Elsevier

Biosystems

Volume 151, January 2017, Pages 21-26
Biosystems

A new integrated symmetrical table for genetic codes

https://doi.org/10.1016/j.biosystems.2016.11.004 Get rights and content

Abstract

Degeneracy is a salient feature of genetic codes, because there are more codons than amino acids. The conventional table for genetic codes suffers from an inability of illustrating a symmetrical nature among genetic base codes. In fact, because the conventional wisdom avoids the question, there is little agreement as to whether the symmetrical nature actually even exists. A better understanding of symmetry and an appreciation for its essential role in the genetic code formation can improve our understanding of nature’s coding processes. Thus, it is worth formulating a new integrated symmetrical table for genetic codes, which is presented in this paper. It could be very useful to understand the Nobel laureate Crick’s wobble hypothesis — how one transfer ribonucleic acid can recognize two or more synonymous codons, which is an unsolved fundamental question in biological science.

Introduction

The discovery of double-helix molecular structure of deoxyribonucleic acid (DNA) by Watson and Crick (1953) is one of landmarks in the history of science. It represents the birth of molecular biology. On the cellular level, the living organisms are classified into prokaryotes and eukaryotes. The prokaryotes are unicellular life forms while the eukaryotes include human, animal and fungus. All prokaryotic and eukaryotic cells share a common process by which information encoded by a gene is used to produce the corresponding protein. This process is called protein biosynthesis and accomplished in two steps: transcription and translation.

During transcription, DNA is transcribed into ribonucleic acid (RNA). DNA carries the genetic information, while RNA is used to synthesize proteins. DNA consists of a strand of bases, namely Adenine (A), Thymine (T), Guanine (G) and Cytosine (C), whereas RNA has A, G, C and Uracil (U) instead of T. Then, translation occurs where proteins (molecules composed of a long chain of amino acids) are built upon the codons in RNA. Each codon, which is a set of three adjoined nucleotides (triplet), specifies one amino acid or termination signal (Crick et al., 1961).

There are 20 amino acids, namely Histidine (His/H), Arginine (Arg/R), Lysine (Lys/K), Phenylalanine (Phe/F), Alanine (Ala/A), Leucine (Leu/L), Methionine (Met/M), Isoleucine (Ile/I), Tryptophan (Trp/W), Proline (Pro/P), Valine (Val/V), Cysteine (Cys/C), Glycine (Gly/G), Glutamine (Gln/Q), Asparagine (Asn/N), Serine (Ser/S), Tyrosine (Tyr/Y), Threonine (Thr/T), Aspartic acid (Asp/D) and Glutamic acid (Glu/E). For the formation of proteins in living organism cells, it is found that each amino acid can be specified by either a minimum of one codon or up to a maximum of six possible codons. In other words, different codons specify the different number of amino acids. A table for genetic codes is a representation of translation for illustrating the different amino acids with their respectively specifying codons, that is, a set of rules by which information encoded in genetic material (RNA sequences) is translated into proteins (amino acid sequences) by living cells. There are a total of 64 possible codons, but there are only 20 amino acids specified by them. Therefore, degeneracy is a salient feature of genetic codes. Genetic information is stored in DNA in the form of sequences of nucleotides which is made clearly in the double-helix model, but it does not provide any clue on how one transfer ribonucleic acid (tRNA) can recognize two or more synonymous codons. Therefore, deciphering the genetic codes becomes a problem. Up to now, it is still unable to find out the reason or explanation for these kinds of characteristics and relationships between codons and amino acids. Therefore, it has always been an interesting area for us to explore and obtain any explanation further.

The table for genetic codes allows us to identify a codon and the individual amino acid assigned to the codon by nature. These assignment tables may come in a variety of forms, but they all suffer from an inability of illustrating a symmetrical nature among genetic base codes. In fact, because the conventional wisdom avoids the question, there is little agreement as to whether the symmetrical nature actually even exists. A better understanding of symmetry and an appreciation for its essential role in the genetic code formation can improve our understanding of nature’s coding processes. Thus, it is worth formulating a new integrated symmetrical table for genetic codes.

Section snippets

Genetic codes

The genetic codes for translation can be categorized into two main categories: nuclear and mitochondrial codes, which are the genetic codes of nuclear deoxyribonucleic acid (nDNA) and mitochondrial deoxyribonucleic acid (mtDNA) respectively. Each category has various different genetic codes for the translation of a particular class, genus or species of living organisms. Not all organisms can use standard nuclear code for translation and some organisms of the same family can have the different

Symmetrical genetic codes

In standard nuclear code (Nirenberg and Matthaei, 1961), the arrangement of amino acid assignment is not random, presumably as the product of evolution to enhance stability in the face of mutation (Freeland and Hurst, 1998, Freeland et al., 2000, Freeland et al., 2003, Sella and Ardell, 2006), tRNA misloading (Yang, 2004, Jestin and Soulé, 2007, Seligmann, 2010b, Seligmann, 2011, Seligmann, 2012), frame shift (Seligmann and Pollock, 2004, Itzkovitz and Alon, 2007, Seligmann, 2007, Seligmann,

An integrated table for genetic codes

In view of the symmetrical and asymmetrical characteristics of all 16 rearranged genetic codes, there is a question that many may raise whether a perfect symmetrical genetic code is the origin or ultimate product of evolutionary progress. The total 16 sets of genetic codes that are used in different biological species may give us the clue of how the evolutionary process happened. Today various species are quite different in terms of appearance, but they may have the same ancestor. Therefore, a

Concluding remarks

As shown in Fig. 4, the STOP (*) codon of standard nuclear code is mutated to other amino acids in almost every non-standard code. The only two that do not contain STOP (*) codon mutation are alternative yeast nuclear code (N4) and thraustochytrium mitochondrial code (M8). This seems to imply that, the STOP (*) codon is the most unstable codon in genetic codes, or could be seen as an empty shell, which could easily be replaced by the nearby amino acids. It is worth mentioning to this end that

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