Trypsin: Definition, Function & Mechanism of Action

Instructor: Laura Foist

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

Trypsin is one of the enzymes used to digest proteins. It is very similar to another protein digestion enzyme, chymotrypsin. In this lesson we'll learn more about trypsin, what it does, and how it works.

What is Trypsin?

When we eat protein, the body uses several enzymes to break it down into individual amino acids, which can be absorbed into the body. One of the most studied enzymes is chymotrypsin, but another protein digestion enzyme is trypsin. Chymotrypsin and trypsin are very similar enzymes, thus when studying trypsin it is often in comparison to chymotrypsin.

One of the main differences between trypsin and chymotrypsin is which amino acids residues it selects for. Chymotrypsin cleaves the protein at the c-terminal of aromatic amino acids while trypsin cleaves the protein at the c-terminal of the basic amino acids lysine and arginine.

Structural Comparison

The structure of trypsin and chymotrypsin are very similar. In fact the active site pockets are almost identical, with the actual amino acid residues involved in the mechanism reaction being exactly the same: serine, histidine, and aspartic acid.

Yet there is one important difference between the two structures. We know that chymotrypsin needs to select for the aromatic amino acids, which are hydrophobic, while trypsin needs to select for the basic amino acids, which contain a positive charge. In order to accomplish this, the specificity pocket of chymotrypsin includes a serine at position 189 while trypsin contains an aspartic acid in that position. This seems like a very small difference, but serine is not polar, thus it will allow hydrophobic amino acids into the pocket. While aspartic acid has a negative charge, this would attract the positive charge on the basic molecules of lysine and arginine. In fact when this serine in trypsin is replaced with aspartic acid, it no longer selects for lysine and arginine.

Mechanism of Trypsin

Since the active site is exactly the same in trypsin and chymotrypsin, the mechanism is exactly the same for both as well. There are four steps in this mechanism:

Step 1

First, the hydrogen on the OH of serine is removed, thus forming a negative charge on the oxygen. The negative charge can attack the peptide bond, with the extra electrons going onto the oxygen:


Step 1


Step 2

The electrons on the oxygen can easily reform a carbon-oxygen double bond, but then another bond with carbon needs to be kicked off. In this case the carbon-nitrogen bond forming the peptide is broken. The nitrogen gets a hydrogen from the histidine nitrogen. Now the first protein residue has been released from the enzyme:


Step 2


Step 3

The peptide bond was broken but the reaction isn't done because the other half of the protein (the section with the basic amino acid) is still attached to the enzyme. The last two steps are in order to help the enzyme release this second half of the protein.

In order to accomplish this, water is added. The hydrogen from the water goes onto the histidine and the OH attaches to the carboxyl carbon, against putting a negative charge onto oxygen:


Step 3


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