Finding the net charge of amino acid
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Re: Finding the net charge of amino acid
How did you arrive at 4?
NH3+KAPRMCOO
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]=pHpK or log[NH2]\[NH3+]=pHPK
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??
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]=pHpK or log[NH2]\[NH3+]=pHPK
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??
Re: Finding the net charge of amino acid
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 Cterminal 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 HendersonHasselbach 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 HendersonHasselbach for questions about "% ionized" or "fraction of sample in some or the other ionization state" etc.
Sorry, you do have the complete HendersonHasselbach 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.
Sorry, you do have the complete HendersonHasselbach 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.
I should correct a mistake I made. The way I said to calculate pI's is partially wrong. For amino acids with nonionizable side chains, it is correct that the pI is the average of the pKa's of the alphaamino and alphacarboxyl 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 alphacarboxyl and the gammacarboxyl groups, not the average of all three pK's. Sorry if I misled anyone.

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Re: Finding the net charge of amino acid
I have difficulty in evaluating the bands sspecially lower than 500 bp.
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