Polynucleotide Biosynthesis

The synthesis of nucleotide triphosphates required for polynucleotide chain building is a complex process which will not be considered in full detail here. The biosynthetic routes for purine and pyrimidine nucleosides are somewhat different and commence with 5 phosphoribosyl-l-pyrophos-phate and carbamyl phosphate, respectively. These two materials undergo successive enzyme-catalysed reactions, linking at times with compounds encountered in other biochemical cycles, and utilising ATP in several stages. Polynucleotides can be synthesised by purely chemical means in the laboratory (Chapter 10.4). 

FIGURE 11.34 Cruciform arrangement from palindromic sequences. 

The 5 phosphoribosyl-l-pyrophosphate required for purine synthesis is obtained from ATP and ribose-5-phosphate by reaction (11.39). Glutamine, which is also required, is obtained from glutamic acid by reaction (11.44), and the latter is obtained from a - oxoglutaric acid by reaction (11.124). The last reaction links the Krebs cycle with amino acid metabolism. 

Pyrimidine biosynthesis commences with a reaction between carbamyl phosphate and aspartic acid to give carbamyl aspartic acid which then nndergoes ring closure and oxidation to orotic acid. A reaction then occurs between orotic acid and 5-phosphoribosyl pyrophosphate to give orotidine-5-phosphate which on decarboxylation yields uridine-5-phosphate (UMP). By means of two successive reactions with ATP, UMP can then be converted into UTP and this by reaction with ammonia can give rise to cytidine triphosphate, CTP (11.126). 

Deoxy-CTP can be obtained by reduction of CDP with NADPH, followed by phosphorylation. The overall reactions for production of deoxyribonucleoside triphosphates can be summarised as (11.127). 

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In addition to the roles of nucleotides and their derivatives and products in intermediary metabolism and in polynucleotide biosynthesis, some nucleotides can also regulate a wide variety of enzyme reactions and metabolic processes in doing so, they are not themselves metabolized in the reaction. For reviews dealing with the vast literature on metabolic regulation, see references 30-32. 

Messenger RNA (mRNA) (Section 28 11) A polynucleotide of nbosethat reads the sequence of bases in DNA and inter acts with tRNAs in the nbosomes to promote protein biosynthesis... 

Cellular Protein Biosynthesis. The process of cellular protein biosynthesis is virtually the same in all organisms. The information which defines the amino acid sequence of a protein is encoded by its corresponding sequence of DNA (the gene). The DNA is composed of two strands of polynucleotides, each comprising some arrangement (sequence) of the four nucleotide building blocks of the nucleic acids adenine (A), thymine (T),... 

Nucleic acids are the molecules of the genetic apparatus. They direct protein biosynthesis in the body and are the raw materials of genetic technology (see Genetic engineering). Most often polynucleotides are synthesized microbiologicaHy, or at least enzymatically, but chemical synthesis is possible. 

Since the chemistry of nucleic acids was last discussed in this Series,1 publications on the subject have appeared at an unprecedented rate. Degradation products have been further investigated and their structures are more firmly established. Moreover, studies of the properties of these materials have led to a fuller understanding of the behavior of polynucleotides. Emphasis will be laid on the organic chemistry of nucleic acids, and many physicochemical investigations will not be discussed. The period under review has seen the beginning of an understanding of the biosynthesis of nucleic acids, but space does not allow of a consideration of this aspect of the subject. 

These three compounds exert many similar effects in nucleotide metabolism of chicks and rats [167]. They cause an increase of the liver RNA content and of the nucleotide content of the acid-soluble fraction in chicks [168], as well as an increase in rate of turnover of these polynucleotide structures [169,170]. Further experiments in chicks indicate that orotic acid, vitamin B12 and methionine exert a certain action on the activity of liver deoxyribonuclease, but have no effect on ribonuclease. Their effect is believed to be on the biosynthetic process rather than on catabolism [171]. Both orotic acid and vitamin Bu increase the levels of dihydrofolate reductase (EC 1.5.1.4), formyltetrahydrofolate synthetase and serine hydroxymethyl transferase in the chicken liver when added in diet. It is believed that orotic acid may act directly on the enzymes involved in the synthesis and interconversion of one-carbon folic acid derivatives [172]. The protein incorporation of serine, but not of leucine or methionine, is increased in the presence of either orotic acid or vitamin B12 [173]. In addition, these two compounds also exert a similar effect on the increased formate incorporation into the RNA of liver cell fractions in chicks [174—176]. It is therefore postulated that there may be a common role of orotic acid and vitamin Bj2 at the level of the transcription process in m-RNA biosynthesis [174—176]. 

The Chemistry of Nucleic Acid Biosynthesis Describe three properties common to the reactions catalyzed by DNA polymerase, RNA polymerase, reverse transcriptase, and RNA replicase. How is the enzyme polynucleotide phos-phorylase similar to and different from these three enzymes ... 

Finally, novel nucleic acid catalysts have also been selected from random sequence pools (reviewed in Ref. 19). Joyce and co-workers have manipulated the function of the Group I self-splicing ribozyme, selecting variants that can utilize calcium or cleave DNA from partially randomized pools [20,21], Lorsch and Szostak [22] selected a polynucleotide kinase ribozyme from a completely random sequence pool that flanked a previously selected ATP binding site. Many of the novel ribozymes can catalyze reactions that are relevant to protein biosynthesis, bolstering arguments that translation may have arisen in a putative RNA world. For example, Lohse and Szostak [23] have selected ribozymes that can carry out an acyl transfer reaction, while Illangasekare et al. [24] have isolated a... 

Base-pair hydrogen bonding of the Watson-Crick type is fundamental in all biological processes where nucleic acids are involved. These processes, which are chiefly DNA replication and protein biosynthesis [650, 651], were understood only at the molecular level when Watson and Crick discovered the three-dimensional structure of DNA [27, 527J. This structure consists of two polynucleotide chains running in opposite directions (antiparallel), and twisted into a right-handed double helix. The hydrophobic purine and pyrimidine bases are stacked in the center... 

As far as we know, no reports are available that summarize our present knowledge of the bacterial nucleotides and nucleosides. This review will deal with the nucleosides and low-molecular nucleotides isolated from bacterial systems, their structure, and the function of some of these substances in synthetic processes (but the biosynthesis of polynucleotides is not included). In addition, the enzymic action of cell-free extracts on nucleosides and low-molecular nucleotides has been considered. 

Specific inhibition of templated biosynthesis by electroneutral polynucleotide analogs can be achieved even with complex templates Messenger RNA coding for globin, similarly to other messenger RNA molecules, contains a polyadenylate sequence located... 

From the above discussion, it appears that zinc may have its primary effect on zinc-dependent enzymes that regulate the biosynthesis and catabolic rate of RNA and DNA. In addition, zinc may also play a role in the maintenance of polynucleotide conformation. Sandstead et al. (99) observed abnormal polysome profiles in the liver of zinc-deficient rats and mice. Acute administration of zinc appeared to stimulate polysome formation both in vivo and in vitro. This finding is supported by the data of Femandez-Madrid, Prasad, and Oberleas (42), who noted a decrease in the polyribosome content of zinc-deficient connective tissue from rats and a concomitant increase in inactive monosomes. 

A new dibenzodiazepine alkaloid, diazepinomicin 265, was isolated from the culture of a marine actinomycete of the genus Micromonospora Compound 265 showed modest anti-microbial activity against selected Gram-positive bacteria with MICs of about 32 pg mL". The method of expression the biosynthetic pathway genes in transformed host cells, and the novel polynucleotide sequences and their encoded proteins involved in the biosynthesis of 265 were discussed. Derivatives of 268 were prepared. ... 

Examination of the urine of subjects receiving EATDA showed that several, if not all, of the urinary purines were excreted in increased amounts. There was, furthermore, no change in the mode of excretion of urates or in the proportion disposed of extrarenally (S12). The suggestion has been made (K18) that the fundamental mechanism of action of these compounds is the blocking of the incorporation of newly synthesized adenine into polynucleotides and/or coenzymes, with the production of an undefined deficiency state. This block could stimulate a compensatory increase in purine biosynthesis. The excess purines would not be utilizable and, therefore, would be excreted from the cells, and the normal degradation by enzymes would convert this material to uric acid. 

Polarity of DNA synthesis DNA polymerase adds nucleotide units to 3 -OH of the pre-existing chain. Thus DNA biosynthesis (likewise RNA biosynthesis) proceeds in one chemical direction, from the 5 to the 3 end. This directionality has given rise to the convention that polynucleotide sequences are read from left to right in the 5 3 direction. 

Section 26.11 Three RNAs are involved in gene expression. In the transcription phase, a strand of messenger RNA (mRNA) is synthesized from a DNA template. The four bases A, G, C, and U, taken three at a time, generate 64 possible combinations called codons. These 64 codons comprise the genetic code and code for the 20 amino acids found in proteins plus start and stop signals. The mRNA sequence is translated into a prescribed protein sequence at the ribosomes. There, small polynucleotides called transfer RNA (tRNA), each of which contains an anticodon complementary to an mRNA codon, carries the correct amino acid for incorporation into the growing protein. Ribosomal RNA (rRNA) is the main constituent of ribosomes and appears to catalyze protein biosynthesis. 

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