When the machinery of translation reaches a stop signal, a non-functional protein chain is released. Immediately after their release, protein chains are subject to a variety of modifications. The first of these so called posttranslational modifications is common to all proteins and consists in the folding of the protein chain in its unique three-dimensional structure. Some proteins are further subjected to other modifications like, for instance, the chemical modification of some amino acids which greatly enriches the language of proteins, the formation of covalent bonds between particular amino acids, and the removal of some fragments to shorten the chain length. Finally, some folded protein chains (subunits) must aggregate with other subunits to form a multi-subunit protein. Such multi-subunit proteins include many of the most important enzymes and transport proteins in the cell. These proteins are said to have a quaternary structure, the highest level of protein organization.

What is important to understand here, is that each level of protein organization is built on the lower levels, and everything is dictated by the primary structure of the protein, which obviously is ultimately dictated by the gene. Another important thing is that when a protein chain folds itself, amino acids separated by long stretches in the linear chain might be brought together in the final three-dimensional structure; the opposite might also happen and neighbor amino acids in the protein chain may face completely different moieties and be involved in distinct aspects of the structure or functionalities of the protein. Finally, the most important fact about protein structure and function is that the function of a particular protein is dictated by its unique three-dimensional structure, which is ultimately dictated by the sequence of the gene. Note, however, how far a protein is from its DNA sequence! Such is the power of simple transformations and the beauty of emergence.

The expression trees of GEP are also the products of simple transformations and the results are equally overwhelming. We will also see that, in GEP, the expression trees also fold in particular ways, bringing together elements distant in the gene, and separating others that were close. We will also see that some expression trees have a quaternary structure, being composed of smaller subunits (sub-expression trees) which are linked together by different kinds of posttranslational interactions.