The Second Major Transition The Origin of Proteins

Proteins are the key building blocks of all living structures, as well as the engines of countless reactions that go on within those structures. For all their extraordinary versatility, however, there is one thing they cannot do. Unlike genes, they cannot be their own templates. It is simply not possible to make proteins by copying other proteins. The transition from spontaneous to manufactured molecules, therefore, was relatively simple for genes but much more complex for proteins. Manufactured genes could be made simply by copying natural genes, and all that was required to that purpose were molecules which had a polymerase-like activity. Manufactured proteins, instead, could not be made by copying, and yet the information to make them had to come from molecules that can be copied, because only those molecules can be inherited. The information for manufacturing proteins, therefore, had to come from genes, so it was necessary to bring together a carrier of genetic information (a messenger RNA), a peptide-bondmaker (a piece of ribosomal RNA) and molecules that could carry both nucleotides and amino acids (the transfer RNAs). The first protein-makers, in short, had to bring together three different types of molecules (messenger, ribosomal and transfer RNAs), and were therefore much more complex than copymakers.

The outstanding feature of the protein-makers, however, was not the number of components. It was the ability to ensure a one-to-one correspondence between genes and proteins, because without it there would be no biological specificity, and without specificity there would be no heredity and no reproduction. Life as we know it simply would not exist without a one-to-one correspondence between genes and proteins.

Such a correspondence would be automatically ensured if the bridge between genes and proteins could be determined by stereochemistry, as one of the earliest models suggested, but that is not what happens in Nature. The bridge is always provided by molecules of transfer RNA, first called adaptors, that have two recognition sites: one for a group of three nucleotides (a codon) and another for an amino acid. In this case, a one-to-one correspondence could still be guaranteed automatically if one recognition site could determine the other, but again that is not what happens. The two recognition sites of the adaptors are physically separated in space and are chemically independent. There simply is no necessary link between codons and amino acids, and a one-to-one correspondence between them can only be the result of conventional rules. Only a real code, in short, could guarantee biological specificity, and this means that the evolution of the translation apparatus had to go hand in hand with the evolution of the genetic code.

Protein synthesis arose, therefore, from the integration of two different processes, and the final machine was a code-and-template-dependent-peptide-maker, or, more simply, a codemaker. The second Major Transition of the history of life is generally described as the origin of proteins, but it would be more accurate to say that it was the origin of codemaking, or the origin of codemakers, the first molecular machines that discovered molecular coding and started populating the Earth with codified proteins.

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