BB ch6, p1

Enzyme

A biological catalyst, usually a protein, that accelerates thermodynamically favorable reactions in cells.

Catalyst (Biological)

A substance that increases the rate of a biochemical reaction without being consumed, exemplified by enzymes.

Cofactor

An additional non-protein chemical component (metal ion or organic molecule) required for enzymatic activity.

Coenzyme

A complex organic cofactor that transiently carries specific functional groups during catalysis.

Apoenzyme

The protein portion of an enzyme, inactive until combined with its necessary cofactors or coenzymes.

Holoenzyme

The catalytically active enzyme containing both the apoenzyme and its required cofactors/coenzymes.

Metal Ion Cofactor

An inorganic ion (e.g., Zn²⁺, Mg²⁺, Fe²⁺) that participates in an enzyme’s catalytic mechanism.

Oxidoreductase

Enzyme class (EC 1) that catalyzes electron-transfer reactions such as oxidations and reductions.

Transferase

Enzyme class (EC 2) that catalyzes group-transfer reactions between molecules.

Hydrolase

Enzyme class (EC 3) that catalyzes hydrolysis reactions, transferring functional groups to water.

Lyase

Enzyme class (EC 4) catalyzing addition to or removal of groups from double bonds without hydrolysis or oxidation.

Isomerase

Enzyme class (EC 5) that catalyzes intramolecular rearrangements to form isomers.

Ligase

Enzyme class (EC 6) forming new C-C, C-O, C-S, or C-N bonds via condensation reactions coupled to ATP cleavage.

Activation Energy (ΔG‡)

The free-energy barrier that must be overcome for a reaction to proceed; lowered by enzymes.

Standard Free Energy Change (ΔG'°)

The difference in free energy between reactants and products under standard biochemical conditions; determines equilibrium.

Lock-and-Key Model

Early enzyme model (Fischer, 1894) proposing a rigid, pre-formed complementarity between enzyme and substrate.

Induced Fit Model

Modern model where substrate binding induces conformational changes that align catalytic groups in the enzyme.

Binding Energy (ΔGB)

Free energy released from non-covalent interactions between enzyme and substrate in the transition state, driving catalysis.

Entropy Reduction

Catalytic strategy where enzyme binding decreases substrate freedom, increasing effective concentration and reaction rate.

General Acid-Base Catalysis

Enzymatic mechanism involving proton donation or acceptance by amino-acid side chains other than water.

Catalytic Residue

Amino-acid side chain directly participating in the chemical transformation in an enzyme’s active site.

pKa Perturbation in Protein

Shift in an amino-acid side chain’s pKa due to its microenvironment within a folded enzyme.

Michaelis-Menten Equation

v₀ = (Vmax [S])/(Km + [S]); fundamental expression relating initial rate to substrate concentration for many enzymes.

Substrate Saturation Curve

Plot of v₀ versus [S] showing hyperbolic dependence and transition from first-order to zero-order kinetics.

Steady-State Assumption

Michaelis-Menten premise that [ES] remains constant during the initial phase of an enzyme reaction.

Km (Michaelis Constant)

Substrate concentration at which v₀ is half of Vmax; reflects enzyme-substrate binding affinity.

Vmax

Theoretical maximal velocity reached when all enzyme active sites are saturated with substrate.

kcat (Turnover Number)

Number of reaction cycles an enzyme molecule completes per second at saturation; equals Vmax/[Et].

Catalytic Efficiency (kcat/Km)

Second-order rate constant describing enzyme performance at low [S]; also called the specificity constant.

Diffusion Limit

Upper boundary (~10⁸–10⁹ M⁻¹s⁻¹) for kcat/Km governed by how fast enzyme and substrate can collide in solution.

Lineweaver-Burk Plot

Double-reciprocal plot (1/v versus 1/[S]) yielding a straight line to determine Km and Vmax graphically.

Competitive Inhibition

Reversible inhibition where inhibitor competes with substrate for the active site, increasing apparent Km only.

Uncompetitive Inhibition

Inhibitor binds only to ES complex, decreasing both apparent Km and Vmax proportionally.

Mixed Inhibition (Noncompetitive)

Inhibitor can bind E or ES with different affinity, altering both Km and Vmax in a non-parallel manner.

Inhibition Constant (Ki)

Equilibrium constant describing the affinity of an inhibitor for an enzyme or ES complex.

Apparent Km

Observed Km in the presence of inhibitor, reflecting altered substrate affinity under inhibition.

Apparent Vmax

Observed maximal velocity in the presence of inhibitor, lower than true Vmax in certain inhibition types.

Rate Enhancement

Factor by which an enzyme increases reaction rate compared to the uncatalyzed reaction, often up to 10¹⁷-fold.

Transition State

High-energy, unstable arrangement of atoms occurring during a reaction; stabilized by enzymes.

Transition State Stabilization

Primary catalytic strategy where enzyme binds the transition state more tightly than substrate or product.

First-Order Reaction

Reaction whose rate is directly proportional to the concentration of one reactant.

Zero-Order Reaction

Reaction whose rate is independent of reactant concentration, observed at enzyme saturation.

ES Complex (Enzyme-Substrate Complex)

Transient intermediate formed upon substrate binding to enzyme’s active site.

Reaction Progress Curve

Plot of substrate or product concentration versus time for an enzyme-catalyzed reaction.

Turnover Rate

Same as kcat; frequency with which an enzyme converts substrate to product per active site.

Specificity Constant

Alternate term for kcat/Km, reflecting both catalytic speed and substrate binding specificity.

Proton Donor (Catalysis)

Acidic group (e.g., Glu, Asp) that donates a proton during general acid catalysis.

Proton Acceptor (Catalysis)

Basic group (e.g., His, Lys) that accepts a proton during general base catalysis.

Catalase

Diffusion-controlled enzyme that decomposes hydrogen peroxide with a kcat ~4 × 10⁷ s⁻¹.

Carbonic Anhydrase

Zinc-dependent enzyme converting CO₂ and water to bicarbonate; exhibits kcat up to 10⁶ s⁻¹.

Diffusion-Controlled Enzyme

Enzyme whose kcat/Km approaches the diffusion limit, operating at near-perfect catalytic efficiency.

Substrate Binding Pocket

Region of an enzyme’s active site providing shape and chemical complementarity to its substrate.

Thermodynamic Favorability

Condition where ΔG'° is negative; reaction is energetically possible but may still be slow without catalysis.

Kinetic Control

Regulation of reaction rates through enzymes regardless of the reaction’s thermodynamic potential.

Metabolic Function

Physiological role of enzymes in orchestrating biochemical pathways necessary for life.

Ion Cofactor

Metal ion such as Cu²⁺, K⁺, or Mn²⁺ essential for enzyme structure or catalytic activity.

Prosthetic Group

Tightly bound cofactor or coenzyme integral to an enzyme’s active site and not easily removed.

Pyruvate Kinase

K⁺/Mg²⁺-dependent enzyme catalyzing the final step of glycolysis, converting phosphoenolpyruvate to pyruvate.

Cytochrome Oxidase

Cu²⁺/Fe²⁺-dependent enzyme in the electron-transport chain that reduces O₂ to H₂O.

Hexokinase

Mg²⁺-dependent enzyme phosphorylating glucose during glycolysis; exhibits low Km for glucose.

Urease

Ni²⁺-containing enzyme that hydrolyzes urea into ammonia and carbon dioxide.

Orotidine Monophosphate Decarboxylase

Enzyme achieving one of the largest known rate enhancements (~10¹⁷-fold) by decarboxylating OMP to UMP.

Stickase (Hypothetical)

Imaginary enzyme used to illustrate induced fit and binding-energy concepts in catalysis.

RecA Protein

ATPase involved in DNA repair; noted for high catalytic efficiency near diffusion limit.

Catalytic Perfection

State where kcat/Km approaches the diffusion limit, indicating maximal possible enzymatic efficiency.

Brain Hexokinase

Isoform with very low Km for glucose, ensuring high affinity in neuronal tissue.

Steady-State Concentration

Condition in which the formation and breakdown rates of ES are equal, keeping [ES] constant.

Briggs-Haldane Modification

Refinement of Michaelis-Menten kinetics introducing the steady-state assumption rather than rapid equilibrium.

Substrate Concentration Effect

Dependence of reaction velocity on [S], showing first-order behavior at low [S] and saturation at high [S].

Reaction Velocity (v₀)

Initial rate of product formation measured before significant substrate depletion or product accumulation.

ES Breakdown to Product (k₂)

Rate constant for conversion of ES complex to free enzyme and product in Michaelis-Menten kinetics.

Saturation Effect

Phenomenon where increasing [S] no longer raises reaction rate because all enzyme active sites are occupied.

Group Transfer Reaction

Type of reaction catalyzed by transferases involving movement of functional groups between molecules.

Hydrolysis Reaction

Chemical process of cleaving bonds through the addition of water, catalyzed by hydrolases.

Enzyme Classification Number

Numerical code (EC number) assigned by the International Union of Biochemistry and Molecular Biology to categorize enzymes by reaction type.