Peptide synthesis is most often done using the C-to-N synthesis method. With this method, a carboxyl group of incoming amino acid is coupled to the N-terminus of a growing peptide chain. During the synthesis, the N-terminus of the incoming amino acid is coupled to the C-terminus of the protein chain.
Since the nature of in vitro protein synthesis is very complex, the additional amino acids added to the growing peptide chain takes place in a precise, step by step and cyclic manner. In as much as the common peptide synthesis processes have some critical differences, they all adhere to the same step by step method in the addition of amino acids to the growing peptide chain.
Amino acids have several reactive groups and due to this, peptide synthesis must be done with great caution to avoid causing side reactions which might reduce the length of the peptide chain. To allow for the formation of peptides with very little side reactions, chemical groups are developed to batch together the amino acid reactive groups and in the process, the functional groups are thus protected from the nonspecific side reactions.
Purified amino acids which in peptide synthesis are first reacted with the protective groups before the synthesis begins, after which the specific protective synthesis group is eliminated from the newly added amino acid after coupling so that the next incoming amino acid can be bounded together to the increasing peptide chain in the proper alignment. This is the process known as peptide de-protection in the synthesis of amino acids.
After the peptide synthesis is over, all the remaining protective groups are taken away from the nascent peptides. Most of the times, three types of protective groups are used and this normally depend the specific type of peptide synthesis used.