Biochemistry: Enzymes

Comprehensive vocabulary flashcards covering the biochemistry of enzymes, including catalytic properties, kinetics, models of binding, factors affecting activity, inhibition types, regulation, isozymes, clinical plasma enzymes, and cofactor classifications.

Enzyme

A group of organic catalysts consisting of globular proteins present inside living cells that can act independently of the cell, characterized by high molecular weight, heat lability, non-dialyzability, and a colloidal nature.

Substrate

The specific organic substance upon which an enzyme acts.

Product

The organic substance formed as a result of the catalytic action of an enzyme.

Co-Enzyme

An organic, low-molecular-weight molecule that is loosely bound to an enzyme, essential for catalytic activity, and functions as an intermediate carrier of electrons, atoms, or functional groups (also considered a second substrate or co-substrate).

Absolute Specificity

A form of enzyme specificity where an enzyme acts only on one single, distinct substrate (for example, lactase acting exclusively on lactose).

Group (Structural) Specificity

A form of enzyme specificity where an enzyme acts on a special type of bond at a specific site attached to particular chemical groups (for example, pepsin cleaving bonds next to the $\text{NH}_2$ of aromatic amino acids, and trypsin cleaving bonds next to the $\text{COOH}$ of basic amino acids).

Relative Specificity

A property where an enzyme acts at different rates on one type of bond found in chemically related compounds (for example, pancreatic lipase hydrolyzing alpha-ester bonds at positions 1 and 3 of triglycerides).

Optical (Stereochemical) Specificity

The property wherein enzymes exhibit absolute specificity for particular optical isomers ($\text{D}$ or $\text{L}$) or specific bond configurations (such as amylase hydrolyzing $\alpha\text{-1,4}$ glycosidic linkages versus cellulase hydrolyzing $\beta\text{-1,4}$ glycosidic linkages).

Transition State

An unstable, high-energy arrangement of atoms in which chemical bonds are actively in the process of being formed or broken.

Activation Energy

The energy barrier required to elevate reactant molecules from their ground state to the transition state.

Active Site

A specific sequence of amino acids on an enzyme containing both a binding site and a catalytic site, providing the machinery required to bind substrate and catalyze the reaction.

Binding Site

The pocket or region within the active site that holds the substrate in the proper position using weak, non-covalent interactions.

Catalytic Site

The specific pocket or cleft within an enzyme's active site where the chemical transformation of substrate to product actually takes place.

Lock and Key Model (Rigid Model)

A model of enzyme-substrate binding proposing that the active site is pre-shaped and rigid, fitting the substrate in a complementary lock-and-key fashion to confer high specificity.

Induced Fit Model (Flexible Model)

A model of substrate binding proposing that the substrate induces a conformational change in the enzyme's active site upon binding to achieve a precise fit.

Enzyme Unit ($\text{U}$)

The amount of enzyme that converts one micromole ($1\,\mu\text{mol}$) of substrate per liter of sample per minute ($\text{U/L}$).

Michaelis Constant ($K_m$)

The substrate concentration that produces half-maximal reaction velocity ($\frac{1}{2} V_{\max}$), which is inversely proportional to enzyme affinity ($K_m \propto \frac{1}{\text{affinity}}$).

Optimum Temperature

The specific temperature at which enzymatic reaction velocity is maximal, typically ranging from $25\,^\circ\text{C}$ to $40\,^\circ\text{C}$ for mammalian enzymes, with an ideal optimum of $37\,^\circ\text{C}$.

Optimum pH

The pH value at which appropriate charges are present on both the enzyme and substrate, allowing enzymatic activity to reach its maximum velocity.

Zymogen (Proenzyme)

An inactive enzyme precursor that requires the proteolytic cleavage and removal of an inhibitory masking peptide to unmask its catalytic site and become active (e.g., pepsinogen converting to pepsin).

Competitive Inhibition

A reversible inhibition where an inhibitor closely resembles the substrate in structure, binds reversibly to the active site to form an $\text{EI}$ complex, increases the apparent $K_m$, leaves $V_{\max}$ unchanged, and can be overcome by increasing substrate concentration.

Reversible Non-Competitive Inhibition

A form of inhibition where an inhibitor binds reversibly to a site distinct from the active site on either the free enzyme or the enzyme-substrate complex, reducing $V_{\max}$ while leaving $K_m$ unaffected.

Irreversible Non-Competitive Inhibition (Enzyme Poison)

An inhibition where an inhibitor binds covalently to an essential group of the enzyme regardless of substrate concentration, permanently destroying catalytic activity (e.g., iodoacetate reacting with the $\text{-SH}$ group).

Allosteric Site

A regulatory site on an enzyme distinct from the active site that binds small organic molecules non-covalently, producing conformational changes that alter the catalytic activity of the active site.

Feedback Inhibition

A regulatory mechanism in which the end product of a multi-step enzymatic pathway binds non-covalently to the allosteric site of the first enzyme in the pathway, reversibly inhibiting its activity.

Inducer

A substance, such as a substrate or a hormone, that stimulates gene expression to increase the cellular synthesis of a specific enzyme.

Repressor

A substance, such as the reaction product or a hormone, that inhibits gene expression to decrease or halt the synthesis of a specific enzyme.

Constitutive Enzymes

Enzymes that are continuously synthesized and maintained at a constant concentration in the cell regardless of environmental or physiological conditions.

Rate Limiting Enzyme

The regulatory enzyme that possesses the lowest $V_{\max}$ in a biochemical pathway, typically occurring early to dictate the overall rate of the pathway.

Committed Step Enzyme

The first irreversible enzyme that is entirely unique to a specific metabolic pathway.

Isoenzymes (Isozymes)

Oligomeric enzymes that catalyze the identical biochemical reaction but possess different quaternary combinations of subunits, distinct amino acid sequences, different tissue distributions, differing kinetic properties ($K_m$ and $V_{\max}$), and different electrophoretic mobilities.

Functional Plasma Enzymes

Enzymes synthesized by the liver and normally present in high concentrations in blood plasma, where they perform specific physiological roles on substrates circulating in the bloodstream (e.g., thrombin, plasmin, lipoprotein lipase).

Non-Functional Plasma Enzymes

Enzymes that have no physiological role in blood plasma and are normally present only at low levels due to routine cell turnover, whose levels rise markedly following cellular damage or death.

Apoenzyme

The protein portion of a conjugated enzyme that is catalytically inactive without its non-protein cofactor.

Holoenzyme

The complete, catalytically active conjugated enzyme complex consisting of the apoenzyme joined to its cofactor.

Prosthetic Group

A non-protein cofactor that is firmly and stably attached to an enzyme through covalent or strong non-covalent bonds.

Ribozyme

A catalytic segment of ribonucleic acid (RNA) that displays enzymatic activity in the absence of proteins, requiring divalent cations like $\text{Ca}^{2+}$ or $\text{Mg}^{2+}$ as cofactors.

Metal-Activated Enzymes

Enzymes that have an absolute requirement for a metal ion to enhance their catalytic activity, where the metal is weakly bound and easily removed during purification.

Metalloenzymes

Enzymes containing a tightly bound metal ion integrated into the protein structure during synthesis, the removal of which causes complete denaturation of the enzyme (e.g., carbonic anhydrase requiring zinc).