Twenty Canonical Amino Acids of the Genetic Code: The Arithmetical Regularities. Part I

Shcherbak, V.I.

doi:10.1006/jtbi.1993.1096

Cited by 23 publications

(21 citation statements)

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“…Shcherbak (1993Shcherbak ( , 1994Shcherbak ( , 2003, Rakočević (2004), and Downes and Richardson (2002). Recently, Perez (2010) showed that the human genome as a whole single strand was of a fractal type with regard to frequency of codons.…”

Section: Some General Viewsmentioning

confidence: 98%

Numeral series hidden in the distribution of atomic mass of amino acids to codon domains in the genetic code

Wohlin¹

2015

Journal of Theoretical Biology

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The distribution of codons in the nearly universal genetic code is a long discussed issue. At the atomic level, the numeral series 2x(2) (x=5-0) lies behind electron shells and orbitals. Numeral series appear in formulas for spectral lines of hydrogen. The question here was if some similar scheme could be found in the genetic code. A table of 24 codons was constructed (synonyms counted as one) for 20 amino acids, four of which have two different codons. An atomic mass analysis was performed, built on common isotopes. It was found that a numeral series 5 to 0 with exponent 2/3 times 10(2) revealed detailed congruency with codon-grouped amino acid side-chains, simultaneously with the division on atom kinds, further with main 3rd base groups, backbone chains and with codon-grouped amino acids in relation to their origin from glycolysis or the citrate cycle. Hence, it is proposed that this series in a dynamic way may have guided the selection of amino acids into codon domains. Series with simpler exponents also showed noteworthy correlations with the atomic mass distribution on main codon domains; especially the 2x(2)-series times a factor 16 appeared as a conceivable underlying level, both for the atomic mass and charge distribution. Furthermore, it was found that atomic mass transformations between numeral systems, possibly interpretable as dimension degree steps, connected the atomic mass of codon bases with codon-grouped amino acids and with the exponent 2/3-series in several astonishing ways. Thus, it is suggested that they may be part of a deeper reference system.

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Section: Some General Viewsmentioning

confidence: 98%

Numeral series hidden in the distribution of atomic mass of amino acids to codon domains in the genetic code

Wohlin¹

2015

Journal of Theoretical Biology

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“…Shcherbak showed that a specific classification of the protein amino acids (AAs), "canonical" amino acids within the genetic code (GC), reveals some arithmetical regularities and stated that "the physical nature of such a phenomenon is so far not clear" (Shcherbak, 1993). There is a similar statement of A. Verkhovod in his work on the same subject and published a few months later: "The nature of these mechanisms is presently unknown" (Verkhovod, 1994).…”

Section: Analogies With Quantum Physicsmentioning

confidence: 71%

“…On all the said and some other similar investigations of mathematical regularities of the GC one can see the following works: (Sukhodolets, 1985;Leunissen and De Jong, 1986;Koruga, 1992;Madox, 1992Madox, , 1994Shcherbak, 1993Shcherbak, -2008Damjanović, 1998Damjanović, -2006Qiu and Zhu, 2000;Yang, 2004;Dragovich, 2006Dragovich, -2012Negadi, 2009Negadi, -2014Castro-Chavez, 2010Mišić, 2011;Petoukhov, 2014;2016;Wohlin, 2015;Rakočević, 1988Rakočević, -2014.…”

Section: Some Other Mathematical Formalismsmentioning

confidence: 99%

Analogies of genetic and chemical code

Rakočević

2018

Polyhedron

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Abstract. Starting from the previously established hypothesis on the existence of "the coherence of the chemical and genetic code" (Rakočević, 1991), new facts and new insights on the existence of essential analogies between the genetic and chemical code are presented, whereby the chemical code is derived from the original Mendeleev's work on the periodic system of chemical elements. When, namely, the 14 lanthanides are scheduled into 14 groups of Periodic system of chemical elements (PSE) (Rakočević, 1991), in accordance to Mendeleev's original manuscript tables, then are revealed some very specific mathematical and chemical regularities within the PSE; among others, PSE appears to be a code -the chemical code -in an entity analogy with the terrestrial genetic code. These regularities correspond to the mathematical regularities within the genetic code. Between others relations, it appears also a correspondance between the distribution of codons in the Genetic Code Table and the distribution of chemical elements in the PSE with respect to their even/odd parity and stability/instability of the isotopes. Based on the significant mathematical expressions it is showed a new essence of coding formalism in natural code as such: it cannot be reduced only to two alphabets (which are consequences, and not the cause); a natural code is such an essence that can be represented by an appropriate mathematical expression, which contains a sequence from the series of natural numbers within itself. From this follows that both are natural codes, the Genetic code as well as the Periodic system of chemical elements (PSE).

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“…An assumption is that different types of amino acids are needed to achieve the desired functions in proteins. Although these 20 amino acids can traditionally be grouped according to their side-chain physicochemical properties (non-polar, polar uncharged, polar negatively charged or acidic, polar positively charged or basic, aromatic and non-aromatic), their yet unclear physicochemical property has since inspired tremendous excellent research and speculation (Weber and Miller, 1981;Swanson, 1984;Shcherbak, 1993;Rakocevic and Jokic, 1996;Dufton, 1997;Pastushenko and Pastushenko, 1997;Davydov, 1998).…”

Section: Categorizations Of Amino Acids According To Their β-Carbon Smentioning

confidence: 99%

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

Yang

2005

Orig Life Evol Biosph

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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 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.

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Twenty Canonical Amino Acids of the Genetic Code: The Arithmetical Regularities. Part I

Cited by 23 publications

References 0 publications

Numeral series hidden in the distribution of atomic mass of amino acids to codon domains in the genetic code

Numeral series hidden in the distribution of atomic mass of amino acids to codon domains in the genetic code

Analogies of genetic and chemical code

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

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