Amino Acid Charge Question

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SyrianHero

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How do you go about reasoning through a question like this: What is the net charge of the peptide Arg–Ala–Phe–Leu at pH 8?

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There are only five carboxylic acids that have side chains that can be charged: two carboxylic acid ones and three basic ones. At a pH greater than the carboxylic acids' pKa, the carboxylic acids act as, well, acids and are deprotonated, giving you a negative charge. Otherwise, they remain protonated and are not charged. At a pH lower than a basic amino acid's pKa, it acts as a base and is protonated, giving you a positive charge.

So, the carboxylic acid amino acids are aspartic and glutamic acid. The basic ones are lysine, arginine, and histidine. Of the ones you listed, only one can be charged - arginine. Since the pKa of arginine is 12.5, it's going to be protonated and thus have a positive charge. Now, you can't forget the amino and carboxylic acid terminuses. The amino terminus has a pKa of 9.7 and the carboxylic acid terminus has a pKa of 2.0. So the amino terminus will be protonated and the carboxylic acid terminus will be deprotonated.

These are the only charges on the peptide chain and so if you add them up, you get +1.
 
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For all amino acids, the -COOH group has a pka around 2 and the -NH3+ group has a pka from 9-11. So for the nonpolar amino acids, a pH from around 3 to 8 will give a neutral charge (COO- and NH3+). The positively charged amino acids have pkas above 10 except for histidine, so from pka 3-8 they will be +1 (COO- NH3+ NH3+).

So the molecule you mentioned at pH 8 will look like:
(N terminus)Arg–Ala–Phe–Leu(C terminus)
NH3+-NH3+-no charge-no charge -no charge-COO-

This gives a net +1 charge
 
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For all amino acids, the -COOH group has a pka around 2 and the -NH3+ group has a pka from 9-11.

Just to clarify - this only matters for amino acids at the end of the peptide chain, i.e. the terminuses. This is because the amino and carboxylic acid terminuses on the intermediate amino acids in the peptide chain are used in the linkages. Just a minor point, but it might help make everything less confusing for the OP.
 
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There are only five carboxylic acids that have side chains that can be charged: two carboxylic acid ones and three basic ones. At a pH greater than the carboxylic acids' pKa, the carboxylic acids act as, well, acids and are deprotonated, giving you a negative charge. Otherwise, they remain protonated and are not charged. At a pH lower than a basic amino acid's pKa, it acts as a base and is protonated, giving you a positive charge.

So, the carboxylic acid amino acids are aspartic and glutamic acid. The basic ones are lysine, arginine, and histidine. Of the ones you listed, only one can be charged - arginine. Since the pKa of arginine is 12.5, it's going to be protonated and thus have a positive charge. Now, you can't forget the amino and carboxylic acid terminuses. The amino terminus has a pKa of 9.7 and the carboxylic acid terminus has a pKa of 2.0. So the amino terminus will be protonated and the carboxylic acid terminus will be deprotonated.

These are the only charges on the peptide chain and so if you add them up, you get +1.

Shouldn't histidine (Pka 6.0) be "acidic" in physiological PH of ~7 ?
 
Histidine tends to act as a base in many reactions, in many reactions the pka of histidne changes based on what amino acids are around, more so than lysine and arg, histindine from what I have seen, can act as an acid or based at physiological ph
 
Histidine tends to act as a base in many reactions, in many reactions the pka of histidne changes based on what amino acids are around, more so than lysine and arg, histindine from what I have seen, can act as an acid or based at physiological ph

Yes, that is why His is said to act as a biological buffer.
 
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