Question

explain the relationship between amino acids, peptide bonds, and protons

Answer 1

I think I can help with some of this question: amino acids are the building blocks of proteins and they are joined together at the ribosome into polypeptides. The peptide bonds are the bonds between the amino acids (also known as amide bonds). Peptide bonds are formed by what is known as a condensation reaction (because water is produced). In this condensation reaction the carboxyl group and the amino group are joined together so peptides can be described in terms of N to C direction.

As for protons, do you really mean proteins? These are either single polypeptides or complexes of two or more peptides.