m6 p4

Overview of Enzymes

  • Enzymes: Biological catalysts that accelerate chemical reactions necessary for life under physiological conditions.

    • Without enzymes, metabolic reactions would occur at extremely slow rates; some needing millions of years, rendering life impossible.

    • Enzymes increase reaction rates without being consumed or altering equilibrium concentrations of substrates and products.

    • Most enzymes are proteins; some, known as ribozymes, are composed of RNA.

  • Enzyme Kinetics: A quantitative analysis of enzyme function to probe reaction mechanisms and compare efficiency across related enzymes under diverse conditions.

Module 6 Overview

  • Topic 1: Overview of Enzymes - Chapter 7.1

  • Topic 2: Enzyme Function - Chapter 7.2

  • Topic 3: Enzyme Mechanisms - Chapter 7.2

  • Topic 4: Enzyme Reactions - Chapter 7.3

  • Topic 5: Enzyme Kinetics - Chapter 7.4

Enzyme Reactions

  • Regions of Substrate Binding Pockets in Serine Proteases: Reflect specificity for amino acids adjacent to the scissile bond.

    • Ser and Asp residues present in the specificity pocket are different from those in the catalytic triad.

Chymotrypsin: A Classic Serine Protease

  • Chymotrypsin is a serine protease involved in digestion by cleaving the peptide backbone of dietary proteins.

  • Structure: Made of three polypeptide chains derived from a single chain by cleavage.

  • Catalytic Triad: Comprises Ser195, His57, and Asp102, forms a hydrogen-bonded network necessary for catalysis.

Mechanism of Chymotrypsin Action
First Phase (Steps 1-3): Formation of a Covalent Acyl-Enzyme Intermediate

  1. Substrate binds to the enzyme active site.

  2. His57 removes a proton from Ser195, rendering serine a nucleophile.

  3. Nucleophilic attack occurs on the carbonyl carbon of the peptide, leading to the initial cleavage and release of the carboxyl-terminal peptide fragment.

Second Phase (Steps 4-6): Enzyme Regeneration

  1. Water enters the active site; His57 acts as a general base, removing a proton from water.

  2. The formed OH- ion attacks the carbonyl carbon of the acyl-enzyme intermediate, resulting in the second tetrahedral intermediate.

  3. His57 donates a proton to the amino group of the substrate, cleaving the second product (amino-terminal fragment) and regenerating the catalytic triad.

Enolase: Catalysis via Metal Ions

  • Enolase: A metalloenzyme with two divalent metal ions required at each active site, located within a cleft of the enzyme's alpha/beta domain.

    • Mechanism:

    • Step 1: Lys345 acts as a general base, deprotonating 2-phosphoglycerate (2-PGA).

    • Step 2: Stabilization of the increased negative charge occurs through interactions with Mg$^{2+}$ ions in the enzyme.

    • Step 3: Glu211 acts as a general acid, donating a proton to the intermediate which results in the formation of phosphoenolpyruvate (PEP).

HMG-CoA Reductase: A Key Enzyme in Cholesterol Biosynthesis

  • HMG-CoA Reductase: A tetrameric enzyme critical in the cholesterol biosynthetic pathway.

    • Mechanism: Reduction of HMG-CoA thioester is carried out through two hydride transfer steps utilizing two NADPH molecules as coenzymes.

    • The active site stabilizes the transition state to facilitate the enzymatic reaction.

Statin Drugs: Inhibition of HMG-CoA Reductase

  • Statin Drugs: Effective treatments for atherosclerosis that lower serum LDL levels.

    • Each statin compound exhibits functional groups that resemble the substrate HMG-CoA, demonstrating their mechanism of action as inhibitors of HMG-CoA reductase.