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Introduction to Physiology and Basic Concepts (Ch. 1–2)

  • Anatomy vs physiology
    • Anatomy: study of body structure with mastery of anatomical terminology
    • Physiology: science of body functions; subdivisions by organ systems or responses (e.g., renal physiology, cardiovascular physiology; exercise physiology; pathophysiology)
    • Often focuses at cellular and molecular level; life depends on chemical reactions in cells
    • To study physiology, need basic physical principles (electrical currents, pressure, movement) and chemical principles
  • Core principle: form reflects function
    • Function always reflects structure; what a structure can do depends on its form
  • Levels of organization (from smallest to largest)
    • Subatomic particles → Atom → Molecule → Macromolecule → Organelle → Cell → Tissue → Organ → Organ System → Organism
    • Cell is the smallest unit capable of all life processes
  • Matrix (extracellular material)
    • Matrix components: fibers (fibrous proteins) and ground substance (tissue fluid, extracellular fluid, interstitial fluid)

Four Major Tissue Types

  • Epithelial: protection, secretion, absorption, excretion
    • Covers body surfaces; lines internal organs; forms glands
    • Distinguishing characteristics: no blood vessels; rapid cell division; cells tightly packed
  • Connective: binds, supports, protects; fills spaces; stores fat; produces blood cells
    • Widely distributed; includes cartilage, bone, blood, adipose
    • Distinguishing characteristics: good blood supply; cells farther apart; extracellular matrix present
  • Muscle: movement
    • Attached to bones, walls of hollow organs, heart; ability to contract in response to stimuli
  • Nervous: conducts impulses for coordination, regulation, integration, sensory reception
    • Brain, spinal cord, nerves; cells communicate with one another; extracellular matrix composition differences
  • Matrix components summary: fibers + ground substance

Organ Systems and Their Integration (Figure 1.2 concept)

  • Circulatory: transport of materials between all cells of the body (heart, vessels, blood)
  • Digestive: conversion of food into transportable particles; elimination of some wastes (stomach, intestine, liver, pancreas)
  • Endocrine: coordination via regulatory molecule synthesis and release (glands such as thyroid, adrenal; thymus, spleen, lymph nodes)
  • Integumentary: protection from environment (skin)
  • Immune: defense against foreign invaders
  • Musculoskeletal: support and movement (skeletal muscles, bone)
  • Nervous: coordination via electrical signals; rapid control
  • Respiratory: exchange of O2 and CO2 with external environment (lungs, airways)
  • Reproductive: perpetuation of species (ovaries, uterus, testes)
  • Urinary: maintenance of water/osmolarity; waste removal (kidneys, bladder)
  • Inter-system integration: signaling networks (nervous + endocrine) coordinate activities; hollow organ interiors can be part of external environment

Function and Mechanism (Chapter 1, 1.2)

  • Teleological (functional) perspective: asks why a process occurs; explains purpose
  • Mechanistic (causal) perspective: asks how the process occurs; explains mechanism
  • Example: Red blood cells (RBCs)
    • Teleological: Why transport oxygen? because cells need oxygen
    • Mechanistic: How? oxygen binds to hemoglobin inside RBCs
  • Translational research: integrates mechanistic science with clinical application

Homeostasis and Internal Environment (Ch. 1, 1.4–1.5)

  • Homeostasis: maintenance of a relatively stable internal environment
    • Dynamic state of equilibrium; constantly readjusting within limits
    • Restores changes back to normal when perturbed
  • Critical variables (regulated variables): environmental factors for cells, materials for cells, and intercellular communication factors
  • Regulated variables are kept within a range (setpoints) rather than a single value
  • Disease and pathophysiology: failure to maintain homeostasis; example: diabetes mellitus (high blood glucose)
  • Internal body environment definitions
    • Extracellular fluid (ECF): fluid outside cells; buffer between outside world and intracellular fluid (ICF)
    • Interstitial fluid, plasma, cerebrospinal fluid, synovial fluid, etc.
    • Intracellular fluid (ICF): fluid inside cells
  • Mass balance and steady state (Chapter 1, 1.5; mass balance concept in Page 10)
    • Law of mass balance: steady state where intake + production = output + excretion + metabolic removal
    • Load: amount of a substance in the body
    • Gain: intake from outside or metabolic production
    • Loss: excretion or metabolic removal
    • Mass flow: rate of transport of a substance through or into/out of the body
    • Excretion clears substances from the body; clearance = volume of blood cleared of a substance per unit time
  • Mass balance in open vs closed systems (Figure 1.6 concept)
    • Open system: input = output for constant level
    • Body mass balance: input (intake, production) vs output (excretion, removal) determines body load
  • Homeostasis vs equilibrium
    • Plasma is a dynamic steady state; materials move between ECF and ICF with no net long-term movement between compartments during steady state
    • Disequilibrium exists when disturbances occur
  • Control systems and homeostasis (1.5, 1 of 2)
    • Regulated variables kept near a setpoint by control mechanisms
    • Local control: restricted to tissue or cell
    • Reflex control: long-distance signaling via nervous and/or endocrine systems; response loops
    • Key roles: input signal (afferent), integrating center, output signal, effector
  • Feedback loops
    • Negative feedback: restores variable toward setpoint; homeostatic; stabilizes
    • Positive feedback: reinforces original stimulus; not homeostatic; often for infrequent events (e.g., labor contractions, clotting cascade, lactation)
  • Feedforward control: anticipates change before it occurs (e.g., mouth watering when smelling bread, heart rate increase with stairs)
  • Reflex pathway example (Figure 1.10): aquarium temperature control loop illustrating sensor, integrating center, and actuator responses
  • Oscillation around setpoint (Figure 1.11): many homeostatic processes exhibit bounded fluctuations around setpoints

Chemistry and Physics Fundamentals (Ch. 2 and related)

Atoms, Elements, and Basic Chemistry (Chapter 2 overview)

  • Element: pure substance that cannot be created or broken down by ordinary chemical means
    • Periodic table lists all known elements
    • Four elements make up ~96% of the body; most abundant: O, C, H, N
  • Atoms: basic building blocks; composed of protons, neutrons (nucleus) and electrons (orbiting)
  • Molecules and compounds
    • Molecule: two or more atoms bonded together
    • Compound: substance composed of two or more different elements bonded
    • Examples: H2O, C6H12O6, DNA
  • Periodic table notes (as in Figure 2.1/2.2 visuals): common symbols and rows/columns (for exam familiarity) including Na, K, Ca, Mg, Cl, etc.
  • Subatomic particles
    • Proton: positive charge, in nucleus; atomic number = number of protons
    • Neutron: neutral; in nucleus
    • Electron: negative charge; occupy electron shells around nucleus

Chemical Bonds and Electron Roles

  • Chemical bonds arise from energy relationships between electrons of reacting atoms
  • Electrons and electron shells (energy levels)
    • Atoms can have up to 7 electron shells; shells fill from the inside out
    • Valence shell: outermost shell; electrons here participate in chemical reactions
  • Octet rule (8-electron valence rule) with exceptions (H and He want 2 electrons in first shell)
  • Ionic bonds
    • Transfer of valence electrons → formation of cations and anions; electrostatic attraction binds opposite charges
    • Example: Na transfer to Cl → Na+ and Cl- form NaCl (ionic bond)
  • Covalent bonds
    • Sharing of valence electrons between atoms
    • Single bond (2 electrons), double bond (4 electrons), triple bond (6 electrons)
    • Two types: polar covalent and nonpolar covalent
  • Nonpolar covalent bonds: equal sharing of electrons
  • Polar covalent bonds: unequal sharing due to electronegativity differences; creates dipole
  • Hydrogen bonds: attractive force between a positively polarized hydrogen and a highly electronegative atom in another molecule; not a true bond but a strong dipole–dipole interaction; critical in water structure and biopolymers (proteins, DNA)
  • Bonding continuum (ionic → polar covalent → nonpolar covalent) and what they imply about molecule polarity and reactivity

Formation of Ionic and Covalent Bonds (examples)

  • Ionic bond formation example
    • Na (1e in outer shell) donates 1e to Cl (7e in outer shell) → Na+ and Cl− form NaCl
  • Covalent bond formation examples
    • Methane: CH4 formed by carbon sharing four electron pairs with four hydrogens (CH4)
    • Oxygen gas: O2 involves a double covalent bond (O=O)
    • Nitrogen gas: N2 involves a triple covalent bond (N≡N)
  • Nonpolar covalent example: CO2, long-chain fatty acids
  • Polar covalent example: H2O (O more electronegative than H)

Solutions, Solubility, and Noncovalent Interactions

  • Solutions: true homogeneous mixtures where solute is dissolved in solvent (usually water in biology)
  • Solvent vs solute
    • Solvent: water (universal solvent in biology)
    • Solute: the dissolved substance (e.g., glucose in blood plasma)
  • Solubility: ease with which a solute dissolves in a solvent
  • Hydrophilic vs hydrophobic:
    • Hydrophilic: polar or ionic; soluble in water
    • Hydrophobic: nonpolar; not soluble in water
  • Noncovalent interactions include hydrogen bonds, ionic bonds, and van der Waals forces; essential for protein folding, DNA structure, membranes
  • pH and acid–base chemistry
    • Acids: donate H+; e.g., HCl → H+ + Cl−; electrolytes in water
    • Bases: accept H+; e.g., NaOH → Na+ + OH−; hydroxide ions increase basicity
    • pH scale: log scale; pH = -log10([H+]); neutral pH = 7; acidic pH < 7; basic pH > 7
    • Buffers resist pH changes by releasing or binding H+; carbonic acid–bicarbonate system (important blood buffer):
      ext{CO}2 + ext{H}2 ext{O}
      ightleftharpoons ext{H}2 ext{CO}3
      ightleftharpoons ext{H}^+ + ext{HCO}_3^-
    • Normal blood pH range: approx. 7.35 ext{ to } 7.45; kidneys, lungs, and buffers regulate pH
  • Acids and bases properties summary (Table-like points)
    • Acids: donate protons, ionize in water, conduct electricity, turn blue litmus red, sour taste, corrosive
    • Bases: accept protons, dissociate to give OH−, conduct electricity, turn red litmus blue, bitter/slippery

Functional Groups and Major Biomolecule Building Blocks

  • Functional groups: recurring groups of atoms that move between molecules as a unit; determine reactivity
  • Four major biomolecule classes (biomolecules are organic molecules)
    • Carbohydrates
    • Lipids
    • Proteins
    • Nucleotides
  • Polymers and monomers
    • Polymers: large molecules made of repeating monomer units
    • Monomers: can bond to form polymers
  • Conjugated and modified biomolecules
    • Conjugated proteins (e.g., lipoproteins): proteins combined with another biomolecule (lipids)
    • Glycosylated molecules (glycoproteins, glycolipids): proteins/lipids with carbohydrate groups

Lipids and Fatty Acids

  • Lipids: insoluble in water; nonpolar; dissolve in other lipids
  • Functions: energy storage, insulation, protection
  • Lipids classes
    • Triglycerides: most abundant in humans; glycerol backbone with three fatty acids
    • Phospholipids: amphiphilic (phosphate-containing head hydrophilic; fatty acid tails hydrophobic) → essential for membranes
    • Steroid hormones (cortisol, aldosterone, testosterone, estrogen, progesterone, vitamin D)
    • Phospholipids and fat-soluble vitamins (A, D, E, K)
  • Fatty acids
    • Saturated: single bonds; straight chains; pack tightly; solid at room temp
    • Unsaturated: one or more double bonds; kinked chains; liquid at room temp
    • Omega-3 and Omega-6: essential unsaturated fatty acids
    • Trans fats: hydrogenated unsaturated fats with unhealthy properties
  • Key structural note: fatty acids have a carboxyl group; carbon chains determine properties

Carbohydrates

  • Functions: major cellular fuel (glucose); structural roles (ribose in RNA)
  • General formula: contain C, H, O with H:O in ~2:1 ratio
  • Classes
    • Monosaccharides: single sugars (e.g., glucose, fructose, galactose; ribose, deoxyribose)
    • Disaccharides: two monosaccharides (e.g., sucrose, maltose, lactose)
    • Polysaccharides: many monosaccharides (e.g., starch, cellulose, glycogen)
  • Notable examples
    • Glucose (dextrose): C6H12O6
    • Ribose vs deoxyribose: RNA sugar is ribose; DNA sugar is deoxyribose
  • Visual representations: Fischer projections and ring forms shown in figures to illustrate structures

Proteins

  • Abundance and roles
    • 20–30% of cell mass; most varied functions of any molecules
    • Contain C, H, O, N, sometimes S and P
  • Monomer units: amino acids (20 standard ones) with variable R groups
    • All amino acids share a common backbone: amino group (-NH2), carboxyl group (-COOH), hydrogen, and a unique R group attached to the central carbon
  • Protein structure levels
    • Primary structure: amino acid sequence linked by peptide bonds
    • Secondary structure: α-helix, β-pleated sheet, β-turn stabilized by hydrogen bonds
    • Tertiary structure: further folding; describes 3D shape of single polypeptide
    • Quaternary structure: assembly of multiple polypeptides into a functional unit
  • Protein forms and functions (examples)
    • Structural proteins: collagen (tensile strength in connective tissue)
    • Enzymes: catalyze biochemical reactions; names often end in -ase
    • Transport proteins: carry substances (hemoglobin transports O2)
    • Contractile proteins: actin and myosin in muscle contraction
    • Regulatory proteins: transcription factors, receptors, signaling molecules
    • Defensive proteins: antibodies
  • Protein interactions and binding
    • Binding site (active site for enzymes, receptor binding sites, transporters)
    • Ligand vs substrate: ligand binds to protein; substrate binds to enzymes or transporters
    • Specificity: proteins bind specific ligands; induced-fit model explains conformational changes upon binding
    • Binding reversibility and affinity
  • Denaturation
    • Loss of 3-D structure and function due to pH changes or temperature
    • Often reversible if conditions return to normal; can be irreversible in extreme cases (e.g., cooking an egg)
  • Enzymes
    • Globular proteins; act as biological catalysts; lower activation energy
    • Do not get consumed in reactions
    • Apoenzyme (protein portion) + cofactor/coenzyme (non-protein component)
    • Enzyme specificity and naming often ends with -ase
  • Modulation of enzyme activity
    • Activation: proteolytic activation (e.g., pepsinogen → pepsin), cofactors (ions, vitamins), allosteric modulators, covalent modification
    • Inhibition: competitive inhibitors vs irreversible antagonists;
    • Allosteric modulation and covalent modulation (e.g., phosphorylation)
  • Factors affecting enzyme/activity and reaction rates
    • Amount of protein and amount of ligand
    • Saturation: maximum rate when all enzyme sites are occupied
    • Temperature and pH: physical modulators
    • Reaction rate vs protein/ligand concentrations (illustrated by activation curves and saturation graphs)
    • Concept of transport maximum (Tm) and saturation kinetics
  • Protein complexes and multisubunit assemblies
    • Subunits can be identical or different; molecular complexes held together by noncovalent interactions
    • Changes in 3D structure can abolish function

Nucleic Acids

  • Nucleotides are the monomers; polymers are nucleic acids
  • DNA (deoxyribonucleic acid)
    • Double-stranded, helical; located in cell nucleus; 46 chromosomes (23 from each parent)
    • Sugar: deoxyribose; bases: adenine (A), thymine (T), cytosine (C), guanine (G)
    • Base-pairing rules: A pairs with T; G pairs with C
    • Antiparallel orientation: 5' to 3' ends run opposite on the two strands
  • RNA (ribonucleic acid)
    • Single-stranded; sugar: ribose; bases: A, U, C, G (uracil replaces thymine)
    • Functions: mRNA (messenger) carries genetic information; tRNA (transfer) brings amino acids; rRNA (ribosomal) forms the ribosome
  • ATP and energy carriers
    • ATP (adenosine triphosphate): energy currency; produced from glucose and other fuels; structure: adenine + ribose + three phosphate groups
    • ADP and AMP as energy carriers (cycles with phosphorylation)
  • Nucleotides and energy transfer
    • Nucleotides like NAD, FAD, cAMP carry energy or signals for cellular processes

Buffers, Acids, and Bases (Expanded)

  • Buffers maintain pH by buffering H+ in solution; they can release H+ when pH rises or bind H+ when pH falls
  • Carbonic acid–bicarbonate buffer system is especially important in blood
    • Reaction: ext{CO}2 + ext{H}2 ext{O}
      ightleftharpoons ext{H}2 ext{CO}3
      ightleftrightarrow ext{H}^+ + ext{HCO}_3^-
  • pH considerations
    • pH is a logarithmic scale: a one-unit change represents a tenfold change in H+ concentration
    • Practical ranges: normal blood pH ~ 7.35–7.45; extremes are life-threatening due to effects on enzyme activity and electrical signaling

Key Quantities and Constants (for exam familiarity)

  • Avogadro’s number: N_A = 6.02 imes 10^{23} ext{ mol}^{-1}
  • One mole equals: 1 ext{ mole} = 6.02 imes 10^{23} ext{ molecules}
  • Molarity: M = rac{ ext{moles of solute}}{ ext{liters of solution}} ext{ (mol/L)}
  • Gram molecular weight (molar mass): the mass in grams per mole of a substance (e.g., glucose = 180 ext{ Da} = 180 ext{ g/mol})
  • pH and [H+]: ext{pH} = - ext{log}_{10}([H^+]); ext{ thus } [H^+] = 10^{- ext{pH}} ext{ M}
  • Dissociation constant for binding interactions (Kd): K_d = rac{[P][L]}{[PL]}
    • Large Kd = low affinity; small Kd = high affinity
  • Units and basic conversions: 1 L, 1 M, 1 mmol/L ≡ 1 mM

Reactions, Synthesis, and Degradation (Organic Chemistry in Physiology)

  • Chemical reactions involve formation, rearrangement, or breaking of bonds
  • Reactants → Products; balanced equations show stoichiometry
    • Example: H2 + Cl2 → 2 HCl (illustrative; actual stoichiometry varies by reaction)
  • Types of chemical reactions
    • Synthesis: more complex structure formed
    • Decomposition: bonds broken to form simpler molecules
    • Exchange: bonds broken and new bonds formed
    • Reversible: products can revert to reactants; chemical equilibrium when forward and reverse rates equal
  • Dehydration synthesis and hydrolysis (examples in carbohydrate synthesis and digestion)
    • Dehydration synthesis: monomers joined with removal of OH from one monomer and H from another, releasing water (H2O)
    • Example: joining glucose and fructose to form sucrose, water released
    • Hydrolysis: covalent bonds broken by adding water; monomers released
  • Biochemical energy and metabolism
    • ATP as energy currency; energy captured from breakdown of glucose and other fuels

Biochemical and Physiological Relevance (Chapter 1–2 integration)

  • Homeostasis and energy balance
    • How macromolecules (carbohydrates, lipids, proteins, nucleic acids) supply energy and structural materials for cells to maintain dynamic steady state
  • Signaling and regulation
    • Hormones (endocrine) and neurotransmitters (nervous) as regulatory molecules in reflex control and homeostasis
  • Real-world relevance
    • Pathophysiology: disease states disrupt homeostatic mechanisms (e.g., diabetes alters glucose homeostasis)
    • Diet and exercise impact multiple systems (circulatory, respiratory, endocrine) via integrated physiology

Quick Summary of Key Connections to Real-World Scenarios

  • Negative feedback keeps variables near setpoints (e.g., body temperature, blood glucose) and maintains stability
  • Positive feedback drives rapid, temporary processes (e.g., labor contractions, blood clotting)
  • Feedforward responses anticipate changes (e.g., salivation when smelling food, increased heart rate with exercise anticipation)
  • Enzymes enable body’s biochemistry to occur efficiently at physiological temperatures; activation energy is a gatekeeper for reaction rates
  • Buffer systems keep intracellular and extracellular pH within narrow limits essential for enzyme activity and ion channel function
  • Lipids provide energy storage, insulation, and membrane structure; phospholipids form amphiphilic membranes; steroids regulate gene expression and other functions
  • Nucleic acids encode, transmit, and translate genetic information; ATP and other nucleotides transfer energy and information within the cell
  • Protein structure dictates function; denaturation disrupts function; binding interactions govern signaling, metabolism, transport, and regulatory processes

Quick Reference Tables/Notes (to memorize)

  • Key ions (Table 2.2 style): Na+, K+, Ca2+, Mg2+; Cl−, HCO3−, HPO4^2−, SO4^2−
  • pH values and their implications
    • pH 7.0 is neutral; deviations impact enzyme activity and electrical signaling
    • Buffers maintain pH by reversible binding/releasing H+
  • Base and acid properties summary
    • Acids donate H+; bases accept H+; both are electrolytes when dissolved in water
  • Base-pairing in DNA
    • A pairs with T; G pairs with C; 3 H-bonds for G–C, 2 H-bonds for A–T
  • Protein structure levels (primary → quaternary) and their functional implications
  • Reversible binding and ligand affinity concepts
    • Ligand vs substrate; specificity and induced fit
    • Allosteric modulation and covalent modification influence binding and activity
  • Energy currency and metabolism
    • ATP structure and role; energy transfer from glucose metabolism

End of Notes