Enzyme Structure, Kinetics, Catalysis, and Inhibition

Vocabulary practice flashcards covering enzyme classification, active site characteristics, reaction thermodynamics, Michaelis-Menten kinetics, and modes of enzyme inhibition.

Oxidoreductases

Enzymes that catalyze oxidation-reduction reactions involving the transfer of electrons (such as dehydrogenases, oxidases, and reductases; e.g., lactate dehydrogenase).

Transferases

Enzymes that catalyze group transfer reactions between molecules, such as the transfer of functional groups like phosphate (kinases) or amino groups (transaminases; e.g., protein kinase A).

Hydrolases

Enzymes that catalyze hydrolysis reactions where functional groups are transferred to water, breaking bonds such as amides (proteases), esters (lipases), phosphates (nucleases), or acetals (glycosylases; e.g., chymotrypsin).

Lyases

Enzymes that catalyze the addition or elimination of chemical groups to form double bonds without hydrolysis or oxidation (e.g., decarboxylases, dehydrases, aldolase, and fumarase).

Isomerases

Enzymes that catalyze intramolecular group transfers and isomerization reactions, altering stereogenic centers or connectivity (e.g., epimerases, mutases, and triose phosphate isomerase).

Ligases

Enzymes that catalyze the ligation of two substrates to form new chemical bonds coupled to the hydrolysis of $ATP$ (e.g., carboxylases, synthetases, and aminoacyl-tRNA-synthetase).

Active Site

A 3-D cleft or crevice on an enzyme formed by residues from different parts of the linear sequence, mostly rich in nonpolar residues where water is excluded unless acting as a reactant, serving as the region where substrates and prosthetic groups bind.

Catalytic Groups

Specific amino acid residues within an enzyme's active site that directly participate in the making and breaking of bonds, typically possessing polar or charged side chains functioning as acids, bases, nucleophiles, or electrophiles.

Lock and Key Model

A model proposed by Emil Fisher in 1890 proposing that the active site of the unbound enzyme is preformed and structurally complementary in shape to the substrate prior to binding.

Induced Fit Model

A model proposed by Daniel E. Koshland in 1958 stating that the enzyme undergoes a conformational change upon substrate binding, forming a shape complementary to the substrate only after initial weak binding to position catalytic groups correctly.

Holoenzyme

A catalytically active, complete enzyme unit consisting of the protein component (apoenzyme) combined with its required non-amino acid component (cofactor or coenzyme).

Apoenzyme

The catalytically inactive protein/amino acid portion of an enzyme that requires an associated cofactor or coenzyme to form an active holoenzyme.

Cosubstrate

A small organic cofactor (coenzyme) that transiently associates with an enzyme during a reaction, often acting as a mobile carrier for electrons or functional groups (e.g., $NAD^+$).

Prosthetic Group

A non-amino acid cofactor that is permanently and tightly bound to an enzyme, often via covalent bonds or very strong coordinate covalent interactions (e.g., heme in hemoglobin/cytochrome c).

Standard Free Energy Change of Reaction ($\Delta G^{\circ\prime}$)

The thermodynamic energy difference between reactants and products at standard conditions ($pH = 7$), which determines spontaneity and relates to the equilibrium constant via $\Delta G^{\circ\prime} = -RT \ln K_{eq}'$, providing no information regarding reaction rate.

Activation Energy ($\Delta G^\ddagger$)

The free energy barrier required to initiate the conversion of reactants into the transition state; reaction rates are inversely proportional to this energy threshold.

Transition State ($\text{TS}^\ddagger$)

The most unstable, highest-energy transient chemical species along the reaction coordinate where chemical bonds are in the process of being formed and broken.

Stickase Model

A conceptual model illustrating that an enzyme accelerates reactions by having an active site that is complementary to the transition state (destabilizing and bending the substrate) rather than complementary to the substrate itself.

Initial Velocity ($V_0$)

The reaction rate measured at the beginning of an enzymatic reaction ($\Delta[P]/\Delta t$) when substrate is first added and the reverse reaction is negligible ($k_{-2}$ can be ignored).

Maximal Velocity ($V_{max}$)

The highest rate of an enzyme-catalyzed reaction attained when all enzyme active sites are fully saturated with substrate ($[ES] = [E]_{tot}$), calculated as $V_{max} = k_{cat}[E]_{tot}$.

Michaelis Constant ($K_M$)

The substrate concentration at which the reaction velocity is half-maximal ($V_0 = \frac{1}{2}V_{max}$); it reflects the substrate-binding affinity of an enzyme, defined mathematically as $K_M = \frac{k_{-1} + k_2}{k_1}$.

Turnover Number ($k_{cat}$)

The first-order rate constant of the rate-determining step at saturating substrate concentrations ($k_{cat} = k_2 = \frac{V_{max}}{[E]_{tot}}$), representing the number of substrate molecules converted to product per active site per unit time.

Catalytic Efficiency ($k_{cat} / K_M$)

The second-order rate constant measuring the apparent specificity and catalytic power of an enzyme under physiological conditions where substrate is limiting ($[S] \ll K_M$).

Diffusion-Controlled Limit

The theoretical maximum rate for an enzyme-substrate collision in aqueous solution ($10^8 - 10^9\,M^{-1}s^{-1}$), achieved by catalytically perfect enzymes that catalyze a reaction nearly every time they encounter substrate.

Steady-State Assumption

The condition in enzyme kinetics where the concentration of the enzyme-substrate complex ($[ES]$) remains constant over time because its rate of formation equals its rate of breakdown ($\frac{d[ES]}{dt} = 0$).

Lineweaver-Burk Equation

The double-reciprocal transformation of the Michaelis-Menten equation, $\frac{1}{V_0} = \frac{K_M}{V_{max}}\frac{1}{[S]} + \frac{1}{V_{max}}$, yielding a linear plot with a slope of $\frac{K_M}{V_{max}}$, a y-intercept of $\frac{1}{V_{max}}$, and an x-intercept of $-\frac{1}{K_M}$.

Competitive Inhibition

A reversible inhibition mode where an inhibitor structurally resembles the substrate and competes for binding at the active site; it increases apparent $K_M$ ($K_M^{app} = \alpha K_M$) while leaving $V_{max}$ unchanged, and can be overcome by high substrate concentrations.

Noncompetitive Inhibition

A reversible allosteric inhibition mode where the inhibitor binds to a site distinct from the active site on both free enzyme ($E$) and the $ES$ complex with equal affinity; it decreases $V_{max}$ ($V_{max}^I = \frac{V_{max}}{\alpha}$) while leaving $K_M$ unchanged, and cannot be overcome by high $[S]$.

Inhibition Constant ($K_I$)

The equilibrium dissociation constant for the enzyme-inhibitor complex ($EI \rightleftharpoons E + I$), given by $K_I = \frac{[E][I]}{[EI]}$; a smaller value indicates tighter binding and a more potent inhibitor.

Modification Factor ($\alpha$)

The quantitative factor $\alpha = 1 + \frac{[I]}{K_I}$ by which kinetic parameters ($K_M$ in competitive inhibition, or the denominator of $V_{max}$ in noncompetitive inhibition) are altered in the presence of an inhibitor.

Transition State Analog

A stable compound designed to mimic the transition state geometry and charge distribution of an enzymatic reaction, binding to the active site orders of magnitude more tightly than the substrate (low $K_I$ in the nanomolar range).

Abzyme

A catalytic antibody generated using a transition state analog as an immunogen/antigen, possessing enzymatic catalytic capabilities that accelerate specific reactions up to $10^8$-fold.

Group-Specific Reagent

An irreversible inhibitor that modifies specific amino acid functional groups; an example is diisopropylphosphofluoridate (DIPF), which covalently reacts with catalytic serine residues in acetylcholinesterase and serine proteases.

Affinity Label

An irreversible enzyme inhibitor that is structurally similar to the substrate and docks in the active site, where its reactive moiety covalently modifies an essential catalytic residue (e.g., TPCK modifying His 57 in chymotrypsin).

Suicide Inhibitor

A mechanism-based irreversible inhibitor that binds as an unreactive substrate analog until the enzyme's catalytic machinery converts it in situ into a chemically reactive intermediate that permanently inactivates the enzyme (e.g., fluorouracil converted to F-dUMP targeting thymidylate synthase).

Penicillin

A $\beta$-lactam antibiotic that acts as a transition state analog and suicide inhibitor, covalently and irreversibly modifying an active-site serine of bacterial glycopeptide transpeptidase to disrupt peptidoglycan cell-wall synthesis.

Aspirin (Acetylsalicylic Acid)

An irreversible inhibitor of prostaglandin $H_2$ synthase (cyclooxygenase/COX) that covalently transfers an acetyl group to Ser 530, physically blocking arachidonate from entering the active site.

Methotrexate

A competitive inhibitor and structural analog of dihydrofolate that binds dihydrofolate reductase (DHFR) approximately 1000-fold more tightly than the substrate, inhibiting purine/pyrimidine biosynthesis in cancer chemotherapy.

Catalytic Triad

The conserved constellation of Asp 102, His 57, and Ser 195 residues in serine proteases (such as chymotrypsin) that work together via a hydrogen-bonding network to deprotonate Ser 195 into a potent alkoxide nucleophile.