Nucleic acids phosphate transfer

In addition to its functions in bone, energy transfer, and nucleic acids, phosphate serves to prevent the leakage of biochemicals from the cell. The phosphate groups of nucleotides, intermediates of glycolysis, and vitamin Bg greatly impair the... 

Ribulose 5-phosphate is the substrate for two enzymes. Ribulose 5-phosphate 3-epimerase alters the configuration about carbon 3, forming another ketopentose, xylulose 5-phosphate. Ribose 5-phosphate ketoisom-erase converts ribulose 5-phosphate to the corresponding aldopentose, ribose 5-phosphate, which is the precursor of the ribose required for nucleotide and nucleic acid synthesis. Transketolase transfers the two-carbon... 

Classical gene transfer methods still in use today are diethylamino ethyl (DEAE)-dextran and calcium phosphate precipitation, electroporation, and microinjection. Introduced in 1965, DEAE-dextran transfection is one of the oldest gene transfer techniques [2]. It is based on the interaction of positive charges on the DEAE-dextran molecule with the negatively charged backbone of nucleic acids. The DNA-DEAE-dextran complexes appear to adsorb onto cell surfaces and be taken up by endocytosis. 

Magnesium has its role intimately intertwined with phosphate in many phosphoryl transfer reactions, as Mg-ATP in muscle contraction, in the stabilization of nucleic acid structures as well as in the catalytic activity of ribozymes (catalytic RNA molecules). It also serves as a structural component of enzymes, and is found as the metal centre in chlorophylls, which absorbs light energy in photosynthesis. 

The alkylating agents can transfer an alkyl radical to a suitable receptor site. Alkylation of DNA within the nucleus represent the major interactions which will lead to cell death. These agents react chemically with sulfhydryl, carboxyl, amino and phosphate groups of other cellular nucleophiles in the cells which make them unavailable for the normal metabolic reactions. Alkylating agents react with nucleic acid and inhibit... 

A similar situation is found in the structure of putrescine diphosphate " (a model system for amine-nucleic acid interactions) which divides into layers of HjPOJ anions bridged by protonated putrescine (1,4-diamino-n-butane) cations. In a real biological system (yeast phenylalanine transfer RNA) phosphate residues are found to be enveloped by the polyamine spermine [NH2(CH2)jNH(CH2)4NH(CH2)jNH2] which again adopts a linear, nonchelating conformation. ... 

The biological functions of the nucleic acids involve the participation of metal ions. In particular K+ and Mgr+ stabilize the active nucleic acid conformations. Mg2+ also activates enzymes which are involved in phosphate transfer reactions and in nucleotide transfer. The monomeric nucleotides are also involved in a number of metabolic processes and here again metal ions are implicated. Consequently, there has been considerable attention focussed on the coordination properties of these molecules as a means of understanding the mechanism of the metal ion involvements. A number of reviews are available which cover the studies on metal interactions.113 117... 

Polynucleotide polymerases, or nucleotidyl transferases, are enzymes that catalyze the template-instructed polymerization of deoxyribo- or ribonu-cleoside triphosphates into polymeric nucleic acid - DNA or RNA. Depending on their substrate specificity, polymerases are classed as RNA- or DNA-dependent polymerases which copy their templates into RNA or DNA (all combinations of substrates are possible). Polymerization, or nucleotidyl transfer, involves formation of a phosphodiester bond that results from nucleophilic attack of the 3 -OH of primer-template on the a-phosphate group of the incoming nucleoside triphosphate. Although substantial diversity of sequence and function is observed for natural polymerases, there is evidence that many employ the same mechanism for DNA or RNA synthesis. On the basis of the crystal structures of polymerase replication complexes, a two-metal-ion mechanism of nucleotide addition was proposed [1] during this two divalent metal ions stabilize the structure and charge of the expected pentacovalent transition state (Figure B.16.1). 

FIGURE 9.71 Pentose phosphate pathway. The pentose phosphate pathway is used for the metabolism of various sugars. It is required for the biosynthesis of ribose 5-phosphate (a component of ATP, GTP, CTP, UTP, TTP, and the nucleic acids). The pentose phosphate pathway is used for the reduction of NADP. Thiamin pyrophosphate is a cofactor for two enzymes of the pathway, as indicated by TPP. The circled groups are the two-carbon units transferred by TPP. 

Phosphate esters show important thermal susceptibility (Fig. 1). Dialkyl phosphates, such as those found in nucleic acids (Fig. 2), decompose with the initial loss of one alkyl group, the concomitant transfer of protons, followed by the elimination of the second alkyl group and the subsequent loss of water. This thermal instability of phosphoesters has been used in the analysis of nucleic acids. Thus the pyrolysis that usually precedes the recording of a mass spectrum permits cleavage of the polymeric phosphoesters (nucleic acids), followed by phosphate extrusions, producing nucleotides or simple nucleosides as fragment ions. 

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