Enzymes: Classification, Mechanisms, and Catalysis

Enzymes and Enzyme Mechanisms

Learning Objectives

Enzymes are biological catalysts that accelerate chemical reactions in living organisms. This section covers their classification, mechanisms of action, and the principles underlying enzyme catalysis.

• Describe the six major enzyme classifications: Oxidoreductases, transferases, hydrolases, lyases, isomerases, and ligases, each defined by the type of reaction they catalyze.

• Define and describe the roles of enzyme-related terms: zymogen/proenzyme, coenzyme, co-factors, prosthetic group, apoenzyme, holoenzyme, active site, transition state, and induced fit.

• Explain how enzymes catalyze reactions: Focus on activation energy, transition state stabilization, and the role of the enzyme-substrate complex.

• Explain the induced fit and lock-and-key models: Describe how enzymes recognize and bind substrates.

• Apply the Michaelis-Menten equation: Use it to calculate enzyme kinetics and understand enzyme efficiency.

• Contrast graphical representations of enzyme kinetics: Lineweaver-Burk plots and their use in analyzing enzyme inhibition.

• Compare and contrast different types of inhibitors: Competitive, noncompetitive, uncompetitive, and mixed inhibitors.

Enzyme Classification

Types of Enzymes

Enzymes are classified by the reactions they catalyze. The six major classes are:

Class	Reaction Catalyzed
Oxidoreductases	Transfer of electrons (hydride ions or H atoms)
Transferases	Group transfer reactions
Hydrolases	Hydrolysis reactions (transfer of functional groups to water)
Lyases	Cleavage of C–C, C–O, C–N, or other bonds by elimination, leaving double bonds or rings, or addition of groups to double bonds
Isomerases	Transfer of groups within molecules to yield isomeric forms
Ligases	Formation of C–C, C–S, C–O, and C–N bonds by condensation reactions coupled to cleavage of ATP or similar cofactors

Holoenzyme: The complete, catalytically active enzyme with its cofactor(s). Apoenzyme: The protein component of an enzyme, without its cofactor.

Enzyme Structure and Function

Cofactors and Coenzymes

Many enzymes require non-protein components for activity:

• Cofactor: An inorganic ion (e.g., Mg2+, Fe2+) or a complex organic molecule (coenzyme) required for enzyme activity.

• Coenzyme: A complex organic or metalloorganic molecule that acts as a transient carrier of specific functional groups.

• Prosthetic group: A cofactor or coenzyme that is tightly or covalently bound to the enzyme.

How Enzymes Work: General Mechanisms

Chemical Reactions

A simple enzymatic reaction can be written as:

• $S + E \rightarrow ES \rightarrow EP \rightarrow E + P$

• Where S = substrate, E = enzyme, P = product, ES = enzyme-substrate complex, and EP = enzyme-product complex.

Enzymes and Reaction Equilibrium

• Enzymes accelerate the attainment of equilibrium but do not shift the equilibrium position.

• They increase reaction rates by lowering the activation energy.

Energy Changes (Thermodynamics)

• Reactions proceed via a transition state, which has higher free energy than reactants or products.

• The difference in free energy between the transition state and the substrate or product ($\Delta G^{\ddagger}$) is the activation energy.

• $\Delta G^{\ddagger} = G_{TS} - G_{S}$

• Enzymes lower $\Delta G^{\ddagger}$, increasing reaction rates.

• Standard free energy change ($\Delta G^\circ$) determines reaction spontaneity.

• $\Delta G^\circ = -RT \ln K_{eq}$

Enzyme-Substrate Complex (ES)

• The formation of ES is often the rate-controlling step.

• Enzymes bind substrates at the active site via multiple weak interactions.

• Increasing substrate concentration beyond saturation does not increase reaction rate (enzyme is saturated).

Active Site and Models of Enzyme Action

Active Site

• Region that binds the substrate and contains catalytic functional groups.

• Active site is typically a 3D cleft or pocket formed by amino acid residues.

• Active sites are highly specific for their substrates.

Models of Enzyme-Substrate Interaction

• Lock and Key Model (Emil Fischer): Enzyme and substrate have complementary shapes, fitting together like a key in a lock.

• Induced Fit Model (Daniel Koshland): Enzyme changes conformation upon substrate binding, wrapping around the substrate to stabilize the transition state.

Role of Binding Energy in Catalysis

Binding Energy and Transition State Stabilization

• Multiple weak, non-covalent interactions between enzyme and substrate stabilize the transition state.

• Binding energy ($\Delta G_b$) is used to lower activation energy and increase reaction rate.

• Enzymes are highly specific due to the precise arrangement of binding sites.

Summary Table: Enzyme Terms and Definitions

Term	Definition
Zymogen/Proenzyme	Inactive precursor of an enzyme, activated by cleavage
Coenzyme	Organic molecule required for enzyme activity
Cofactor	Non-protein component required for enzyme activity
Prosthetic group	Tightly bound cofactor or coenzyme
Apoenzyme	Protein part of an enzyme, without cofactor
Holoenzyme	Complete, active enzyme with cofactor
Active site	Region of enzyme where substrate binds and reaction occurs
Transition state	High-energy state during reaction, stabilized by enzyme
Induced fit	Conformational change in enzyme upon substrate binding

Additional info:

• Enzyme kinetics, including Michaelis-Menten and Lineweaver-Burk plots, are essential for quantifying enzyme activity and inhibition.

• Enzyme inhibition can be competitive, noncompetitive, uncompetitive, or mixed, each affecting enzyme kinetics differently.