Enzymes: Structure, Function, Thermodynamics, and Regulation

Comprehensive vocabulary flashcards covering enzyme biochemistry, thermodynamics, kinetic models, active-site dynamics, regulation, and denaturation.

Enzyme

A biological protein that accelerates chemical reactions in living organisms without being consumed or permanently changed in the process.

Catalyst

A substance that speeds up a chemical reaction without being used up or altered, enabling it to be recycled and reused repeatedly.

Substrate

The specific reactant molecule (such as lactose or $H_2O_2$) that binds to an enzyme's active site to undergo a chemical transformation.

Active Site

A specially shaped hollow or cleft within an enzyme's tertiary or quaternary structure where the biochemical reaction takes place and the substrate binds.

Induced Fit

The dynamic conformational change in an enzyme's active site before, during, and after substrate binding to optimize interaction and tightly grasp the reactant.

Enzyme-Substrate Complex

The temporary intermediate molecular complex formed when a substrate molecule occupies and binds to the active site of an enzyme.

Product

The resulting molecule or molecules formed and released from the enzyme's active site following the catalytic synthesis or breakdown of a substrate.

Enthalpy ($\Delta H$)

The total heat content or chemical potential energy stored within the chemical bonds of a system's molecules.

Exothermic Reaction

A reaction in which the reactants have more stored chemical potential energy than the final products, releasing excess energy into the surroundings as heat or light.

Endothermic Reaction

A reaction in which the products contain more stored energy than the initial reactants, requiring continuous absorption of thermal energy from the surroundings.

Entropy ($S$)

A thermodynamic measure of randomness, molecular disorder, or the total number of ways energy can be distributed among particles in a system.

Second Law of Thermodynamics

A physical law stating that the total entropy of the universe is constantly increasing, driving systems spontaneously from states of high order to states of high disorder.

Endergonic Reaction

A non-spontaneous biochemical reaction occurring within cells that requires a net input of energy to proceed.

Exergonic Reaction

A reaction that releases free energy into its environment, functioning as the energetic inverse of an endergonic process.

Denaturation

The disruption of a protein's secondary, tertiary, or quaternary structure by environmental stressors (such as high temperatures or extreme pH), rendering it unfolded and non-functional.

Buffer

A chemical solution that resists changes in pH by neutralizing added acids or bases, maintaining a stable internal environment.

Amphoteric

The property of a molecule or substance that enables it to act chemically as either an acid or a base.

Neutralization

A reaction between an acid and a base that produces a solution with a pH typically close to neutral ($\text{pH } 7$).

Invertase

The enzyme investigated by Maud Menten and Leonard Michaelis that catalyzes the hydrolysis of sucrose into glucose and fructose.

ATP Synthase

A multimeric enzyme featuring a rotating gamma subunit rotor that mechanically deforms adjacent catalytic beta subunits to synthesize ATP from ADP and inorganic phosphate ($\text{P}_i$) via a proton gradient.

Pepsin

A gastric protease consisting of 327 amino acid residues that uses active-site aspartate residues to cleave peptide bonds adjacent to aromatic amino acids like phenylalanine and tyrosine.

Pepsinogen

The inactive zymogen precursor secreted by the stomach prior to activation into the digestive enzyme pepsin.

Cofactor

A small, inorganic non-protein chemical component (such as iron in heme or other metal ions) essential for an enzyme's catalytic activity.

Coenzyme

An organic helper molecule, frequently derived from dietary vitamins such as thiamine (Vitamin B1), required for enzymatic function.

Competitive Inhibition

A regulatory mechanism where an inhibitor molecule structurally mimics the substrate and binds directly to the active site, physically blocking substrate entry.

Non-Competitive (Allosteric) Inhibition

A regulatory mechanism where an inhibitor binds to a secondary allosteric site, altering the 3D conformation of the active site so the substrate cannot properly bind.

Allosteric Site

A specific regulatory binding region on an enzyme separate from the catalytic active site.

Catalase

An antioxidant enzyme present in nearly all eukaryotic cells that decomposes toxic hydrogen peroxide ($2H_2O_2 \rightarrow 2H_2O + O_2$) at an estimated speed of 40 million molecules per second.

Protein Tyrosine Phosphatases

A family of enzymes researched by Canadian biochemist Michel Tremblay that regulate cellular growth, differentiation, and oncogenesis.

Amylase

A digestive enzyme, such as salivary amylase, that breaks down complex starch polysaccharides into simpler sugars near an optimal $\text{pH } 7$.