Pentose-1,5-diphosphates

Although there are a number of inefficient steps in most proposed prebiotic syntheses of ribotides, the major objection to RNA as the primogenitor of life has been the relatively small yield of ribose in the formose reaction, a simple condensation of glycoaldehyde. Muller et a/.,18 however, have discovered a variation of the formose reaction that produces a limited mix of pentose diphosphates in which the ribose forms predominate (52 14 23 11, ribose arabinose lyxose xylose). Although many critical chemical roadblocks remain (such as the extremely low yield of pyrimidine nucleosides following the condensation of ribose and free bases), this advance belies the previously held view that products of the formose reaction are necessarily so chemically diverse that they are the carbohydrate analog of petroleum. 19... 

Consider one complete revolution of the carbon cycle, shown in Fig. 6. Each reaction occurs at least once. Three molecules of pentose diphosphate (fifteen carbon atoms) react with three molecules of carbon dioxide giving six molecules of PGA or eighteen... 

The synthesis of pentose-2,4-diphosphate referred to above gave the best yields of a ribose derivative. Thus, the search for an effective synthesis leading to necessary starting materials such as glycol aldehyde phosphate (GAP) was important Krishnamurthy et al. (1999, 2000) reported new synthetic routes to GAP glycol aldehyde is allowed to react with amidotriphosphate (AmTP) in dilute aqueous solution. The triphosphate derivative is formed from trimetaphosphate and NH4OH. 

The deoxyribonucleotides, except for deoxythymidine nucleotide, are formed from the ribonucleotides by the action of an enzyme complex, which comprises two enzymes, ribonucleoside diphosphate reductase and thioredoxin reductase (Figure 20.11). The removal of a hydroxyl group in the ribose part of the molecule is a reduction reaction, which requires NADPH. This is generated in the pentose phosphate pathway. (Note, this pathway is important in proliferating cells not only for generation... 

Some bacteria that lack the usual aldolase produce ethanol and lactic acid in a 1 1 molar ratio via the "heterolactic fermentation." Glucose is converted to ribulose 5-phosphate via the pentose phosphate pathway enzymes. A thiamin diphosphate-dependent "phosphoketolase" cleaves xylulose 5-phosphate in the presence of inorganic phosphate to acetyl phosphate and glyceraldehyde 3-phosphate. 

The formation of deoxyribose, die pentose moiety of deoxyribonucleic acid, can occur directly from ribose while the latter is in the form of a nucleotide diphosphate. Deoxyribose-5-phosphate can also be formed by condensation of acetaldehyde and glyceraldehyde-3-phosphate. 

Photosynthesis. The formation of carbohydrates in green plants by the process of photosynthesis is described in ihc entry on Photosynthesis. The synthetic mechanism involves the addition of carbon dioxide to ribulose-1,5-diphosphate and the subsequent formation of two molecules of 3-phosphoglyccric acid which are reduced to glyceraldehyde-3-phosphate. The triose phosphates are utilized to again from ribulose-5-phosphates by enzymes of the pentose phosphate cycle Phosphorylation or ribulose-5-phosphate with ATP regenerates ribulose-1.5-diphosphate to accept another molecule of carbon dioxide. See also Phosphorylation (Photosynthetlc). 

A number of lyases are known which, unlike the aldolases, require thiamine diphosphate (TDP) as a cofactor in the transfer of acyl anion equivalents [389-391], but proceed via enolate-type intermediates by a mechanism that resembles the classical benzoin addition. The most important representative is the transketolase (EC 2,2.1.1) [392] which stems from the oxidative pentose... 

Alternatively, ribulose (D-eryt/iro-pentulose) 5-phosphate may be iso-merized to ribose 5-phosphate with pentose phosphate isomerase, but the same isomerase will convert D-ribose 5-phosphate into D- ryt/zro-pentulose 5-phosphate, the equilibrium being displaced by phosphorylation to the diphosphate (involving three enzyme systems). 

In a very imaginative piece of research Frost and coworkers have developed a plasmid-based method for synthesizing aromatic amino acids, by incorporating the genes that code for the enzymes that perform the series of conversions from D-fructose-6-phosphate to D-erythrose-4-phosphate to 3-deoxy-D-arabinoheptulosonic acid-7-phos-phate (DAHP) near each other on a plasmid that can be transformed in E. coli. The enzymes are the thiamin diphosphate-dependent enzyme transketolase in the nonoxida-tive pentose shunt and DAHP synthase. The DAHP is then converted to the cyclic dehydroquinate, a precursor to all aromatic amino acids L-Tyr, L-Phe and L-Trp165,166 (equation 27). 

Later studies established the coenzyme role of thiamin diphosphate in transketolase in the pentose phosphate pathway. More recent studies have shown that thiamin triphosphate acts to regulate a chloride channel in nerve tissue. 

Figure 3 Biosynthetic pathways. (A) In the terpenoid coupling reaction, isomers of isopentenyl pyrophosphate are joined with the loss of pyrophosphate, leading to a linear intermediate that is cyclized to a terpenoid skeleton, as shown for the diterpene taxol. (B) In the polysaccharide coupling reaction, hexose and pentose monomers are joined with the loss of a nucleoside diphosphate, as shown for the epivancosaminyl-glucose disaccharide of vancomycin. (C) In the first step of the nonribosomal peptide coupling reaction, an aminoacyl adenylate is transferred to a carrier protein or thiolation domain (denoted T ) with loss of adenosine monophosphate. In the second step, this carrier protein-tethered aminoacyl group is coupled to the amine of an aminoacyl cosubstrate, forming a peptide bond, as shown for two residues in backbone of vancomycin. (D) In the polyketide coupling reaction, the loss of carbon dioxide from a two or three-carbon monomer yields a thioester enolate that attacks a carrier protein-tethered intermediate, forming a carbon-carbon bond as shown for the polyketone precursor of enterocin.

In the presence of formaldehyde (0.5 mol equiv.), sugar phosphates were formed in up to 45% yield, with pentose-2,4-diphosphates dominating over hexose triphosphates by a ratio of 3 1 (Scheme 13.2, Route B). The major component was found to be D,L-ribose-2,4-diphosphate with the ratios of ribose-, arabinose-, lyxose-, and xylose-2,4-diphosphates being 52 14 23 11, respectively. The aldomerization of 2 in the presence of H2CO is a variant of the formose reaction. It avoids the formation of complex product mixtures as a consequence of the fact that aldoses, which are phosphorylated at the C(2) position, cannot undergo aldose-ketose tautomerization. The preference for ribose-2,4-diphosphate 5 and allose-2,4,6-triphosphate formation might be relevant to a discussion of the origin of ribonucleic acids. 

In the presence of formaldehyde (0.5 mol-equiv.) sugar phosphates were formed in up to 45% yield, with pentose 2,4-diphosphates dominating over hexose triphosphates by a ratio of 3 1 (O Scheme 2, route B). The preference for ribose 2,4-diphosphate 5 and allose 2,4,6-triphosphate formation might have significance for the discussion concerning the origin of ribonucleic acids. 

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