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تسجيل مستخدم جديدGenetic Code: Four-Codon and Non-Four-Codon Degeneracy
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Miloje M. Rakocevic
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In this work it is shown that 20 canonical amino acids (AAs) within genetic code appear to be a whole system with strict distinction in Genetic Code Table (GCT) into some different quantums: 20, 23, 61 amino acid molecules. These molecules distinction is followed by specific balanced atom number and/or nucleon number distinctions within those molecules. In this second version two appendices are added; also a new version of Periodic system of numbers, whose first verson is given in arXiv:1107.1998 [q-bio.OT].
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In this work it is shown that 20 canonical amino acids (AAs) within genetic code appear to be a whole system with strict AAs positions; more exactly, with AAs ordinal number in three variants; first variant 00-19, second 00-21 and third 00-20. The or
dinal number follows from the positions of belonging codons, i.e. their digrams (or doublets). The reading itself is a reading in quaternary numbering system if four bases possess the values within a specific logical square: A = 0, C = 1, G = 2, U = 3. By this, all splittings, distinctions and classifications of AAs appear to be in accordance to atom and nucleon number balance as well as to the other physico-chemical properties, such as hydrophobicity and polarity.
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 non-complements) are observed now together with two further possible splittings into 4 x 5 and 5 x 4 amino acids.
Models of codon evolution are commonly used to identify positive selection. Positive selection is typically a heterogeneous process, i.e., it acts on some branches of the evolutionary tree and not others. Previous work on DNA models showed that when
evolution occurs under a heterogeneous process it is important to consider the property of model closure, because non-closed models can give biased estimates of evolutionary processes. The existing codon models that account for the genetic code are not closed; to establish this it is enough to show that they are not linear (meaning that the sum of two codon rate matrices in the model is not a matrix in the model). This raises the concern that a single codon model fit to a heterogeneous process might mis-estimate both the effect of selection and branch lengths. Codon models are typically constructed by choosing an underlying DNA model (e.g., HKY) that acts identically and independently at each codon position, and then applying the genetic code via the parameter $omega$ to modify the rate of transitions between codons that code for different amino acids. Here we use simulation to investigate the accuracy of estimation of both the selection parameter $omega$ and branch lengths in cases where the underlying DNA process is heterogeneous but $omega$ is constant. We find that both $omega$ and branch lengths can be mis-estimated in these scenarios. Errors in $omega$ were usually less than 2% but could be as high as 17%. We also assessed if choosing different underlying DNA models had any affect on accuracy, in particular we assessed if using closed DNA models gave any advantage. However, a DNA model being closed does not imply that the codon model constructed from it is closed, and in general we found that using closed DNA models did not decrease errors in the estimation of $omega$.
This paper presents, for the first time, four diversity types of protein amino acids. The first type includes two amino acids (G, P), both without standard hydrocarbon side chains; the second one four amino acids, as two pairs [(A, L), (V, I)], all w
ith standard hydrocarbon side chains; the third type comprises the six amino acids, as three pairs [(F, Y), (H, W), (C, M)], two aromatic, two hetero aromatic and two hetero non-aromatic); finally, the fourth type consists of eight amino acids, as four pairs [(S, T), (D, E), (N, Q), (K, R)], all with a functional group which also exists in amino acid functional group (wholly presented: H2N-.CH-COOH; separately: OH, COOH, CONH2, NH2). The insight into existence of four types of diversity was possible only after an insight into the existence of some very new arithmetical regularities, which were so far unknown. Also, as for showing these four types was necessary to reveal the relationships between several key harmonic structures of the genetic code (which we presented in our previous works), this paper is also a review article of the authors researches of the genetic code. By this, the review itself shows that the said harmonic structures are connected through the same (or near the same) chemically determined amino acid pairs, 10 pairs out of the 190 possible.
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