[kekie]

So if you have a generic amino acid (R group just shown as 'R'), and you start increasing the pH (making it more basic) then you'd go through the following phases;

Right?

But when I see explanations of peptide bonding, it looks like there is a NH2 (deprotonated) and a COOH (protonated).

Since things proceed from left to right as shown above (pKa of COOH is 2.2, pKa of NH3 is 9.5) how could that exist?

[Yggdrasil]

The type of reaction mechanisms you're looking at are simplifications of what actually goes on during biological peptide bond formation.  In reality, the carboxy terminus of the amino acid or peptide is linked to a transfer RNA via an ester bond.  This tRNA ester is a much better leaving group than the hydroxyl leaving group that is typically drawn in the simplified reaction mechanism.  So, while the reaction does require a deprotonated amine, it does not also require a protonated carboxyl, since the carboxyl group is not present during the actual reaction on the ribosome.

[kekie]

Thanks!