Foundational Concepts in Biology

Foundational Concepts

• The August Krogh Principle: A biological problem can be conveniently studied in a specific animal model.
• Allometry: Studies how organism size relates to part size.
  • Positive allometry (α > 1): Organ growth faster than body.
  • Negative allometry (α < 1): Organ growth slower than body.
• Physiological Phenotype: Influenced by genotype and environment.
  • Phenotypic plasticity: Changes in phenotype due to environmental factors.
  • Ontogenetic changes: Changes during growth and development.
  • Reversible acclimation: Responses to controlled environmental changes.
  • Acclimatization: Responses to natural environmental variations.
• Metazoans: Develop from embryos with ectoderm, endoderm, sometimes mesoderm, and reproduce sexually or asexually (sexual reproduction leads to greater variation).
• Metabolic pathways: Enzyme-catalyzed reactions converting substrates to products.
  • Anabolic pathways: Synthetic.
  • Catabolic pathways: Degradative.
  • Metabolism: Sum of all anabolic and catabolic pathways.

Cellular Energy and Metabolism

• Cells store energy in reducing energy and high-energy covalent bonds.
• Carbohydrates (e.g., glucose): Used for energy and biosynthesis.
  • Polysaccharides (e.g., glycogen): Energy storage.
  • Polysaccharides (e.g., chitin, cellulose): Structural molecules.
  • Glycogenesis: Glycogen synthesis.
  • Glycogenolysis: Glycogen breakdown.
• Glucose metabolism:
  • Glycolysis (cytoplasm): Anaerobic, produces pyruvate, ATP, NADH.
  • Pyruvate oxidation (mitochondria): Forms acetyl-CoA.
  • NADH oxidation: Redox shuttles transport reducing equivalents to mitochondria.
  • Anaerobic conditions: NADH oxidized to lactate.
• Lipids (carbon backbone): Energy storage, cell structure, signaling.
  • Fatty acids: Dense energy storage, broken down by β-oxidation in mitochondria.
• Ketones: Produced from fatty acids when acetyl-CoA can't be fully oxidized; alternative fuel.
• Tricarboxylic acid cycle (TAC): Breaks down acetyl-CoA, generating NADH, FADH2, GTP.
• Oxidative phosphorylation (mitochondria): Proton gradient drives ATP synthesis by F1F0ATPase.
• Phosphocreatine: High-energy phosphate source, especially in muscle.
• Metabolic rate measurement: 31P-NMR spectroscopy tracks ATP turnover.
• Respiratory quotient (RQ): Ratio of CO2 production to O2 consumption.
  • RQ near 0.7: Lipid oxidation.
  • RQ near 1.0: Carbohydrate oxidation.

Whole-Organism Physiology

• Multicellularity: Specialized cells, tissues, organs, and organ systems arise.
• Comparative physiology: Examines animal adaptations to environments, evolutionary relationships.
• Metabolic rate: Energy usage rate.
  • Basal Metabolic Rate (BMR): Minimum metabolic rate in homeotherms at rest.
  • Standard Metabolic Rate (SMR): BMR of poikilotherms at a defined temperature.
  • Resting Metabolic Rate (RMR): Metabolic rate of an animal at rest.
  • Maximum Aerobic Metabolic Rate (VO2max): Maximum sustainable oxygen consumption during exercise.
  • Field Metabolic Rate: Actual metabolic rate in a natural habitat.
• Scaling of metabolic rate: Whole-animal metabolic rate increases with size, but mass-specific metabolic rate is higher in smaller animals (MR = a (mass)^b).
• Heat fluxes: Metabolism, convection, radiation, evaporation.
  • Evaporative cooling: Depends on water volume and heat of vaporization.
  • Conduction: Depends on thermal conductivity.
• Surface area to volume ratio: Influences heat exchange.
• Regional endothermy: Maintains higher temperatures in specific areas via vascular countercurrent heat exchangers.
• Hypometabolic phases (hibernation, torpor): Reduced metabolic energy demands.

Thermal Adaptation

• Thermal tolerance:
  • Eurytherms: Wide temperature tolerance.
  • Stenotherms: Narrow temperature tolerance.
• Thermogenesis: Heat production (ion pumping, "leaky" membranes). Endotherm plasma membranes leakier than ectotherms.
• Cold adaptation:
  • Psychrotrophs: Thrive at low temperatures.
  • Cold-adapted enzymes: Flexible structures for maintaining activity.
  • Antifreeze proteins: Prevent ice crystal formation.
  • Freeze-tolerant animals: Control ice crystal growth.

Digestion and Absorption

• Digestive systems: Differ between monogastric and ruminant species. Gastric glands secrete HCl and digestive enzymes.
• Gut microflora: Essential for digesting substances (e.g., cellulose).
• Absorption: Increased surface area by villi. Sugar uptake constraints, glucose/fructose mix more effective.
• Lipogenesis: Fat synthesis.
• Lipolysis: Fat breakdown.
• Hormonal control: Insulin stimulates glucose uptake, lipogenesis, suppresses lipolysis.

Circulatory and Respiratory Systems

• Circulatory systems: Closed (mammalian) or open (insect).
• Gas exchange: Oxygen diffusion into blood, transport by hemoglobin, diffusion into tissues, mitochondrial utilization. Insects use tracheal systems.
• Respiratory pigments (e.g., hemoglobin, Hb): Cooperative oxygen binding.
  • P50: Partial pressure for 50% heme saturation.
• Bohr effect: pH, temperature, CO2 affect hemoglobin oxygen affinity.
• High altitude adaptations: Hyperventilation, increased 2,3-DPG release.
• Ventilation mechanisms: Axial musculoskeletal oscillations. Bird lungs (parabronchi) unidirectional airflow.
• Hypoxic Pulmonary Vasoconstriction (HPV): Constricts arterioles in hypoxic environments.

Osmoregulation and Excretion

• Osmotic pressure: Pressure needed to offset solute movement across a membrane. Water moves from high to low concentration.
  • Hypotonic solutions: Water intake by cells.
  • Hypertonic solutions: Water loss from cells.
• Electrolyte balance: Extracellular high Na⁺, intracellular high K⁺.
• Mammalian kidney: Juxtamedullary and cortical nephrons for urine production.
  • Iso-osmotic urine: Little modification.
  • Hyperosmotic urine: Water retention.
  • Hypo-osmotic urine: Water loss.
• Water storage: Fat is a dense water source. Protein catabolism can provide water.
• Renin-Angiotensin-Aldosterone (RAA) system: Blood pressure control.
  • Angiotensin II: Vasoconstriction.
  • Aldosterone: Na⁺ and water retention.
• Hypertension: Elevated blood pressure due to excessive Na⁺ intake.

Electrophysiology and Neural Signaling

• Electrical concepts: Current (I), voltage (V), resistance (R). Biological systems behave like DC and AC circuits (Ohm’s Law: I=V/R).
• Membrane potential: Higher intracellular K⁺. Nernst equation predicts potential for a single ion.
• Perturbing membrane potential:
  • Hyperpolarization: Current into cell (Vm more negative).
  • Depolarization: Current out of cell (Vm more positive).
• Action Potential (AP): Threshold stimulus needed for AP; all-or-nothing phenomenon.
• Hodgkin cycle: Positive feedback cycle with voltage-gated Na⁺ and K⁺ channels. Na/K ATPase maintains ion concentrations.
• Refractory period: Period after AP with lower excitability (absolute and relative periods).
• Length constant: Distance for signal to decay by 63%. Affected by myelination.
• Saltatory conduction: Myelin increases resistance, reduces capacitance, AP jumps between nodes of Ranvier.
• Synaptic transmission:
  • Ligand-gated channels: Ligand binding opens ion channels.
  • Voltage-gated calcium channels: AP causes Ca²⁺ influx, neurotransmitter release.
  • Post-synaptic potentials (PSPs): Excitatory (EPSP) or inhibitory (IPSP).
  • Signal integration: Spatial and temporal summation at the axon hillock.
• Synaptic facilitation: Stronger EPSPs after successive stimulation pulses.

Sensory Systems and Muscle Physiology

• Sensory receptors: Convert stimuli to membrane potential changes. Types include chemoreceptors, mechanoreceptors, photoreceptors, electroreceptors, magnetoreceptors, and thermoreceptors (classified by location and stimulus).
• Stimulus encoding: Modality, location, intensity (AP frequency), duration (tonic vs. phasic neurons).
• Muscle structure: Sarcomeres (actin and myosin).
• Muscle contraction: APs, T-tubules, calcium release from SR, calcium binding to troponin.
• Muscle twitch: Single motor neuron stimulation.
• Temporal summation: Increasing stimulation frequency increases force.
• Muscle fiber types: Red (fatigue-resistant, aerobic), white (high-power output).
• Motor unit: Single motor neuron and innervated fibers.
• Muscle types: Phasic (twitch), tonic (graded potential). Smooth muscles can change shape.
• Invertebrate muscles: Arthropods use striated muscle in functions vertebrate smooth muscle performs.