Enzyme Structure, Classification, and Kinetics in Biochemistry

Enzymes: Structure, Function, and Classification

Introduction to Enzymes

Enzymes are biological catalysts that accelerate chemical reactions in living organisms. They are essential for metabolic processes and are highly specific for their substrates. Enzymes are typically proteins, though some RNA molecules also exhibit catalytic activity (ribozymes).

• Definition: Enzymes are macromolecules that catalyze biochemical reactions by lowering the activation energy required.

• Substrate: The molecule upon which an enzyme acts.

• Active Site: The region of the enzyme where substrate binding and catalysis occur.

• Cofactors and Coenzymes: Non-protein molecules (e.g., NAD, FAD, metal ions) required for enzyme activity.

• Holoenzyme: The complete, active enzyme with its cofactor.

• Apoenzyme: The protein part of an enzyme, without its cofactor.

Enzyme Structure

Enzymes can be classified based on their structure as either monomeric (single subunit) or multimeric (multiple subunits). The arrangement of subunits can affect enzyme function and regulation.

• Monomeric Enzymes: Consist of a single polypeptide chain.

• Multimeric Enzymes: Composed of two or more polypeptide chains (subunits).

• Active Site: Typically a pocket or groove on the enzyme surface where substrate binding occurs.

• Allosteric Sites: Sites other than the active site that can regulate enzyme activity.

Enzyme Kinetics and Graphical Behavior

Enzyme activity can be studied by measuring the rate of substrate conversion to product. The relationship between substrate concentration and reaction rate is often depicted graphically.

• Michaelis-Menten Kinetics: Most enzymes display a hyperbolic relationship between reaction rate and substrate concentration.

• Graphical Representation: The rate of enzyme activity increases with substrate concentration until a maximum velocity (Vmax) is reached.

Equation:

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

• Vmax: Maximum reaction velocity.

• Km: Michaelis constant; substrate concentration at half-maximal velocity.

Enzyme Specificity and Types of Reactions

Enzymes are highly specific for their substrates and the reactions they catalyze. Specificity arises from the precise interaction between the enzyme's active site and the substrate.

• Substrate Specificity: Enzymes bind specific substrates due to complementary shape and chemical properties.

• Reaction Specificity: Enzymes catalyze specific types of chemical reactions.

• Types of Specificity:

  • Transfer of molecules (e.g., acid-base catalysis)

  • Optimum temperature and pH for activity

  • Interaction with specific amino acid residues

Enzyme Classification

The Enzyme Commission (EC) classifies enzymes into six major classes based on the type of reaction they catalyze.

Class	Type of Reaction	Example
Oxidoreductases	Oxidation-reduction reactions	Dehydrogenases
Transferases	Transfer of functional groups	Kinases
Hydrolases	Hydrolysis reactions	Proteases
Lyases	Addition/removal of groups to form double bonds	Decarboxylases
Isomerases	Isomerization reactions	Racemases
Ligases	Joining of two molecules with ATP hydrolysis	DNA ligase

Enzyme Activity and Selectivity

Enzymes exhibit selective ability, meaning they catalyze specific reactions for particular substrates. This selectivity is due to the precise fit between the enzyme and substrate, often described by the "lock and key" or "induced fit" models.

• Lock and Key Model: The substrate fits exactly into the active site of the enzyme.

• Induced Fit Model: The enzyme changes shape upon substrate binding to achieve optimal fit.

Enzyme Inhibition

Enzyme activity can be regulated by inhibitors, which decrease or prevent enzyme function. Inhibitors can be reversible or irreversible, and are classified based on their interaction with the enzyme.

• Competitive Inhibitors: Bind to the active site, competing with the substrate.

• Non-competitive Inhibitors: Bind to a site other than the active site, altering enzyme activity.

• Allosteric Inhibitors: Bind to allosteric sites, causing conformational changes that affect activity.

Example: The inhibition of succinate dehydrogenase by malonate is a classic example of competitive inhibition.

Summary Table: Types of Enzyme Inhibition

Type	Binding Site	Effect on Vmax	Effect on Km
Competitive	Active site	No change	Increases
Non-competitive	Allosteric site	Decreases	No change
Uncompetitive	Enzyme-substrate complex	Decreases	Decreases

Additional info: The notes expand on the basic principles of enzyme structure, function, and inhibition, providing context for their role in metabolism and regulation. The classification and kinetic models are foundational for understanding enzyme behavior in biochemical pathways.