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Why is Cysteine and Tyrosine used to calculate a sequence isoelectric point?
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+ Bioinformatics
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Nicolae Palibroda
Why is Cysteine and Tyrosine used to calculate a sequence isoelectric point?
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.
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.
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.More
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.More
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.More
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:
5.97.9.74than glycine.3.22than glycine.Every side chain has more or less contribution to the IEP of the amino acid. In your question
5.075.66And every amino acid has more or less contribution to the IEP of a protein.
References:
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:
5.97.9.74than glycine.3.22than glycine.Every side chain has more or less contribution to the IEP of the amino acid. In your question
5.075.66And every amino acid has more or less contribution to the IEP of a protein.
References:
More
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