Topic 5 - Enzyme Catalysis

Enzyme

A biological catalyst that accelerates reactions without being permanently changed.

Enzyme composition

Most enzymes are proteins; some contain RNA.

Substrate

A specific molecule upon which an enzyme acts.

Enzyme specificity

An enzyme typically acts on only one or a few types of substrate.

Enzyme fidelity

Enzymes rarely recognize improper substrates or produce incorrect products.

Active site

The small region of an enzyme where substrate binds and the reaction occurs.

Substrate binding

Substrates bind reversibly at the active site through multiple weak interactions.

Transition state

The highest-free-energy form along a reaction pathway, with bonds forming and breaking.

Activation free energy

The free-energy difference between reactants and the transition state; it determines reaction rate.

Enzyme effect on activation energy

Enzymes lower activation energy by stabilizing the transition state.

Enzyme effect on equilibrium

Enzymes accelerate attainment of equilibrium without changing the equilibrium constant.

Enzyme effect on reaction free energy

Enzymes do not change the free-energy difference between reactants and products.

Proximity and orientation

Enzymes bring substrates together and align them for productive reactions.

Catalytic proton transfer

Active-site groups can donate or accept protons during catalysis.

Transition-state analogues

Compounds resembling transition states that bind tightly and act as competitive inhibitors.

Cofactor

A metal ion or coenzyme required for or enhancing an enzyme's activity.

Enzyme pH optimum

Each enzyme has an optimal pH; extreme pH can alter catalytic groups or denature it.

Enzyme temperature optimum

Reaction rate rises with temperature until the enzyme becomes unstable.

Chymotrypsin

A pancreatic serine protease that hydrolyzes peptide bonds during digestion.

Chymotrypsin specificity

It cleaves peptide bonds after phenylalanine, tryptophan, or tyrosine residues.

Serine protease catalytic triad

Serine, histidine, and aspartic acid cooperate in catalysis.

Chymotrypsin: initial attack

Histidine removes a serine proton, enabling serine to attack the peptide carbonyl.

Chymotrypsin: peptide bond cleavage

A tetrahedral intermediate breaks down, releasing the carboxyl-terminal peptide fragment.

Acyl-enzyme intermediate

The amino-terminal peptide fragment is covalently attached to chymotrypsin's serine.

Chymotrypsin: deacylation

Histidine activates water to attack the acyl-enzyme, releasing the remaining peptide fragment.

Oxyanion hole

Stabilizes the oxyanion formed in chymotrypsin's tetrahedral intermediates.

Zymogen

An inactive enzyme precursor that can be activated by cleavage.

Serine protease zymogen activation

Cleavage causes a conformational change that enables substrate binding and aligns catalytic residues.

Enzyme kinetics

The study of how factors such as substrate concentration influence reaction rates.

Initial velocity, v₀

The reaction rate measured before much product has formed.

Substrate saturation

At high substrate concentration, the enzyme approaches its maximum reaction rate.

Michaelis-Menten equation

v₀ = Vmax[S]/(KM + [S]).

Vmax

The maximal reaction velocity at a given enzyme concentration.

Vmax and enzyme concentration

Doubling enzyme concentration doubles Vmax.

Michaelis constant, KM

The substrate concentration at which the reaction rate is half Vmax.

KM and substrate affinity

A lower KM corresponds to higher substrate affinity.

KM and enzyme concentration

KM is independent of enzyme concentration.

Lineweaver-Burk plot

A plot of 1/v₀ against 1/[S] that linearizes Michaelis-Menten data.

Reversible inhibition

An inhibitor binds noncovalently and can be removed from the enzyme.

Irreversible inhibition

An inhibitor forms a covalent bond with the enzyme, permanently blocking activity.

Competitive inhibition

An inhibitor competes with substrate for binding at the enzyme's active site.

Competitive inhibition kinetics

Competitive inhibition increases KM without changing Vmax and can be overcome by excess substrate.

Allostery

Binding at one protein site alters activity at another, often distant, site.

Allosteric feedback

A pathway product can inhibit an earlier enzyme, reducing pathway activity.