Enzymes – Structure, Function & Regulation

Vocabulary flashcards covering enzyme structure, types, mechanisms, regulation, classes, and key biochemical terms drawn from the lecture notes.

Metabolism

The sum of all chemical reactions occurring within a cell or organism.

Enzyme

A specific, mostly protein-based biological catalyst that speeds up a chemical reaction without being consumed.

Biological Catalyst

Any substance, such as an enzyme, that lowers activation energy and accelerates biochemical reactions.

Active Site

The charge-bearing, three-dimensional pocket on an enzyme where the substrate binds and catalysis occurs.

Substrate

The reactant molecule that an enzyme acts upon and converts into product.

Binding Site

Region of the active site whose amino acids hold the substrate in place by weak interactions.

Catalytic Site

Region of the active site whose amino acids perform the chemical transformation of the substrate.

Cofactor

A non-protein helper (metal ion or organic molecule) required by some enzymes for activity.

Activator

A detachable inorganic cofactor—usually a metal ion such as Mg²⁺ or Zn²⁺—that aids enzyme function.

Coenzyme

A detachable organic cofactor, often vitamin-derived (e.g., NAD⁺, FAD, ATP), that carries chemical groups or electrons during catalysis.

Prosthetic Group

A permanently and covalently bound organic cofactor (e.g., haem in cytochromes) essential for enzyme activity.

Apoenzyme

The protein portion of an enzyme that is inactive until its cofactor binds.

Holoenzyme

The complete, catalytically active enzyme complex consisting of apoenzyme plus its required cofactor.

Ribozyme

An RNA molecule with catalytic activity, such as peptidyl transferase in ribosomes.

Metalloenzyme

An enzyme whose activity depends on a tightly bound metal ion within its structure.

Activation Energy

The minimum energy that reactant molecules must acquire to reach the transition state; lowered by enzymes.

Enzyme–Substrate (ES) Complex

Transient association formed when a substrate binds to the enzyme’s active site prior to catalysis.

Lock-and-Key Model

Emil Fischer’s model stating that a rigid, complementary fit exists between enzyme active site and its single specific substrate.

Induced Fit Model

Daniel Koshland’s model in which the active site flexibly molds around the substrate, enabling catalysis and broader specificity.

Turnover Number

The number of substrate molecules converted to product by a single enzyme molecule per second (can be up to 100,000).

Optimum Temperature

The temperature at which an enzyme catalyzes a reaction at its maximum rate (≈37 °C for most human enzymes).

Denaturation (Thermal)

Loss of an enzyme’s tertiary or quaternary structure—and activity—due to excessive heat disrupting hydrogen bonds.

Minimum Temperature

Low temperature at which an inactive enzyme regains activity upon warming; enzymes are not denatured here.

Optimum pH

The narrow pH range at which an enzyme achieves maximal catalytic activity (e.g., pepsin at pH 2, trypsin at pH 8).

Competitive Inhibition

Reversible inhibition where a substrate-like molecule competes for binding at the active site, blocking catalysis (e.g., malonate vs succinate).

Non-Competitive Inhibition

Inhibition in which a molecule binds to an allosteric site, altering enzyme conformation and preventing product formation; may be reversible or irreversible.

Allosteric Site

A specific site on an enzyme, distinct from the active site, where regulatory molecules bind to modulate activity.

Feedback Inhibition

Type of reversible non-competitive inhibition in which the end product of a metabolic pathway inhibits an early enzyme in that pathway.

Irreversible Inhibitor

A molecule that permanently inactivates an enzyme by covalently modifying its active or allosteric site (e.g., cyanide on cytochrome oxidase).

Oxidoreductase

Enzyme class (EC 1) that catalyzes oxidation-reduction reactions by transferring electrons or hydrogen atoms.

Transferase

Enzyme class (EC 2) that transfers specific functional groups—except hydrogen—between molecules (e.g., hexokinase).

Hydrolase

Enzyme class (EC 3) that cleaves bonds by addition of water, performing hydrolysis (e.g., pepsin, amylase).

Lyase

Enzyme class (EC 4) that breaks specific covalent bonds or removes groups without hydrolysis, often forming double bonds (e.g., histidine decarboxylase).

Isomerase

Enzyme class (EC 5) that catalyzes intra-molecular rearrangements, converting one isomer to another (e.g., phosphohexose isomerase).

Ligase (Synthetase)

Enzyme class (EC 6) that joins two molecules with new covalent bonds using energy from ATP (e.g., DNA polymerase).

Protease

General term for enzymes that hydrolyze proteins into peptides or amino acids (e.g., trypsin).

Lipase

Enzyme that hydrolyzes lipids into fatty acids and glycerol (e.g., pancreatic lipase).

Carbohydrase

Enzyme that catalyzes the breakdown of carbohydrates into simpler sugars (e.g., amylase, lactase).

Nuclease

Enzyme that degrades nucleic acids into nucleotides (e.g., DNase, RNase).

Activator Metal Ion

A detachable inorganic cofactor whose binding converts an enzyme’s active site from nonfunctional to functional (e.g., Mg²⁺ for hexokinase).