Table of Contents
Biomolecules Gateway Page
Jmol Tutorial

In this module:

Enzymes' Capabilities
Models of Enzyme Action
Enzyme Kinetics
Competitive Inhibition
Noncompetitive Inhibition
An Enzyme at Work
Protease Inhibitors

An Enzyme at Work

The digestive enzyme pepsin is an example of the class of enzymes known as aspartyl proteases. Proteases are enzymes that hydrolyze peptide bonds. Aspartyl proteases use two aspartate groups in the active site to cleave the bond. (See the Proteins 1 module to see what peptide bonds and aspartate are.)

Click on the step numbers below to see the mechanism proposed for pepsin. Click on the mouse at left to clear the images and text.

A water molecule () is held in the active site by a hydrogen bond to Asp125. The net charge in the active site is -1.
When substrate binds, several things happen at once. One proton of the bound water molecule is removed by Asp25 (). The oxygen atom of the water molecule starts to form a bond to the carbonyl carbon (), and the p electrons move onto the carbonyl oxygen (). The amine nitrogen removes a proton from Asp25 ().
The carbonyl carbon is now in a tetrahedral transition state (). The overall charge of the enzyme-substrate complex is still -1.

An electron pair on the negatively charged oxygen atom moves back into a p bond with the carbonyl carbon () as the peptide bond between that carbon and the amine nitrogen breaks (). The positive charge on Asp25's carboxyl carbon is neutralized by an electron pair on the negatively charged oxygen ().
The peptide bond has been broken. The fragment with a new N-terminus is free to diffuse away, as is the fragment with the new C-terminus if the hydrogen bond between it and Asp125 is broken.

The water molecule bound in the active site of pepsin is called a cofactor . Many enzymes use cofactors such as water, Zn2+, Fe2+, and derivatives of vitamins in their reactions.

The structure of rhizopuspepsin, an aspartyl protease very similar to pepsin, is shown at right. This structure shows the enzyme binding a competitive inhibitor (wireframe model), in this case a short peptide with one of the peptide bonds reduced to a -CH2-NH- group, so that the enzyme cannot cleave it.

An Enzyme at Work