Genetic Code as a Coherent System

Rakočević, Miloje M.

doi:10.14704/nq.2011.9.4.502

Cited by 11 publications

(21 citation statements)

References 13 publications

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“…If we exclude the number of hydrogen atoms, that is hydrogen protons (58 + 59 = 117) of all 20 side chains, then remain 569 protons + 569 neutrons. At the same time, from Sukhodolets' system (Table C.2 in this paper in relation to Table 7, p. 830 in Rakočević, 2011b) follows a symmetrical division of AAs into two sub-classes with 58 and 59 hydrogen atoms, respectively.…”

Section: Another Similaritiesmentioning

confidence: 85%

“…Tables 4.1 & 4.2 in: Rakočević, 1991, or Tables 18 & 20 in: Rakočević, 1997b.) (The Reference: Rakočević, 1997b one can see in website: www.rakocevcode.rs)…”

Section: The Problem Of Lanthanides Arrangement In the Psementioning

confidence: 99%

“…21 [The GC satisfies the golden mean, over the set of all atoms (Rakočević, 1998b(Rakočević, , 2011b as well as through the number of carbon atoms in 20 amino acids (Yang, 2000).] This should in particular be kept in mind for further testing "a new standpoint for addressing questions of selection vs random drift in the evolution of the code" (Swanson, 1984).…”

Section: Some Additional Observationsmentioning

confidence: 99%

“…this regularity of the hydrogen atoms within amino acids (in relation to natural number sequence) with the regularity of total number of atoms within nucleotides in standard GCT: within 64 codons (192 nucleotides) there are 2 x 3456 atoms; 3456 in two inner as well as in two outer columns.] (Rakočević, 2011b) Table C.2. The Sukhodolets' system of amino acids in a 4 x 5 arrangement.…”

Section: Acknowledgementmentioning

confidence: 99%

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Analogies of Genetic and Chemical Code

Rakočević¹

2017

Preprint

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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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Section: Another Similaritiesmentioning

confidence: 85%

“…Tables 4.1 & 4.2 in: Rakočević, 1991, or Tables 18 & 20 in: Rakočević, 1997b.) (The Reference: Rakočević, 1997b one can see in website: www.rakocevcode.rs)…”

Section: The Problem Of Lanthanides Arrangement In the Psementioning

confidence: 99%

Section: Some Additional Observationsmentioning

confidence: 99%

Section: Acknowledgementmentioning

confidence: 99%

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Analogies of Genetic and Chemical Code

Rakočević¹

2017

Preprint

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“…On the other hand, if TM is written adequately, systemic and systematically, 2 as TMA, then, on both sides of the main diagonal, there are the numbers: 0, 2, 6, 12, 20, ... (Table 1.1 in Rakočević, 2011b), which represent the values for "q" in the equation of the generalized golden mean (Spinadel, 1998(Spinadel, , 1999Rakočević, 2004bRakočević, , 2011b. It follows from this that it can be understood why the amino acid (genetic) code is determined by the golden mean (Rakočević, 1998(Rakočević, , 2011b) (Remark 2).However, if we note that the said numbers on the main diagonal of TM, taken in a double amount (0, 4, 12, 24, 40, ...), represent the first cathete in the Pythagorean-Diophantine triangle set, and increased by one -the hypotenuse of the same triangles: 1, 5, 13, 25, 41, ... [The second cathete is "taken" from the set of odd natural numbers, respectively.] Thus, it is possible to understand why the amino acid (genetic) code was determined by the first (3-4-5) PythagoreanDiophantine triangle (Shcherbak, 1994).…”

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Genetic code: Chemical Distinctions of Protein Amino Acids

Rakočević¹

2017

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Abstract. In the work it is shown that 20 protein amino acids ("the canonical amino acids" within the genetic code) appear to be a whole and very symmetrical system, in many ways, all based on strict chemical distinctions from the aspect of their similarity, complexity, stereochemical and diversity types. By this, all distinctions are accompanied by specific arithmetical and algebraic regularities, including the existence of amino acid ordinal numbers from 1 to 20. The classification of amino acids into two decades (1-10 and 11-20) appears to be in a strict correspondence with the atom number balances. From the presented "ideal" and "intelligent" structures and arrangements follow the conclusions that the genetic code was complete even in prebiotic conditions (as a set of 20 canonical amino acids and the set of 2+2 pyrimidine / purine canonical bases, respectively); and the notion "evolution" of the genetic code can only mean the degree of freedom of standard genetic code, i.e. the possible exceptions and deviations from the standard genetic code. [This is the second version with minimal interventions in the text. In addition, one passage was added in front of the second star, with quoting of T. Jukes. Added is Remark 4 and a more adequate shading in the From a chemical point of view the first step of classification of protein amino acids (AAs), "the canonical amino acids" within genetic code, must be the classification into aliphatic and aromatic AAs, where on a hierarchical scale of changes by similarity and complexity, aliphatic AAs must precede the aromatic. For the same reason of the chemical hierarchy, within the class of aliphatic AAs at the beginning must be the hydrocarbon AAs (possesing in the side chain carbon and hydrogen, or hydrogen only, in the case of glycine), and at the end two sulfur AAs, quite different from preceded non-sulphuric AAs. This means that two sulfur AAs [as last in class of aliphatic AAs] must be found in a direct contact to the aromatic ones.In further course of sequencing of AAs, in terms of changes by similarity, from the aspect of the AAs singlets and/or doublets, i.e. pairs, it should be considered appropriate distinctions in three areas: in the hydrocarbon, aromatic, and that between them. In the set of aromatic AAs, Phe came first, as the simplest, followed by Tyr, and Trp, all three with possession of a benzene ring. At the very end ultimately must be His, the only one who does not possess the aromatic benzene ring. In the set of hydrocarbon AAs, at the very beginning must be Gly as the simplest one. Follows Ala as the first possible case of hydrocarbon series with an open carbon chain. Then come Val and Pro, both with three carbon atoms in the side chain, rather than Leu and Ile with four carbon atoms. By this, Val with half-cyclic chain precedes Pro with cyclic one; also Ile precedes Leu, as more similar with Pro. [The details of the relationship between Val and Pro, see in: Rakočević & Jokić, 1996; on the relationship between Pro and Ile, in: Rakočević 1998, Survey 4,...

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The Cipher of the Genetic Code

Rakočević

2018

Biosystems

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Genetic Code as a Coherent System

Cited by 11 publications

References 13 publications

Analogies of Genetic and Chemical Code

Analogies of Genetic and Chemical Code

Genetic code: Chemical Distinctions of Protein Amino Acids

The Cipher of the Genetic Code

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