Yes, mathematically pKa = -log (Ka), while Ka represents the ionization equilibrium constant for a given ionic species. For that, Ka = [H+]x [A-] / [HA]. But what that means? Well, it means that this acid or base, when in solution, will ionize in the proportions given by its Ka. In other words, Ka actually becomes a measure of how much an ionic substance (acid or base) will ionize in aqueous solution. This property is intrinsic for each substance and can be affected by pH or temperature, because both of them can change the equilibrium between ionized and non-ionized forms (Ka).
So what’s pKa for? It represents the exactly same thing, but easier to represent in numbers and graphics than Ka itself. pKa, or simply pK, represents the tendency towards ionization for a given acidic/basic substance or group. However attention must be paid here, as we’re dealing with -log(Ka), have in mind that lower pK values indicate acidic species that easily ionize, while higher pK values indicate basic species, that do the exact opposite, to remain protonated. Making it simple, the lower the pK, the stronger the acid.
Amino-acids are weak acids and pK will not affect their structure, but their charge. As pK is influenced by pH, changing the pH of a solution can change charges of ionizable groups in amino-acids. In a free amino-acid solution it does not interfere with their structure. However when considering amino-acids residues in a protein, changes in pH may disturb ionic interactions between charged residues (simply because their charges will also change) and thus, lead to protein denaturation.
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