Enzymes: Kinetics, Mechanisms, and Regulation

Comprehensive vocabulary flashcards covering enzyme terminology, cofactors, transition states, kinetics equations, enzyme classes, catalytic mechanisms, and regulation.

Energy of Activation

The energy necessary for reactants to reach the high-energy transition state in a chemical reaction.

Transition State

A high-energy conformation that bridges the initial reactant state to the final product state and enables product formation.

Apoenzyme

An enzyme without its required cofactor bound, leaving the enzyme catalytically inactive.

Haloenzyme

An active enzyme form consisting of the protein portion bound to its required cofactor.

Cofactor

Small non-protein molecules or metal ions required by many enzymes to perform catalytic reactions.

Active Site

The three-dimensional binding pocket of an enzyme where substrate binding and catalysis take place.

Allosteric Site

A secondary binding site on an enzyme distinct from the catalytic active site, utilized for regulation.

Isozymes

Multiple forms of an enzyme originating from distinct genes that share similar sequences and catalyze the same chemical reaction.

OMP Decarboxylase

An enzyme catalyzing decarboxylation of orotidine monophosphate, boasting a nonenzymatic half-life of $78,000,000\text{ years}$ and a rate enhancement of $1.4 \times 10^{17}$.

Coenzymes

Small organic cofactor molecules, often derived from vitamins, that participate in enzymatic reactions and can be restored after catalysis.

NAD+ and NADP+

Niacin-derived coenzymes where oxidized $NAD^+$ / reduced $NADH$ function in catabolic pathways (like the electron transport chain), and $NADP^+$ / $NADPH$ function in anabolic pathways.

FMN and FAD

Flavin mononucleotide and flavin adenine dinucleotide, riboflavin-derived prosthetic groups covalently or tightly bound to enzymes that participate in oxidoreduction reactions by transferring electron pairs ($FMNH_2$ and $FADH_2$).

Pyridoxal Phosphate

A vitamin $B_6$-derived coenzyme involved in amino acid transamination reactions that undergoes modification and restoration by the enzyme during catalysis.

Adenosine Triphosphate (ATP)

A central biochemical nucleotide synthesized de novo in mammalian cells that provides chemical energy through terminal phosphate cleavage and serves as an allosteric regulator.

Three-Point Attachment Model

The interaction mechanism where a symmetrical substrate binds to an asymmetric active site at three specific positions to enable stereospecific catalysis.

Michaelis-Menten Equation

The standard rate equation $V = \frac{V_{\text{max}} \times [S]}{[S] + K_M}$ describing how reaction velocity ($V$) depends on substrate concentration ($[S]$), maximal velocity ($V_{\text{max}}$), and the Michaelis constant ($K_M$).

Michaelis Constant ($K_M$)

The substrate concentration ($[S]$) at which reaction velocity reaches $\frac{V_{\text{max}}}{2}$, inversely reflecting the binding strength of the enzyme-substrate ($ES$) complex.

Lineweaver-Burk Plot

A double-reciprocal plot of $\frac{1}{V}$ versus $\frac{1}{[S]}$ based on $\frac{1}{V} = \frac{K_M}{V_{\text{max}}} \times \frac{1}{[S]} + \frac{1}{V_{\text{max}}}$, where the y-intercept equals $\frac{1}{V_{\text{max}}}$, the x-intercept equals $-\frac{1}{K_M}$, and the slope equals $\frac{K_M}{V_{\text{max}}}$.

Ethanol Sensitivity

A condition resulting from a single amino acid mutation that inactivates mitochondrial aldehyde dehydrogenase (low $K_M$), causing facial flushing and tachycardia due to acetaldehyde accumulation as only cytoplasmic aldehyde dehydrogenase (high $K_M$) operates.

Feedback Inhibition

A metabolic control pathway in which downstream product accumulation inhibits an upstream enzyme to down-regulate pathway activity.

Allosteric Enzyme

An enzyme regulating a committed or rate-limiting step of a pathway that contains non-active regulatory binding sites sensitive to effector molecules.

Competitive Inhibitor

A reversible inhibitor structurally resembling the substrate that binds directly to the active site, increasing apparent $K_M$ while leaving $V_{\text{max}}$ unchanged.

Uncompetitive Inhibitor

An inhibitor that binds exclusively to the enzyme-substrate ($ES$) complex, lowering both $V_{\text{max}}$ and apparent $K_M$.

Noncompetitive Inhibitor

An inhibitor that binds to a distal site on both free enzyme ($E$) and enzyme-substrate complex ($ES$), reducing $V_{\text{max}}$ while leaving $K_M$ unchanged.

Transition State Inhibitor

An inhibitor that binds irreversibly to the active site with extreme stability by mimicking the high-energy geometry of the reaction transition state.

Suicide Inhibitor

A competitive irreversible inhibitor designed as a substrate mimic that covalently attaches to active site residues during catalysis.

Protein Phosphorylation

The addition or removal of a phosphate group ($PO_4$) to serine, threonine, or tyrosine residues, serving as the primary mechanism for regulating protein function.

Kinase

A transferase enzyme that catalyzes the transfer of a phosphate group from a nucleoside triphosphate (such as $ATP$) to a substrate.

Phosphatase

An enzyme that removes a phosphate group ($PO_4$) moiety from a protein or molecule.

Oxidoreductases

Class 1 enzymes that catalyze oxidation-reduction reactions by transferring electrons between substrates (e.g., Cytochrome P450).

Transferases

Class 2 enzymes that catalyze the transfer of functional chemical groups (such as amino or phosphate groups) from one molecule to another.

Hydrolases

Class 3 enzymes that cleave chemical bonds by adding water ($-OH$ and $-H$) under physiological conditions.

Lyases

Class 4 enzymes that catalyze carbon-carbon or carbon-nitrogen bond cleavage or addition across double bonds without hydrolysis or oxidation.

Synthase vs. Synthetase

Synthases are lyase enzymes forming new bonds without $ATP$, while synthetases are ligase enzymes forming bonds requiring $ATP$ consumption.

Isomerases

Class 5 enzymes that rearrange functional groups, double bonds, or stereocenters within a single molecule.

Mutases

A subclass of isomerases that shift a functional group, such as a phosphate group, from one carbon position to another within the same molecule.

Epimerases and Racemases

Subclasses of isomerases; epimerases invert stereochemistry around one asymmetric carbon in multi-center molecules, while racemases interconvert D- and L- stereoisomers with one chiral center.

Ligases

Class 6 enzymes that join two carbon atoms or molecules together using energy derived from $ATP$.

General Acid and General Base Catalysis

Enzyme mechanisms operating at physiological pH where amino acids (e.g., histidine) donate or accept protons to promote partial charges for catalysis.

Carbonyl Charge Stabilization

A catalytic mechanism wherein a carbonyl group ($C=O$) adjacent to a carbon atom stabilizes an accumulating negative charge in the reaction transition state.