scholarly journals System-directed pairing of protein amino acids. Part II

2021 ◽  
Author(s):  
Miloje M. Rakočević

In this second part of the paper, the pairs of protein amino acids (AAs), canonical in the genetic code (GC) in the three system-arrangements (OS, DS and AS), presented in the first part, are compared with the Table of chemical similarity of AAs (Table 1 in Part I). The obtained results are such that it makes sense to speak about an ORiginal CHEmical STandard (Orchest), valid not only for amino acids but for life complete.

2019 ◽  
Author(s):  
Miloje M. Rakočević

The paper starts from the established facts about a system consisting of 20 protein amino acids (AAs), arranged according to a hierarchy of chemical similarity (Rakočević, 2019). There, it was shown that the number of atoms in the side chains of AAs given in the arrangement of 5 x 4 is such that it represents a mirror image in a specific way generated sequence of numbers: 02, 13, 24, 16, 05 (20, 31, 42, 61, 50 ). Further in the paper new insights have been preseted to show that mirror symmetry is in many respects an essential feature of the genetic code.


2019 ◽  
Author(s):  
Miloje M. Rakočević

Searching for the answer to the question why – in the generating of the genetic code – only mirror symmetrical left and not right amino acids (AAs) were selected, in a previous work we showed the existence of a double Boolean "triangle" in mirror symmetry, with superposition of the top vertices: 00 -11-22 / 22-11-00 → 00-11-22-11-00 [0 as 000; 1 as 001; 2 as 010] (Rakočević, 2019a). The resulting sequence, summed with the binary sequence of a 6-bit binary tree, split with a mirror in the middle (101/010) [as in Dirac's positron / electron mirror], results in a sequence of decimal number system: 02-13-24-16-05, where a smaller number (010 = 2) was added three times and a larger number (101 = 5) twice (Survey 1). The mirror image of the obtained decimal sequence (20-31-42-61-50) is 100% consistent with the arrangement of protein AAs, arranged according to strict chemical similarity (Rakočević, 2019a, Table 3). Starting from this result, the paper of which this is a supplement, presents new insights and new examples of mirror symmetry valid for the genetic code, showing that mirror symmetry is also in other respects an essential feature of the genetic code. In this Supplement are given the further new insights.


2017 ◽  
Author(s):  
Miloje M. Rakocevic

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 Table inside Box 2.]


2021 ◽  
Author(s):  
Miloje M. Rakočević

In this second part of the short communication (Ref. 2), we give an argument more in favor of the validity of the precognition status of the final result of my 40 years of genetic code researches. It is shown that the changes in the number of atoms in the system-arrangements of protein amino acids, in relation to the Gaussian number (51) and the Dürer number (34 and 68, respectively), correspond to the changes in the products of number 5 in the Multiplication Table of the decimal number system. On the other hand, with the same changes (in the products of number 5), two unconscious narrations, said in the first part of this communication, correspond one hundred percent.


2021 ◽  
Author(s):  
Miloje M. Rakočević

The idea of this review paper is as follows. If it can be shown (and it can!) that the pairing of protein amino acids is system-directed (determined), then the hypothesis of a prebiotically determined genetic code (Rakočević, 2004a) gets its full meaning. The hypothesis is supported by the fact that all these pairings come to the fore primarily through classes and subclasses of amino acid molecules. What is, however, unexpected and even unbelievable from the point of view of current science is the fact that the quantities, i.e. number of atoms (in a direct or indirect relation to the number of nucleons), in these classes and subclasses, are determined by Gauss’ number 51 (51 = 3 x 17), or Gauss’ sequence: 51 ± 10, 51 ± 20, 51 ± 30, 51 ± 40 and 51 ± 50; also by Dürer’s number 34 (34 = 2 x 17), even more either by its double value, 68; or by Dürer’s sequences: 34 ± 10, 34 ± 5 and 68 ± 10, 68 ± 5. Since the hypothesis refers to constituents – amino acids and nucleotides – it follows that in terms of the type and number of constituents, it makes no sense to talk about evolution of GC, but only about its generating. [Generated, not degenerated code!] It makes sense to talk about the evolution of the genetic code only from the "moment" when the resulting peptide and nucleotide chains enter into chemical reactions and interactions; although even then it can be said that this is just a second phase of GC generation.


2017 ◽  
Author(s):  
Miloje M. Rakočević

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 "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.


2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Daniele Carlesso ◽  
Stefania Smargiassi ◽  
Elisa Pasquini ◽  
Giacomo Bertelli ◽  
David Baracchi

AbstractFloral nectar is a pivotal element of the intimate relationship between plants and pollinators. Nectars are composed of a plethora of nutritionally valuable compounds but also hundreds of secondary metabolites (SMs) whose function remains elusive. Here we performed a set of behavioural experiments to study whether five ubiquitous nectar non-protein amino acids (NPAAs: β-alanine, GABA, citrulline, ornithine and taurine) interact with gustation, feeding preference, and learning and memory in Apis mellifera. We showed that foragers were unable to discriminate NPAAs from water when only accessing antennal chemo-tactile information and that freely moving bees did not exhibit innate feeding preferences for NPAAs. Also, NPAAs did not alter food consumption or longevity in caged bees over 10 days. Taken together our data suggest that natural concentrations of NPAAs did not alter nectar palatability to bees. Olfactory conditioning assays showed that honey bees were more likely to learn a scent when it signalled a sucrose reward containing either β-alanine or GABA, and that GABA enhanced specific memory retention. Conversely, when ingested two hours prior to conditioning, GABA, β-alanine, and taurine weakened bees’ acquisition performances but not specific memory retention, which was enhanced in the case of β-alanine and taurine. Neither citrulline nor ornithine affected learning and memory. NPAAs in nectars may represent a cooperative strategy adopted by plants to attract beneficial pollinators.


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