Enzyme Mechanism, Catalysis, Kinetics, and Regulation

Vocabulary flashcards covering enzyme mechanisms, catalytic strategies, kinetics, inhibition, regulatory mechanisms, and basic bioenergetics based on the provided lecture materials.

Active Site

A specialized pocket or domain in an enzyme that provides a specific environment for substrate binding and where the catalytic reaction occurs.

Cofactor

One or more inorganic ions, such as $\text{Fe}^{2+}$, $\text{Mg}^{2+}$, $\text{Mn}^{2+}$, or $\text{Zn}^{2+}$, required by an enzyme for catalytic activity.

Coenzyme

A complex organic or metalloorganic molecule that acts as a transient carrier of specific functional groups or electrons during enzymatic reactions.

Prosthetic Group

A coenzyme or metal ion cofactor that is very tightly or covalently bound to the enzyme protein.

Holoenzyme

A complete, catalytically active enzyme together with its bound coenzyme and/or metal ions.

Apoenzyme

The protein portion of a holoenzyme that lacks its required cofactor or coenzyme, also referred to as an apoprotein.

Oxidoreductases

Class 1 enzymes that catalyze the transfer of electrons, such as hydride ions or $\text{H}$ atoms.

Transferases

Class 2 enzymes that catalyze group transfer reactions.

Hydrolases

Class 3 enzymes that catalyze hydrolysis reactions by transferring functional groups with the elimination or addition of water.

Lyases

Class 4 enzymes that catalyze the cleavage of $\text{C–C}$, $\text{C–O}$, $\text{C–N}$, or other bonds by elimination, leaving double bonds or rings, or addition of groups to double bonds.

Isomerases

Class 5 enzymes that catalyze the transfer of groups within molecules to yield isomeric forms.

Ligases

Class 6 enzymes that catalyze the formation of $\text{C–C}$, $\text{C–S}$, $\text{C–O}$, and $\text{C–N}$ bonds by condensation reactions coupled to cleavage of $\text{ATP}$ or similar cofactors.

Translocases

Class 7 enzymes that catalyze the movement of molecules or ions across membranes or their separation within membranes.

Ground State

The starting point for either the forward or reverse chemical reaction.

Transition State ($\neq$)

The point in a reaction coordinate diagram at which decay to substrate or product is equally likely.

Activation Energy ($\text{Δ}G^\neq$)

The difference between the ground state energy level and the transition state energy level.

Rate-Limiting Step

The step in a reaction sequence with the highest activation energy and the slowest rate.

Binding Energy ($ ext{Δ}G_B$)

The free energy derived from noncovalent enzyme-substrate interactions used by enzymes to lower activation energy.

Lock and Key Hypothesis

An early theory proposing that an enzyme active site is structurally complementary to its substrate.

Induced Fit

Conformational changes in an enzyme upon substrate binding that optimize stabilizing interactions with the transition state.

Nucleophile

An electron-rich functional group that donates an electron pair to an electrophile to form a covalent bond.

Electrophile

An electron-deficient functional group that accepts an electron pair from a nucleophile to form a covalent bond.

Desolvation

The replacement of the solvation shell of structured water around a substrate with weak noncovalent bonds inside the enzyme active site.

Specific Acid-Base Catalysis

Catalysis that uses only the $\text{H}^+$ ($\text{H}_3\text{O}^+$) or $\text{OH}^-$ ions present in water.

General Acid-Base Catalysis

Proton transfers mediated by weak acids or weak bases other than water.

Covalent Catalysis

A catalytic mechanism involving the formation of a transient covalent bond between the enzyme or coenzyme and the substrate.

Metal Ion Catalysis

Catalysis where metal ions serve as structural templates, Lewis acids, or redox agents to orient substrates or stabilize charged transition states.

Catalytic Triad

A specific set of three amino acid residues ($\text{Asp}^{102}$, $\text{His}^{57}$, and $\text{Ser}^{195}$ in chymotrypsin) that cooperate in the active site to enable peptide cleavage.

Acylation Phase

The first phase of chymotrypsin catalysis in which the peptide bond is cleaved and an ester linkage forms between the peptide carbonyl carbon and the enzyme.

Deacylation Phase

The second phase of chymotrypsin catalysis in which the ester linkage is hydrolyzed by water, regenerating the free enzyme.

Pre-Steady State

The initial transient period of an enzymatic reaction during which the enzyme-substrate complex ($\text{ES}$) rapidly builds up.

Steady State

The period during an enzymatic reaction when the concentration of the enzyme-substrate complex ($\text{ES}$) and other intermediates remains constant.

Initial Velocity ($V_0$)

The reaction rate at time $t = 0$, measured when substrate concentration is regarded as constant.

Michaelis Constant ($K_m$)

The substrate concentration at which the initial reaction velocity $V_0$ is equal to $\frac{1}{2} V_{\text{max}}$.

Turnover Number ($k_{\text{cat}}$)

The maximum number of substrate molecules converted to product per unit time per enzyme active site ($k_{\text{cat}} = \frac{V_{\text{max}}}{[E_t]}$).

Specificity Constant ($k_{\text{cat}}/K_m$)

An apparent second-order rate constant used as a measure of an enzyme's catalytic efficiency.

Lineweaver-Burk Plot

A double-reciprocal plot of $\frac{1}{V_0}$ versus $\frac{1}{[S]}$ that yields a straight line for enzymes obeying Michaelis-Menten kinetics.

Competitive Inhibition

Reversible inhibition where an inhibitor competes directly with the substrate for the active site, increasing apparent $K_m$ while leaving $V_{\text{max}}$ unchanged.

Uncompetitive Inhibition

Reversible inhibition where an inhibitor binds only to the $\text{ES}$ complex at a site distinct from the active site, decreasing both $V_{\text{max}}$ and apparent $K_m$.

Mixed Inhibition

Reversible inhibition where an inhibitor binds to either free enzyme or the $\text{ES}$ complex at a non-active site, decreasing $V_{\text{max}}$ while apparent $K_m$ may increase or decrease.

Suicide Inactivator

A mechanism-based inactivator that undergoes initial catalytic steps before being converted into a reactive compound that binds irreversibly to the enzyme.

Regulatory Enzyme

An enzyme whose catalytic activity increases or decreases in response to specific metabolic signals.

Allosteric Enzyme

An enzyme whose activity is regulated through reversible, noncovalent binding of modulators at sites other than the active site.

Homotropic Modulator

An allosteric modulator that is identical to the substrate of the enzyme.

Heterotropic Modulator

An allosteric modulator that is a molecule different from the substrate of the enzyme.

Protein Kinase

An enzyme that catalyzes the transfer of a phosphoryl group from $\text{ATP}$ to specific amino acid residues such as $\text{Ser}$, $\text{Thr}$, $\text{Tyr}$, or $\text{His}$.

Phosphoprotein Phosphatase

An enzyme that removes phosphoryl groups from target proteins via hydrolytic cleavage.

Zymogen

An inactive protein precursor that requires proteolytic cleavage to become an active enzyme.

Bioenergetics

The quantitative study of energy transductions and transformations in living systems.

Gibbs Free Energy ($G$)

A thermodynamic state function representing the amount of work a system can perform at constant temperature and pressure.

Enthalpy ($H$)

A thermodynamic property reflecting the heat content and the number and kinds of chemical bonds in reactants and products.

Entropy ($S$)

A thermodynamic property that quantitatively measures randomness or disorder in a system.

Exergonic Reaction

A chemical reaction that releases free energy ($\text{Δ}G < 0$) and proceeds spontaneously.

Endergonic Reaction

A chemical reaction that absorbs free energy ($\text{Δ}G > 0$) and requires an energy input to proceed.