Enzymology

3.

Principles of Enzyme Catalysis

3.1.

Chemical Reaction Energetics

3.1.1.

Gibbs Free Energy

3.1.1.1.

Definition and Significance

3.1.1.2.

Exergonic Reactions

3.1.1.3.

Endergonic Reactions

3.1.2.

Reaction Equilibria

3.1.2.1.

Equilibrium Constant

3.1.2.2.

Relationship to Free Energy

3.1.2.3.

Effect of Enzymes on Equilibrium

3.2.

Transition State Theory

3.2.1.

The Transition State

3.2.1.1.

Characteristics of the Transition State

3.2.1.2.

Energy Profile of Reactions

3.2.2.

Activation Energy

3.2.2.1.

Energy Barrier to Reaction

3.2.2.2.

Temperature Dependence

3.2.3.

How Enzymes Lower Activation Energy

3.2.3.1.

Stabilization of Transition State

3.2.3.2.

Alternative Reaction Pathways

3.2.3.3.

Binding Energy Utilization

3.3.

Models of Enzyme-Substrate Interaction

3.3.1.

The Lock-and-Key Model

3.3.1.1.

Rigid Complementarity

3.3.1.2.

Historical Significance

3.3.1.3.

3.3.2.

The Induced-Fit Model

3.3.2.1.

Conformational Changes upon Binding

3.3.2.2.

Dynamic Nature of Binding

3.3.3.

Modern Perspectives on Binding

3.3.3.1.

Conformational Selection

3.3.3.2.

Population Shift Model

3.4.

Catalytic Mechanisms and Strategies

3.4.1.

Proximity and Orientation Effects

3.4.1.1.

Bringing Substrates Together

3.4.1.2.

Correct Alignment for Reaction

3.4.1.3.

Entropic Advantages

3.4.2.

Acid-Base Catalysis

3.4.2.1.

General Acid Catalysis

3.4.2.2.

General Base Catalysis

3.4.2.3.

Specific Acid-Base Catalysis

3.4.2.4.

Role of Amino Acid Side Chains

3.4.3.

Covalent Catalysis

3.4.3.1.

Formation of Enzyme-Substrate Intermediates

3.4.3.2.

Nucleophilic Catalysis

3.4.3.3.

Electrophilic Catalysis

3.4.3.4.

Examples of Covalent Catalysis

3.4.4.

Metal Ion Catalysis

3.4.4.1.

Charge Stabilization

3.4.4.2.

Redox Reactions

3.4.4.3.

Lewis Acid Catalysis

3.4.5.

Electrostatic Catalysis

3.4.5.1.

Stabilization of Charged Intermediates

3.4.5.2.

Preorganization of Active Site

3.4.6.

Strain and Distortion

3.4.6.1.

Induction of Substrate Strain

3.4.6.2.

Facilitation of Bond Cleavage

3.4.6.3.

Ground State Destabilization

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2. Enzyme Structure and Composition

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4. Enzyme Kinetics