The Difference Between Trypsin & Chymotrypsin

Instructor: Laura Foist

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

Trypsin and chymotrypsin are two very similar enzymes that perform similar functions. In this lesson we will explore how they are different and what in the structure causes the difference. Updated: 01/20/2022

Enzyme Overview

Enzymes fulfill a multitude of purposes. They allow our body to work and operate in the manner that we have come to rely on. For example, in digestion our body can't simply absorb the chunks of food that we chew up because the pieces are too big. So there are several enzymes to help break the food into smaller 'chunks'.

Protein needs to be broken into individual amino acids in order for the body to absorb the nutrients. Two of the main enzymes involved in this process are trypsin and chymotrypsin.

Both of these enzymes come from the pancreas and act in the duodenum (the portion right between the stomach and small intestines, or the first section of the small intestines). They start the process of breaking proteins into individual amino acids. They are very similar in structure and function, but have a few unique differences, such as where they cleave the protein.


The main difference between chymotrypsin and trypsin is the amino acids they select for.

  • Chymotrypsin is the enzyme that selects for the aromatic amino acids: phenylalanine, tryptophan, and tyrosine.
  • Trypsin is the enzyme that selects for the basic amino acids: lysine and arginine.

Both cut from the c-terminal of the protein. In a protein each amino acid residue contains two sides, the n-terminal and the c-terminal. The n-terminal refers to the nitrogen-terminal, or the side of the amino acid that has the nitrogen. The c-terminal refers to the carbon-terminal, or the side of the amino acid that has the carbon.

So, for example, chymotrypsin will only cut the protein on the side of phenylalanine that has the carbon not on the side with the nitrogen.

In a single protein there will be several amino acid residues for each enzyme to act on. But each amino acid is only going to select for their specific amino acids and cut the protein in that position:

Trypsin and chymotrypsin each cleave the protein at different points
Cutting the protein

How Are Amino Acids Selected?

So, how does each enzyme select for their specific amino acids? It's all about having a good fit. The structure of each enzyme is very specific and only certain amino acids are allowed into the active site. Once in the active site the mechanism of action for both enzymes is exactly the same, so the enzyme needs to select for specific amino acids prior to getting to the active site.

We often think of enzymes acting as a lock and key mechanism, where it won't work unless the substrate with the perfect shape comes along:

We often think about enzymes as operating with a lock and key model
Lock and key model

If we change the enzyme even slightly then it won't select for the same substrate as before, but a new substrate:

Even a slight change in the enzyme will change its specificity
Change enzyme

This is similar to the difference between the structure of trypsin and chymotrypsin. They are very similar enzymes, but there are slight differences in their structures in order to allow trypsin to select for lysine and arginine while chymotrypsin selects for phenylalanine, tryptophan, and tyrosine.


The main difference occurs at position 189. For chymotrypsin this amino acid residue is serine while in trypsin it's aspartic acid.

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