Comprehensive Study Notes for ANP College: Molecular Interactions, Cellular Metabolism, Membrane Dynamics, Endocrine, Nervous, Sensory, Blood, and Respiratory Physiology

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Protein Structure and Function

Levels of Protein Structure

Proteins are complex molecules essential for structure and function in living organisms. Their function is determined by their structure, which is organized into four hierarchical levels:

Primary Structure: The linear sequence of amino acids in a polypeptide chain, held together by peptide bonds.
Secondary Structure: Local folding patterns such as α-helix and β-pleated sheet, stabilized by hydrogen bonds between backbone atoms.
Tertiary Structure: The three-dimensional folding of a single polypeptide, maintained by disulfide bonds, hydrogen bonds, ionic bonds, and hydrophobic interactions.
Quaternary Structure: The assembly of multiple polypeptide subunits into a functional protein complex (e.g., hemoglobin, potassium channels).

Protein Activation: Proteins may require activation by proteolytic cleavage or binding of cofactors/ligands. For example, trypsinogen is an inactive precursor of trypsin, and many enzymes require cofactors such as calcium.

Ligand: Any molecule or ion that binds to a protein, often to regulate its function (e.g., opening a channel).

Atoms, Ions, and Chemical Bonds

Atomic Structure and Ions

Protons: Positively charged particles in the nucleus.
Neutrons: Neutral particles in the nucleus.
Electrons: Negatively charged particles in orbitals/shells around the nucleus.
Ions: Atoms that have gained or lost electrons. Cations are positive (e.g., Na+, K+), Anions are negative (e.g., Cl-).

Chemical Bonds

Ionic Bonds: Formed when one atom donates an electron to another, creating oppositely charged ions that attract.
Covalent Bonds: Atoms share electrons to achieve stability.
Hydrogen Bonds: Weak attractions between polar molecules, crucial for DNA base pairing and water's surface tension.

pH, Acids, Bases, and Buffers

pH Scale and Buffer Systems

pH: Measures hydrogen ion concentration. pH < 7 is acidic, pH = 7 is neutral, pH > 7 is basic (alkaline).
Acids: Release H+ ions (e.g., HCl).
Bases: Accept H+ ions or release OH-.
Bicarbonate Buffer System: Maintains blood pH. The reaction is:
Exercise and pH: Intense exercise increases lactate and H+, lowering pH (acidosis).

Carbohydrates, Lipids, and Nucleic Acids

Carbohydrates

Composed of monosaccharides (simple sugars).
Polysaccharides: Long chains of sugars (e.g., glycogen in animals).
Glucose: Primary molecule for ATP production.

Lipids

Include triglycerides, steroids, cholesterol, and phospholipids (with hydrophilic head and hydrophobic tail).

Nucleic Acids and Nucleotides

Made of nucleotides, each with a five-carbon sugar, phosphate group, and nitrogenous base.
DNA: Contains deoxyribose; RNA: Contains ribose.
Base Pairing: Cytosine pairs with guanine.
ATP: Main energy-transfer molecule.
Functions: Energy transfer, genetic information, signaling (e.g., cAMP).

Enzymes and Cellular Metabolism

Enzyme Function and Regulation

Enzymes are protein catalysts that speed up chemical reactions by lowering activation energy.
Require specific binding sites for substrates, forming enzyme-substrate complexes.
Cofactors: Non-protein helpers (e.g., calcium) required for enzyme activity.
Inhibition: Competitive inhibitors block the active site; noncompetitive inhibitors bind elsewhere, altering enzyme shape.
Enzymes can be denatured by heat or pH changes.

Types of Enzymes

Hydrolases: Catalyze hydrolysis reactions (add/subtract water).
ATP Synthase: Generates ATP using H+ gradient in the electron transport chain (ETC).

Cellular Respiration Pathways

Glycolysis: Occurs in cytosol; converts glucose to pyruvate.
Intermediate Step: Pyruvate to acetyl-CoA in mitochondrial matrix.
Krebs Cycle (Citric Acid Cycle): In mitochondrial matrix; produces NADH, FADH2, and CO2.
Electron Transport Chain (ETC): On inner mitochondrial membrane; uses oxygen as final electron acceptor to produce ATP.

Overall Equation for Aerobic Respiration:

Red blood cells lack mitochondria and rely solely on glycolysis for ATP.
Low oxygen (hypoxia) leads to lactic acid production from pyruvate.
During starvation, fats are broken down first (lipolysis), then proteins (gluconeogenesis).

Protein Synthesis (Gene Expression)

Transcription: DNA to mRNA in the nucleus, catalyzed by RNA polymerase.
Translation: mRNA binds to ribosome; tRNA brings amino acids matching mRNA codons.
Gene: Sequence of DNA coding for a protein or RNA product.
Example: DNA triplet ATC → mRNA codon UAG; mRNA codon CAU pairs with tRNA anticodon GUA.

Membrane Dynamics and Transport

Fluid Compartments and Membrane Properties

Extracellular Fluid (ECF): Includes interstitial fluid (surrounds cells) and plasma (liquid part of blood).
Intracellular Fluid (ICF): Fluid inside cells.
Permeability: Ability of membrane to allow substances to pass; depends on membrane composition and transport proteins.

Transport Mechanisms

Simple Diffusion: Passive movement of small, nonpolar molecules (e.g., O2, CO2) across the lipid bilayer.
Facilitated Diffusion: Passive, uses carrier proteins; no ATP required.
Active Transport: Requires ATP; moves substances against concentration gradient (e.g., Na+/K+ pump).
Osmosis: Passive movement of water from low to high solute concentration.
Exocytosis: Vesicular transport of large molecules out of the cell using ATP.

Membrane Potential

Resting Membrane Potential: About –70 mV in neurons, maintained by Na+/K+ pump and K+ leak channels.
Depolarization: Membrane potential becomes less negative (e.g., Na+ influx).
Repolarization: Return to resting potential (e.g., K+ efflux).

Endocrine System and Hormone Regulation

Hormone Pathways and Functions

Calcium Balance: Regulated by PTH (raises Ca2+), calcitonin (lowers Ca2+), and calcitriol (increases absorption).
Thyroid Hormone Regulation: TSH from anterior pituitary stimulates thyroid hormone synthesis; TPO enzyme adds iodine to thyroglobulin.
RAAS Pathway: Renin (kidney) → angiotensinogen (liver) → angiotensin I → ACE (lung) → angiotensin II → aldosterone (adrenal cortex) → increased Na+ reabsorption.
Posterior Pituitary: Releases oxytocin (milk ejection, uterine contraction) and ADH (water retention).
Anterior Pituitary: Releases TSH, ACTH, LH, FSH, GH, prolactin.
Parathyroid Hormone: Acts on bone, kidney, and indirectly intestine to raise blood Ca2+.
Aldosterone: Increases Na+ reabsorption, K+ excretion in kidneys.
Insulin and Glucagon: Regulate blood glucose; insulin lowers, glucagon raises.

Nervous System: Neurons and Glia

Neuronal Function and Action Potentials

Glial Cells: Support neurons; microglia act as immune cells, Schwann cells (PNS) and oligodendrocytes (CNS) produce myelin.
Action Potential: Rapid depolarization (Na+ influx), repolarization (K+ efflux), and return to resting potential.
Absolute Refractory Period: No new action potential can be generated.
All-or-None Principle: Action potentials fire fully or not at all.
Myelination: Increases conduction speed via saltatory conduction.
Neurotransmitter Release: Triggered by Ca2+ influx at axon terminal; released by exocytosis.
Excitatory vs. Inhibitory Neurotransmitters: Excitatory (e.g., open Na+ channels), Inhibitory (e.g., open K+ or Cl- channels).

Central Nervous System: Brain Anatomy and Physiology

Brain Structure and Function

Protection: Meninges, skull, cerebrospinal fluid (CSF).
Energy Needs: High glucose and oxygen demand; supplied by blood.
Corpus Callosum: Connects cerebral hemispheres.
Choroid Plexus: Produces CSF.
Medulla Oblongata: Controls vital autonomic functions.
Reticular Formation: Regulates arousal, sleep-wake cycles, muscle tone.
Vagus Nerve: Mixed cranial nerve for internal organs.
Hypothalamus: Homeostasis, hormone regulation, behavioral drives.
Hippocampus: Learning and memory.
Perception: Integration of sensory stimuli.
Basal Ganglia, Motor Cortex, Cerebellum: Movement control.
Amygdala: Center for emotions.
Epinephrine: Enhances fight-or-flight response.

Sensory Physiology: Special Senses

General Sensory Pathways

All sensory pathways (except olfaction) relay through the thalamus.

Receptors and Sensory Modalities

Nociceptors: Detect pain.
Chemoreceptors: Detect chemicals.
Mechanoreceptors: Detect pressure, vibration, stretch.
Thermoreceptors: Detect temperature changes.

Hearing and Equilibrium

Middle ear bones (malleus, incus, stapes) amplify sound.
Sound waves → tympanic membrane → vibrations → cochlea.
Hair cells in cochlea transduce vibrations; highest frequencies detected at cochlear base.
Semicircular canals detect rotational acceleration; utricle and saccule detect linear acceleration.

Vision

Light enters through pupil; lens shape controlled by ciliary muscle.
Fovea: Area of sharpest vision.
Retinal pigment (retinal) derived from vitamin A.
Blind spot: Where optic nerve exits retina.

Taste and Smell

Five primary tastes: sweet, salty, sour, bitter, umami.

Metabolism and Energy Balance

Glucose and Lipid Metabolism

Glycogen: Storage form of glucose in liver and muscle.
Gluconeogenesis: Synthesis of glucose from noncarbohydrate sources.
Lipolysis: Breakdown of fats into glycerol and fatty acids.
Beta-oxidation: Fatty acids → Acetyl-CoA; Ketogenesis: Acetyl-CoA → ketone bodies.
Ketone Bodies: Produced during high fat metabolism (starvation, diabetes).

Pancreatic Hormones

Alpha cells: Secrete glucagon (raises blood glucose).
Beta cells: Secrete insulin (lowers blood glucose).
D cells: Secrete somatostatin (regulates digestion).

Diabetes and Metabolic Effects

Insulin deficiency → high blood glucose, increased fat metabolism, risk of ketoacidosis.
Fat is the most energy-dense storage molecule.

Blood and Hematopoiesis

Red Blood Cells (Erythrocytes)

Transport O2 and CO2; contain hemoglobin (four globin chains, each with heme and iron).
Produced in red bone marrow, stimulated by erythropoietin (EPO) from kidneys.
Lifespan ~120 days; removed by spleen and liver.
Hematocrit: % of blood volume occupied by RBCs.

Plasma and Proteins

Plasma: ~90% water, contains albumins, globulins, fibrinogen.
Transferrin transports iron; ferritin stores iron.

Platelets and Coagulation

Platelets form plugs and release clotting factors.
Coagulation cascade: Intrinsic (collagen exposure) and extrinsic (tissue factor) pathways converge to form fibrin.
Fibrinolysis breaks down clots after repair.
PT (Prothrombin Time) tests extrinsic pathway (factor VII).

Respiratory System: Mechanics and Gas Exchange

Alveoli and Gas Exchange

Type II alveolar cells: Produce surfactant to reduce surface tension and prevent alveolar collapse.
Alveoli are the primary site of O2 and CO2 exchange.

Ventilation Mechanics

Inhalation: Diaphragm and external intercostals contract, expanding thoracic cavity and drawing air in.
Exhalation: Muscles relax, thoracic volume decreases, air is expelled.
Air moves from high to low pressure.

Pulmonary Volumes

Volume	Description
Tidal Volume (TV)	Normal breath volume
Inspiratory Reserve Volume (IRV)	Extra air inhaled after normal inhalation
Expiratory Reserve Volume (ERV)	Extra air exhaled after normal exhalation
Residual Volume (RV)	Air remaining after maximal exhalation
Vital Capacity (VC)	Total air that can be forcefully inhaled and exhaled
Total Lung Capacity (TLC)	Maximum lung volume
Functional Residual Capacity (FRC)	Air left after normal exhalation

Oxygen and Carbon Dioxide Transport

O2 is mostly carried by hemoglobin; its binding is affected by CO2, temperature, and pH (Bohr effect).
CO2 is mainly transported as bicarbonate (HCO3-), some binds to hemoglobin, some dissolves in plasma.
Oxygen-hemoglobin dissociation curve shifts right with increased CO2, temperature, or decreased pH.

Acid-Base Balance

Hyperventilation causes respiratory alkalosis (CO2 loss).
Kidneys compensate by excreting bicarbonate.
Increased CO2 stimulates ventilation to restore balance.

Surfactant

Reduces alveolar surface tension, preventing collapse and reducing work of breathing.