Catalysis by serine proteases — Identify the primary nucleophile that initiates peptide bond cleavage in the catalytic cycle

Introduction:
Serine proteases (e.g., chymotrypsin, trypsin, elastase) catalyze peptide bond hydrolysis through a conserved catalytic triad. This question focuses on the nucleophile that initiates the acylation step of catalysis.

Given Data / Assumptions:

• The catalytic triad comprises Ser, His, and Asp (or Glu in some families).
• Nucleophilic attack on the carbonyl carbon forms a tetrahedral intermediate.
• Hydrolysis proceeds in two stages: acylation and deacylation.

Concept / Approach:
During acylation, the Ser hydroxyl is deprotonated by His to generate a reactive alkoxide, which attacks the peptide carbonyl. Water becomes the nucleophile only in the second stage (deacylation) to release the acyl-enzyme intermediate and regenerate free enzyme.

Step-by-Step Solution:

Verification / Alternative check:
Covalent inhibition by fluorophosphonates selectively labels the active-site Ser, supporting its role as the primary nucleophile in acylation. Kinetic solvent isotope effects further distinguish steps involving water in the second half-reaction.

Why Other Options Are Wrong:

Common Pitfalls:
Conflating acylation and deacylation; assuming water initiates all protease reactions; overlooking the role of His and Asp in activating Ser.

Final Answer:
Serine (active-site Ser as an alkoxide) is the primary initiating nucleophile.