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Finding the net charge of amino acid

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Finding the net charge of amino acid

Postby nic852 » Mon Sep 29, 2008 8:28 pm

How do you calculate the the net charge of glutamate amino acid at a pH of 99
Last edited by nic852 on Fri Oct 03, 2008 1:54 am, edited 1 time in total.
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Postby mith » Mon Sep 29, 2008 9:49 pm

just assign charges.
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Re: Finding the net charge of amino acid

Postby nic852 » Mon Sep 29, 2008 11:01 pm

For the alpha amino group since pka>pH the charge would be +1. For the alpha carboxyl group since the pKa<pH the charge would be -1. I'm confused what to do with the pKA(s) of the side chain groups??
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Re: Finding the net charge of amino acid

Postby blcr11 » Tue Sep 30, 2008 1:10 am

The side chain of Alanine is aliphatic--essentially a hydrocarbon. The -CH3 protons don't dissociate. The side chain of Alanine is electrically neutral at all pH's
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Re: Finding the net charge of amino acid

Postby nic852 » Tue Sep 30, 2008 1:44 am

Does this mean that based on the information I gave, the net charge of alanine at pH=8 is (+1) from alpha amino group plus (-1) from alpha carboxyl group which is equal to 0. (+1)+(-1)=0. Is this correct?
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Postby blcr11 » Tue Sep 30, 2008 2:05 am

Yes. Free Alanine will have a net charge of zero between pH 2 to pH 9, roughly.
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Postby nic852 » Tue Sep 30, 2008 3:32 am

Something is not right because none of the answers are 0. So the net charge of alanine based on the information I gave cannot be zero. I'm missing something.

What am I missing? Don't you use the Henderson Hasselbach equation somehow to calculate the net charge?
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Re: Finding the net charge of amino acid

Postby blcr11 » Tue Sep 30, 2008 12:07 pm

I'm a little puzzled, I guess. You haven't been given the specific pKa's for alanine and yet you are supposed to come up with some sort of fractional charge, as in % ionized or something like that? The pKa's for alanine are 2.3 for the acid group and 9.7 for the amino group. The formal pI of alanine is 6.0. The pI is calculated from the two pKa's as ( pKa1 + pKa2 )/2. If there were three titratable groups this would involve all three pKa's and the denomimator would be "3" rather than "2" and so on.

The only ionic species present when the pH = pI is the zwitterion where both the amino group and the carboxylate are ionzed--the amino group is +1 and the carboxylate is -1. As you move above the pI, the proton is lost from the amino group and the alanine has a net -1 charge. But not all molecules will instantly lose the proton. Only when you get above the basic pKa (9.2) will all of the alanines carry a net charge of -1. If you need to calculate the ratio of (alanine)-0 to (alanine)-1 then you could use the Henderson-Hasselbach equation, but it could get complicated as you have two, coupled acid-base equilibria going on. You could assume that the pKa at 2.3 is irrelevant and only use the equilibrium at pH 9.7 (or 9, if that's what your prof intends). It didn't seem to me like the question was asking for such a detailed analysis of the titration curve. At pH's between the two pKa's, it is true, at least to a first approximation, that the net charge of alanine is roughly zero. It is only strictly zero at the pI. As you move away from the pI and get closer to one of the pKa's that becomes less and less true. Within, say, 2 pH units of the pKa you could use the Henderson-Hasselbach equation to estimate the ratio of charged to uncharged species. The net charge per molecule, though, can only be 0,-1,+1.
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Postby blcr11 » Tue Sep 30, 2008 12:29 pm

If you assume the data of pKa = 9, and that the acidic equilibrium is not important, at pH 8 roughly 10% of the alanine carries a net charge of -1 while 90 % remain zwitterionic (net charge = 0). If you use the actual pKa for alanine, then even less alanine carries a net charge--maybe 1-2% of the alanines are net -1.
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Postby nic852 » Tue Sep 30, 2008 3:19 pm

So, how would you find the net charge of a peptide such as MARSA at ph of 99?
Last edited by nic852 on Fri Oct 03, 2008 1:54 am, edited 1 time in total.
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Re: Finding the net charge of amino acid

Postby blcr11 » Tue Sep 30, 2008 5:16 pm

You've got to try it first. Because it is a peptide, you only need to consider the terminal alpha-amino and terminal alpha carboxylate. Then you need to consider all the side chains and decide whether or not they will contribute to any charged species. This means putting together the amino acid name with it's one-character symbol and then associating the right chemistry with the side chain.
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Postby nic852 » Wed Oct 01, 2008 2:34 am

I've been trying to solve the last question for a couple of hours and I got a net charge of -4 which is wrong. Can someone please help me with this problem?
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