1. Notes about genetic code, Note 1: Four diversity types of protein amino acids
Miloje M. Rakočević
Full professor of Faculty of Science, University of Niš, Serbia;
Now retired, on the Address: Milutina Milankovica 118/ 25
11070 Belgrade, Serbia
(E-mail: milemirkov@nadlanu.com)
Abstract
For the first time, in this Note is presented the existence of four diversity types of protein amino acids (AAs). Fist type with two AAs (G; P); second with four AAs (A, L; V, I); third with six AAs (F, Y, H, W; C, M); and fourth type with eight AAs (S, T, D, E; N, Q; K, R).
2. The Genetic Code via Gödel Encoding
T. Négadi* Physics Department, Faculty of Science, Oran University, 31100, Es-Sénia, Oran, Algeria
Abstract:
The genetic code structure into distinct multiplet-classes as well as the numeric degeneracies of the latter are revealed by a two-step process. First, an empirical inventory of the degeneracies (of the shuffled multiplets) in two specific equal moieties of the experimental genetic code table is made and transcribed in the form of a sequence of integers. Second, a Gödel Encoding procedure is applied to the latter sequence delivering, as an output, a Gödel Number the digits of which, from the decimal representation, could remarkably describe the amino acids and the stops and allow us also to compute the exact degeneracies, class by class. The standard and the vertebrate mitochondrial genetic codes are considered and their multiplet structure is fully established.
3. The Genetic Code Degeneracy and the Amino Acids Chemical Composition are Connected
Tidjani Négadi
Abstract
We show that our recently published Arithmetic Model of the genetic code based on Gödel Encoding is robust against symmetry transformations; specially Rumer’s one U´G, A´C and constitutes a link between the degeneracy structure and the chemical composition of the 20 canonical amino acids. As a result, several remarkable atomic patterns involving hydrogen, carbon, nucleon and atom numbers are derived. This study has no obvious practical application(s) but could, we hope, add some new knowledge concerning the physico-mathematical structure of the genetic code.
Key Words: genetic code, degeneracy, Gödel encoding, symmetry, atomic composition
FREE PDF GRATIS: NeuroQuantology 2009; 1 : 181-187
4. The genetic code multiplet structure, in one number
Tidjani Négadi
Physics Department, Faculty of Sciences,
Oran University, Oran, 31100, Algeria
physicants@aol.com1
Abstract:
The standard genetic code multiplet structure as well as the correct degeneracies, class by class, are all extracted from the (unique) number 23!, the order of the permutation group of 23 objects.
FREE PDF GRATIS: ArXiv
5. The multiplet structure of the genetic code, from one and small number
Tidjani Négadi
Département de Physique, Faculté des Sciences,
Université d’Oran, 31100, Oran, Algérie
Email : tnegadi@gmail.com
Website : http://negadi.webs.com
Abstract
In this short paper, we show that the multiplet structure of the standard genetic code is derivable from the total number of nucleotides contained in 64 codons, 192, a small number. The degeneracy class-number is derived as the number of numbers coprime to the number of Family-Boxes involved for the quartets, the doublets and the singlets. Those for the triplet and the sextets are computed as simple linear combinations of the preceding ones. Some interesting consequences are also presented.
FREE PDF GRATIS: ArXiv
6. Genetic Code Table: A note on the three splittings into amino acid classes
Miloje M. Rakočević
Faculty of Science, University of Niš (now retired, on the Address: Milutina Milankovica 118, 11070 Belgrade, Serbia (e-mail: m.m.r@eunet.yu;
or: milemirkov@nadlanu.com; www.sponce.net or www.rakocevcode.rs)
Abstract
This note represents the further progress in understanding the determination of the genetic code by Golden mean (Rakocevic, 1998). Three classes of amino acids that follow from this determination (the 7 "golden" amino acids, 7 of their complements, and 6 noncomplements) are observed now together with two further possible splittings into 4 x 5 and 5 x 4 amino acids.
FREE PDF GRATIS: ArXiv
7. Origin and evolution of the genetic code: The universal enigma
Eugene V. Koonin* and Artem S. Novozhilov
Article first published online: 31 DEC 2008
DOI: 10.1002/iub.146
Copyright © 2008 International Union of Biochemistry and Molecular Biology, Inc.
IUBMB Life
Volume 61, Issue 2, pages 99–111, February 2009
Keywords: genetic code; translation; evolution
Abstract
The genetic code is nearly universal, and the arrangement of the codons in the standard codon table is highly nonrandom. The three main concepts on the origin and evolution of the code are the stereochemical theory, according to which codon assignments are dictated by physicochemical affinity between amino acids and the cognate codons (anticodons); the coevolution theory, which posits that the code structure coevolved with amino acid biosynthesis pathways; and the error minimization theory under which selection to minimize the adverse effect of point mutations and translation errors was the principal factor of the code's evolution. These theories are not mutually exclusive and are also compatible with the frozen accident hypothesis, that is, the notion that the standard code might have no special properties but was fixed simply because all extant life forms share a common ancestor, with subsequent changes to the code, mostly, precluded by the deleterious effect of codon reassignment. Mathematical analysis of the structure and possible evolutionary trajectories of the code shows that it is highly robust to translational misreading but there are numerous more robust codes, so the standard code potentially could evolve from a random code via a short sequence of codon series reassignments. Thus, much of the evolution that led to the standard code could be a combination of frozen accident with selection for error minimization although contributions from coevolution of the code with metabolic pathways and weak affinities between amino acids and nucleotide triplets cannot be ruled out. However, such scenarios for the code evolution are based on formal schemes whose relevance to the actual primordial evolution is uncertain. A real understanding of the code origin and evolution is likely to be attainable only in conjunction with a credible scenario for the evolution of the coding principle itself and the translation system. © 2008 IUBMB IUBMB Life, 61(2): 99–111, 2009
FREE PDF GRATIS: IUBMB Life
