Ribose-2-phosphate

We can contrast these methods using the data shown in Figure 9.30, which were obtained by searching the Cambridge Structural Database for the ribose phosphate fragment also shown... 

Fig. 9.30 Ribose phosphate fragment used to extract data from Cambridge Structural Database and eight sets 0 torsion angle values for tj and r. ...

Distance matrix for eight ribose phosphate fragments. 

Figure 26.6 Vitamin B12 (a) a corrin ring showing a square-planar set of N atoms and a replaceable H, and (b) simplified stmcture of B12. In view of the H displaced from the corrin ring, the Co-C bond, and the charge on the ribose phosphate, the cobalt is formally in the - -3 oxidation state. This and related molecules are conveniently represented as r...

In theory, periodate oxidation could have given a clear-cut answer as to the composition of the isomeric mixture of deoxy ribose phosphates. The 4-phosphate (73), devoid of vicinal diol groups, should be resistant to periodate the 3-phosphate (74) should reduce one and only one molar equivalent of the oxidant and yield one molar equivalent of both formaldehyde and the phosphorylated dialdehyde (75), whereas the 5-phosphate (76) could be expected to reduce one molar equivalent of periodate relatively rapidly, followed by a slower overoxidation reaction owing to the oxidation of malonaldehyde, formed as a result of the glycol cleavage. 

Attempts to separate the isomeric deoxy ribose phosphates by ion exchange techniques met with no success this may be because of the fact that eluents having a pH lower than 5 were not used, as migration of phosphomonoesters is known to be acid catalysed, and, because of the free sugar involved, alkaline eluents could not be considered. 

In terms of their molecular structures, the nucleotide and protein realms are usually considered to be rather independent of each other. However, these two families of molecules are covalently linked in the translational aminoacyl- RNAs and ribonucleoproteins as well as in the nucleoproteins involved in cellular and viral replication. In these hybrid biomolecules, a (deoxy)ribose phosphate moiety serves as the structural connection between the nucleoside and peptide moieties. 

D-Ribose Nucleic acids. Structural elements of nucleic acids and coenzymes, eg, ATP, NAD, NADP, flavo-proteins. Ribose phosphates are intermediates in pentose phosphate pathway. ... 

THE PENTOSE PHOSPHATE PATHWAY GENERATES NADPH RIBOSE PHOSPHATE (Figure 20-1)... 

Base X = H Nucleoside X = Ribose or Deoxyribose Nucleotide, Where X = Ribose Phosphate... 

One obvious way in which to attach a nitroxide group to B12 is to simple alkylate Cob(I)aiamin with a suitable nitroxide derivative. This would result in having the nitroxide covalently bound to the corrinoid at the upper axial coordination position of the cobalt. Such a procedure is outlined in Fig. 19. In this reaction 4-bromoacetamido 2,2,6,6-tetra-methylpiperidine-N-oxyl is used to alkylate Cob(I)alamin. This results in a Co(III)-nitroxalkylcobalamin. The corresponding cobinamide can then be produced by hydrolyzing the ribose-phosphate linkage (119). 

Adenine (A) Cytosine (C) Guanine (G) Thymine (T) Adenine (A) Cytosine (C) Guanine (G) Uracil (U) Deoxyribose Ribose Phosphate groups... 

Efforts were concentrated mainly on the backbone of RNA, i.e., the sequence phosphate - D-ribose - phosphate - D-ribose - phosphate, which needed to be simplified without losing the most important RNA functions, such as base pairing and information transfer. 

As Fig. 6.11 shows, the normal ribose phosphate chain of native RNA is replaced by the simpler backbone of polyamide polymers. The laboratory synthesis of these new polymers has been carried out. 

It is assumed that tholins also played an important role in the PAH world hypothesis. The PAH world could have existed as a pre-RNA world on the primeval Earth. It is suggested that PAHs can undergo stacking, thus forming structures to which nucleobases are chemically bound (to OH functions which are formed by photochemical derivatisation of the PAHs). The PAH stacks replace the more complex phosphate-D-ribose-phosphate chains in the nucleic acids (Ehrenfreund et al., 2006). 

Phosphoglucomutase acts not only on D-glucose and D-mannose phosphates (see p. 204) but also on D-ribose phosphates, the interconversion of D-ribosyl phosphate and D-ribose 5-phosphate being similarly accelerated by D-glucose 1,6-diphosphate,193 which appears to generate D-ribose 1,5-diphos-phate as cofactor.199(a) (b) (o) D-Ribose 5-phosphate is formed from D-ribose and ATP in the presence of yeast ribokinase.m... 

Those nucleosides found in the nucleic acids DNA and RNA involve the joining of ribose of deoxyribose to a purine or a pyrimidine base. One such nucleoside is adenosine, in which a nitrogen of adenine is linked to carbon 1 of the pentose, ribose. In this form it is a component of RNA but as a phosphory-lated derivative of adenosine (e.g. ATP), which is a high energy compound, it fulfils an important role in metabolism. The dinucleotides NAD and NADP are two cofactors necessary for many enzymic transformations and these also contain /V-glycosides of ribose phosphate. Other important nucleosides are found... 

Phosphoribosylpyrophosphate (PRPP) synthetase is one of the very few enzymes which transfer a pyrophosphoryl group from ATP in one step. When the synthesis is carried out in lsO-enriched water, lsO is incorporated into the PRPP, but not into AMP.91 The lsO in the PRPP arises from a pre-exchange between the H2180 and the ribose phosphate, and hence the results confirm that fission of the /5-P—O bond takes place. PRPP and ATP are starting materials in the biosynthesis of histidine, and Ai-(5 -phospho-D-ribosyl)adenosine triphosphate (29) is an intermediate. The... 

NMN is basically half of the NAD+ molecule nicotinamide ribose phosphate. NADP+ is NAD+ bearing a phosphate group at C3 of the ribose group attached to the adenine. The redox chemistry is the same in all three forms of the coenzymes. NAD+ is the form most frequently employed for biochemical oxidation reactions in catabohsm and NADP+ (in its reduced form NADPH) is the form usually employed for biochemical reduction reactions in anabohsm. NMN is employed infrequently. 

B. Kuhnast, F. Dolle, F. Vaufrey, F. Hinnen, C. Crouzel, B. Tavitian, Fluorine-18 labeling of oligonucleotides bearing chemically-modified ribose-phosphate backbones, J. Label. Compds Radiopharm. 43 (2000) 837-848. 

Adenine (A) Adenine (A) Deoxyribose RIbose Phosphate groups... 

The aqueous electron will react rapidly with all four of the nucleobases. Reaction of the aqueous electron with deoxyribose or ribose phosphate is 2 orders of magnitude lower, so the dominant interaction is with the bases. 

There seems, however, to be a problem with the above reasoning. If all the free radical damage ends up on the DNA bases, then one has problems explaining significant lesions such as single-strand breaks. How then does one explain strand breaks The question could be rephrased by asking if there could be damage to the ribose-phosphate which is difficult to detect. 

In RNA these bases are attached to the ribose phosphate chain as shown in Figure B. Synthetic polynucleotides can be produced that are like RNA in every respect except that they contain only one of the four bases they are called Poly A, Poly C, and Poly U. Poly G unfortunately cannot be prepared in high molecular weight form hence Poly I (in which the guanine amino groups have been removed) is prepared instead. 

Figure B. Attachment of the four bases to the ribose phosphate chain...

The routes involved in the formation of the various furan sulphides and disulphides involve the interaction of hydrogen sulphide with dicarbonyls, furanones and furfurals. Possible pathways are shown in Scheme 12.8. Furanthiols have been found in heated model systems containing hydrogen sulphide or cysteine with pentoses [56-58]. 2-Methyl-3-furanthiol has also been found as a major product in the reaction of 4-hydroxy-5-methyl-3(2H)-furanone with hydrogen sulphide or cysteine [21, 59]. This furanone is formed in the Maillard reaction of pentoses alternatively it has been suggested that it may be produced by the dephosphorylation and dehydration of ribose phosphate, and that this may be a route to its formation in cooked meat [21, 60]. 

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