On the Structural Regularity in Nucleobases and Amino Acids and Relationship to the Origin and Evolution of the Genetic Code
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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.
Keywordsamino 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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- Alberty, S.: 2001, Physical Chemistry, 3rd ed., John Wiley & Sons, Inc., Chapter 11, p. 418.Google Scholar
- Cedergren, R. and Miramontes, P.: 1996, The Puzzling Origin of the Genetic Code, Trends Biochem. Sci. 21, 199–200. Erratum in: 1996, Trends Biochem. Sci. 21, 396. Comment in: 1997, Trends Biochem. Sci. 22, 49–50.Google Scholar
- Eigen, M. and Schuster, P.: 1979, The Hypercycle: A Principle of Natural Self-Organization, Springer-Verlag, Heidelberg.Google Scholar
- Nelson, D. L. and Cox, M. M.: 2000, Lehninger Principles of Biochemistry, Worth Publishers, New York.Google Scholar
- Woese, C. R.: 1967, The Genetic Code, Harper & Row, New York.Google Scholar
- Yang, C. M. and Chen, Y.: 2000, Protein Only or Virino? Chin. Sci. Bull. 45, 285–289.Google Scholar
- Yang, C. M.: 2000, An “i-4, i, i+4” “Reductive and Nucleophilic Zipper” Shared by Both Prion Protein and Beta-Amyloid Peptide Sequences Supports a Common Putative Molecular Mechanism, Chem. J., Internet http://www.chemistrymag.org/cji/2000/027035le.htm.
- Yang, C. M., Li, W., Hang, Q. and Cheng, J. P.: 2001, Protein Chemical Biology in Neurodegenerative Disorders, Prog. Nat. Sci. 1, 673–681.Google Scholar
- Yang, C. M.: 2002, Physical Organic Chemistry in Neurodegenerative Diseases, Chem. J. Chin. Univ. 23, 243–250.Google Scholar
- Yang, C. M.: 2003, On the quasi-icosikaioctagon (quasi-28-gon) Symmetry and Presumed Evolutionary Axes of the Genetic Code, http://preprint.chemweb.com/biochem/0306003, submitted for publication.