Why are acidic amino acid side chains acidic?

[nucleargirl]

I have been trying to work this out over 2 days now and I just don't understand!
The side chains of Aspartic acid and Glutamic acid both have the reactive group COO^-.
I don't understand how the COO^- is an acidic group! To me, I can see how it could be a basic group - the H⁺ binds to the COO^- and becomes COOH. But how does COO^- donate a H⁺ ion?


And the same question for the basic amino acid side chains. How is NH3⁺ a basic group? Doesn't NH3⁺ become NH2 in solution and therefore donates a H⁺??

 

[Ygggdrasil]

You are right, the carboxylate (-COO^-) on glutamate and aspartate would act as a base and the ammonium group (-NH₃⁺) of lysine would act as an acid. However, biologists just classify these amino acids based on the behavior of their neutral forms. So, glutamic acid and aspartic acid have a carboxylic acid (-COOH) that acts as an acid and lysine has an amino group (-NH₂) that acts as a base. Alternatively, you can think of classifying the side groups by their pKa. The side group of glutamate and aspartate has a low pKa value while the side chains of arginine and lysine have high pKa values.

 

[Yanick]

They are considered acidic side chains because they contain the carboxylic acid functional groups (-COOH). The reason you see them drawn or written as the carboxylate forms is because the pKa of carboxylic acids is around 4-5, at physiological pH's (~7) the carboxylate form predominates. This is also why they may be referred as Aspartic Acid (-COOH) or Aspartate (-COO^-).*

The same can be said for Lysine. The pKa of ammonium (NH₄⁺) is around 9. This means that at pH ~7, the ammonium form predominates over the ammonia form.*

So you will typically see amino acids or peptides drawn with the carboxylates deprotonated and the amine groups protonated.

*These statements hold strictly true for free amino acids in solution. Once we are talking about peptides and proteins and such, pKa's can have drastically different values for the same functional group. Other amino acid may aid to stabilize or destabilize certain forms and the pKa may be off by a few units. Therefore its not strictly true that an aspartate is ALWAYS deprotonated at pH ~7.

 

[nucleargirl]

huh, so actually the amino acids have the COOH and NH₂ side chains when they are not in solution? and then when they are in solution they become COO^- or NH₃⁺?

 

[Yanick]

Well yes and no. Because the pKa's of carboxylic acids and amine groups are far enough away from each other, its almost a necessity that one of them be a salt (-COONa) if the other is in its neutral form (-NH₂). So it pretty much depends on the conditions, but yes when things are solid (not dissolved in some polar solvent), they don't have charges so you either have to have a charge with a counter ion (Na+ or Cl- for example) of you need the "protonation status" to yield a neutral charge, IE protonated acid groups or deprotonated amine groups.

My little footnote on the bottom regarding the pKa's changing depending on the environment still assumes aqueous environment, just whole peptides or proteins (with the tertiary/quaternary structure) instead of free amino acids.