I am having a brain fart about amino acids...

[Doctor_Strange]

The amino acids have been changed to G D C M but ignoring the net charge part, I am blanking out: at a pH of 7, the COOHs of all the AA get deprotonated or no? What about the side chains?

This is like a simple concept that I am forgetting I think....

EDIT: So I remember about the amine group and that at pH of 7 they remain protonated, but the side chains of D C and M remain protonated?

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[aldol16]

When pH > pKa, what happens? And vice versa?

 

[Doctor_Strange]

When pH > pKa, what happens? And vice versa?

Hey, so I literally remembered after posting this--when pH is greater than the pKa it gets deprotonated and vice versa remains protonated, but the pKa of the side of , for example, Cysteine, at a pH of 7 would remain protonated?? I know that accoridng to my mneomonic only D E and H R K are the only charged AAs but is the charged status assuming at zwitteron always? That must be the convention, no?

 

[Doctor_Strange]

To clarify my current understanding:

• The acidic and basic AAs are the only ones with a charge--everything else does not have a charge (but can be polar still)
• But, if the question asked what is the charge of R at a pH of 11 I would not know the answer, because I do not know what the pKa of its basic side chain is (amines get deprotoanted at around pKa 9, so the pKa of R's side chain would have to be greater, I just would not know by how much...

 

[theonlytycrane]

The pKa of arg ~ 12.5. So at pH = 11, pH < pKa and the proton is on.

 

[Doctor_Strange]

The pKa of arg ~ 12.5. So at pH = 11, pH < pKa and the proton is on.

I have not memorized the pKas of the various acidic an drastic aa is it worth to do so?

 

[theonlytycrane]

No, as long as you know that the carboxylic acids (asp and glu) have lower pKas than the basic amino acids. If it's specific you'll probably have enough from the passage to figure it out or it will just be a relative ordering type of thing.

 

[aldol16]

Hey, so I literally remembered after posting this--when pH is greater than the pKa it gets deprotonated and vice versa remains protonated, but the pKa of the side of , for example, Cysteine, at a pH of 7 would remain protonated?? I know that accoridng to my mneomonic only D E and H R K are the only charged AAs but is the charged status assuming at zwitteron always? That must be the convention, no?

No, you do not have to assume zwitterion. Most of the time, these will come up in peptides on the MCAT and in a peptide, there are no free carboxylic acids or amines except at the C- or N-termini. Therefore, the side chain contributes all of the charge when the amino acid is on a peptide and the peptide charge is the net charge of the side chains plus the charges of the C- and N-termini.

You can do this exercise at any pH, given that you know that the pKa of the carboxyl group is around 2 and the pKa of the amino group is about 9. Everything else you should know at least as "basic" or "acidic," although knowing the pKas will be helpful in biochemistry (lower yield on the MCAT, I suppose).