AP Biology Unit 3 Enzymes: How Biological Catalysts Work and What Affects Them

Enzyme

A biological catalyst (usually a protein) that speeds up cellular chemical reactions without being permanently consumed; its function depends on its 3D shape.

Catalyst

A substance that increases reaction rate by lowering activation energy without changing the overall energy difference between reactants and products or the reaction’s equilibrium.

Structure–function relationship (enzymes)

The principle that an enzyme’s specific 3D structure determines what it can bind and how well it catalyzes; changes in structure often change function.

R group (side chain)

The variable part of an amino acid that gives it chemical properties (nonpolar, polar, charged) and drives protein folding and binding.

Ribozyme

An RNA molecule that catalyzes a chemical reaction (an example that not all enzymes are proteins).

Primary structure

The amino acid sequence of a protein; even a single substitution can alter folding or active-site chemistry.

Secondary structure

Local protein folding patterns (alpha helices and beta sheets) stabilized mainly by hydrogen bonds.

Tertiary structure

The overall 3D shape of one polypeptide, stabilized by R-group interactions (hydrophobic interactions, ionic bonds, hydrogen bonds, and sometimes disulfide bridges).

Quaternary structure

A functional protein formed by multiple polypeptide subunits assembled together (not present in all enzymes).

Active site

The enzyme region where the substrate binds and catalysis occurs; a flexible 3D arrangement of amino acids that helps stabilize the transition state.

Substrate

The reactant an enzyme acts on; only substrates with sufficient shape and chemical complementarity bind effectively.

Induced fit model

Model in which substrate binding causes a slight conformational change in the enzyme’s active site, improving binding and positioning catalytic groups.

Activation energy (Ea)

The energy required to reach the transition state; enzymes speed reactions primarily by lowering this barrier.

Transition state

A high-energy, unstable arrangement of atoms at the peak of the energy barrier between reactants and products; enzymes lower Ea by stabilizing it.

Cofactor

Any non-protein component required for enzyme activity (e.g., inorganic ions like Mg2+ or Zn2+, or organic molecules).

Coenzyme

An organic cofactor (often vitamin-derived) that assists enzyme function, commonly by carrying electrons or functional groups.

Prosthetic group

A cofactor that is tightly and strongly (often permanently) bound to an enzyme.

Allosteric site

A regulatory binding site separate from the active site; binding there changes enzyme shape and alters activity.

Feedback inhibition

Pathway regulation in which a final product binds allosterically to an early enzyme and reduces its activity to prevent overproduction.

Enzyme saturation

A condition at high substrate concentration where most active sites are occupied; reaction rate plateaus because adding more substrate has little effect.

Competitive inhibitor

A molecule that resembles the substrate and competes for the active site; its effect can often be reduced by increasing substrate concentration.

Noncompetitive (allosteric) inhibitor

An inhibitor that binds away from the active site (often allosterically), changing enzyme shape and reducing activity; increasing substrate does not fully overcome it.

Denaturation

Loss of a protein’s functional 3D shape (often from disrupted noncovalent interactions), typically reducing or eliminating enzyme activity.

Optimum temperature (enzyme)

The temperature at which enzyme activity is highest due to a balance between increased molecular motion and avoidance of heat-driven denaturation.

pH optimum (enzyme)

The pH at which an enzyme works best; pH changes alter amino acid protonation/charge, affecting bonding, folding, and active-site chemistry.