Topic 5: Enzyme Function

Comprehensive vocabulary flashcards covering metabolic pathways, thermodynamics, free energy, ATP coupling, and enzyme mechanics and regulation.

Metabolism

The sum of all the chemical reactions that occur within a living cell, tissue, or organism.

Metabolic pathway

A series of sequential steps beginning with a starting molecule (a metabolite) where each step is catalyzed by a specific enzyme to yield a final product.

Catabolic pathway

A metabolic pathway that releases energy by breaking down complex molecules into simpler compounds, such as cellular respiration breaking down sugars into $CO_2$ and water.

Anabolic pathway

A metabolic pathway that consumes energy to build complex molecules from simpler compounds, such as the synthesis of amino acids.

Kinetic energy

The form of energy associated with the relative motion of objects or moving things.

Thermal energy

A type of kinetic energy associated with the random movement of atoms or molecules that generates heat.

Potential energy

Energy that is not kinetic, dependent upon an object's location or structural arrangement of electrons within chemical bonds.

Chemical energy

A form of potential energy available in molecules for release during a chemical reaction.

First Law of Thermodynamics

The principle stating that energy cannot be created or destroyed, only converted or transformed (also referred to as the Principle of Conservation of Energy).

Second Law of Thermodynamics

The physical principle stating that every energy transfer or transformation increases the entropy (disorder) of the universe.

Free energy ($G$)

The portion of a system's energy that is available to do work when temperature and pressure are uniform throughout.

Change in free energy ($\Delta G$)

The difference between the final free energy state of products and the initial free energy state of reactants, calculated as $\Delta G = G_{\text{final}} - G_{\text{initial}}$.

Exergonic reaction

A spontaneous chemical reaction where the reactants have more free energy than the products, releasing energy to the surroundings with a $\Delta G < 0$.

Endergonic reaction

A non-spontaneous chemical reaction where the reactants have less free energy than the products, requiring an input of energy with a $\Delta G > 0$.

Energy coupling

The cellular strategy of using the energy released from an exergonic process to drive an endergonic reaction, typically mediated by ATP.

Phosphorylated intermediate

A molecule that has received a phosphate group transferred covalently from ATP, making it less stable and possessing higher free energy.

Activation energy ($E_A$)

The initial amount of energy that reactant molecules must absorb to contort their bonds into an unstable transition state where bonds can break.

Catalyst

A chemical agent that selectively accelerates the rate of a reaction without being consumed by the process.

Enzyme

A macromolecule (typically a protein) acting as a biological catalyst that speeds up chemical reactions by lowering the activation energy ($E_A$) without altering the reaction's $\Delta G$.

Substrate

The specific reactant molecule upon which an enzyme binds and acts during a catalytic reaction.

Active site

The specific 3D pocket or groove on an enzyme formed by specific amino acid R-groups where the substrate binds and catalysis takes place.

Induced-fit model

The concept that the active site and substrate are not rigid matches initially, but rather substrate entry induces a conformational change in the enzyme that enfolds the substrate snugly.

Cofactor

A nonprotein helper required for catalytic activity consisting of an inorganic metal atom or ion.

Coenzyme

An organic nonprotein helper molecule, such as a vitamin, required by an enzyme to facilitate catalysis.

Enzyme saturation

The state reached when all available active sites of an enzyme population are bound to substrate molecules, causing the rate of reaction to plateau.

Denaturation

The loss of a protein's native three-dimensional folded structure caused by extreme changes in environmental conditions, such as high temperature or pH shifts, leading to loss of biological function.

Competitive inhibitor

A regulatory molecule that mimics the substrate's shape and binds directly to the active site, competing with the substrate and slowing down the reaction rate.

Noncompetitive inhibitor

An inhibitor molecule that binds to an enzyme at a location away from the active site, altering the enzyme's shape so that the active site functions less effectively or not at all.

Allosteric activation

The binding of a regulatory molecule to a distinct regulatory site on an enzyme complex that stabilizes its active conformation.

Allosteric inactivation

The binding of an inhibitory regulatory molecule to a regulatory site on an enzyme complex that stabilizes its inactive conformation.

Cooperativity

A type of allosteric regulation in multisubunit enzymes where substrate binding to one active site locks all remaining subunits in their active conformations.

Feedback inhibition

A metabolic control mechanism where the final product of a pathway allosterically binds to and inhibits an early enzyme in the sequence to prevent unnecessary synthesis.