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In the protonated form of lysine, the positive charge is localized on one nitrogen atom. In...

In the protonated form of lysine, the positive charge is localized on one nitrogen atom. In the protonated form of arginine, the charge is delocalized on 3 nitrogen atoms. Why does this explain why the side chain of arginine has higher pKa than the side chain of lysine?

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Answer #1

Arginine has a pKa of 13.8 while Lysine has a pKa of 10.5 of protonation.

as pKa increases acidity decreases or the deprotonation decreases. Also stability increases.

The very high pKa of Arg results from delocalization of the positive charge within the π-bonded system of the side chain guanidinium ion. This increases the stability of the protonated form thus higher pKa

This contrasts within Lys in case of which the charge is focused on the terminal aliphatic amino group and the side chain is readily deprotonated in proteins as this localised charge destabilizes the molecule forcing it to deprotonate.

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