Arginine is positively charged at physiological pH, with a pK value for its side chain of 12.5. The pK is the pH at which 50% of the side chains are protonated. At lower pH the proportion that are protonated rises, as the proton concentration increases. As the pK of the arginine side chain is so much higher than physiological pH, they are almost completely protonated.
Another amino acid that can accept protons at physiological pH, and therefore become positively charged, is histidine. The pK of the histidine side chain is 6.0, and is modified by the local environment. This is much closer to physiological pH, enabling histidine to act as a reversible proton carrier, e.g. in haemoglobin.
Dibasic amino acids with positively charged side chains are cystine, ornithine, arginine and lysine. In cystinuria a defect of the dibasic amino acid transporter in the renal tubule leads to excess quantities of all of these amino acids being present in the urine, when cystine rises to concentrations that are insoluble, leading to the formation of cystine stones.
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