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Chemically polar amino acids have an uneven (AKA polar) distribution of electrons over their surface.

Charged amino acids have a charged ion in their structure. This is probably where my knowledge is a little shaky!

I guess I am confused at this point. Does this just mean that charged amino acids are really polar amino acids? If that is correct that would explain why I have seen histidine categorised as a charged amino acid, but has no clear ions.

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    $\begingroup$ You can see this post on why histidine has a low tendency to form ion compared to other positively charged amino acids. $\endgroup$
    – WYSIWYG
    Commented May 15, 2015 at 6:28
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    $\begingroup$ A related question: biology.stackexchange.com/questions/23763/… $\endgroup$
    – inf3rno
    Commented May 17, 2015 at 16:40

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All amino acids with side chains that are charged at physiological pH are, by definition, also amino acids with polar side chains (e.g., lysine or glutamic acid). The converse is not true; in other words not all amino acids with polar side chains are necessarily amino acids with side chains that are charged at physiological pH (e.g., threonine or asparagine). The pKa of the nitrogen in histidine's imidazole ring is quite close to physiological pH, and in some situations would be charged and in other environments would be uncharged. In either case it would be considered polar (or largely hydrophilic in nature).

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