Polymerization nucleotides

Figure 10.13 Phosphoryl-transfer reactions. The figure shows (a) nucleotide polymerization, (b) nucleic acid hydrolysis, (c) first cleavage of an exon-intron junction by group I ribozyme (d) and by a group II ribozyme, (e) strand transfer during transposition and (f) exon ligation during RNA splicing. (From Yang et al., 2006. Copyright 2006, with permission from Elsevier.)...

A second major area of biochemical importance concerns study of nucleotide polymerization to produce ribonucleic acids (RNA) and deoxyribonucleic acids (DNA). Genes, the basis for inherited characteristics, are contained in DNA double-helical sections incorporated into coiled and supercoiled DNA structures. Genomics, the study of the total genetic assemblage of any species, is now a well-known topic to all, especially with the announcement of the sequencing of the human genome in 2001. More information on this topic is given in Section 2.3.6. 

DNA Polymerase I (DNA Pol I) from E. coli is the best characterized of all the DNA polymerases and, as far as DNA sequencing is concerned, is by far the most widely used. The purified enzyme is a single polypeptide chain of molecular weight 109,000 daltons containing approximately 1000 amino acid residues. The turnover number is about 667 nucleotides polymerized per molecule of enzyme per min at 37°C. One atom of zinc per molecule of enzyme appears to be required for the activity of the enzyme. 

DNA polymerase and 5 - 3 exonuclease functions of the enzyme. Nucleotide hydrolysis in the 5 - 3 direction concomitant with nucleotide polymerization results in translocation of the position of the discontinuity by a process termed nick translation (Fig. 2) (30). Discontinuities or nicks in DNA can be introduced into intact DNA by limited digestion with pancreatic DNase I, which generates 3 -hydroxyl termini in double-stranded DNA. If radioactive nucleotides are used in the reaction with DNA polymerase 1, randomly and uniformly labeled DNA is produced (31). 

The two metal ions are held in place by three conserved aspartic acid residues. The fact that catalysis is mediated exclusively by metal ions with no direct participation of amino acid side chains suggests that nucleotide polymerization may have originated before the evolution of proteins. Specifically, the two metals may have been chelated by RNA in the primordial RNA World that is thought to have operated before the evolution of proteins. 

As an additional example of enzymatic specificity, consider the enzyme DNA polymerase, which synthesizes a polymer of the four basic nucleic acid units (adenosine, guanosine, thymosine, and cytosine) on a template strand of DNA. This enzyme exhibits an extraordinarily high degree of fidelity in the copies it produces typically <1 error per 10 nucleotides polymerized. 

The poly(A) tail is a stretch of 100-200 adenosine nucleotides polymerized onto the 3 end of a mRNA by the enzyme poly(A) polymerase. 

Brishammar, S. and N. Juntti RNA-synthesizing enzymes in healthy and TMV-infected tobacco leaves. Separation and properties of enzymes catalyzing nucleotide polymerization Arch. Biochem. Biophys. 164 (1974) 218-223. 

Simulations of the Zn world could also start from other entry points . Under the above described conditions, (photo)polymerization of pre-formed nucleotides (or nucleosides in the presence of phosphite) could be studied at the ZnS surfaces. The encouraging results that were obtained upon studying the (photo)polymer-ization reactions atTi02 surfaces [94], suggest that nucleotide polymerization at illuminated ZnS surfaces could proceed with an acceptable quantum yield. 

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