Enzyme Structure, Function, and Kinetics: A Comprehensive Review

Structure of an enzyme

A folded polypeptide with primary, secondary, tertiary, and sometimes quaternary structure, containing an active site formed by specific amino acid residues;

How enzyme structure regulates biological processes

The active site's shape and chemistry determine which substrates bind; enzymes also have regulatory sites, undergo conformational changes (induced fit), respond to pH/temp, and can be activated or inhibited;

Function of an enzyme

To increase the rate of biochemical reactions by stabilizing the transition state and providing a lower-activation-energy pathway;

How enzyme function regulates biological processes

By speeding specific reactions, enzymes control pathway timing, flux, and metabolic responses to cellular signals;

How enzymes perform catalysis

They bind substrates, form enzyme-substrate complexes, orient molecules correctly, use catalytic residues (acid-base, covalent, or metal-ion), stabilize transition states, and release product;

Monomer that makes up enzymes

Amino acids;

Effect of enzymes on reaction rate

They increase reaction rate dramatically by lowering activation energy and increasing the number of successful collisions;

Enzyme-catalyzed reaction

A reaction in which an enzyme binds substrate, lowers activation energy, and accelerates conversion to products through an alternative pathway;

Activation energy: catalyzed vs uncatalyzed

Catalyzed reactions have lower activation energy; uncatalyzed reactions have a higher energy barrier and therefore proceed slower;

Free energy change (ΔG): catalyzed vs uncatalyzed

ΔG is the same for both; enzymes do not change the energy difference between reactants and products;

Reaction rate: catalyzed vs uncatalyzed

Enzyme-catalyzed reactions occur much faster—often millions of times faster—than uncatalyzed reactions;

Do enzymes change Gibbs free energy? (True/False)

False; enzymes do not change ΔG, only the activation energy;

Active site

A 3-D pocket where substrates bind and catalysis occurs; formed by specific amino acids brought together by protein folding;

Induced fit model

The enzyme changes shape slightly upon substrate binding, aligning catalytic residues and increasing catalytic efficiency;

Transition state stabilization

Enzymes bind and stabilize the transition state more strongly than the substrate, greatly lowering activation energy;

Michaelis-Menten kinetics

Describes how reaction velocity depends on substrate concentration; includes Vmax, Km, and kcat;

Vmax

The maximum reaction velocity when the enzyme is saturated with substrate;

Km

The substrate concentration at which reaction rate is half of Vmax; often reflects enzyme-substrate affinity;

kcat (turnover number)

The number of substrate molecules converted to product per enzyme molecule per second when the enzyme is fully saturated;

Catalytic efficiency (kcat/Km)

A measure of how efficiently an enzyme converts substrate into product, especially at low substrate concentration;

Competitive inhibition

Inhibitor binds active site; raises Km, Vmax unchanged;

Noncompetitive inhibition

Inhibitor binds allosteric site; lowers Vmax, Km unchanged;

Uncompetitive inhibition

Inhibitor binds only ES complex; lowers both Km and Vmax;

Factors affecting enzyme activity

Temperature, pH, salinity, substrate concentration, cofactors, inhibitors, and allosteric regulators;

Allosteric regulation

Regulation via molecules binding to non-active sites, causing conformational changes that increase or decrease enzyme activity;

Zymogen (proenzyme)

An inactive enzyme precursor activated by proteolytic cleavage (e.g., trypsinogen → trypsin);

Cofactors and coenzymes

Non-protein helpers (metal ions, vitamins, NAD⁺, FAD) required for enzyme activity;

Effect of temperature on enzymes

Rate increases with temperature up to an optimum; high heat denatures the enzyme and decreases rate;

Effect of pH on enzymes

Each enzyme has an optimal pH; outside this range, ionization of amino acids changes and the enzyme may lose function;