Biochemistry: Chapter 9 - Mechanisms and Inhibitors

Vocabulary practice flashcards generated from Biochemistry Chapter 9 lecture notes covering catalytic strategies, enzyme kinetics, types of inhibitors, and the chymotrypsin catalytic mechanism.

Nucleophile

A chemical group or atom attracted to regions of positive charge in other molecules that participates in chemical reactions by donating electrons to electrophiles.

Electrophile

An electron-deficient chemical group attracted to negative charge that participates in chemical reactions by accepting electrons from nucleophiles.

Covalent Catalysis

A catalytic strategy in which the active site contains a reactive group (usually a powerful nucleophile) that becomes temporarily covalently modified during catalysis.

General Acid–Base Catalysis

A catalytic strategy in which a molecule other than water plays the role of a proton donor or acceptor.

Metal Ion Catalysis

A catalytic mechanism in which a metal ion serves as an electrophilic catalyst to stabilize a negative charge, generates a nucleophile by increasing acidity, increases substrate binding energy, or serves as an enzyme cofactor.

Catalysis by Approximation

A strategy that enhances reaction rates for reactions with multiple substrates by bringing them into proximity and proper orientation on a single enzyme binding surface.

Binding Energy

The full complement of binding interactions between an enzyme and a substrate, which is maximal only when the substrate is in the transition state.

Endotherms

Organisms (such as humans) that maintain a constant body temperature, thereby minimizing the effect of ambient temperature changes on enzyme activity.

Ectotherms

Organisms that assume the temperature of their ambient environment, making external temperature an important regulator of their biological and biochemical activity.

Optimal pH

The specific pH at which an enzyme displays maximal catalytic activity, correlating with the environment of the enzyme.

Irreversible Inhibition

Enzyme inhibition characterized by the inhibitor covalently binding to target enzymes and failing to dissociate at any appreciable rate.

Reversible Inhibition

Enzyme inhibition characterized by noncovalent interactions between the inhibitor and the target, allowing the enzyme–inhibitor complex to dissociate.

Competitive Inhibition

A type of reversible inhibition where the inhibitor competes directly with the substrate for binding to the enzyme active site, increasing the apparent $K_M$ ($K_M^{\text{app}}$) without changing $V_{\max}$.

Uncompetitive Inhibition

A substrate-dependent reversible inhibition where the inhibitor binds exclusively to the enzyme–substrate ($\text{ES}$) complex, lowering both $V_{\max}$ (to $V_{\max}^{\text{app}}$) and $K_M$ (to $K_M^{\text{app}}$).

Pure Noncompetitive Inhibition

Reversible inhibition where the inhibitor binds equally well to the free enzyme or the enzyme–substrate complex, lowering $V_{\max}$ to $V_{\max}^{\text{app}}$ while leaving $K_M$ unchanged.

Mixed Noncompetitive Inhibition

Reversible inhibition where the inhibitor binds preferentially to either the free enzyme or the enzyme–substrate complex, altering both $V_{\max}$ (to $V_{\max}^{\text{app}}$) and $K_M$ (to $K_M^{\text{app}}$).

Transition-State Analogs (TSAs)

Compounds that structurally resemble the transition state of a catalyzed reaction and function as highly potent competitive inhibitors.

Group-Specific Reagents

A category of irreversible inhibitors that react with specific amino acid side chains (R groups) on enzyme molecules.

Diisopropylphosphofluoridate (DIPF)

A group-specific reagent that irreversibly inhibits chymotrypsin by modifying a single serine residue (Ser 195) and also inactivates acetylcholinesterase.

Affinity Labels

Reactive substrate analogs that structurally resemble an enzyme's substrate and covalently bond to active-site residues to irreversibly inhibit the enzyme.

Tosyl-L-phenylalanine chloromethyl ketone (TPCK)

An affinity label for chymotrypsin that binds to the active site via its phenylalanine side chain and covalently modifies Histidine 57 to inhibit enzyme activity.

Mechanism-Based (Suicide) Inhibitors

Chemically modified substrates that bind to an enzyme's active site and are processed by the catalytic mechanism to generate a reactive intermediate that permanently inactivates the enzyme.

Penicillin

A suicide inhibitor composed of a thiazolidine ring fused to a reactive $\beta$-lactam ring that mimics the $\text{D-Ala-D-Ala}$ peptide moiety to irreversibly inhibit glycopeptide transpeptidase.

Peptidoglycan

A bacterial cell wall macromolecule consisting of linear polysaccharide chains cross-linked by short peptides that provides mechanical support against osmotic pressure.

Proteases

Also known as proteolytic enzymes; a class of enzymes that catalyze the cleavage of proteins into small peptides and amino acids via hydrolysis.

Chymotrypsin

A proteolytic enzyme that selectively cleaves peptide bonds on the carboxyl-terminal side of large hydrophobic amino acids (such as Trp, Tyr, Phe, Met, and Ile) using covalent catalysis.

Chromogenic Substrate

A substrate analog used to monitor enzyme kinetics that generates a colored product upon enzyme cleavage.

p-Nitrophenolate

A yellow-colored product formed during the cleavage of N-acetyl-L-phenylalanine p-nitrophenyl ester by chymotrypsin, used to monitor enzyme activity.

Acyl-Enzyme Intermediate

A covalent complex formed during chymotrypsin catalysis where the acyl group of the substrate becomes temporarily attached to Serine 195.

Catalytic Triad

A set of three key residues (Serine 195, Histidine 57, and Aspartate 102) in the active site of chymotrypsin that promote nucleophilic cleavage of peptide bonds.

Oxyanion Hole

A site in the active site of chymotrypsin that stabilizes the negative charge on the oxygen atom of the unstable tetrahedral intermediate via backbone NH group hydrogen bonds.

S1 Pocket

A deep, hydrophobic pocket in chymotrypsin that accommodates long, uncharged amino acid side chains (such as phenylalanine and tryptophan) to position adjacent peptide bonds for cleavage.