I'm not really sure what you are asking, but I'll try.
The side-chains of the ionizable amino acids most certainly are ionized in a way determined by the pH of the solution that they are in.
Now, if you are asking about how we often represent the formation of a peptide bond, let me take a shot. First, the formation of a peptide bond is often shown as:
---COOH + NH2---- --> ---CONH--- + H2O
Where the -OH from the carboxyl group and one H-- from the amino group form water. And here, the amino acids are shown in their unionized forms.
Just as valid (as shown in some texts) is:
---COO- + H3N+---- --> ---COHN--- + H2O
Where the O of the carboxyl and 2 H from the NH3+ are remove to form water.
In reality, peptide bonds are not formed in this manner, but are formed during the translation process where the amino acid is first covalently linked to a tRNA and then the growing polypeptide is transferred from one tRNA onto the amino acid on the next. In this process, the water is formed in the earlier step of linking the amino acid to the tRNA and not actually during the formation of the peptide bond.
Not sure if this helps or not....