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					In order to help some of you out with the idea of signing charges, I put this together. Let’s start with the simple case of
ammonia/ammonium:
                           NH4+               NH3 + H+

The pKa of NH4+ is 9.25. That means in a solution with a pH of 9.25 the [NH3] = [NH4+]. If we lower the pH ([H+] goes
up), we push the equilibrium above to the left, and the [NH4+] goes up. If we raise the pH, the H+ will react with the
base, and the equilibrium is pushed to the right, and the [NH4+] down.

It is important to note that a pH is based on the [H+], and you must have a volume (e.g. L) to have a concentration (e.g
molar). It doesn’t make sense to discuss the pH of a molecule because there is no volume associated with a molecule.

At a pH well below 9.25 (e.g. 7), the charge on the molecules essentially in every case is is +1. The equilibrium is to the
left. At a pH well above (e.g. 11), the charge on the molecules essentially in every case is is 0, and the equilibrium is to
the right.

For amino acids and peptides, we have multiple ionizable groups. For our purposes, we will treat them independently,
and as if the pKa’s don’t change (e.g. We will assume the pKa of the aspartic acid side chain is the same in a dipeptide
as it is in free aspartic acid). You should be able to look a the pH and pK a for each group individually and assign the
charge on that group at that pH, and then sum them for all of the ionizable groups in the molecule.

Remember, the pKa is the pKa associated with LOSING ONE PROTON. The pKa of NH4+ is 9.25. The pKa of NH3 (NH3
losing one proton to go to NH2-) is much higher.

Your book actually does something I don’t like. It gives you the amino acids in the deprotonated form for the carboxylic
acids, and then gives you the pKa for the protonated form. Remember, those carboxylic acid groups will have a proton
on them. The pKa of those protons is low (~2 for the non-side chain carboxylic acids) so they come off at pretty low
pH’s so you will get the form shown in the book at most pH, but at LOW pHs, they can be protonated.

To assign the charges for the different amino acids, you have to be able to identify the ionizable groups. For the most
part we are talking about carboxylic acids and amines. His is different, but we talked about it specifically in class. For
Tyr, it is the phenolic (benezne ring) hydroxyl group that is ionizable and for Cys it is sulfhydryl group (the sulfur) that is
ionizable at relevant pHs.

Hope this helps some.

				
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posted:12/3/2011
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