So when we find the net charge we look up the pka in the table. But we need to k

Question

So when we find the net charge we look up the pka in the table. But we need to know our ionizable groups which are arg and lys x2 Do you just need the pka of arg and lys?? I think of all? I think the rest would be neutral at ph of 7 except for the ionizible? I think all the groups have a pka, even though some are very close to neutral. I found the table he is talking about. Remember how every aa has two pkas, one for the carboxyl group and one for the amino group? Nvm I see what you are talking about, cys, tyr, asp, glutamate, lysine, and arg all have side chain pkas. Is that what we use? Im really not sure for this one For amino acids with acidic side chains, you use the average of the lower pka's. For amino acids with basic side chains, you use the average of the two higher pka's. The only two that are that way are lysine and arginine (both basic and positive) I remember vaguely talking about this in class now This video says you only use the ones that have a side chain. Do we want to leave it and ask tomorrow? Or calculate it? And then ask tomorrow? Or how are we proceeding We have to do it for both pH 7 and 12.5 to the Oh at ph of 7 its easy. NH3 will have a +1 charge. Arg will have a plus one charge. So will the two lysines. The c terminus will have a -1 charge. So I think it will have a +3 charge at a ph of 7. I think the pkas are used to tell if the side chain will be protonated or not at that ph. Yes if the pH pka, deprotonated? And if ph = pka, net charge of zero? But I think for the two aa's you have to find the pl.

Explanation / Answer

A correlation can be made between the net charge with the pKa for those amino acids in which the side chain does not have an ionizable group, the pI is the average pKa values of the - NH3 and -COOH.
However, in the case of arg and lys, the side chain also has an ionizable (basic) group with a pKa value. In such cases where there is an ionizable group in the side chain, all three pKa values are considered.

The arg, and lys can be characterized by the average of pKa value of side chain and the pKa value of NH3.

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