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Finding the net charge of amino acid

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Re: Finding the net charge of amino acid

Postby blcr11 » Wed Oct 01, 2008 8:41 am

How did you arrive at -4?
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Postby nic852 » Thu Oct 02, 2008 2:51 am

NH3+---KAPRM---COO-

K=Lysine has a charged R group
A=ALanine nonpolar so not charged
P=Proline (nonpolar) so not charged
R=Arginine R group positive)
M=nonpolar

using this formula log[COO-]\[COOH]=pH-pK or log[NH2]\[NH3+]=pH-PK

the alpha amino group has a charge of +1 based on the above formula
Lysine has a charge of +1 based on the above formula
Arginine has a charge of +1 based on the above formula
the alpha carboxyl group has a charge of -1 based on the above formula

so (+1)+(1)+1+(-1)=+2 so net charge of the peptide is +2 not -4

Am i doing this right??? Is my work right??
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Re: Finding the net charge of amino acid

Postby blcr11 » Thu Oct 02, 2008 9:42 am

Looks good to me. You only need to consider the terminal NH2 and COOH groups, as you've done. All the others are forming amide bonds with the next amino acid in the polypeptide and don't substantially contribute to the pH equilibria. The only other titratable groups are on the side chains and you've correctly identified K and R as the only relevant residues for this peptide. There are trhee positive charges (the free amino terminus and the 2 basic amino acid side chains) and one negative charge (the C-terminal carboxylate) for a net charge of +2. I don't know that you need to use the other formulae you listed but if they help you in some way, fine. These look like part of the Henderson-Hasselbach equation or part of the expression for the Ka or Kb, but I'm not sure what you mean by them. You're getting the correct answer, at least in my opinion. For just the net charge on a peptide, in general you just do the arithematic, saving Henderson-Hasselbach for questions about "% ionized" or "fraction of sample in some or the other ionization state" etc.

Sorry, you do have the complete Henderson-Hasselbach equation there. I didn't look at the formulae carefully enough. As I said, though, I doubt you really have to use them for this kind of problem, but it doesn't hurt and it certainly is a useful equation to understand.
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Postby blcr11 » Sat Oct 04, 2008 12:52 pm

I should correct a mistake I made. The way I said to calculate pI's is partially wrong. For amino acids with non-ionizable side chains, it is correct that the pI is the average of the pKa's of the alpha-amino and alpha-carboxyl groups. It is NOT true, though, that the pI of an amino acid with a titratable side chain is the average of the three pKa's. The pI is the average pKa of the two "like" groups. So, for glutamic acid, for example, the pI is the average of the pKa's of the alpha-carboxyl and the gamma-carboxyl groups, not the average of all three pK's. Sorry if I misled anyone.
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Postby debbie4christ » Tue May 28, 2013 8:12 pm

please, i need help with this question. Estimate the net charge of a polypeptide chain at physiological pH 7.4 and at pH 5.0 Ala-Arg-Val-His-Asp-Gln
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Postby JackBean » Wed May 29, 2013 1:56 pm

list the prononizable groups, find their pKa and define their charge at desired pH. Then just sum the charges and you get your result.
http://www.biolib.cz/en/main/

Cis or trans? That's what matters.
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Re: Finding the net charge of amino acid

Postby Richard02 » Mon Jul 08, 2013 6:58 am

I have difficulty in evaluating the bands sspecially lower than 500 bp.
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Postby JackBean » Mon Jul 08, 2013 12:13 pm

What? This is about amino acid's charges, not electrophoresis.
http://www.biolib.cz/en/main/

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