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. The primary structure is linear. Interactions between atoms in the amino acids lead to folding that forms the proteins final complex shape. Here the amino acids are; asparagine (orange), glutamine (yellow), histidine (green), leucine (blue), cysteine (brown) and glycine (cyan).