enzyme catalysis notes

7.1 Introduction

  • Enzymes as catalysts exceed chemical catalysts in substrate and reaction specificity.

  • Interactions in binding between enzyme and substrate include:

    • Covalent bonds

    • Hydrogen bonds

    • Ionic interactions

    • Ion-dipole interactions

    • Dipole-dipole interactions

    • Charge transfer interactions

    • Hydrophobic interactions

    • Van der Waals interactions

  • Mechanisms of enzyme catalysis are crucial for accelerating reaction rates.

Objectives

  • Understand enzyme-substrate binding interactions.

  • Explain acid-base catalysis.

  • Discuss specific examples such as chymotrypsin and lysozyme.

  • Analyze the interactions between enzyme and substrate.

7.2 General Features

  • Enzymes manipulate reactions more effectively than most catalysts by reducing activation energy.

  • Free energy change in enzyme catalysis is expressed as G = H - TS, where:

    • H = Enthalpy

    • S = Entropy

  • The active site, where catalysis occurs, has a 3D structure that protects substrates and aids catalysis.

7.2.1 Proximity and Orientation

  • Key mechanisms enhancing reactions: proximity and orientation of molecules.

  • Proximity effect:

    • Molecules bind close together on the enzyme surface, enhancing concentration and reducing entropy loss.

  • Orientation effect:

    • Correct alignment of reactive groups is vital for optimizing reaction conditions.

  • Enhanced reaction rates by factors of ~5 to ~107 are possible through these effects.

7.2.2 Strain and Distortion

  • Binding energy drives enzyme mechanisms by overcoming transition state barriers.

  • Induced fit leads to substrate distortion, increasing reactivity towards the transition state.

  • Strain can also affect enzyme conformation, enhancing binding and reaction rates.

7.2.3 Acid-Base Catalysis

  • Acid-base reactions involve proton transfer via side chains of amino acids.

  • Two categories of acid-base catalysis:

    1. Specific acid-base catalysis: Involves only H+ or OH- from solvent.

    2. General acid-base catalysis: Involves various acids or bases present in solution.

  • Rate enhancement is achieved by altering pKa in the active site, contributing to catalysis.

7.2.4 Covalent Catalysis

  • Involves formation of transient covalent bonds between enzyme and substrate.

  • Key stages:

    1. Formation of covalent bond with the nucleophile.

    2. Electrophilic catalyst extraction of electrons.

    3. Elimination of the catalyst.

  • Nucleophilic groups play crucial roles, altering reaction pathways for enhanced rates.

7.2.5 Mechanism of Action of Chymotrypsin

  • Chymotrypsin gets activated from chymotrypsinogen, cleaving peptide bonds.

  • Key amino acids in the active site include Asp-102, His-57, and Ser-195, which form a catalytic triad.

  • Mechanism involves:

    1. Nucleophilic attack on substrate.

    2. Formation of unstable tetrahedral intermediates.

    3. Hydrolytic cleavage regenerating the active enzyme.

7.2.6 Mechanism of Lysozyme Action

  • Lysozyme hydrolyzes polysaccharides that comprise bacterial cell walls.

  • Mechanistic pathway involves:

    1. Binding of substrate at specific sites (A-F).

    2. Distortion and activation through the half-chair conformation.

    3. Catalytic action by Glu-35 and Asp-52 facilitating bond cleavage.

7.2.7 Metal-Activated Enzymes and Metalloenzymes

  • Metal ions play significant roles as catalytic cofactors.

  • Classifications:

    • Metal-activated enzymes: Require metal for activation (e.g., Hexokinase).

    • Metalloenzymes: Metal tightly bound, essential for function (e.g., carboxypeptidase).

  • Metal ions assist in stabilizing transition states and orienting substrates.

7.2.8 Transition State Analogues

  • Enzymes preferentially bind transition states to facilitate reactions.

  • Transition state analogues resemble intermediates in enzyme reactions, acting as potent inhibitors.

  • These analogues aid in understanding enzyme mechanisms and designing new drugs.

7.3 Summary

  • Enzymes greatly accelerate reactions by lowering activation energy and enhancing substrate binding.

  • Mechanisms include:

    • Proximity and orientation effects reducing entropy.

    • Acid-base catalysis aiding in substrate transformation.

    • Covalent catalysis stabilizing transition states.

  • Chymotrypsin and lysozyme serve as key examples of enzyme mechanisms.

  • Metal ions are critical to many enzymes' catalytic activities.

  • Transition state analogues provide insights and have potential therapeutic applications.

7.4 Terminal Questions

  1. Justify: 'Binding energy is the major driving force in enzyme catalyzed mechanisms'.

  2. Distinguish specific from general acid-base catalysis.

  3. Explain lysozyme mechanism of action.

  4. Differentiate metal-activated enzymes from metalloenzymes.

7.5 Answers

  • Self-Assessment Questions provide corrective feedback on understanding key concepts and mechanisms mentioned in the summary.

7.6 Suggested Readings

  1. "Lehninger Principles of Biochemistry" by David L. Nelson and Michael M. Cox.

  2. "Harper’s Illustrated Biochemistry" by Robert K. Murray et al.

  3. "Principles of Biochemistry" by Donald J Voet and Judith G. Voet.

  4. Additional works provide comprehensive insights into enzyme science and biochemistry.