BIO 361 Lecture Notes - Lecture 11: Electronegativity, Enzyme, Deprotonation

• School: Stony Brook University
• Department: Biology
• Course: BIO 361
• Professor: Stephen Glynn, Sanford Simon

Document Summary

Biochemistry professor sanford simon stony brook summer 2016. The carbonyl oxygen and amide nitrogen are electronegative, while the carbonyl carbon is partially positive, which makes it very susceptible for nucleophilic attack (major step of peptide cleavage) The specificity pocket is not the site of substrate binding. Elastase is not as specific as chymotrypsin and trypsin due to its shallower pocket. Overlay of three different proteases showing conservation of catalytic triad. The order of the catalytic residues is different in different serine proteases. Unlikely that these difference would result from a common ancestor, demonstrating convergent evolution due to the differences in protein sequences of enzymatic primary structures. His57 deprotonates ser195 to create nucleophile (general base catalysis) Nucleophilic attack creates a covalent intermediate (covalent catalysis) Formation of the tetrahedral intermediate is the transition state. Ser195 is ideally placed to carry out nucleophilic attack on the carbonyl group of the scissile peptide bond (proximity and orientation)