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Chymotrypsin: Definition, Structure & Mechanism

Instructor: Laura Foist

Laura has a Masters of Science in Food Science and Human Nutrition and has taught college Science.

Chymotrypsin is an enzyme used for digesting proteins. In this lesson we will learn what types of proteins it digests and how it digests those proteins.

Digesting Proteins

Imagine you just had a nice juicy steak, cooked to perfection and perfectly seasoned. There was probably quite the party going on in your mouth, but what happens to that meat after it leaves the mouth? There are several steps throughout the digestive tract to break down the protein in that steak into pieces that can be absorbed into the body. One of these steps is chymotrypsin. Chymotrypsin is an enzyme found in the duodenum that selectively cleaves (cuts) off pieces of amino acids from the protein chain.

Specifically chymotrypsin cleaves phenylalanine, tyrosine, and tryptophan bonds, or in other words the aromatic amino acids. It cleaves these amino acids starting from the C-terminus of the protein.

Chymotrypsin Structure

The structure of chymotrypsin selectively cleaves aromatic amino acids due to the hydrophobic pocket at the active site. This means that only sections of the protein that are hydrophobic (such as aromatic portions) will favorably go into this pocket for the reaction to occur.

In the active site there are three amino acids which participate in the reaction: aspartic acid, histidine, and serine.

The active site of chymotrypsin is a hydrophobic pocket containing three amino acid residues, asparagine, histidine, and serine.
Active site

Other amino acids in the enzyme act to stabilize the protein during the reaction process, including a glycine.

Chymotrypsin Mechanism

Once an aromatic amino acid finds its way into the chymotrypsin hydrophobic pocket then the reaction which cleaves the peptide bond can occur.

Step 1

First the oxygen on the aspartic acid draws electrons away from the histidine by sharing the hydrogen with the nitrogen. This causes the other nitrogen in the ring to take the hydrogen away from the OH on serine. The negative charge on this oxygen can then attack the peptide bond, with the extra electrons going onto the oxygen:


Step 1


Step 2

When the electrons from the oxygen's negative charge reform the carbon-oxygen double bond the carbon-nitrogen bond of the peptide is broken. The nitrogen takes the hydrogen from the nitrogen on histidine. This releases this portion of the protein, it has now broken off from the rest of the protein:


Step 2


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