File:Common Periodic Table of Codons & Amino Acids.jpg

Background The Proteomic Code revitalizes a very old dilemma and dispute about the origin of the genetic code, represented by Carl Woese and Francis Crick. Is there any logical connection between any properties of an amino acid on the one hand and any properties of its genetic code on the other? Carl Woese [1] argued that there was stereochemical matching, i.e., affinity, between amino acids and certain triplet sequences. He therefore proposed that the genetic code developed in a way that was very closely connected to the development of the amino acid repertoire, and that this close biochemical connection is fundamental to specific protein–nucleic acid interactions. Crick [2] considered that the basis of the code might be a “frozen accident”, with no underlying chemical rationale. He argued that the canonical genetic code evolved from a simpler primordial form that encoded fewer amino acids. The most influential form of this idea, “code co-evolution,” proposed that the genetic code co-evolved with the invention of biosynthetic pathways for new amino acids [3].

Construction A periodic table of codons has been designed [4] where the codons are in regular locations. The table has four fields (16 places in each) one with each of the four nucleotides (A, U, G, C) in the central codon position. Thus, AAA (lysine), UUU (phenylalanine), GGG (glycine) and CCC (proline) were placed into the corners of the fields as the main codons (and amino acids) of the fields. They were connected to each other by six axes. The resulting nucleic acid periodic table showed perfect axial symmetry for codons. The corresponding amino acid table also displaced periodicity regarding the biochemical properties (charge and hydropathy) of the 20 amino acids, and the position of the stop signals. The table emphasizes the importance of the central nucleotide in the codons, and predicts that purines control the charge while pyrimidines determine the polarity of the amino acids. This prediction was experimentally tested.

Importance These results give a clear-cut answer for the Woese vs Crick dilemma: there is a connection between the codon structure and the properties of the coded amino acids. The second (central) codon base is the most important determinant of the amino acid property. The codon/amino acid co-evolution is an important argument for the Proteomic Code.

References 1. Woese CR: Chapters 6-7. In: The Genetic Code. The Molecular Basis for Genetic Expression. New York: Harper & Row: 1967:156-160. 2. Crick FHC: The origin of the genetic code. J Mol Biol 1968, 38:367-379. 3. Wong JT: Evolution of the genetic code. Microbiology 1988, 5:174-181. 4. Biro JC, Benyo B, Sansom C, Szlavecz A, Fordos G, Micsik T, Benyo Z: A common periodic table of codons and amino acids. Biochem Biophys Res Commun 2003, 306:408-415.

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