As the pH increases, the amino group looses a proton. Proteins are formed by a condensation reaction that joins the amino group of one amino acid with the carboxyl group of another. The resulting bond is a type of covalent bond called a peptide bond.Thus, proteins are also called polypeptides-because they contain oodles of peptide bonds.rimary structure-Refers to the sequence of amino acids in the protein. Once formed, the protein immediately folds and takes on a particular 3D configuration (see below). The shape of the protein is determined by the sequence of amino acids (the primary structure). Let s use pop beads to model a protein.