Enzymes and Catalysis Overview

Study Notes

Covalent Catalysis: Enzymes contain a reactive group (nucleophile) that temporarily binds to the substrate. Potential nucleophiles include unprotonated histidine imidazole, amino groups, thiolates, and the R groups of serine, glutamate, and aspartate.
General Acid-Base Catalysis: Molecules, other than water, act as proton donors (acids) or acceptors (bases). The group that donates a proton must later accept a proton to regenerate the enzyme. Potential residues include histidine imidazole, amino groups, cysteine thiol, glutamate, aspartate, lysine, tyrosine, and arginine.
Catalysis by Approximation: Enzymes catalyze reactions between two substrates by bringing them together in their active site. This decreases the entropy of the system and speeds up the reaction.
Metal Ion Catalysis: Metal ions can play various roles in catalysis, including stabilizing negative charges on intermediates, facilitating nucleophile formation, and acting as bridges between the enzyme and substrate.

Chymotrypsin: A digestive enzyme synthesized in the pancreas. It cleaves peptide bonds after bulky aromatic residues like phenylalanine, tyrosine, and tryptophan.
Carbonic Anhydrase: Adds water to carbon dioxide.
Restriction Endonuclease (EcoRV): Hydrolyzes DNA at specific sites.
Myosin: Hydrolyzes ATP.

It's a digestive enzyme synthesized in the pancreas.
It is involved in protein turnover.
It cleaves peptide bonds after bulky, aromatic residues.
It speeds up a slow reaction by making the carbonyl group more susceptible to nucleophilic attack by water.
It uses covalent catalysis (assisted by general base catalysis).

Acylation Phase: The first substrate (protein/peptide) binds. The serine nucleophile attacks the carbonyl of the peptide bond, releasing the amine component (C-terminus of the protein).
Deacylation Phase: The second substrate (water) binds. Water attacks the carbonyl group of the original peptide bond, releasing the carboxylic acid component (N-terminus of the protein).