Protein primary structure, illustration. The primary structure of a protein is the sequence of amino acids that form its polypeptide chain. The amino acids are joined by covalent bonds known as peptide bonds. They are formed when the alpha carboxyl group (grey and red) of an amino acid reacts with the alpha amino group (blue) of another amino acid, releasing a water molecule. The repeating structure of amino groups, alpha carbons (yellow) and carboxyl groups form the backbone of the polypeptide. Side chains (green), known as R groups, project from the backbone and determine the type of amino acid. The primary structure is linear. Interactions between atoms in the amino acids lead to folding that forms the proteins final complex shape. Here, from left to right the amino acids are; asparagine, glutamine, histidine, leucine, cysteine and glycine.