Re: do pepsin and alcalase break down different amino acids in gelatin?

Hi Natalie,

There are 3 things that we need to look at to answer your question.

1. What is gelatin?
Wikipedia tells us that gelatin is a substance created by the prolonged boiling of connective tissue - skin, bones, cartilage. This means that it's a complicated mixture of substances. Much of it is formed from the major protein in these types of tissue, which is called collagen. Collagen, in turn, is a fibrous protein that contains a high proportion of the amino acids glycine and proline.
This last point is important - the types of amino acid in a protein can determine whether it is a good substrate for a protease.
2. What is pepsin?
Pepsin is a protease - an enzyme that degrades proteins to peptides. Proteases are enzymes and most enzymes have a specificity for substrates - that is, some proteins will be more susceptible to degradation by pepsin than others. There are 2 things that you need to know about pepsin. First, it prefers to cut proteins in a particular position - the N-terminal side of a hydrophobic amino acid residue. It will not cut near peptide bonds that contain valine, alanine or glycine. Second, pepsin works best at an acidic pH, about 2.
3. What is alcalase?
I have to admit that alcalase was a new term to me. It's a commercial name for a protease called subtilisin Carlsberg, which is an alkaline protease. As the name suggests this protease works best at alkaline pH (7-9). It has a rather broad range of specificity - it cleaves on the C-terminal side of up to 6 different amino acid residues. Take a look at the enzyme properties page to find out more about it.

The MadSci team tell me that you already have some information on how copper ions affect the activity of these enzymes, so I'll skip over that part of the question. Briefly, my understanding is that copper activates pepsin and I'm not aware of any studies that document either activation or inhibition of alcalase by copper.