Enzymes Overview and Classification

Study Notes

Enzymes

Enzymes are biological catalysts.
Most enzymes are proteins, except a few catalytic RNA molecules (ribozymes).
They speed up reactions by lowering the activation energy.
They participate in the reaction but return to their original state after the reaction is completed.
They are specific to particular reactions and substrates.

Intended Learning Outcomes

Describe enzyme classification, nomenclature, and structure.
Identify coenzymes, isoenzymes, and cofactors.
Understand enzyme mechanism of action and factors affecting reaction rate.
Identify enzyme inhibitors.

Enzyme Specificity

Absolute Specificity: Enzymes catalyze only one specific reaction on one specific molecule (e.g., uricase, urease, catalase).
Relative Specificity: One enzyme acts on a group of compounds with the same type of bonds (e.g., lipase acts on ester bonds of triacylglycerols and phospholipids).

Enzyme Classification

Oxidoreductases: Catalyze oxidation-reduction reactions (e.g., alcohol dehydrogenase).
Transferases: Catalyze the transfer of functional groups (other than hydrogen) between substrates (e.g., Choline acyltransferase).
Hydrolases: Catalyze hydrolysis of a bond by adding water (e.g., peptidases and proteinases like trypsin and chymotrypsin).
Lyases: Catalyze group elimination to form double bonds (e.g., fumarase).
Isomerases: Catalyze the interconversion of isomers by rearranging atomic groupings without altering molecular weight or the number of atoms (e.g., aldoses and ketoses).
Ligases: Catalyze bond formation coupled with ATP hydrolysis (e.g., acetyl-CoA carboxylase).

Enzyme Nomenclature

Enzymes are classified based on the chemical type and mechanism of the reaction they catalyze.
Each enzyme has a code number (EC) with four digits, indicating the class, subclass, sub-subclass, and specific enzyme.
Example: EC 2.7.1.1 (Class 2 - transferase; Subclass 7 - transfer phosphate; Subsubclass 1 - phosphate acceptor is alcohol; Final digit - enzyme hexokinase).

Cofactors and Coenzymes

Some enzymes require small molecule cofactors for their action.
Cofactors:
- Metal ions (Cu²⁺, Fe³⁺, Zn²⁺).
- Organic molecules (coenzymes).
Coenzymes:
- Cosubstrates (transiently associated).
- Prosthetic groups (permanently associated).

Types of Coenzymes

Coenzymes are categorized based on the group transferred.
Type 1: Coenzymes for transfer groups other than hydrogen.
- Pyridoxal phosphate (B6): amino group transfer.
- Tetrahydrofolate: one carbon group transfer.
- Thiamin pyrophosphate (B1): aldehyde transfer.
- Biocytin (from biotin): carboxylation reactions.
Type 2: Coenzymes for transferring hydrogen.
- Nicotinamide coenzymes (NAD⁺, NADP⁺) from niacin for oxidation-reduction reactions.
- Flavin coenzymes (FMN, FAD) from riboflavin (B2) for oxidation-reduction reactions.
- Coenzyme Q.

Apoenzyme and Holoenzyme

Holoenzyme is the complete, active enzyme comprising an apoenzyme (protein portion) and a cofactor (non-protein portion).

Active Site

The catalytic site (active site) is a specific region within the enzyme where substrate binding and catalysis occur.
The active site has a specific shape and chemical properties.
Two models describe active site interaction: lock-and-key (rigid template) and induced fit (Koshland).

Isoenzymes

Isoenzymes are physically distinct forms of the same enzyme, present in different cell types/tissues.
They have the same catalytic activity but differ in electrophoretic mobility.
May differ in their substrate affinity.
Example: Lactate dehydrogenase (LDH) exists as five isoenzymes (LDH1-5).

Factors Affecting Enzyme Activity

Temperature: Optimal temperature increases reaction velocity; above the optimal temperature, the enzyme denatures.
pH: Moderate changes affecting the ionic state of the enzyme/substrate; optimal pH ranges from 5-9 except some enzymes like pepsin.
Enzyme concentration: Reaction velocity is directly proportional to enzyme concentration.
Substrate concentration: Initial velocity increases with substrate concentration, reaching a maximum velocity when the enzyme is saturated with substrate (Vmax).
Inhibitors: Substances that reduce enzyme activity; irreversible or reversible (competitive, uncompetitive, noncompetitive).

Michaelis-Menten Equation

Describes relationship between initial velocity (V_i), substrate concentration ([S]), and constants: V_max, K_m.
K_m: substrate concentration for half-maximal velocity (½ V_max).

Lineweaver-Burk Plot

A double reciprocal plot derived from Michaelis-Menten equation.
Used to estimate V_max and K_m from the plot's intercept/slope.

Enzyme Inhibitors

Inhibitors reduce enzyme activity.
- Irreversible inhibitors: Bind covalently to enzymes or destroy crucial functional groups.
- Reversible inhibitors: Bind non-covalently and can be removed.
  - Competitive: Compete with the substrate for the active site.
  - Uncompetitive: Bind to the enzyme-substrate complex (ES).
  - Noncompetitive: Bind to a site other than the active site.

Enzyme Regulation

Enzyme Availability: The rate of its synthesis; rate of its degradation.
Enzyme Activity:
- Allosteric effectors: Molecules that bind to regulatory sites (allosteric sites) away from the active site, altering enzyme activity.
- Covalent Modification: Attachment or removal of chemical groups (e.g., phosphorylation/dephosphorylation) to the enzyme.
- Limited Proteolysis: Activation of inactive enzymes (proenzymes) through controlled proteolytic cleavage.

Enzymes Overview and Classification

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Questions and Answers

Enzymes are biological catalysts that accelerate chemical reactions.

Most enzymes are composed of lipids.

What is the name for the region of an enzyme where catalysis takes place?

Which of the following is NOT a factor affecting enzyme activity?

What is the term for a molecule that binds to an enzyme and inhibits its activity?

Which type of inhibitor binds to the active site of an enzyme and competes with the substrate?

Uncompetitive inhibitors bind only to the enzyme-substrate complex, not to the free enzyme.

Non-competitive inhibitors bind at a site other than the active site of the enzyme and have no structural resemblance to the substrate.

What is the name given to the inactive precursor form of an enzyme?

Enzymes are affected by temperature, pH, and substrate concentration. Therefore, they are not specific for their reactions.

Which of the following is NOT a type of coenzyme?

The Michaelis-Menten equation describes the relationship between the initial velocity of an enzyme-catalyzed reaction and the substrate concentration.

The (K_m) value is the substrate concentration that produces half the maximum velocity of an enzyme-catalyzed reaction.

What is the name of the plot that is used to determine the (K_m) and (V_{max}) values of an enzyme reaction?

Allosteric enzymes are regulated by the binding of effectors to a site other than the active site.

Study Notes

Enzymes

Intended Learning Outcomes

Enzyme Specificity

Enzyme Classification

Enzyme Nomenclature

Cofactors and Coenzymes

Types of Coenzymes

Apoenzyme and Holoenzyme

Active Site

Isoenzymes

Factors Affecting Enzyme Activity

Michaelis-Menten Equation

Lineweaver-Burk Plot

Enzyme Inhibitors

Enzyme Regulation

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