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In the following peptide:

enter image description here

I want to know the net charge of the peptide at pH=1.

According to me the as the solution is acidic so every nitrogen will get protonated.

Hence the number of charge = number of Nitrogen atom

Am I doing it in correct way?

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You are on the right track, but not every nitrogen atom will be protonated - only those that are basic. None of the nitrogen atoms in amide groups are basic. Neither is the nitrogen atom in the indole side chain on tryptophan. Only one nitrogen is basic for each of the imidazole side chain of histidine and the guanidine side chain of arginine.

Thus, the positive charge in acid is more correctly determmine by the number of basic side chains plus the N-terminus amine.

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  • $\begingroup$ Why they are not basic $\endgroup$ – Icandoahandstand99 Jan 16 '17 at 5:32
  • $\begingroup$ why these are not basic i.imgur.com/H2knPtC.png $\endgroup$ – Icandoahandstand99 Jan 16 '17 at 5:37
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    $\begingroup$ @help Amides exist in resonance ($\ce{RC(=O)N(H)R' <-> RC(-O^-)=N+(H)R'}$) which delocalizes the lone pair, making it not basic. $\endgroup$ – DHMO Jan 16 '17 at 13:56

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