Hi,

There is a bit of information on this in the post Quick determination of charged peptides in a neutral environment by Justine in the OChem forum.

A quick excerpt from this:

To best answer this type of question at any pH, it is good to know the pKas of amino acid side chains (D, E, K, H, C, R, Y), as well as the pKas of the N and C termini (or NH2 and COOH). Depending on how much time you have, I would recommend memorizing structures of amino acids and their pKas with a software like Anki.

When your pKa is higher than the pH, the side chain will be deprotonated. From this and the structure of the amino acid, you can determine its charge. You would then do the method that I had shown above to get the peptide charge.

As for the question itself:

I cannot find this half length exam as the one I find is on CARS not chem, but I can give you a quick method (I just won't be able to show you elimination).

For a cysteine, we have 3 groups of interest:

1) COOH which has a pKa of around 3-4 (a little more acidic than a regular COOH)
2) NH2 which has a pKa of around 9
3) SH which has a pKa of around 8 (memorized from flashcards)

The first thing I do is consider the pH. At pH 12, it's quite basic, so I would expect most of these groups to be deprotonated. I then consider that if pKa < pH, this group is deprotonated, and go through groups one by one.

1) 3.5 < 4 so COOH is deprotonated to COO-
2) 9 < 12 so NH2 remains NH2, which is its deprotonated form.

This confuses many people as they want to put NH-, but keep in mind that the pKa of 9 corresponds to the specific process of NH2 --> NH3+, and NH- is so basic that it tends not to exist in biological settings.

3) 8 < 12 so SH is deprotonated to S-.

This gives you a 2- overall amino acid at pH 12. Keep in mind that even if you only know the protonation states of 1 and 2 which are constant for most amino acids, you can eliminate down to usually 2 answers (as your side chain is only going to be protonated or deprotonated)

I hope this helps, if you want you can try to explain to me what tyrosine would be at pH 7 and what it would be at pH 12 for practice (or just any given amino acid at any given pH).