Study On Genetic Codes Based On The Theory And Method Of Algebra

The origin and evolution of the genetic code, which is one of nature's best creations, are the hot topics for life science. So far, many authors have explored and made a variety hypothesis of origin of the genetic code from different perspectives on this issue. The mainest forms are the genomic genetic codes and the mitochondrial genetic codes. But there exists mismatch between some biological phenomena and these genetic codes system.In this dissertation, we study protein molecules from the perspective of algebraic. According the relative physical and chemical properties, including the chemical type of base pairs, we introduce a new hypothesis of the origin of genetic codes and obtain some characterizations of bioinformatics.In order to explain the recombining codon better, we further compute the synonymous codon preference under the new classifications. The results show that the algebraic structure and the operation fully demonstrate the important features of biological significance about codons named quasi-amino acids genetic coding. This has avoided some inexplicable events of the genomic genetic codes. This is one of the main innovative ideas in this dissertation.The main contents are listed as follows:We establish the algebraic system with operation based on the protein sequences coded by codon. We prove that it is a distribution lattice of rings theoretically and we introduce a genomic signature method, is called algebraic genomic signature method. We study protein molecules from the view of algebra. According the relative physical and chemical properties, including the chemical type of base pairs, we propose a novel genetic code table named quasi-amino acids coding ZU -16 based on the algebraic theory. The internal relation is well revealed about quasi-amino acids coding. Further, the ( ZU -16,⊕,?) is proved a field theoretically. The results clearly tell that there exist some very close correlations among the properties of the quasi-amino acids and the codon.Based on the results of ZU -16, we analyze the use of preferences of the synonymous codon in 78 human genes (19967 codons). And, we compute the relative usage degree of the synonymous codon based on the quasi-amino acid coding. The result presents human genes clearly show the consistent preference in synonymous codon choice in all codon family based on the quasi-amino acid coding. That is, human gene prefer to use the codons with strong combination of the codon-anticodon, just the codons ending with c, avoiding using the codons with moderate combination. The choice of codon in human genes is not only affected by the isochore and genome in the genome structure,but also still related to the strength of combination with the codon-anticodon. All mentioned above factors are effect on the human genes, all the codon family clearly show the consistent preference to the synonymous codon. Specially, this characteristics is more obvious than based on the genetic codes.Based on the standard Crick genomic genetic codes, we give some main work as following:In Chapter 6, we introduce the concepts of characteristic sequencesσ-,τ– andσ∩τ- for protein. We present the numerical description method of relating amino acid characteristic sequences for protein. Comparing of the characteristic sequences, we get some information about the structural characteristic of amino acids on three kinds of secondary structural classes of proteins: allα- helix, allβ- strand, andαβkind protein, respectively. Finally, the graph representation with numerical description of amino acid characteristic sequences about 18 protein sequences obtained.In Chapter 7, we establish the spherical surface projection and the corresponding spherical surface curve. The structure portray chart of the protein sequence is displayed. A special and important genomic signatures method of protein sequences is obtained by using this spherical surface curve. So the protein structure of the mutation sequence to the gene pathological change to carry on the description analysis is induced.In Chapter 8, we calculate the frequencies of appearance of codon in DNA sequences for alien plants of china, and viewed as genomic signatures, which were illustrated by 2D graphs and 1D histograms. Alien invasive species'DNA sequences are nonrandom and it's signatures are specific: the closer the species are, the more similar the signatures will be. We expect to give some advice on the prevention and control of the alien invasive species.In the end, research prospect are presented.