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Why are the amino acids - cysteine and tyrosine used in isoelectric point calculations for a protein sequence, yet neither of them are positively charged molecules? and are not used in net charge calculations.

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    $\begingroup$ Both have ionisable side chains. $\endgroup$ – canadianer Oct 30 '14 at 17:45
  • $\begingroup$ I still don't know why 7 amino acids are used for isoelectric point and only 5 for net charge? $\endgroup$ – user2679447 Jan 23 '15 at 15:59
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Every amino acid has a different isoelectric point: a pH where they do not carry electric charge. This isoelectric point depends on the side chains:

  • By glycine the side chain $-H$ is neutral (while the amino and carbonic acid groups are not) so the IEP is 5.97.
  • By lysine the side chain $-(CH_2)_4\mbox{-}NH_2$ is alkaline $[R\mbox-NH_2 + H^+ \rightleftharpoons R\mbox-NH_3^+]$, so it will have a more alkaline IEP 9.74 than glycine.
  • By glutamic acid the side chain $-(CH_2)_2\mbox -COOH$ is acidic $[R\mbox -COOH \rightleftharpoons R\mbox -COO^- + H^+]$, so it will have a more acidic IEP 3.22 than glycine.

Every side chain has more or less contribution to the IEP of the amino acid. In your question

  • the side chain of cysteine $-CH_2\mbox-SH$ is a weak acid $[R\mbox-SH \rightleftharpoons R\mbox-S^- + H^+]$ so the IEP is 5.07
  • the side chain of tyrosine $-CH_2\mbox-Ph\mbox-{\scriptsize (p)}OH$ is an even weaker acid $[R\mbox-OH \rightleftharpoons R\mbox-O^- + H^+]$ so the IEP is 5.66

And every amino acid has more or less contribution to the IEP of a protein.

References:

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    $\begingroup$ Plus the phenyl group (or any group) can also exert effects on the ionizability of the amino acid (inductive and resonance effects). It is also incorrect to calculate pI of the entire protein from the sum of its parts. $\endgroup$ – WYSIWYG Oct 31 '14 at 4:36
  • $\begingroup$ @WYSIWYG Yes, I think they just want to roughly estimate the value of pI. $\endgroup$ – inf3rno Oct 31 '14 at 11:50
  • $\begingroup$ I only want a simple linear equation for pI. I still don't understand how if net charge/pI are more or less the same thing. Why you would use D,E,H,K,R for net charge and D,E,H,K,R and C,Y for isoelectric point? Sorry I'm not a biologist or a chemist. $\endgroup$ – user2679447 Oct 31 '14 at 13:15
  • $\begingroup$ @user2679447 en.wikipedia.org/wiki/Isoelectric_point The net charge depends on the pH, the pI of the protein/amino acid is the pH where the net charge is zero. So pI and net charge are completely different things. $\endgroup$ – inf3rno Oct 31 '14 at 14:43

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