The Mystery of Stop-Codons....

Each different tRNA in an organism would have to be encoded by a different gene, each of which would either arise independently or as a variation of the first tRNA gene. Either way, they would have arisen one by one.

The transfer RNA (tRNA) multigene family comprises 20 amino acid-accepting groups, many of which contain isoacceptors. The addition of isoacceptors to the tRNA repertoire was critical to establishing the genetic code, yet the origin of isoacceptors remains largely unexplored. A model of tRNA evolution, termed tRNA gene recruitment, was formulated. It proposes that a tRNA gene can be recruited from one isoaccepting group to another by a point mutation that concurrently changes tRNA amino acid identity and messenger RNA coupling capacity.

In certain proteins, non-standard amino acids are substituted for standard stop codons, depending upon associated signal sequences in the messenger RNA: UGA can code for selenocysteine and UAG can code for pyrrolysine as discussed in the relevant articles. Selenocysteine is now viewed as the 21st amino acid, and pyrrolysine is viewed as the 22nd. A detailed description of variations in the genetic code can be found at the NCBI web site.

AGA and AGG (AGR) are arginine codons in the universal genetic code. These codons are read as serine or are used as stop codons in metazoan mitochondria.

While some groups of single-celled organisms & organelles do use a slightly different coding system to that used in most prokaryotes and (IIRC) all eukaryotes, it is not the case that veterbrate and invertebrate codings are different.

The genetic code, understood as the specific assignment of amino acids to nucleotide triplets, might have preceded the existence of translation.Amino acids were utilized as cofactors by ribozymes in a metabolically complex RNA world. Specific charging ribozymes linked amino acids to corresponding RNA handles, which could basepair with different ribozymes, via an anticodon hairpin, and so deliver the cofactor to the ribozyme.Growing of the ”handle’ into a presumptive tRNA was possible while function was retained and modified throughout.A stereochemical relation between some amino acids and cognate anticodons/codons is likely to have been important in the earliest assignments.

A coherent pattern of evolution will be seen to emerge in which addition of a new amino acid to the code typically followed path extension, tRNA diversification to a new acceptor, expansion in synthetase specificity and selection for each synthesized protein.

The coevolution hypothesis (Wong, 1975, 1976) requires that precursors among coded amino acids entered the code before their products. In this section, the time of entry of each amino acid into the code has been estimated from the number of reactions in its biosynthetic pathway. A phased pattern of synthesis emerges, in the sense that physicochemically divergent amino acids appear at divergent stages of code evolution. This has significant implications for code evolution and the origin of life.