Amino acid with alkaline side chains

This class of amino acids includes those amino acids who have in their side chain an alkaline functional group. This means that these amino acids tend to have positive charge on their side chain as the alkali groups tend to pick up H+. As a result, they usually establish ionic bonds (or salt bridges) with amino acids with negatively charged side chains There are 3 amino acids belonging to this class:

Lysine - This amino acid has in its side chain a primary amine, that means, an amine group which is bonded to only one carbon, while the remaining nitrogen substituents are hydrogen atoms. The amine group is the main alkaline group in biochemistry (more information on this post). Lysine is the primary site of glycosylation of proteins, and in this case, the established connections are N-glycosidic bonds.

 

Arginine - This amino acid has in its side chain a more complex alkali functional group, called guanidine. This is a functional group comprising 3 nitrogen atoms, which displays electronic resonance, and they can be protonated.

Histidine - This amino acid has a cyclic structure in its side chain, more specifically an imidazole ring. It is a heterocycle composed of nitrogen and carbon atoms, in which one of the nitrogens can be protonated. Histidine has a particularly important feature in biochemistry: it is the only amino acid that has substantial buffering capacity at physiological pH (between 6.5 and 7.5), since its pKa is about 6. In this regard, it should be noted, firstly, that the pKa of histidine changes, as this amino acid is inserted into different polypeptide chains, but usually it is not much different from the original value (isolated histidine). Also, the fact that it is important to have a pKa close to physiological pH, relates to the ability of histidine to exist in medium in its acid and alkaline forms at the physiological pH, functioning as an acid-base pair conjugate.