Chapter 9/10 - Enzymatic Catalysis and Kinetics Review Flashcards

A comprehensive set of vocabulary flashcards covering enzyme properties, classification, catalytic mechanisms (acid-base, covalent, metal ion), specific enzyme examples (lysozyme, serine proteases), and enzyme kinetics including Michaelis-Menten parameters and inhibition types.

Active site

A pocket or cleft in an enzyme ideally shaped to bind specific substrates and participate in the chemical reaction that transforms them into products.

Enzymology

The study of enzymes, originating from 19th-century investigations of fermentation and digestion.

Ribozymes

RNA molecules that possess enzymatic activity, such as ribosomal RNA which catalyzes peptide bond formation.

Transition state

The point of highest free energy in a reaction progress where bond breaking and formation occur simultaneously.

Free energy of activation ($\Delta G^{\ddagger}$)

The difference in free energy between the reactants and the transition state ($X^{\ddagger}$).

Rate-determining step

The step in a multistep reaction with the greatest activation energy that acts as a bottleneck for the overall process.

Binding energy

A source of free energy derived from the formation of weak non-covalent interactions between an enzyme and its substrate used to lower activation energy.

Induced fit

A phenomenon where an enzyme undergoes conformational changes upon substrate binding to properly position functional groups for catalysis.

Stereospecificity

The ability of an enzyme to differentiate between prochiral groups or act only on a specific enantiomer due to the complementarity of its binding site.

Oxidoreductases

The first major class of enzymes according to the IUBMB, which catalyze oxidation-reduction reactions.

Transferases

The second major class of enzymes, responsible for the transfer of functional groups.

Hydrolases

The third major class of enzymes, which catalyze hydrolysis reactions.

Lyases

The fourth major class of enzymes, which catalyze group elimination to form double bonds.

Isomerases

The fifth major class of enzymes, which catalyze isomerization reactions.

Ligases

The sixth major class of enzymes, which catalyze bond formation coupled with ATP hydrolysis.

Translocases

The seventh major class of enzymes, involved in the movement of molecules or ions across or within membranes.

Cofactor

Small molecules, which may be metal ions or organic coenzymes, that associate with enzymes to expand their chemical palette.

Holoenzyme

A catalytically active enzyme-cofactor complex.

Apoenzyme

The enzymatically inactive protein portion of an enzyme that remains after its cofactor is removed.

General acid catalysis

A catalytic mechanism where proton transfer from an acid lowers the free energy of a reaction's transition state.

Covalent catalysis

A mechanism that accelerates reaction rates through the transient formation of an enzyme-substrate covalent bond, usually featuring a nucleophile.

Lysozyme

An enzyme that destroys bacterial cell walls by hydrolyzing $\beta(1 \rightarrow 4)$ glycosidic linkages between NAM and NAG residues.

Catalytic triad

A hydrogen-bonded constellation of three invariant residues (Ser195, His57, and Asp102) found in the active site of serine proteases.

Oxyanion hole

A pocket in serine proteases that stabilizes the negative charge of the tetrahedral intermediate through hydrogen bonding with backbone NH groups.

Zymogens

Inactive enzyme precursors, such as trypsinogen or chymotrypsinogen, that require proteolytic cleavage to become active.

Reaction velocity ($v$)

The instantaneous rate of appearance of product or disappearance of reactant, measured in units like $M \cdot s^{-1}$.

Michaelis constant ($K_M$)

The substrate concentration at which the reaction velocity is half-maximal ($V_{max}/2$).

Turnover number ($k_{cat}$)

The catalytic constant representing the number of reaction processes each active site catalyzes per unit time ($k_{cat} = V_{max}/[E]_T$).

Catalytic efficiency

The ratio $k_{cat}/K_M$, which measures how efficiently an enzyme converts substrate to product; the upper limit is the diffusion-controlled limit ($10^8$ to $10^9\,M^{-1} \cdot s^{-1}$).

Lineweaver-Burk plot

A double-reciprocal plot of $1/v_o$ versus $1/[S]$ used to determine $V_{max}$ and $K_M$ values.

Competitive inhibitor

A substance that competes with the substrate for the active site, increasing the apparent $K_M$ while leaving $V_{max}$ unchanged.

Uncompetitive inhibitor

An inhibitor that binds only to the enzyme-substrate (ES) complex, decreasing both $V_{max}$ and $K_M$ in equal proportion.

Mixed inhibitor

An inhibitor that binds to both the free enzyme and the ES complex, decreasing $V_{max}$ and either increasing or decreasing the apparent $K_M$.