Expert: Florence M Rollwagen - 10/14/2008

Question
All enzymes are highly specific both in the reaction they catalyze and in their choice of substrates.  Substrate specificity can be for a specific molecule or a class of molecules.  Subtilisin is a bacterial protease that can cleave any peptide bond.  Trypsin, on the other hand splits peptide bonds only on the carboxyl side of lysine and arginine groups.  What differences might you predict in the active site of these two enzymes?  Think in terms of substrate structure, too.

I was thinking in terms of shape of but I wasnt really sure if there was some sort of partial charge repelling or attracting one another.

Please help.

Answer
Hi Andrew:  Thanks for your question.

To answer thie question, you need to search the charge and pH of each amino acid.  Enzymes bind the substrate on the basis of shape and charge, so a positive charge on an amino acid will bond with a negative charge on the enzyme.  

Create an image of the amino acids (lysine, arginine) at neutral pH (why neutral?) and then set the binding site of the enzyme against that.

Here are some websites that will help you:

http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1413572

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/Enzymes.html

http://www.biologyguide.net/bya1/bya1-10-5.htm

Hope this helps!  Write back if you have more questions.

FM Rollwagen, PhD