevents tight packing at low temps and restricts movement at high temps.
  • Transport Proteins:
    • Channel Proteins: Hydrophilic tunnel (e.g., aquaporins for water).
    • Carrier Proteins: Change shape to shuttle passengers across.
  • Tonicity:
    • Isotonic: No net movement.
    • Hypertonic: Higher solute concentration outside; cell shrivels.
    • Hypotonic: Lower solute concentration outside; cell swells (Turgid in plants, Lysed in animals).
  • Active Transport: Uses ATP to pump against a gradient. The Sodium-Potassium Pump maintains high [K+][K^{+}] and low [Na+][Na^{+}] inside cells.
METABOLISM AND ENZYMES
  • The Two Laws of Thermodynamics:
    1. Energy cannot be created or destroyed, only transformed.
    2. Every energy transfer increases the entropy (disorder) of the universe.
  • Free Energy: The portion of a system's energy that can perform work.
    • ΔG=G<em>final−G</em>initial\Delta G = G<em>{final} - G</em>{initial}.
  • ATP Cycle: ATP is a renewable resource; hydrolysis to ADP + Pi is exergonic (ΔG=−7.3 kcal/mol\Delta G = -7.3 \, \text{kcal/mol}).
  • Enzymes: Act by lowering the Activation Energy (EAE_{A}) barrier.
    • Environmental factors: Each enzyme has an optimal temperature and pH.
CELLULAR RESPIRATION
  • Glycolysis: Oxidizes glucose to pyruvate. Occurs in cytosol even without O2O_{2}.
    • Net yield: 2 ATP (via substrate-level phosphorylation) and 2 NADH.
  • Pyruvate Oxidation: Pyruvate enters mitochondria and is converted to Acetyl CoA, releasing CO2CO_{2}.
  • The Citric Acid Cycle (Krebs): Further oxidizes fuel.
    • Per turn (2 turns per glucose): 1 ATP, 3 NADH, 1 FADH2.
  • Oxidative Phosphorylation:
    • Electron Transport Chain (ETC): Electrons from NADH/FADH2 drop in free energy as they pass through complexes to Oxygen (final electron acceptor), forming H2OH_{2}O.
    • Chemiosmosis: H+H^{+} gradient (Proton-Motive Force) flows through ATP Synthase to generate bulk ATP.
PHOTOSYNTHESIS
  • Light Reactions: Occur in the thylakoid membrane.
    • Split water to provide electrons (e−e^{-}) and protons (H+H^{+}).
    • Generate ATP and NADPH.
  • Calvin Cycle: Occurs in the stroma.
    • Phases: Carbon Fixation, Reduction, Regeneration.
    • For 1 G3P sugar, the cycle uses 3 CO2CO_{2}, 9 ATP, and 6 NADPH.
  • C4 and CAM: Solutions to photorespiration. C4 separates fixation and cycle in different cells; CAM separates them by time (day/night).
CELL COMMUNICATION
  • Receptors:
    • GPCRs: Work with the help of a G protein that binds GTP.
    • Ligand-gated ion channels: Open or close in response to a signal.
  • Second Messengers: Small, nonprotein, water-soluble molecules. Examples: Cyclic AMP (cAMP) and Calcium ions (Ca2+Ca^{2+}).
  • Protein Kinases: Enzymes that transfer phosphates from ATP to protein (phosphorylation).
THE CELL CYCLE
  • Interphase: Accounts for 90% of the cycle.
    • G1: Growth.
    • S: DNA synthesis (replicates chromosomes).
    • G2: Preparation for division.
  • Mitotic Phase:
    • Prophase: Chromatin condenses.
    • Metaphase: Chromosomes line up at the plate.
    • Anaphase: Sister chromatids part.
  • Regulation: Controlled by Cyclins and Cdks (Cyclin-dependent kinases). The M checkpoint ensures all chromosomes are attached to spindle fibers before anaphase.
MEIOSIS AND GENETICS
  • Meiosis I: Reductive division (2n→n2n \rightarrow n). Homologous chromosomes pair up and exchange segments (crossing over).
  • Genetic Variation: Produced by Independent Assortment, Crossing Over, and Random Fertilization.
  • Probability:
    • Multiplication Rule: Probability of two independent events occurring together.
    • Addition Rule: Probability of any one of two or more exclusive events.
  • Sex-Linked Genes: Usually refers to genes on the X chromosome. Fathers pass X-linked alleles to daughters but not to sons.
DNA REPLICATION AND GENE EXPRESSION
  • DNA Replication Enzymes:
    • Helicase: Unwinds parental double helix.
    • Topoisomerase: Relieves over-winding strain.
    • DNA Pol III: Synthesizes new DNA strand.
    • DNA Pol I: Removes RNA primer and replaces it with DNA.
  • Transcription: Synthesis of RNA under direction of DNA.
    • Promoter: Sequence where RNA polymerase attaches.
    • TATA Box: A crucial promoter DNA sequence in eukaryotes.
  • Translation: The mRNA message is decoded into a protein.
    • tRNA: Carries specific amino acids and has an anticodon complementary to mRNA codons.