Biochemistry: Enzyme Properties, Kinetics, and Regulation

Comprehensive vocabulary flashcards covering basic characteristics, classification, kinetic models, active site mechanisms, kinetic plots, regulation, and therapeutic/diagnostic applications of enzymes.

Simple Enzymes

Enzymes composed entirely of protein components.

Holoenzymes

Complex or conjugated enzymes consisting of a protein part (apoenzyme) combined with a non-protein part (cofactor).

Apoenzyme

The protein portion of a conjugated enzyme or holoenzyme.

Cofactor

The non-protein portion of a conjugated enzyme required for catalytic activity.

Prosthetic Group

A small inorganic molecule or metal ion tightly bound to an apoenzyme.

Coenzyme

A large organic molecule, frequently derived from vitamins, that is loosely bound to an apoenzyme.

Energy of Activation ($E_a$)

The energy barrier required to initiate a chemical reaction, which enzymes lower to accelerate reaction rates.

Oxidoreductases

Class 1 enzymes that catalyze oxidation and reduction reactions through the transfer of electrons, charges, and hydrogen ($H^+$) ions.

Transferases

Class 2 enzymes that transfer chemical groups from one molecule to another or within a single molecule.

Hydrolases

Class 3 enzymes that cleave substrate molecules by breaking chemical bonds in the presence of water.

Lyases

Class 4 enzymes that split substrate molecules via nonhydrolytic processes without using water, leaving double bonds or adding groups to double bonds.

Isomerases

Class 5 enzymes that interconvert isomeric molecules through intramolecular rearrangements.

Ligases

Class 6 enzymes that join two molecules together, creating chemical bonds at the expense of a nucleoside triphosphate such as ATP.

Enzyme Commission (EC) Number

A numerical system consisting of four decimal-separated numbers assigned to classify enzymes by general class, subclass, sub-subclass, and complete systematic name.

Constitutive Enzymes

Enzymes that are synthesized continuously and present in constant amounts in the cell regardless of environmental conditions.

Inducible Enzymes

Enzymes whose production is genetically controlled and induced only when a specific substrate or cellular need is present.

Active Site

A 3-dimensional cleft, cavity, or region in an enzyme that takes up a small part of total enzyme volume and binds substrates via specific amino acid side chains to participate in catalysis.

Rigid Template Model

The Lock-and-Key Model postulated by Emil Fischer in 1894, stating that the active site contains amino acid residues arranged in a complementary 3D surface pre-formed to fit the substrate.

Induced Fit Model

The active site model postulated by Daniel E. Koshland Jr. in 1958, stating that enzyme active sites undergo conformational changes upon substrate binding to align amino acid side chains.

Proximity and Orientation Effects

A catalytic mechanism wherein reacting groups are brought into close spatial proximity and oriented properly to promote favorable orbital overlap and product formation.

Desolvation Effects

A catalytic mechanism in which water molecules surrounding the substrate dissociate as the substrate is sequestered into a hydrophobic active site pocket.

Acid-Base Catalysis

A catalytic mechanism where amino acid side chains on the enzyme act as proton donors and proton acceptors to facilitate chemical transformations.

Covalent Catalysis

A catalytic mechanism where nucleophilic amino acid side chains on the enzyme attack electrophilic groups on the substrate to form temporary covalent intermediate bonds.

Metal Coordination Effects

A catalytic mechanism where metal ions act as Lewis acids (electrophiles) to accept electron pairs, form coordination bonds, and stabilize negative charges or intermediates.

Competitive Inhibitors

Reversible inhibitors that resemble the substrate and bind directly to the active site; overcome by increasing substrate concentration, resulting in an increased $K_m$ and an unaffected $V_{\max}$.

Non-Competitive Inhibitors

Reversible inhibitors that bind to an allosteric site distinct from the active site on both free enzyme and ES complex; cannot be overcome by increasing substrate concentration, resulting in an unaffected $K_m$ and a reduced $V_{\max}$.

Uncompetitive Inhibitors

Reversible inhibitors that bind exclusively to the Enzyme-Substrate ($ES$) complex, resulting in both a reduced $K_m$ and a reduced $V_{\max}$.

Enzyme Activity

The quantitative measure of enzymatic catalysis expressed as $\mu\text{mol substrate/min}$, corresponding to the conversion of $1\,\mu\text{mol}$ of substrate per minute under specified conditions.

Specific Activity

Enzyme catalytic rate normalized per milligram of total protein, expressed as $\mu\text{mol substrate/min/mg enzyme}$.

Katal (kat)

An SI unit of enzyme activity representing the amount of activity that transforms $1\text{ mole}$ of substrate per second ($\text{mol substrate/sec}$).

Turnover Number ($K_{cat}$)

The number of substrate molecules converted to product per unit time on a single enzyme molecule when the enzyme is fully saturated, expressed as $\mu\text{mol substrate/min/}\mu\text{mol enzyme}$.

Steady State Assumption

The kinetic premise by Briggs and Haldane asserting that the concentration of the $ES$ complex remains constant during initial velocity ($V_0$) measurement because its rate of formation equals its rate of breakdown.

Michaelis Constant ($K_m$)

The substrate concentration at which initial reaction velocity ($V_0$) reaches $\frac{1}{2} V_{\max}$; an inverse measure of enzyme-substrate affinity.

Lineweaver-Burk Plot

A double-reciprocal linear graph plotting $\frac{1}{V_0}$ against $\frac{1}{[S]}$ with a slope of $\frac{K_m}{V_{\max}}$, a y-intercept of $\frac{1}{V_{\max}}$, and an x-intercept of $-\frac{1}{K_m}$.

Ordered Sequential Reactions

A Cleland notation mechanism for multi-substrate reactions requiring a compulsory sequence for substrate binding and subsequent product release.

Random Sequential Reactions

A Cleland notation mechanism for multi-substrate reactions in which substrates bind and products release in no obligatory order.

Ping-Pong Reactions

A Cleland notation mechanism where intermediate products are released before all substrates bind, causing the enzyme to alternate between two distinct interconvertible forms ($E$ and $F$).

Allosteric Effectors

Substances that regulate enzyme activity by binding to allosteric sites physically distinct from the catalytic sites, triggering conformational changes.

K-Class Allosteric Enzymes

Allosteric enzymes in which the effector alters the Michaelis constant ($K_m$) without changing maximum velocity ($V_{\max}$).

V-Class Allosteric Enzymes

Allosteric enzymes in which the effector alters maximum velocity ($V_{\max}$) without changing the Michaelis constant ($K_m$).

Homotropic Interactions

Allosteric interactions in which the binding of one substrate to a protomer affects the binding of the identical substrate to another protomer in an oligomeric enzyme.

Heterotropic Interactions

Allosteric interactions in which the binding of one substrate or ligand affects the binding of a different substrate or ligand to the protomers.

Calmodulin

A eukaryotic calcium-binding control protein that senses intracellular calcium levels and activates target enzymes upon binding calcium.

Zymogens

Inactive proenzyme precursors converted irreversibly into active enzymes by proteolytic cleavage of one or a few specific peptide bonds.

Isoenzymes

Multiple physical forms of the same enzyme that catalyze the same reaction but differ in amino acid composition, chemical properties, and tissue distribution.

Streptokinase

A therapeutic enzyme drug used clinically to dissolve blood clots in acute myocardial infarction and Deep Venous Thrombosis (DVT).

Glucose Oxidase

An enzyme immobilized on commercial biosensor test strips in handheld glucometers to quantify blood glucose concentrations.