Unit 1: Ecology, Homeostasis, and Biostatistics

Animal Behavior and Homeostasis

Animal behavior and homeostasis are fundamental concepts in biology, describing how organisms interact with their environment and maintain internal stability. Behaviors can be innate or learned, and homeostasis is regulated by feedback mechanisms.

• Innate Behaviors: Genetically inherited actions performed without prior experience. Example: Fixed action patterns triggered by a sign stimulus.

• Directed Movements:

  • Kinesis: Non-directional change in activity rate or turning frequency in response to a stimulus.

  • Taxis: Directional movement toward (positive) or away from (negative) a stimulus (e.g., phototaxis, chemotaxis).

• Learned Behaviors: Modified based on experience (e.g., habituation, classical/operant conditioning, imprinting during a critical period).

• Homeostasis: Maintenance of a dynamic, stable internal physiological environment within narrow limits despite external fluctuations.

• Feedback Loops:

  • Negative Feedback: Counteracts physiological changes to return the system to its target set point (e.g., thermoregulation, insulin/glucagon regulation of blood glucose).

  • Positive Feedback: Amplifies a stimulus to drive a biological process to completion (e.g., oxytocin release during childbirth, ethylene signaling during fruit ripening).

Ecological Levels of Organization

Ecology examines interactions across hierarchical tiers, from individual organisms to the biosphere.

• Organism: Individual living entity.

• Population: Group of individuals of the same species living in a defined area at the same time and capable of interbreeding.

• Community: All interacting populations of different species coexisting within a specified area.

• Ecosystem: Biological community together with all surrounding abiotic factors.

• Biome: Broad regional ecosystems characterized by distinct climate patterns, precipitation, and dominant plant/animal communities.

• Biosphere: The global sum of all ecosystems supporting life on Earth.

• Environmental Factors:

  • Biotic Factors: Living components (e.g., predators, prey, parasites, competitors, mutualists).

  • Abiotic Factors: Non-living physical and chemical variables (e.g., solar radiation, temperature, precipitation, soil composition, pH, dissolved oxygen).

Biomes, Populations, and Ecosystem Dynamics

Biomes are defined by climate and dominant life forms. Population and community ecology examine growth, interactions, and energy flow.

• Major Biomes:

  • Tundra: Permafrost, low precipitation, low biodiversity, short growing season.

  • Taiga (Boreal Forest): Coniferous forests, cold winters, moderate precipitation.

  • Temperate Deciduous Forest: Broadleaf deciduous trees, four distinct seasons, moderate-to-high precipitation.

  • Tropical Rainforest: High annual precipitation, warm temperatures year-round, highest terrestrial biodiversity.

  • Grassland: Seasonal precipitation, dominated by grasses, maintained by periodic fires and herbivory.

  • Desert: Extremely low precipitation, specialized adaptations for water conservation.

  • Aquatic: Marine (oceans, coral reefs, estuaries) and freshwater (lakes, rivers, wetlands).

• Population Ecology:

  • Exponential Growth: Unrestrained growth in an idealized, unlimited environment. Equation:

  • Logistic Growth: Incorporates resource limitation and carrying capacity. Equation:

• Limiting Factors:

  • Density-dependent: Impact increases as population density rises (e.g., disease, competition, predation, waste accumulation).

  • Density-independent: Effects regardless of population density (e.g., natural disasters, seasonal temperature extremes).

• Community Ecology:

  • Interspecific Interactions: Competition (−/−), predation/parasitism/herbivory (+/−), mutualism (+/+), commensalism (+/0).

  • Competitive Exclusion Principle: Two species competing for the same limiting resources cannot coexist indefinitely; leads to resource partitioning or competitive exclusion.

  • Trophic Cascades and Keystone Species: Keystone species exert strong control on community structure disproportionate to their abundance.

• Ecosystem Dynamics:

  • Energy Flow: Unidirectional; only about 10% of energy transfers from one trophic level to the next, 90% lost as heat or unconsumed biomass.

  • Nutrient Cycling: Matter cycles indefinitely through biogeochemical reservoirs (carbon, nitrogen, phosphorus, water cycles).

Unit 2: Chemistry of Life

Monomers vs. Polymers

Biological macromolecules are constructed from smaller subunits called monomers. Polymers are formed by linking monomers in chains.

• Monomers: Small, individual molecular subunits (e.g., glucose, amino acids, nucleotides).

• Polymers: Large macromolecules constructed by covalently linking multiple monomers.

• Macromolecular Relationships:

  • Carbohydrates: Monosaccharides form polysaccharides.

  • Proteins: Amino acids form polypeptides and functional proteins.

  • Nucleic Acids: Nucleotides form polynucleotide chains (DNA and RNA).

  • Lipids: Not true polymers; composed of distinct components (glycerol and fatty acids).

Dehydration Synthesis vs. Hydrolysis

Macromolecules are assembled and broken down by dehydration synthesis and hydrolysis reactions.

• Dehydration Synthesis: Joins two monomers with the loss of a water molecule. Anabolic and endergonic process. General equation:

• Hydrolysis: Cleaves covalent bonds between monomers by adding water. Catabolic and exergonic process. General equation:

Four Organic Macromolecules

Living organisms are built from four main classes of macromolecules: carbohydrates, lipids, proteins, and nucleic acids.

• Carbohydrates:

  • Composition: Carbon, hydrogen, oxygen (approximate ratio C1H2O1).

  • Monomers: Monosaccharides (e.g., glucose, fructose, galactose; formula C6H12O6).

  • Linkage: Glycosidic bonds via dehydration reactions.

  • Disaccharides: Two monosaccharides (e.g., maltose, sucrose, lactose).

  • Polysaccharides:

    • Energy Storage: Starch (plants), glycogen (animals).

    • Structural Support: Cellulose (plants), chitin (fungi, arthropods).

• Lipids:

  • Composition: Predominantly carbon and hydrogen; some contain phosphorus.

  • Characteristics: Non-polar, hydrophobic, insoluble in water.

  • Major Classes:

    • Triglycerides: Glycerol + 3 fatty acids via ester linkages. Saturated (no double bonds, solid), unsaturated (double bonds, liquid).

    • Phospholipids: Glycerol backbone, two fatty acid tails, one phosphate head. Amphipathic; forms cell membranes.

    • Steroids: Four-ring carbon skeleton (e.g., cholesterol, steroid hormones).

• Proteins:

  • Composition: Carbon, hydrogen, oxygen, nitrogen, sulfur.

  • Monomers: Amino acids (20 types).

  • Structure: Central α-carbon, amino group, carboxyl group, hydrogen, variable R-group.

  • Peptide Bonds: Covalent bonds between amino acids.

  • Structural Levels:

    • Primary: Linear sequence of amino acids.

    • Secondary: α-helices and β-sheets stabilized by hydrogen bonds.

    • Tertiary: 3D conformation from R-group interactions.

    • Quaternary: Association of multiple polypeptides (e.g., hemoglobin).

• Nucleic Acids:

  • Composition: Carbon, hydrogen, oxygen, nitrogen, phosphorus.

  • Monomers: Nucleotides (pentose sugar, phosphate group, nitrogenous base).

  • Linkage: Phosphodiester bonds (3' hydroxyl to 5' phosphate).

  • Types:

    • DNA: Deoxyribose sugar; bases A, T, C, G; double helix; hereditary storage.

    • RNA: Ribose sugar; bases A, U, C, G; single-stranded; protein synthesis and gene regulation.

Functional Groups

Functional groups are specific chemical groups attached to carbon skeletons, conferring distinct properties to organic molecules.

• Hydroxyl (−OH): Polar; forms hydrogen bonds; identifies alcohols.

• Carbonyl (−C=O): Polar; found as ketones (internal) or aldehydes (terminal); component of sugars.

• Carboxyl (−COOH): Acidic; donates H+; found in amino acids and fatty acids.

• Amino (−NH2): Basic; accepts H+; found in amino acids.

• Sulfhydryl (−SH): Weakly polar; forms disulfide bridges; characteristic of cysteine.

• Phosphate (−OPO32−): Negative charge; polar; energy transfer (e.g., ATP), nucleic acid backbone.

• Methyl (−CH3): Non-polar; hydrophobic; affects gene expression and molecular shape.

Isomers

Isomers are compounds with the same chemical formula but different structural arrangements.

• Structural Isomers: Differ in covalent arrangement or placement of functional groups (e.g., glucose vs. fructose).

• Cis-Trans Isomers: Differ in spatial arrangement around a double bond.

  • Cis: Similar groups on the same side.

  • Trans: Similar groups on opposite sides.

• Enantiomers: Non-superimposable mirror images due to chiral carbon; exist in D- and L- forms; enzyme specificity for one form.

The Heterotroph Hypothesis

This hypothesis explains the origin of life under prebiotic conditions, leading to the evolution of heterotrophic and autotrophic organisms.

• Prebiotic Conditions: Reducing atmosphere (CH4, NH3, H2, H2O), abundant energy sources (volcanic heat, lightning, UV radiation).

• Evolutionary Progression:

  1. Abiotic synthesis of monomers in primordial soup.

  2. Aggregation into polymers and protocells.

  3. Anaerobic heterotrophs absorbed environmental organic molecules and used fermentation.

  4. Autotrophs evolved to synthesize organic molecules from inorganic carbon (CO2).

  5. Photosynthetic autotrophs released O2, leading to the oxygen revolution and aerobic respiration.

The Stanley Miller Experiment

This experiment tested the Oparin-Haldane hypothesis by simulating prebiotic Earth conditions and demonstrating abiotic synthesis of organic molecules.

• Apparatus: Closed glass system with warm water (ocean), reducing atmosphere (CH4, NH3, H2, H2O), electrical sparks (lightning), condenser (rainfall).

• Findings: Formation of amino acids, urea, organic acids within one week.

• Significance: Demonstrated that organic monomers can arise spontaneously from inorganic gases without preexisting life.

Properties of Water

Water's unique properties are essential for life, resulting from its polarity and hydrogen bonding.

• Polarity & Hydrogen Bonding: Water is polar; oxygen is δ−, hydrogen is δ+. Forms hydrogen bonds with up to four neighbors.

• Cohesion & Surface Tension: Attraction between water molecules; high surface tension supports organisms.

• Adhesion & Capillary Action: Attraction to other polar surfaces; drives capillary action in plants.

• High Specific Heat Capacity: Water absorbs/releases heat before changing temperature; stabilizes climate and internal homeostasis.

• High Heat of Vaporization: Large heat required to vaporize; enables evaporative cooling (transpiration, perspiration).

• Expansion Upon Freezing: Ice is less dense than liquid water; floats and insulates aquatic life.

• Universal Solvent: Water dissolves ions and polar molecules; medium for metabolic reactions.

Unit 3: Cell Membranes and Cell Transport

Structure and Function of the Plasma Membrane

The plasma membrane is a selectively permeable boundary regulating substance movement and maintaining homeostasis. Its structure is described by the fluid mosaic model.

• Phospholipid Bilayer: Amphipathic phospholipids form a bilayer; hydrophobic tails inward, hydrophilic heads outward.

• Membrane Fluidity: Phospholipids move laterally; cholesterol regulates fluidity.

• Membrane Proteins:

  • Integral: Penetrate hydrophobic core; amphipathic.

  • Peripheral: Loosely bound to membrane surface; mostly polar.

  • Lipid Bound: Rare, nonpolar, inside bilayer.

  • Functions: Transport, enzymatic activity, signal transduction, cell-cell recognition, intercellular joining, attachment to cytoskeleton/ECM.

• Carbohydrate Chains: Glycoproteins and glycolipids serve as molecular identification tags.

Selective Permeability

The hydrophobic core of the bilayer determines which substances can cross directly.

• Small nonpolar molecules: (e.g., N2, O2, CO2) cross freely.

• Small polar uncharged molecules: (e.g., H2O) pass slowly.

• Large polar molecules and ions: (e.g., glucose, Na+, K+, Cl−) require transport proteins.

Passive Transport

Passive transport moves substances along their concentration gradient without energy expenditure.

• Simple Diffusion: Net movement down concentration gradient; restricted to small, nonpolar molecules.

• Facilitated Diffusion: Passive movement of polar/charged molecules via transport proteins.

  • Channel Proteins: Hydrophilic corridors (e.g., aquaporins, ion channels).

  • Carrier Proteins: Conformational changes transport specific solutes (e.g., glucose transporters).

• Osmosis: Diffusion of water across a membrane from lower solute to higher solute concentration.

  • Aquaporins: Channel proteins accelerating water movement.

Tonicity and Environmental Effects

Tonicity describes how extracellular solutions affect cell water movement.

• Hypertonic: Higher solute outside; cells lose water.

  • Animal cells: Crenation (shriveling).

  • Plant cells: Plasmolysis (membrane pulls away from wall).

• Hypotonic: Lower solute outside; cells gain water.

  • Animal cells: Swell and may burst (lysis).

  • Plant cells: Turgid (ideal state).

• Isotonic: Equal solute; no net water movement.

  • Animal cells: Normal (flaccid equilibrium).

  • Plant cells: Flaccid (lacks turgor pressure).

Water Potential

Water potential (Ψ) predicts the direction of water movement. Water moves from higher to lower potential.

• Equation:

• Ψ (Water Potential): Measured in bars or MPa; pure water = 0 bars.

• Ψs (Solute Potential): Effect of dissolved solutes; always negative or zero.

• Ψp (Pressure Potential): Physical pressure; positive in turgid plant cells.

Solute Potential Calculation

• Equation:

• i: Ionization constant (e.g., sucrose i=1, NaCl i=2).

• C: Molar concentration (mol/L).

• R: Pressure constant (0.0831 L bar/mol K).

• T: Absolute temperature (K = °C + 273).

Ion Pumps and Primary Active Transport

Active transport uses ATP to move ions against their gradient via carrier proteins.

• Sodium-Potassium Pump (Na+/K+ ATPase): Pumps 3 Na+ out, 2 K+ in per ATP; maintains negative membrane potential.

• Proton Pump: Pumps H+ out; generates proton gradient in plants, fungi, bacteria.

Bulk Transport

Bulk transport moves large particles or volumes via vesicles, requiring ATP.

• Endocytosis: Cell takes in matter by forming vesicles.

  • Phagocytosis: Engulfs large solids or cells.

  • Pinocytosis: Non-specific uptake of fluid and solutes.

  • Receptor-Mediated Endocytosis: Specific uptake via ligand-receptor binding.

• Exocytosis: Vesicles fuse with membrane, releasing contents (e.g., hormones, neurotransmitters, enzymes).