Enzymes: Characteristics, Classification, and Active Sites

Vocabulary flashcards covering enzyme characteristics, classification, active site dynamics, cofactors, catalytic mechanisms, and metabolic regulation mechanisms based on lecture slides.

Ribozymes

RNA-based enzymes, such as ribosomal RNA in ribosomes, which catalyze biochemical reactions despite not being proteins.

Oxidoreductases

A class of enzymes that catalyze oxidation-reduction reactions involving the transfer of electrons between molecules.

Transferases

A class of enzymes that catalyze the transfer of functional groups (such as phosphate, amino, or methyl groups) from one substrate to another.

Hydrolases

A class of enzymes that catalyze the cleavage of chemical bonds through the addition of water (hydrolysis).

Lyases

A class of enzymes that catalyze the cleavage of chemical bonds without using hydrolysis or oxidation.

Isomerases

A class of enzymes that catalyze the rearrangement of atoms within a molecule to convert it into its isomer.

Ligases

A class of enzymes that catalyze the joining of two molecules coupled with the hydrolysis of ATP.

Binding Residues

Amino acid residues in the active site that interact with and position the substrate primarily through noncovalent forces.

Catalytic Residues

Amino acid residues in the active site that directly participate in the chemical reaction by acting as proton donors, acceptors, nucleophiles, or electrophiles.

Lock and Key Model

An enzyme specificity model proposed by Fischer in 1890 stating that the active site has a rigid, pre-formed structure complementary to the substrate.

Induced Fit Model

An enzyme specificity model proposed by Koshland stating that the active site is flexible and alters its conformation upon substrate binding to optimize interaction.

Holoenzyme

A catalytically active enzyme system formed by the combination of an apoenzyme with its required cofactor or coenzyme.

Apoenzyme

The inactive protein component of an enzyme that requires a cofactor or coenzyme to become catalytically active.

Prosthetic Group

A cofactor tightly bound to an apoenzyme via covalent or noncovalent bonds.

Catalysis by Proximity

A catalytic mechanism where the rate of reaction is enhanced by bringing substrates into close spatial proximity and optimal orientation within the active site.

Catalysis by Bond Strain

A catalytic mechanism in which substrate binding distorts target bonds, weakening them and mimicking the transition state to facilitate cleavage.

Covalent Catalysis

A catalytic mechanism where the substrate forms a transient covalent bond with an active-site residue or coenzyme during the reaction pathway.

Isozymes

Distinct structural forms of an enzyme, encoded by different genes, that catalyze the same biochemical reaction.

$$K_m$$

The substrate concentration at which the reaction velocity is equal to $\frac{1}{2}$ of $V_{\max}$, indicating the enzyme's affinity for its substrate.

Rate-Limiting Enzyme

The enzyme catalyzing the slowest, bottleneck step in a metabolic pathway that determines the overall rate of product formation.

First Committed Step

The initial irreversible enzymatic reaction unique to a specific metabolic pathway that commits the substrate to that pathway.

Ubiquitin-Proteasome Pathway

An ATP-dependent pathway responsible for the selective tagging of non-functional or damaged proteins with ubiquitin molecules for degradation by the proteasome.

Allosteric Regulation

The regulation of enzyme activity through the non-covalent binding of effector molecules at a site other than the active site.

Feedback Inhibition

A regulatory process in which the final product of a biosynthetic pathway acts as an allosteric inhibitor on an early enzyme in the same pathway.

K-Series Allosteric Enzymes

Allosteric enzymes in which effector binding alters the enzyme's affinity for substrate ($K_m$) while keeping maximum velocity ($V_{\max}$) constant.

V-Series Allosteric Enzymes

Allosteric enzymes in which effector binding alters catalytic efficiency ($V_{\max}$) while keeping substrate affinity ($K_m$) constant.

Primary Messenger

An extracellular signal molecule, such as a hormone or nerve impulse, that initiates cellular responses by stimulating the generation of intracellular signals.

Secondary Messenger

An intracellular molecule, such as $Ca^{2+}$ or cAMP, produced or released in response to a primary messenger to alter enzyme activity inside the cell.

Partial Proteolysis

An irreversible covalent modification involving the cleavage of specific peptide bonds to convert an inactive zymogen into an active enzyme.

Zymogens

Inactive protein precursors of enzymes that require specific proteolytic cleavage to become catalytically active.

Phosphorylation

A reversible covalent modification process involving the enzymatic addition of a phosphate group to specific amino acid residues on a protein.

Protein Kinases

Enzymes that catalyze the transfer of a terminal phosphoryl group from ATP to specific amino acid residues of target proteins.

Protein Phosphatases

Enzymes that catalyze the hydrolytic removal of phosphate groups from phosphorylated proteins, returning them to their dephosphorylated state.