BIOC 423 Lecture 3: Enzyme Kinetics and Regulation - Chapter 6-7 (Vocabulary)

Vocabulary flashcards covering key concepts from enzyme cofactors, kinetics, transition state, Michaelis–Menten kinetics, and allosteric regulation.

Apoenzyme

An enzyme lacking its bound non-protein cofactor.

Holoenzyme

An enzyme that is bound to its cofactors and is fully active.

Cofactor

Non-protein component required for enzyme activity (includes metal ions and organic molecules like coenzymes).

Prosthetic group

A tightly bound coenzyme that is an integral part of the enzyme.

Cosubstrate

A loosely bound coenzyme that binds and dissociates during catalysis.

Coenzyme

An organic non-protein molecule required for enzyme activity (e.g., NAD+, FAD).

Metal ion cofactor

Inorganic metal ions (e.g., Mg2+, Zn2+) that assist enzyme activity.

Activation energy

The energy barrier that must be overcome for a reaction to proceed; enzymes lower this barrier.

Transition state

The high-energy, unstable arrangement of atoms at the top of the energy barrier; stabilized by the enzyme’s active site.

Active site

The 3D pocket or cleft of an enzyme where the substrate binds and the transition state is stabilized.

Substrate

The molecule that binds to the enzyme and is converted into product.

Enzyme-substrate complex (ES)

The transient complex formed when the enzyme binds its substrate before catalysis.

Gibbs Free Energy (ΔG)

Thermodynamic potential that predicts spontaneity: ΔG < 0 exergonic, ΔG > 0 endergonic; depends on conditions.

Exergonic

Reactions with negative ΔG; spontaneous under given conditions.

Endergonic

Reactions with positive ΔG; require energy input to proceed.

Equilibrium

State where forward and reverse reaction rates are equal; enzymes do not change equilibrium.

Michaelis-Menten model

Kinetic model where E + S ⇄ ES → E + P describes formation of ES and conversion to product, with key parameters k1, k−1, k2.

kcat

Turnover number; rate constant for ES → E + P; often Vmax/[E]T.

Vmax

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

KM (Michaelis constant)

Substrate concentration at which the reaction rate is half of Vmax; reflects enzyme–substrate affinity (lower KM = tighter binding).

Catalytic efficiency (kcat/KM)

Ratio that measures how efficiently an enzyme converts substrate to product, especially at low substrate levels.

Allosteric enzyme

Enzyme showing sigmoidal (cooperative) kinetics, regulated by effectors at allosteric sites.

Allosteric regulation

Regulation of enzyme activity through binding at sites other than the active site, often producing positive or negative effects.

Concerted model

Allosteric model where T and R forms exist; substrate binds to R, leading to cooperative activation and all-or-nothing behavior.

Sequential model

Allosteric model where binding of substrate to one subunit alters the affinity of others in the complex.

First-order reaction

Reaction rate proportional to the concentration of a single limiting reactant.

Second-order reaction

Reaction rate proportional to the product of two reactant concentrations.

Reaction velocity (Vo)

Initial rate of reaction; the rate at which product appears (or reactant disappears) initially.

Michaelis-Menten equation

Vo = (Vmax [S]) / ([S] + KM); describes how rate depends on substrate concentration.

STP (Standard Conditions)

Standard temperature, pressure, and pH used for thermodynamic measurements: T = 298 K, P = 1 atm, pH 7.0.

Activation site

Three-dimensional pocket in the enzyme where activation energy is addressed and stabilization occurs.

Transition-state stabilization

Enzymes lower ΔG‡ by stabilizing the transition state through cumulative weak interactions at the active site.

Allosteric site

Site on an enzyme other than the active site where regulators bind to modulate activity.

Pockets and clefts

Structural features of the active site that provide complementary shape and chemistry to the substrate.

Tense form (T) and Relaxed form (R) in allosteric enzymes

Two conformations in the Concerted model; T is less active, R is more active; regulation shifts balance.

Cooperativity

In allosteric enzymes, binding of substrate at one site influences binding at other sites, enhancing sensitivity to substrate levels.

k1, k−1, k2, kcat

Rate constants in Michaelis–Menten kinetics: k1 ES formation, k−1 ES dissociation, k2 ES to E+P; kcat is turnover.

ES dissociation constant (KM relation)

KM is derived from k−1 and k2 relative to k1 and reflects the balance between dissociation and product formation.

Specificity constant

A measure of how specific an enzyme is for a substrate, often expressed as kcat/KM.