Enzyme Structure, Function, and Regulation

Enzyme Structure and Function

Introduction to Enzymes

Enzymes are biological catalysts that speed up chemical reactions in living organisms by lowering the activation energy required for the reaction. They are typically proteins composed of one or more polypeptide chains and have a specific three-dimensional structure essential for their function.

• Active Site: The region on the enzyme where the substrate binds and the reaction occurs.

• Substrate: The molecule upon which an enzyme acts.

• Enzyme-Substrate Complex: The temporary complex formed when an enzyme binds its substrate.

• Denaturation: Loss of enzyme structure (and function) due to extreme temperature, pH, or salinity.

Example: Catalase is an enzyme that breaks down hydrogen peroxide into water and oxygen.

Factors Affecting Enzyme Activity

Enzyme Concentration

Increasing enzyme concentration generally increases the rate of reaction, provided that substrate is not limiting.

• At constant substrate concentration, increasing enzyme concentration increases reaction rate linearly.

• At constant enzyme concentration, increasing substrate concentration increases reaction rate until a maximum (Vmax) is reached.

Equation:

$\text{Rate} = k[\text{Enzyme}]$ (when substrate is in excess)

Substrate Concentration

As substrate concentration increases, the rate of reaction increases until the enzyme becomes saturated and the rate levels off at Vmax.

• At low substrate concentrations, the rate increases rapidly with increasing substrate.

• At high substrate concentrations, the rate approaches a maximum (Vmax).

Michaelis-Menten Equation:

$v = \frac{V_{max}[S]}{K_m + [S]}$

where $v$ is the reaction rate, $[S]$ is substrate concentration, $V_{max}$ is the maximum rate, and $K_m$ is the Michaelis constant.

Temperature and pH

Each enzyme has an optimal temperature and pH at which it functions most efficiently.

• Increasing temperature generally increases reaction rate up to an optimum, after which the enzyme denatures and activity decreases.

• Each enzyme has a specific pH optimum; deviations can reduce activity or denature the enzyme.

Example: Human enzymes typically function best at body temperature (~37°C) and near-neutral pH.

Denaturation

Extreme conditions (high temperature, extreme pH, high salinity) can disrupt the three-dimensional structure of enzymes, leading to loss of function.

• Normal protein: Maintains functional shape.

• Denatured protein: Loses shape and function.

Enzyme Inhibition

Competitive Inhibition

Competitive inhibitors bind to the active site of the enzyme, competing directly with the substrate. This prevents substrate binding and decreases enzyme activity.

• Can be overcome by increasing substrate concentration.

• Vmax remains the same; Km increases.

Non-Competitive Inhibition

Non-competitive inhibitors bind to a site other than the active site (allosteric site), causing a conformational change in the enzyme that reduces its activity.

• Cannot be overcome by increasing substrate concentration.

• Vmax decreases; Km remains unchanged.

• Many poisons act as non-competitive inhibitors.

Allosteric Enzymes and Regulation

Allosteric Enzymes

Allosteric enzymes are usually composed of two or more polypeptide subunits and can alternate between active and inactive forms. They have regulatory sites (allosteric sites) distinct from the active site.

• Binding of allosteric activators stabilizes the active form.

• Binding of allosteric inhibitors stabilizes the inactive form.

Allosteric Activation and Inhibition

Type	Effect	Example
Allosteric Activation	Activator binds to allosteric site, enzyme becomes active	AMP activating phosphofructokinase
Allosteric Inhibition	Inhibitor binds to allosteric site, enzyme becomes inactive	ATP inhibiting phosphofructokinase

Cofactors and Coenzymes

Role of Cofactors

Some enzymes require non-protein molecules called cofactors to function properly. Cofactors can be inorganic ions or organic molecules (coenzymes).

• Inorganic cofactors: Metal ions such as Fe2+, Mg2+, Cu2+, Zn2+.

• Organic cofactors (coenzymes): NAD+, NADP+, vitamins.

• Example: Catalase requires iron as a cofactor.

Enzymes in Metabolic Pathways

Sequential Reactions

Enzymes often work together in metabolic pathways, where the product of one reaction becomes the substrate for the next.

• Each step is catalyzed by a specific enzyme.

• Intermediates are formed between the initial substrate and final product.

Example Pathway:

$A \xrightarrow{E_1} B \xrightarrow{E_2} C \xrightarrow{E_3} D$

Feedback Inhibition

Metabolic pathways are often regulated by feedback inhibition, where the end product inhibits an earlier enzyme in the pathway to prevent overproduction.

• Ensures efficient use of resources.

• Common in biosynthetic pathways.

Enzyme Activity and Disease

Genetic Mutations and Enzyme Function

Mutations in genes encoding enzymes can lead to altered enzyme function and disease.

• Example: Albinism is caused by a mutation in the tyrosinase enzyme, affecting melanin production.

• Enzyme may function normally at certain temperatures but lose function at others (temperature-sensitive mutations).

Summary Table: Types of Enzyme Inhibition

Type	Binding Site	Effect on Vmax	Effect on Km	Can be Overcome by Substrate?
Competitive	Active site	No change	Increases	Yes
Non-competitive	Allosteric site	Decreases	No change	No