Key track of your ions. Take your favorite protein and run it through an Anion Exchange column. Say it bound very tightly, it will elute very late. If you put it on Cation Exchange column, it would elute early because it didn't have alot of those charges. Don't care whether it's a protein or an amino acid.
Amino acids have both positive and negative charges.
R groups will have different molecular weights. What you deal with is a Charge to Mass Ratio . Separations still possible. You finally have your Favorite Protein 3-D structure most proteins have an Active Site binds some molecule or molecules in the cell, the Substrate Proteins are not static, they do something Enzymes catalyze chemical reactions most of the time, they sort of act as surface catalysts Alcohol lowers inhibitions. That's what the enzyme is doing.