Phosphate groups in nucleotides

FIGURE 13-2 Mcf+ and ATR Formation of Mg2+ complexes partially shields the negative charges and influences the conformation of the phosphate groups in nucleotides such as ATP and ADP... 

Allyl phosphates 332 are deprotectd using HCO2H amine [146] or HSnBu3 [147], The method is applied to the protection and deprotection of the amino and phosphate groups in nucleotides synthesized in the solid phase [148],... 

Building towards models relevant for polymeric DNA and RNA, nucleotides contain a phosphate attached at the 5 or 3 position. The 5 -nucleotides are most commonly studied, for which the phosphate has a pAa 6 for the first protonation step. Unless otherwise noted, throughout this chapter nucleotide will refer to the 5 -phosphate linkage. In nucleotides, metal-phosphate coordination competes with metal-base interactions. Chelate complexes with both phosphate and base coordination can occur when sterically allowed. Thus, transition metal complexes with purine monophosphates tend to exhibit metal coordination to the base N7 position, with apparent hydrogen bonding of coordinated waters to the phosphate. By contrast, more ionic Mg" binds preferentially to the phosphate groups in nucleotide monophosphates. In di- and tri-phosphate complexes such as metal-ATP compounds, the proximity of multiple phosphates generally favors polyphosphate chelate complexes with metal ions. 

Alkyl-S-esters of phosphoric acid are cleaved on oxidation with iodine [16] or periodate, or on hydrolysis under acid conditions, but are stable to sdkali and at neutral pH. These properties have been used to protect terminal phosphate groups in nucleotides [17], and allow specific removal of a number of other protecting groups in other parts of the molecule without the S-dkyl ester being affected. Alkyl-S-phosphates arc obtained via reaction of thiophosphoric acid with the corresponding alkyl hsdides. The S- ilkyl group is then introduced with... 

In each nucleotide monomer of DNA or RNA molecules, a phosphate group is attached to the C-5 hydroxyl of each sugar residue in an ester (anhydride) linkage. These phosphate groups in turn are linked in diester bonds to neighboring sugar groups of adjacent nucleotides... 

Cells also contain nucleotides with phosphate groups in positions other than on the 5 carbon (Fig. 

FIGURE 8-7 Phosphodiester linkages in the covalent backbone of DNA and RNA. The phosphodiester bonds (one of which is shaded in the DNA) link successive nucleotide units. The backbone of alternating pentose and phosphate groups in both types of nucleic acid is highly polar. The 5 end of the macromolecule lacks a nucleotide at the 5 position, and the 3 end lacks a nucleotide at the 3 position. 

Figure 2-13 (A) Stereoscopic view of the nucleotide binding domain of glyceraldehyde phosphate dehydrogenase. The enzyme is from Bacillus stearothermophilus but is homologous to the enzyme from animal sources. Residues are numbered 0-148. In this wire model all of the main chain C, O, and N atoms are shown but side chains have been omitted. The large central twisted P sheet, with strands roughly perpendicular to the page, is seen clearly hydrogen bonds are indicated by dashed lines. Helices are visible on both sides of the sheet. The coenzyme NAD+ is bound at the end of the P sheet toward the viewer. Note that the two phosphate groups in the center of the NAD+ are H-bonded to the N terminus of the helix beginning with RIO. From Skarzynski et al.llla (B) Structural formula for NAD+.

Guanidino group—for example, arginine (R), which may involve in the binding of phosphate groups of nucleotide coenzymes. 

The molecular mechanisms underlying the detrimental effects caused by aluminum have yet to be fully understood [31]. The toxicological mechanisms of aluminum in plants or in animals probably involve alterations in many enzyme activities. There is a large number of proteins which requires nucleoside phosphates as substrates or is regulated by nucleoside phosphates, therefore aluminum can potentially interfere with the normal functions of these proteins [18]. Thus, it is important to understand some reactions that involve aluminum and nucleotides. In this review we are going to focus on the alterations caused by this metal in some enzymes that hydrolyze or transfer phosphate groups of nucleotides, like NTPases, NTPDases, and kinases. 

At this point, it is clear that aluminum can interact with phosphate groups of nucleotides or in enzyme catalytic structures, thus it is probable that many other enzymatic reactions not discussed here could be damaged by aluminum. 

DCC is also used in nucleotide chemistry to esterify a sugar hydroxyl group with a phosphate group in another nucleotide or oligonucleotide unit. Also p-styrene based polymers with a pyridyl-2-ethanol end group are reacted in pyridine with 3 -0-acetyl-desoxythimidine-5 -phosphate in the presence of DCC." The reaction of mono esters of phosphoric acid with alcohols or phenols, in the presence of DCC, affords phosphoric acid diesters in high yield." This reaction is widely used in nucleic acid chemistry. 

In addition to its functions in bone, energy transfer, and nucleic adds, phosphate scrv cs to prevent the leakage of biochcmicals from the cell. The phosphate groups of nucleotides, intermediates of glycolysis, and vitarnin 6 greatly impair the... 

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