Biochemistry Fundamentals – Water, Bonds, Acids-Bases, Proteins, Enzymes & Hemoglobin

A comprehensive set of vocabulary flashcards covering water chemistry, bonding, acid–base concepts, proteins, enzymes, and hemoglobin physiology as presented in the lecture notes.

Intracellular Fluid (ICF)

The fluid contained within cells; makes up about two-thirds of total body water.

Extracellular Fluid (ECF)

All body fluid outside cells; roughly one-third of total body water, composed of interstitial fluid and blood plasma.

Interstitial Fluid

Fluid located between tissue cells; about 80 % of the ECF.

Blood Plasma

Liquid portion of blood; ~20 % of the ECF.

Polar Molecule

A molecule with uneven electron distribution resulting in partial positive and negative ends.

Electronegativity (EN)

An atom’s ability to attract shared electrons; increases left-to-right across a period.

Hydrogen Bond

Weak electrostatic attraction between a hydrogen attached to N, O, or F and a nearby electronegative atom.

Cohesion

Attraction of water molecules to each other due to hydrogen bonding.

Adhesion

Attraction of water molecules to different substances or surfaces.

Surface Tension

Resistance of a liquid’s surface to external force, produced by cohesive interactions.

Osmosis

Net movement of water across a semipermeable membrane from high to low solvent concentration.

Osmotic Pressure

Pressure needed to stop osmosis; governs capillary fluid exchange.

Hydrostatic Pressure

Outward force exerted by a fluid; pushes water out of capillaries.

Oncotic (Colloidal) Pressure

Inward-pulling force generated mainly by plasma proteins; draws water into capillaries.

Hypertonic Solution

Environment where hydrostatic pressure exceeds colloidal pressure, causing cells to shrink.

Isotonic Solution

Environment where hydrostatic and colloidal pressures are equal; cell volume stays constant.

Hypotonic Solution

Environment where colloidal pressure exceeds hydrostatic pressure; water enters, cells swell.

Hydrophilic

‘Water-loving’; dissolves readily in water.

Hydrophobic

‘Water-hating’; non-polar molecules insoluble in water.

Amphipathic Molecule

Contains both polar (hydrophilic) and non-polar (hydrophobic) regions.

Micelle

Spherical aggregate of amphipathic molecules with hydrophobic cores and hydrophilic surfaces.

Hydrophobic Effect

Spontaneous clustering of non-polar molecules in aqueous solution to minimize ordered water shells; drives membrane formation and protein folding.

Ionic Bond (Salt Bridge)

Non-covalent attraction between oppositely charged ions.

Van der Waals Forces

Very weak, distance-dependent attractions between transient dipoles.

Bronsted-Lowry Acid

Proton donor and electron pair acceptor.

Bronsted-Lowry Base

Proton acceptor and electron pair donor.

pH Scale

Logarithmic scale of hydrogen ion concentration; each unit represents a ten-fold change.

Kw (Ion Product of Water)

[H⁺][OH⁻] = 1 × 10⁻¹⁴ at 25 °C.

Ka (Acid Dissociation Constant)

Equilibrium constant measuring strength of a weak acid.

pKa

−log Ka; pH at which an acid is 50 % dissociated.

Henderson–Hasselbalch Equation

Relates pH to pKa and ratio of conjugate base to acid; pH = pKa + log([A⁻]/[HA]).

Buffer

Solution that resists pH change by absorbing or releasing H⁺; e.g., bicarbonate system.

Metabolic Acidosis

Low blood pH with low HCO₃⁻; excess acid or bicarbonate loss.

Metabolic Alkalosis

High blood pH with high HCO₃⁻; excess base or acid loss.

Gastroesophageal Reflux Disease (GERD)

Chronic backflow of stomach acid into esophagus; may erode tooth enamel.

Protein

Polymer of amino acids performing cellular functions; name derives from Greek ‘proteios’ (primary).

Amino Acid

Organic molecule with central α-carbon, amino group, carboxyl group, hydrogen, and variable R-group.

Chirality

Existence of non-superimposable mirror-image forms (L and D) of a molecule.

Zwitterion

Molecule with equal positive and negative charges but net neutrality; typical state of amino acids at pH 7.

Essential Amino Acid

Must be obtained from diet because body cannot synthesize it.

Non-Polar Amino Acid

Has hydrophobic hydrocarbon side chain; tends to cluster inside proteins.

Polar Uncharged Amino Acid

R-group contains electronegative atoms; forms H-bonds but no net charge at pH 7.

Disulfide Bridge

Covalent S–S bond formed by oxidation of two cysteine residues; stabilizes protein structure.

Ketogenic Amino Acid

Carbon skeleton degraded to ketone bodies (e.g., leucine, lysine).

Glucogenic Amino Acid

Carbon skeleton converted to glucose precursors.

Peptide Bond

Amide linkage between carboxyl of one amino acid and amino of next; forms polypeptide chain.

Primary Structure

Linear sequence of amino acids in a polypeptide.

Secondary Structure

Local folding into α-helices or β-pleated sheets stabilized by backbone hydrogen bonds.

Alpha Helix

Right-handed coil with hydrogen bonding every 4 residues along backbone.

Beta Pleated Sheet

Sheet-like arrangement of strands linked by inter-strand hydrogen bonds; parallel or antiparallel.

Motif (Super-secondary Structure)

Combination of secondary structures forming a recognizable pattern with specific function.

Domain

Large, independently folding unit of a protein that can retain function when separated.

Fibrous Protein

Long, structural protein mainly with primary/secondary structure (e.g., collagen, keratin).

Collagen Triple Helix

Three polypeptide chains (rich in Gly-Pro-Hyp) twisted together; major connective-tissue protein.

Vitamin C (Ascorbic Acid)

Cofactor required for hydroxylation of proline and lysine in collagen; deficiency causes scurvy.

Scurvy

Disease of impaired collagen synthesis due to vitamin C deficiency; leads to bleeding gums, weak teeth.

Osteogenesis Imperfecta

Genetic disorder causing brittle bones from defective collagen.

Lupus

Autoimmune disease that attacks collagen; worsened by stress hormone cortisol.

Tertiary Structure

Three-dimensional folding of a single polypeptide, stabilized by various interactions including hydrophobic effect.

Quaternary Structure

Spatial arrangement and interactions of multiple polypeptide subunits in a protein complex.

Hydrophobic Core

Non-polar interior of a folded protein generated by hydrophobic effect.

Denaturation

Unfolding of proteins by heat, pH, or chemicals; destroys secondary, tertiary, quaternary structure but not peptide bonds.

Chaperone Protein

Molecule that assists correct folding or refolding of other proteins.

Enzyme

Protein catalyst that accelerates biochemical reactions without being consumed.

Substrate

Reactant molecule upon which an enzyme acts.

Active Site

Region on enzyme where substrate binds and reaction occurs.

Induced Fit Model

Concept that substrate binding induces conformational change in enzyme to enhance catalysis.

Gibbs Free Energy (ΔG)

Measure of usable energy in a system; dictates spontaneity of reactions.

Activation Energy (ΔG‡)

Energy barrier that must be overcome for reactants to reach transition state.

Vmax

Maximum velocity of an enzyme-catalyzed reaction when enzyme is saturated with substrate.

Km (Michaelis Constant)

Substrate concentration at which reaction rate is half of Vmax; indicates enzyme affinity.

Kcat (Turnover Number)

Number of substrate molecules converted to product per enzyme per second at saturation.

Competitive Inhibitor

Molecule resembling substrate that competes for active site; increases Km but does not change Vmax.

Uncompetitive Inhibitor

Binds only to enzyme-substrate complex; decreases both Km and Vmax.

Noncompetitive Inhibitor

Binds to allosteric site on enzyme or ES complex; lowers Vmax without changing Km.

Suicide (Irreversible) Inhibitor

Covalently binds and permanently inactivates an enzyme (e.g., penicillin targeting transpeptidase).

Beta-Lactam Antibiotic

Class of drugs with β-lactam ring; irreversibly inhibit bacterial cell-wall enzymes.

Allosteric Enzyme

Regulatory enzyme whose activity is modulated by binding of effectors at sites other than active site.

Positive Cooperativity

Binding of a substrate to one subunit increases affinity of other subunits.

Feedback Inhibition

End product of a pathway inhibits first committed enzyme to regulate pathway output.

Concerted Model (MWC)

Allosteric model where subunits exist in T or R state simultaneously; effectors shift equilibrium.

Sequential Model (KNF)

Allosteric model in which subunits change conformation individually upon ligand binding, allowing hybrid states.

Protein Kinase

Enzyme that transfers phosphate from ATP to target molecules, activating or deactivating them.

Protein Phosphatase

Enzyme that removes phosphate groups from proteins.

Zymogen

Inactive enzyme precursor activated by proteolytic cleavage (e.g., chymotrypsinogen → chymotrypsin).

Hypophosphatasia

Genetic disorder of defective alkaline phosphatase causing poor bone and tooth mineralization.

Alkaline Phosphatase (ALP)

Enzyme that hydrolyzes pyrophosphate releasing inorganic phosphate for hydroxyapatite formation.

Pyrophosphate (PPi)

Two linked phosphate groups; inhibits hydroxyapatite; hydrolyzed by ALP.

Paget’s Disease

Bone disorder with excessive remodeling; high ALP levels; treated with bisphosphonates.

Bisphosphonate

Drug class that inhibits osteoclasts to slow bone breakdown.

Hemoglobin (Hb)

Tetrameric allosteric protein in red blood cells transporting O₂, CO₂, and H⁺.

Myoglobin (Mb)

Monomeric oxygen-storage protein in muscle; higher O₂ affinity than Hb.

Heme

Prosthetic group containing iron within a porphyrin ring enabling O₂ binding.

T State (Taut)

Low-affinity, deoxygenated conformation of hemoglobin stabilized by 2,3-BPG.

R State (Relaxed)

High-affinity, oxygenated conformation of hemoglobin.

2,3-Bisphosphoglycerate (2,3-BPG)

Allosteric effector that binds Hb, stabilizing T state and promoting O₂ release in tissues.

Bohr Effect

Decreased Hb O₂ affinity at low pH or high CO₂; facilitates O₂ release in metabolically active tissues.

Carbon Monoxide (CO)

Gas binding Hb 250× stronger than O₂, preventing oxygen transport; major toxin in smoke.

Positive Cooperativity (Hb)

O₂ binding to one subunit increases affinity of remaining subunits.

Fetal Hemoglobin (HbF)

Hb variant (α₂γ₂) with lower 2,3-BPG affinity and higher O₂ affinity to facilitate maternal-fetal transfer.