# On the Importance of Asymmetry in the Phenotypic Expression of the Genetic Code upon the Molecular Evolution of Proteins

^{*}

## Abstract

**:**

## 1. Introduction

^{2}-codes) with the same degeneracy of the SGC.

^{2}-codes. In the sy

^{2}-codes, subsets of amino acids formed orbits according to their codonicity, whilst in the natural code, 20 orbits were observed, i.e., one orbit for each amino acid.

**Definition**

**1.**

**Definition**

**2.**

## 2. Materials and Methods

## 3. Results

## 4. Discussion

## Supplementary Materials

## Author Contributions

## Funding

## Acknowledgments

## Conflicts of Interest

## References

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**Figure 1.**Four possible arrangements of the four nucleotides (A, C, G, U) as the vertices of a square. The four arrangements are not symmetrically equivalent.

**Figure 2.**The standard genetic code (SGC) and three synthetic symmetrical genetic codes. The standard genetic code table (

**a**) and the tables of three symmetric synthetic genetic codes. Changes from the synthetic code 1 (

**b**) to the synthetic code 2 (

**c**) and the synthetic code 3 (

**d**) are shaded in grey.

**Figure 3.**The Amino Acid Neutrality Test Applied to a Hypothetical Protein Obeying the SGC or the Synthetic Codes. The amino acids are ordered according to their codonicity, i.e., from mono-codonic: W (Trp), M (Met); di-codonic: Y (Tyr), C (Cys), E (Glu), K (Lys), Q (Gln), H (His), F (Phe), N (Asn), D (Asp); tri-codonic: I (Ile); tetra-codonic: G (Gly), P (Pro), T (Thr), V (Val); A (Ala); and hexa-codonic: L (Leu), S (Ser), and R (Arg).

Standard Genetic Code | Synthetic Code 1 | Synthetic Code 2 | Synthetic Code 3 | ||
---|---|---|---|---|---|

Phenotypic graph of codons/anticodons | Phenotypic graph of codons/anticodons | Phenotypic graph of codons/anticodons | Phenotypic graph of codons/anticodons | ||

Arrangement 1 | $e$ | ${\mathbb{Z}}_{2}$ | ${\mathbb{Z}}_{2}^{2}$ | ${\mathbb{Z}}_{2}$ | |

Arrangement 2 | $e$ | ${\mathbb{Z}}_{2}$ | ${\mathbb{Z}}_{2}^{2}$ | ${\mathbb{Z}}_{2}$ | $e$ |

Arrangement 3 | $e$ | ${\mathbb{Z}}_{2}$ | ${\mathbb{Z}}_{2}$ | ${\mathbb{Z}}_{2}$ | |

Arrangement 4 | $e$ | ${S}_{3}$ | ${S}_{3}$ | ${\mathbb{Z}}_{2}$ |

Standard Genetic Code | Synthetic Code 1 | Synthetic Code 2 | Synthetic Code 3 | |
---|---|---|---|---|

Phenotypic graph of codons/anticodons | Phenotypic graph of codons/anticodons | Phenotypic graph of codons/anticodons | Phenotypic graph of codons/anticodons | |

Arrangement 1 | N/A | {N, H}, {Q, K}, {L, S}, {F, Y}, {P, T} | {N, H}, {Q, K}, {L, S}, {F, Y}, {P, T} | {N, H}, {Q, K}, {L, S}, {F, W}, {P, T} |

Arrangement 2 | N/A | {A, T}, {R, S}, {N, D}, {C, Y}, {E, K} | {A, T}, {R, S}, {N, D, E, K}/{A, T}, {R, S}, {N, D}, {C, Y}, {Q, H}, {C, Y}, {E, K} | N/A |

Arrangement 3 | N/A | {A, P}, {R, L}, {D, H}, {C, F}, {Q, E} | {A, P}, {R, L}, {D, H}, {C, F}, {Q, E} | {A, P}, {R, L}, {D, H}, {C, F}, {Q, E} |

Arrangement 4 | N/A | {A, P, T}, {R, L, S}, {N, D, H}, {C, F, Y}, {Q, E, K} | {A, P, T}, {R, L, S}, {N, D, H}, {C, F, Y}, {Q, E, K} | {A, P}, {R, L}, {D, H}, {C, F}, {Q, E} |

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**MDPI and ACS Style**

José, M.V.; Zamudio, G.S.
On the Importance of Asymmetry in the Phenotypic Expression of the Genetic Code upon the Molecular Evolution of Proteins. *Symmetry* **2020**, *12*, 997.
https://doi.org/10.3390/sym12060997

**AMA Style**

José MV, Zamudio GS.
On the Importance of Asymmetry in the Phenotypic Expression of the Genetic Code upon the Molecular Evolution of Proteins. *Symmetry*. 2020; 12(6):997.
https://doi.org/10.3390/sym12060997

**Chicago/Turabian Style**

José, Marco V., and Gabriel S. Zamudio.
2020. "On the Importance of Asymmetry in the Phenotypic Expression of the Genetic Code upon the Molecular Evolution of Proteins" *Symmetry* 12, no. 6: 997.
https://doi.org/10.3390/sym12060997