Chao Chen
Abstract: Based on mathematics, biochemistry, molecular biology and other natural sciences, and under the guidance of the thought of “Book of Changes” (YiJing), the four bases in RNA: adenine, guanine, cytosine and urine pyrimidine are considered to be the four elements of yin and yang, namely the taiyang, shaoyang, shaoyin, and taiyin. Sixty-four codons are considered to be sixty-four hexagrams. According to the physical and chemical properties of the bases, combined with the sequence of binary natural numbers, each codon is given a digital code to form a digital RNA codon table. The feature of this table is that according to the change of the second base U, C, G, A of the codon, an ordered non-polar hydrophobic region, non-polar polar region, polar basic region, and polar base are formed. According to the change of the first base U, C, G, A of the codon, four periodic cycles are formed. The digitized codon periodic table reveals the intrinsic relationship between codons and amino acid physicochemical properties, deepens people’s knowledge and understanding of gene expression, and also provides a theoretical basis for innovative gene sequencing methods.
Key words: Genetic Code, Amino acid, Digitizing, Periodic table, YiJing
Life is how proteins exist. Proteins are made up of various amino acids in a specific order. Information about the ordered assembly of amino acids to form proteins is stored in DNA or RNA molecules. Each DNA or RNA molecule is composed of bases, pentose sugars and phosphates. The pentose sugar in DNA is deoxyribose, while the pentose sugar in RNA is ribose; this is the difference between the two structures. DNA and RNA molecules can store and transmit genetic information. The genetic information of life is contained in the sequence of four bases. The so-called gene sequencing is to determine the order of four bases in DNA or RNA molecules. In RNA molecules, the four bases are adenine (A), guanine (G), cytosine (C), and uracil (U), while in DNA molecules, uracil (U) is replaced by thymine (T). Wherein, every three bases constitute a set of codons (Codon), corresponding to a standard amino acid or a termination signal. According to the arrangement formula, these 4 bases are repeatedly arranged at 3 positions in the polynucleotide chain, and finally 64 kinds of codons will be formed, that is, 4^3=64. In the last century, through the efforts of many scientists, the corresponding relationship between the 64 codons and amino acids was discovered one after another, and finally the RNA codon table was compiled by British scientist Clark［1］. According to the base sequences of U, C, A, and G, the table shows the corresponding relationship between the 64 codons and 20 amino acids through artificial arrangement, and summarizes many scientific research achievements in this field at that time. Unfortunately, however, Clarks codon table did not reveal the inner connection and basic principle behind the codon bases and physicochemical properties of amino acids.
his research is based on natural sciences such as mathematics, biochemistry, and molecular biology, as well as the guidance of the “Book of Changes”, to hypothesize that the purine and pyrimidine base pairs of C and G, A and U can be considered yin and yang. The four bases: adenine, guanine, cytosine and uracil map on to the four phenomena, namely the taiyang, shaoyang, shaoyin and taiyin. The sixty-four codons can be explained to match the sixty-four hexagrams, reconstructing the RNA codon table.
To digitize the sixty-four codons, the first step is that the four bases are encoded according to their basic physicochemical properties. The functional group of the base is an important part that determines the chemical properties of its organic matter, its yin-yang properties are determined by the electronegativity of the associated atomic groups. The greater the electronegativity, the more likely the group is negative; the lower the electronegativity, the more likely the group is positive. The electronegativity of oxygen is 3.44, which is greater than 2.55 of carbon, so the carbonyl is negatively charged; the electronegativity of hydrogen is 2.2, which is significantly smaller than 3.04 of nitrogen, so the amino group is positive. Uracil has two carbonyl groups (>C=O), while cytosine has one carbonyl and one amino group (NH2). The carbonyl is negatively charged and belongs to Yin (indicated by 0 in binary mathematics), and the amino group is positively charged and belongs to Yang (expressed by 1). The number 00 is therefore used to represent the two carbonyl groups of uracil, and the number 01 is used to represent one carbonyl group and one amino group of cytosine.
Uracil has two negative carbonyl groups
number 00
cytosine has one negative carbonyl and one
positive amino group, number 01
In the second step, according to the principle［2］of uracil and adenine pairing, and cytosine and guanine pairing, the code of uracil is 00, so the code of adenine can only be 11, so that opposites attract and yin and yang pair up. The coding of cytosine is 01,so the coding of guanine can only be 10, in a way that opposites attract and yin and yang pair with each other.
In the third step, according to the RNA codon table, every three bases constitute a codon, corresponding to an amino acid. Therefore, triplet codons can be expressed digitally. For example, the codon UUU can be expressed with the number 000000, which corresponds to phenylalanine. The codon UUG, represented by the number 000010, corresponds to leucine. Then, according to the binary natural number sequence, the digital amino acid periodic table of genetic code can be compiled. It should be pointed out that this study is entirely based on the knowledge of mathematics, chemistry and molecular biology, without artificial assumptions. Through the natural progression of the Miguazi coding sequence, the corresponding physical and chemical properties of amino acids also appear in non-polar, polar, basic, and acidic orderly changes, and finally form a framework of four regions and four cycles, as shown in the attached table: ［Digital Gene Code – Periodic Table of Amino Acids］.
In the digitized gene code-amino acid periodic table, each codon-amino acid column contains the following basic content: 1. Code from binary natural sequence; 2. Triple codon; 3. Amino acid English single-letter code［3］; 4 .Natural sequence from decimal system; 5. English three-letter code of amino acid; 6. Chinese name of amino acid or termination signal.
1. The digitizing the periodic table of amino acids in the genetic code is divided into 4 regions according to the difference in the second base of the codon: non-polar hydrophobic region, non-polar & polar region, polar basic region, and polar basic acid region［4］, each region contains 4 codons, and the four regions contain 16 codons, forming a cycle. According to the difference of the first base of the codon, it is divided into four cycles of U, C, G, and A, with each cycle containing 16 codons; the four cycles, thus, contain a total of 64 codons. It is stated as follows:
1). Non-polar hydrophobic region: the second base of the triplet codon is uracil (U). Uracil has two negative carbonyl groups, which are yin within yin, and the decoded amino acids are all non-polar hydrophobic amino acids, including phenylalanine, leucine, valine, isoleucine, and methionine . From the perspective of nutrition, these five are essential amino acids for the human body; from the perspective of physical and chemical properties, they are all conservative amino acids, of which leucine, valine, and isoleucine are branched-chain amino acids; phenylalanine is an Aromatic amino acid; methionine (methionine) is the initiation signal.
2). Non-polar polar region:the second base of the triplet codon is cytosine (C). Cytosine has a negative carbonyl group and a positive amino group, thus, containing both yin and yang. It can decode 4 amino acids, of which two are positive polar amino acids: 〖JP+1〗serine and threonine, and two are negative non-polar amino acids: proline and alanine. Although proline and alanine are classified as non-polar amino acids, their isoelectric potentials［5］are 6.3 and 6.02, respectively, which are higher than other non-polar amino acids (usually below 6). In some cases, both are also classified as polar molecules. Therefore, both are more reactive amino acids compared to the rest of the non-polar amino acids.
3). Polar basic region: the second base of the triplet codon is guanine (G). Guanine is a double-ring structure, chemically active, and belongs to yang; it has a positive amino group and a negative carbonyl group, which is more yang and less yin. Most of the amino acids decoded by it are positive polar amino acids and positively charged basic amino acids. Only one negative non-polar amino acid and termination signal. The 4 polar amino acids are: glycine, cysteine, serine, and arginine. Arginine is the most basic standard amino acid, which belongs to the yang of yang. Therefore, they are active amino acids in terms of physicochemical properties. Although tryptophan is a nonpolar amino acid, it is sometimes slightly polar due to its unique side chain［6］.
The solitary yin of tryptophan does not grow, and the solitary yang of arginine does not grow, leading to the termination signal that the extremes of things must be reversed. (The termination signal UGA can decode tryptophan in human mitochondria. The codons AGG and AGA of arginine are termination signals in human mitochondria.) In this periodic table, tryptophan, arginine and termination signals are close neighbors, which shows the internal relationship between them.
4). Polar basic acid region:the second base of the triplet codon is adenine (A). Adenine is also a double-ring structure, which belongs to yang, has a positive amino group, making it yang within yang, and the amino acids decoded by it are all yang amino acids, including 3 kinds of polar amino acids: asparagine, glutamine, tyrosine; 2 basic amino acids (yang within yang): histidine and lysine; 2 acidic amino acids (yin within yang): aspartic acid and glutamic acid. In a certain pH range, asparagine and aspartic acid, glutamine and glutamic acid can be converted into each other［7］. This area also includes two termination signals UAG and UAA. (The termination signals UAG and UAA can be decoded as glutamine in Paramecium.) In this periodic table, asparagine and aspartic acid, glutamine and glutamic acid, glutamine and termination signal are in a neighbor relationship, showing the intrinsic relationship between them.
From the above explanation, it can be seen that the second base in the codon has an important influence on the physicochemical properties of the corresponding amino acid. The second base of the codon determines the physical and chemical properties of the corresponding amino acids and forms a four-region and four-cycle framework, which is an important feature of the new code periodic table.
2. The digital genetic code amino acid periodic table, according to the difference of the first base of the codon, is divided into four sequences: U, C, G, and A; all three aromatic amino acids and termination signals are classified into the U sequence, all acidic amino acids are assigned to the G sequence, and all basic amino acids are assigned to the C and A sequences. Although the second base is important for decoding amino acids, it also requires the participation of the first base. For another example, the four codons whose bases 1 and 2 are C all correspond to proline, and the four codons whose bases 1 and 2 are G all correspond to glycine, and they are not affected by the third base; However, codons whose first and second bases are U or A require the participation of the third base to correctly decode amino acids. The codons of the G and C sequences are relatively stable, probably because the base pairs of C and G have three hydrogen bond supports; while the codons of the U and A sequences are relatively sensitive, because the base pairs of A and U have only two hydrogen bond supports, variant codons are susceptible to microenvironmental influences［8］. From the perspective of the entire periodic table, the codons in the polar basic regions and polar basic acidic regions of U and A sequences are the most sensitive and are easily affected by the microenvironment, and altered code words (altered code words) appear. Existing experiments can prove the conjecture of this periodic table: UGA is a termination signal, but it can decode tryptophan in human mitochondria. AGG and AGA are codons for arginine, but they are termination signals in human mitochondria. UAA and UAG are termination signals, but can decode glutamine in Paramecium. These mutated codons are all in the U and A sequences, and when the microenvironment changes, they mutate into messages with similar neighboring codons. In this periodic table, tryptophan, arginine and the termination signal are neighbors, and glutamine and the termination symbol are also neighbors. According to the codon cycle law revealed in this table, it should not be surprising to find that AAG and AAA become variant codons under certain conditions.
3. According to molecular biology, the codon of messenger ribonucleic acid (mRNA) can determine the corresponding amino acid and benefit from the help of transfer ribonucleic acid (tRNA). tRNA can recognize codons on mRNA and also amino acids. Because the second base of the codon has a strong role in determining the amino acid. If the second base on the messenger ribonucleic acid is uracil (U), which is negative, and the second base on the anticodon of the transfer ribonucleic acid is adenine (A), which is positive, and then the positive transfer ribose nucleic acid is combined with negative amino acid. In this way, opposites attract and the law of yin and yang pairing runs through the entire process of gene expression and protein synthesis. From the perspective of modern science, the positive and negative electromagnetic force (such as ionic bond force, etc.), van der Waals force (such as dispersion force, induction force, etc.), and hydrogen bond force between molecules or groups should be the physical and chemical basis for the matching of yin and yang and the attraction of opposites［9］.
In summary, the digital genetic code table not only includes all the information of the traditional codon table, but also has the following notable features:
1). According to the physical and chemical properties of the base, use the binary natural number sequence to give each codon a digital code. This code is the mathematical expression of the physical and chemical properties of the base, providing a new theoretical basis for digital gene sequencing.
2). According to the conversion of the second base U, C, G, A of the codon, orderly non-polar regions, four-region alternation of non-polar & polar regions, polar basic regions and polar basic acid regions are formed. The second base in the codon has a decisive influence on the physical and chemical properties of the corresponding amino acid, and its degree of influence is arranged in the order of C, U, G, A. When the second base is U or C (especially C), the third base has little effect on codon decoding amino acid; when the second base is G or A (especially A), the third base has an important influence on the decoding ability of the codon.
3). According to the conversion of the first base U, C, G, A of the codon, four cycles of U, C, G, A are formed. Codons with the first base of C and G have a relatively stable ability to decode amino acids; while codons with the first base of U and A are more sensitive and easily affected by the environment, forming mutated codons. Most of these mutated codons are in U and A sequences. When the microenvironment changes, they generate mutated information and have properties similar to adjacent codons.
4). Opposites attract and the law of yin and yang pairing runs through the entire process of gene expression and protein synthesis. The positive and negative electromagnetic force, van der Waals force, and hydrogen bond force between molecules or groups should be the physical and chemical basis for the matching of yin and yang, as well as the attraction of opposites［9］.
These features breathe life into traditional codon tables. The digitization and periodicity of the gene codon table provides a powerful tool for the interpretation and application of molecular biology, while also providing a guiding map for continuing to explore the unknown areas of molecular biology.
Authors:
M.D.，Acupuncturist in Fort Lauderdale, Florida.
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