On the Structural Regularity in Nucleobases and Amino Acids and Relationship to the Origin and Evolution of the Genetic Code |
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Authors: | Email author" target="_blank">Chi?Ming?YangEmail author |
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Institution: | (1) Neurochemistry and System Chemical Biology, Nankai University, Tian Jin, 300071, China |
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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 β-carbon stereochemistry, verified by charge density (at β-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. |
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Keywords: | amino acid classification charge distribution coevolution β -C stereochemistry determinative measure frozen core nitrogen atom hybrid sp2 nucleobase redox potentials rearranged genetic code stereo-electronic factor |
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