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Quickly determining charge of peptides in neutral enviornment
Justine_5420
#1 Posted : Friday, July 03, 2020 2:07:15 AM
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Hello,

Stand-alone question 51 of the chem section bank of the AAMC prep asks "At pH 7, which of the following peptides will bind to an anion-exchange column and require the lowest concentration of NaCl for elution?"

To determine the answer, I'm assuming one must find the overall charge on a peptide of 15 a.a's at a pH of 7. Do you have a quick way of determining the overall charge of peptides with multiple a.a's?

Can we go with the assumption - basic R groups have overall positive charge, acidic R groups have overall negative charge, etc.

Thank you in advance.
INSTR_Katerina_102
#2 Posted : Saturday, July 04, 2020 1:35:49 AM
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Hello,

Stand-alone question 51 of the chem section bank of the AAMC prep asks "At pH 7, which of the following peptides will bind to an anion-exchange column and require the lowest concentration of NaCl for elution?"

To determine the answer, I'm assuming one must find the overall charge on a peptide of 15 a.a's at a pH of 7. Do you have a quick way of determining the overall charge of peptides with multiple a.a's?


Usually what I do for this type of thing is I draw out the peptide in one letter amino acid code (here is an example I've conjured up):

AKYDG

I then remind myself that I have an N and C terminus which will have charges, rewriting this as:

N term-AKYDG-C term

Then I assign charges along each amino acid on the peptide (treating N and C termini seperately)

At pH 7

N term = +1
A = 0
K = +1
Y = -1
D = -1
G = 0
C term = -1

I then sum up all these values, giving an overall peptide charge of -1 for this peptide at pH 7.

Can we go with the assumption - basic R groups have overall positive charge, acidic R groups have overall negative charge, etc.


This works well for pH 7, but falls apart when you are at other pHs as the protonation states of amino acids depend on their pKas.

To better answer this type of question at any pH, it is better to know the pKas of amino acid side chains (D, E, K, H, C, R, Y), as well as the pKas of the N and C termini (or NH2 and COOH). Depending on how much time you have, I would recommend memorizing structures of amino acids and their pKas with a software like Anki.

When your pKa is higher than the pH, the side chain will be deprotonated. From this and the structure of the amino acid, you can determine its charge. You would then do the method that I had shown above to get the peptide charge.

Please let me know if this is unclear.
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