Enzyme kinetics, mechanism, regulation; EC classification; catalytic strategies.
Enzymes
Enzyme
Protein (or catalytic RNA) that accelerates a biochemical reaction by lowering the transition-state free-energy barrier without being…
Active site
Substrate-binding pocket on an enzyme where catalysis occurs. Lined with conserved residues supplying binding energy (hydrogen bonds,…
Catalytic triad (Ser-His-Asp)
Ser-His-Asp triad of serine proteases (chymotrypsin, trypsin, elastase, subtilisin). Asp polarises His which deprotonates Ser; the Ser…
Transition-state stabilisation
Linus Pauling's 1946 theorem of enzyme catalysis: enzymes bind the transition state (‡) more tightly than substrate or product; the tighter…
Michaelis-Menten kinetics
v = Vmax·[S] / (K_M + [S]). Derived from E + S ⇌ ES → E + P under the steady-state approximation (Briggs-Haldane 1925). Describes…
Turnover number k_cat
Maximum number of substrate molecules converted to product per enzyme active site per unit time at saturating [S]: k_cat = Vmax /…
Michaelis constant K_M
Substrate concentration at which v = ½·Vmax. Under rapid-equilibrium assumption K_M ≈ K_d of the ES complex; under steady-state K_M = (k_-1…
Catalytic efficiency k_cat/K_M
Specificity constant — second-order rate constant for E + S → E + P at low [S]. Upper bound set by diffusion: 10⁸–10⁹ M⁻¹·s⁻¹. Enzymes…
Lineweaver-Burk (double-reciprocal) plot
Linearisation of Michaelis-Menten: 1/v = (K_M/Vmax)·(1/[S]) + 1/Vmax. Historically used to read K_M from x-intercept (-1/K_M) and Vmax from…
Competitive inhibition
Inhibitor binds the active site and competes with substrate. Apparent K_M increases by factor (1 + [I]/K_I); Vmax unchanged.…
Non-competitive inhibition
Inhibitor binds a site distinct from the active site with equal affinity to E and ES. Vmax decreases by factor 1/(1 + [I]/K_I); apparent…
Uncompetitive inhibition
Inhibitor binds only the ES complex (not free E). Vmax and apparent K_M decrease in the same ratio. Lineweaver-Burk lines are parallel.…
Allosteric regulation
Modulation of enzyme activity by a ligand binding at a site distinct from the active site, propagated through subunit conformational…
MWC concerted model (Monod-Wyman-Changeux 1965)
Symmetric oligomeric enzyme exists in an equilibrium between an all-T (tense, low affinity) and all-R (relaxed, high affinity) state.…
KNF sequential model (Koshland-Némethy-Filmer 1966)
Substrate binding induces conformational change in the bound subunit only, which propagates through subunit-subunit contacts to alter…
Cooperativity (binding)
Binding of one substrate (or ligand) molecule alters the affinity of remaining sites. Positive cooperativity (n_H > 1) produces sigmoidal…
Hill equation
θ = [S]^{n_H} / (K' + [S]^{n_H}), with n_H the Hill coefficient. n_H = 1 non-cooperative (Michaelis-Menten); n_H > 1 positively cooperative…
Enzyme Commission (EC) classification
Hierarchical EC-number taxonomy of enzymes by reaction type: EC 1 oxidoreductases, EC 2 transferases, EC 3 hydrolases, EC 4 lyases, EC 5…
EC numbers (IUBMB 1961)
IUBMB 1961 + 2024 EC-classification 7-class hierarchy; modern BRENDA + UniProt; computational enzyme-function-prediction.
Induced fit vs lock-and-key
Fischer 1894 lock-and-key + Koshland 1958 induced-fit; modern conformational-selection MWC + KNF allosterism.
Enzyme catalysis (Warshel 1976)
A Warshel 1976 (Nobel 2013) QM/MM enzyme catalysis; modern Schramm-1998 transition-state-stabilization 10^17 acceleration.
Cleland kinetics (1963)
W W Cleland 1963 multisubstrate-enzyme kinetics; modern King-Altman steady-state; Phenex + Dynafit numerical fitting.
Ribozyme (Cech-Altman Nobel 1989)
Cech-Altman 1989 (Nobel 1989) catalytic RNA; modern T tetrahymena intron + RNase P + ribosome PTC.
Directed evolution (Arnold 2018)
F Arnold 2018 (Nobel 2018) directed-evolution; modern computational + ML-guided enzyme-engineering Estell + Romero-Arnold.