Ribose in nucleic acids

Two points thus argue against the participation of ribose in nucleic acid formation the lability of the molecule and the problems with its synthesis (the concentrations of the starting materials are too high). Other, newer and more effective syntheses seem necessary, whereby prebiotic conditions (although these are not known precisely) strongly limit the possibilities. 

Until recently the lactol ring structure of 2-desoxy-D-ribose in nucleic acid had been proved conclusively only for the thymidine nucleoside component and in this case it was furanose in form.26 Subsequently Brown and Lythgoe,27 by application of the periodate oxidation procedure to the 2 -desoxy ribosides of guanine, hypoxanthine, cytosine and thymine, afforded proof of the presence of a furanose sugar in each compound. 

The prefix 2-deoxy indicates the absence of oxygen at carbon 2. Units of D-ribose and 2-deoxy-D-ribose in nucleic acids and most other biological molecules are found almost exclusively in the j8-configuration. 

There are a number of possible ways to stabilize sugars the most interesting one is to attach the sugar to a purine or pyrimidine, i.e., by converting the carbohydrate to a glycoside, but the synthesis of nucleosides is difficult under plausible prebiotic conditions. It has therefore been suggested that ribonucleotides could not have been the first components of prebiotic informational macromolecules (59). This has led to propositions of a number of possible substitutes for ribose in nucleic acid analogues, in what has been dubbed the "pie-RNA World" (60). 

Nucleic Acids. Phosphoms is an essential component of nucleic acids, polymers consisting of chains of nucleosides, a sugar plus a nitrogenous base, and joined by phosphate groups (43,44). In ribonucleic acid (RNA), the sugar is D-ribose in deoxyribonucleic acids (DNA), the sugar is 2-deoxy-D-ribose. 

The sugars are typically ribose (ribonucleic acids, RNA), or 2-deoxyribose (deoxyribonucleic acids, DNA). There are five common bases in nucleic acids adenine (A) thymine (T) uracil (U) cytosine (C) and guanine (G). DNA polymers incorporate the four bases. A, T, C, and G, and RNA, the set A, U, C, and G. 

Section 28.7 Nucleic acids are polynucleotides present in cells. The carbohydrate component is D-iibose in ribonucleic acid (RNA) and 2-deoxy-D-ribose in deoxyribonucleic acid (DNA). 

As is well-known, nucleic acids consist of a polymeric chain of monotonously reiterating molecules of phosphoric acid and a sugar. In ribonucleic acid, the sugar component is represented by n-ribose, in deoxyribonucleic acid by D-2-deoxyribose. To this chain pyrimidine and purine derivatives are bound at the sugar moieties, these derivatives being conventionally, even if inaccurately, termed as pyrimidine and purine bases. The bases in question are uracil (in ribonucleic acids) or thymine (in deoxyribonucleic acids), cytosine, adenine, guanine, in some cases 5-methylcytosine and 5-hydroxymethylcyto-sine. In addition to these, a number of the so-called odd bases occurring in small amounts in some ribonucleic acid fractions have been isolated. 

The most important product of the hexose monophosphate pathway is reduced nicotinamide-adenine dinucleotide phosphate (NADPH). Another important function of this pathway is to provide ribose for nucleic acid synthesis. In the red blood cell, NADPH is a major reducing agent and serves as a cofactor in the reduction of oxidized glutathione, thereby protecting the cell against oxidative attack. In the syndromes associated with dysfunction of the hexose monophosphate pathway and glutathione metabolism and synthesis, oxidative denaturation of hemoglobin is the major contributor to the hemolytic process. 

Figure 1.40 The two forms of sugar residues commonly found in nucleic acids. 3-D-Ribose is the sugar constituent of RNA, while p-D-2-deoxyribose is a component of DNA.

Administration203 to chicks of acetic acid labeled with C14 (in the carboxyl group) gave D-glucose (from the glycogen) labeled equally at C3 and C4, but the D-ribose (from nucleic acids) had more label at C3 than at C2, indicating that in vivo D-ribose does not arise exclusively from hexose by loss of Cl. The 20-30% isotope content of D-ribose formed from D-glucose-l-C14 by Escherichia coli indicates that direct conversion is the major pathway but that a part is probably derived from transketolase action.204 206... 

The nucleotides of RNA and DNA consist of three components a carbohydrate, a phosphate group and an organic nitrogenous base. There are two types of carbohydrate molecule in nucleic acids, both of which are D-pentoses, i.e. contain five carbon atoms. The carbohydrate in RNA is ribose, while DNA contains deoxyribose, which has a hydrogen atom instead of a hydroxyl group attached to the carbon in the 2 position (Figure 13.1). 

Nature is also selective in the geometry involved in nucleic acid synthesis. This specificity involves both the base order and the particular sugar employed. For DNA the employed sugar is (3-2-deoxy-D-ribose, deoxyribose (below left). Deoxyribose has three chiral centers but only one of them is employed in the synthesis of nucleic acids. Ribose, the sugar employed in the synthesis of RNA, has four geometric sites (below right). 

The purine and pyrimidine ring compounds found in nucleic acids are known as "bases," even though some of them have almost no basic character. Nucleosides are the N-glycosyl derivatives of the bases with ribose or 2-deoxyribose. Tire nucleotides are phosphate esters of nucleosides. Similar names are applied to related compounds such as adenosine triphosphate (ATP) that are not present in DNA or RNA. The names of the principal nucleotides from which the nucleic acids are formed are given in Table 5-1. The... 

Many kinds of organisms and some mammalian organs, notably liver, possess an alternative pathway for the oxidation of hexoses which results in a pentose phosphate and carbon dioxide. This pentose can be used as a precursor of the ribose found in nucleic acids or other sugars containing from three to seven carbon atoms which are needed in smaller amounts. The first and third reactions in the pentose phosphate pathway generate NADPH which is a major source of reducing power in many cells. 

The composition and function of desoxyribonucleic acids have been studied extensively in recent years, and wider knowledge of the behavior of 2-desoxy-D-ribose became urgent. In this review developments in nucleic acid chemistry which have led to advances in our knowledge of 2-desoxypentoses (and vice versa) will be stressed. 

A close look at this reaction reveals that in the opposite direction, the reaction is of the phosphorolysis type. For this reason, the enzymes catalyzing the reaction with ribose-l-phosphate are called phosphorylases, and they also participate in nucleic acid degradation pathways. Purine nucleoside phosphorylases thus convert hypoxanthine and guanine to either inosine and guanosine if ribose-l-phosphate is the substrate or to deoxyinosine and deoxyguanosine if deoxyribose-1-phosphate is the substrate. Uridine phosphorylase converts uracil to uridine in the presence of ribose-l-phosphate, and thymidine is formed from thymine and deoxyribose-l-phosphate through the action of thymidine phosphorylase. 

The precise nature of activated Fe-BLM is still a subject of debate however, both Fe(IV)02+ and Fe(V)03+ species have been suggested (15). In any case, activated Fe-BLM is capable of oxidizing many organic substrates, including ribose and deoxyribose in nucleic acids (6). 

The four principal bases of the nucleic acids are uracil and cytosine, which are derivatives of pyrimidine, and adenine and guanine, which are derived from the purine heterocycle (Fig. 15.1). In the nucleic acids, ribose (in ribonucleic acid,... 

These sugars are all part of the pentose phosphate pathway, which is used to form ribose for nucleic acid synthesis in other organisms. The dark reactions have hijacked the pentose phosphate pathway to regenerate RuBP from GAP. 

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