On the Structural Regularity in Nucleobases and Amino Acids and Relationship to the Origin and Evolution of the Genetic Code

Abstract

To explore how chemical structures of both nucleobases and amino acids may have played a role in shaping the genetic code, numbers of sp2 hybrid nitrogen atoms in nucleobases were taken as a determinative measure for empirical stereo-electronic property to analyze the genetic code. Results revealed that amino acid hydropathy correlates strongly with the sp2 nitrogen atom numbers in nucleobases rather than with the overall electronic property such as redox potentials of the bases, reflecting that stereo-electronic property of bases may play a role. In the rearranged code, five simple but stereo-structurally distinctive amino acids (Gly, Pro, Val, Thr and Ala) and their codon quartets form a crossed intersection "core". Secondly, a re-categorization of the amino acids according to their beta-carbon stereochemistry, verified by charge density (at beta-carbon) calculation, results in five groups of stereo-structurally distinctive amino acids, the group leaders of which are Gly, Pro, Val, Thr and Ala, remarkably overlapping the above "core". These two lines of independent observations provide empirical arguments for a contention that a seemingly "frozen" "core" could have formed at a certain evolutionary stage. The possible existence of this codon "core" is in conformity with a previous evolutionary model whereby stereochemical interactions may have shaped the code. Moreover, the genetic code listed in UCGA succession together with this codon "core" has recently facilitated an identification of the unprecedented icosikaioctagon symmetry and bi-pyramidal nature of the genetic code.

A self-referential model for the formation of the genetic code

“…Such strict correspondence could be easily understood if some kind of fit existed between nucleic acid pockets and amino acids. This stereo-chemical hypothesis might be responsible for some of the correspondences (Yang 2005;Legiewicz and Yarus 2005). In fact, the correspondences are mediated by adaptor RNA molecules, the transfer RNAs (tRNA), each one carrying a specific amino acid and bearing a code, a triplet of nucleotides (an anticodon) that matches by base-pairing a triplet in the template mRNA (the codon; Ibba et al 2000;Barbieri 2003).…”

Factors in Protobiomonomer Selection for the Origin of the Standard Genetic Code

“…The association between codons and amino acids could have been affected by the element composition and M (Rosen 1999), by the number of carbon atoms in amino acid side chains (β-carbons), and by the number of C=N bonds in heterocyclic bases: three in A, two in G, one in C, and zero in U (Yang 2005). These stereoelectronic factors might have contributed significantly to the development of symmetry in the genetic code.…”

The Codes of life: the rules of macroevolution

“…Such strict correspondence could be easily understood if some kind of fit existed between nucleic acid surfaces or pockets and the amino acids. This stereochemical hypothesis is not presently in favor for the generation of the whole code but it could have been responsible for some of the correspondences (Yang 2005;Yarus et al 2005). In fact, the correspondences are mediated by adaptor RNA molecules, the transfer RNAs (tRNA), each one carrying a specific amino acid and bearing a code, a triplet of nucleotides (an anticodon) that matches by base-pairing a triplet in the template mRNA (the codon) (Ibba et al 2000;Barbieri 2003).…”