Chapter 8: Enzymes – Biological Catalysts (Biochemistry Study Notes)

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Enzymes: Biological Catalysts

What is a Catalyst?

Catalysts are substances that increase the rate of chemical reactions without being consumed or permanently altered in the process. In biological systems, enzymes serve as highly efficient and specific catalysts.

Definition: A catalyst increases the rate or velocity of a chemical reaction without being changed in the overall process.
Effect on Equilibrium: Catalysts accelerate the approach to equilibrium but do not alter the thermodynamic favorability of the reaction.
Activation Energy: Catalysts lower the activation energy (energy barrier) required for the transition state, facilitating the conversion of substrate to product.
Example: Enzymes such as catalase speed up the breakdown of hydrogen peroxide in cells.

Major Classes of Enzymes

Enzymes are classified based on the type of reaction they catalyze. The six major classes are:

Class	Example (Reaction Type)	Reaction Catalyzed
1. Oxidoreductases	Alcohol dehydrogenase (oxidation with NAD+)	CH3CH2OH + NAD+ → CH3CHO + NADH + H+
2. Transferases	Hexokinase (phosphorylation)	Glucose + ATP → Glucose-6-phosphate + ADP
3. Hydrolases	Carboxypeptidase A (peptide bond cleavage)	Peptide + H2O → Shorter peptide + Amino acid
4. Lyases	Pyruvate decarboxylase (decarboxylation)	Pyruvate → Acetaldehyde + CO2
5. Isomerases	Maleate isomerase (cis-trans isomerization)	Maleate → Fumarate
6. Ligases	Pyruvate carboxylase (carboxylation)	Pyruvate + CO2 + ATP → Oxaloacetate + ADP + Pi

Additional info: These classes are defined by the Enzyme Commission (EC) system and are universally used in biochemistry.

How Enzymes Act as Catalysts: Principles and Examples

Models for Substrate Binding and Catalysis

Lock-and-Key Model: The enzyme's active site is a rigid structure that fits the substrate precisely, like a key in a lock.
Induced Fit Model: The enzyme's active site is flexible and molds itself around the substrate upon binding, enhancing specificity and catalytic efficiency.
Example: Hexokinase undergoes a conformational change upon glucose binding, illustrating the induced fit model.

Mechanisms for Achieving Rate Acceleration

Enzymes accelerate reactions by several mechanisms:

General Acid/Base Catalysis (GABC): Enzyme side chains donate or accept protons to stabilize transition states.
Covalent Catalysis: Enzyme forms a transient covalent bond with the substrate.
Electrostatic Stabilization: Charged groups on the enzyme stabilize charged transition states.
Proximity Effects: Enzyme brings substrates into close proximity and correct orientation.
Preferential Stabilization of the Transition State: Enzyme binds the transition state more tightly than the substrate or product.
Protein Conformational Changes: Structural changes in the enzyme can facilitate catalysis.

Reaction Coordinate Diagram:

Enzyme-catalyzed reactions have a lower activation energy () compared to noncatalyzed reactions.
General equation:

Coenzymes, Vitamins, and Essential Metals

Coenzyme or Cofactor Function in Catalysis

Many enzymes require non-protein helpers called coenzymes or cofactors for catalytic activity. These are often derived from vitamins or are metal ions.

Vitamin	Coenzyme	Reaction involving the coenzyme
Thiamine (B1)	Thiamine pyrophosphate	Activation and transfer of aldehydes
Riboflavin (B2)	Flavin mononucleotide; flavin adenine dinucleotide	Oxidation-reduction
Niacin (B3)	Nicotinamide adenine dinucleotide; nicotinamide adenine dinucleotide phosphate	Oxidation-reduction
Pantothenic acid (B5)	Coenzyme A	Acyl group activation and transfer
Pyridoxine (B6)	Pyridoxal phosphate	Various reactions involving amino acid activation
Biotin	Biotin	CO2 activation and transfer
Lipoic acid	Lipoamide	Acyl group activation; oxidation-reduction
Folic acid	Tetrahydrofolate	Activation and transfer of single-carbon functional groups
Vitamin B12	Adenosyl cobalamin, methyl cobalamin	Isomerization and methyl group transfers

Metal Ions in Enzymes

Metal ions serve as essential cofactors in many enzymes, often stabilizing charged intermediates or participating in redox reactions.

Metal	Example of Enzymes	Role of Metal
Fe	Cytochrome oxidase	Oxidation-reduction
Cu	Ascorbic acid oxidase	Oxidation-reduction
Zn	Alcohol dehydrogenase	Helps bind NAD+
Mn	Histidine ammonia lyase	Aids in catalysis by electron withdrawal
Co	Glutamate mutase	Co is part of cobalamin coenzyme
Ni	Urease	Catalytic site
Mo	Xanthine oxidase	Oxidation-reduction
V	Nitrate reductase	Oxidation-reduction
Se	Glutathione peroxidase	Replaces S in one cysteine in active site
Mg	Many kinases	Helps bind ATP

Enzyme Inhibition

Drugs, Toxins, and Enzymatic Activity

Enzyme inhibitors are molecules that decrease or abolish enzyme activity. Many drugs and toxins act as enzyme inhibitors.

Reversible Inhibitors: Bind noncovalently and can dissociate from the enzyme.
Irreversible Inhibitors: Bind covalently, permanently inactivating the enzyme.
Example: Many prescription drugs are designed as enzyme inhibitors, and some toxins act by inhibiting key enzymes.

Types of Reversible Inhibition

Competitive Inhibition: Inhibitor competes with substrate for binding at the active site. Can be overcome by increasing substrate concentration.
Uncompetitive Inhibition: Inhibitor binds only to the enzyme-substrate (ES) complex, not to the free enzyme, often at a site distinct from the active site.
Mixed (Noncompetitive) Inhibition: Inhibitor can bind to either the free enzyme or the ES complex, usually at a site other than the active site, affecting both substrate binding and catalysis.

Summary Table of Inhibition Types:

Type	Binding Site	Effect on Vmax	Effect on Km
Competitive	Active site (free enzyme)	No change	Increases
Uncompetitive	ES complex	Decreases	Decreases
Mixed/Noncompetitive	Free enzyme or ES complex	Decreases	Variable

Irreversible Inhibition

Mechanism: Inhibitor forms a covalent bond with the enzyme, often at the active site, leading to permanent inactivation.
Example: Diisopropyl fluorophosphate (DFP) irreversibly inhibits acetylcholinesterase, causing paralysis.

The Regulation of Enzyme Activity

Controlling Enzyme Functions in the Cellular Context

Cells regulate enzyme activity through several mechanisms to maintain metabolic balance and respond to environmental changes.

Substrate Level Control: Reaction rate increases with substrate concentration, but large changes in [S] are needed for significant effect.
Regulation at Committed Steps: Feedback inhibition or activation at key control points, often involving allosteric enzymes, is an efficient way to maintain homeostasis.
Covalent Modification: Enzyme activity is regulated by reversible (e.g., phosphorylation) or irreversible (e.g., zymogen activation) covalent changes.

Feedback Inhibition

End product of a metabolic pathway inhibits an earlier step, preventing overproduction.
Example: In amino acid biosynthesis, the final product often inhibits the first enzyme in the pathway.

Allostery

Allosteric Enzymes: Usually multisubunit proteins that change conformation upon binding substrates or effectors.
Homoallostery: Cooperativity in substrate binding (e.g., hemoglobin).
Heteroallostery: Regulation by non-substrate effector molecules.

Covalent Modifications Used to Regulate Enzyme Activity

Reversible Modifications: Phosphorylation (by kinases) and dephosphorylation (by phosphatases) act as on/off switches for enzyme activity.
Irreversible Modifications: Proteolytic cleavage of zymogens activates certain enzymes (e.g., digestive enzymes, blood clotting factors).
Example: Glycogen phosphorylase is activated by phosphorylation.

Nonprotein Biocatalysts: Catalytic Nucleic Acids

Ribonucleic Acids as Enzymes

Ribozymes: RNA molecules that catalyze chemical reactions, such as self-splicing or peptide bond formation in ribosomes.
Evolutionary Significance: The "RNA World" hypothesis suggests that early life used RNA for both genetic information and catalysis before the evolution of DNA and proteins.