Nucleotide Deoxyribonucleotides Purine

The pentose component of naturally occurring nucleotides is ribose or 2-deoxyribose (i.e., ribose with a hydrogen instead of a C-2 —OH). In nucleotides the purine or pyrimidine is attached to C-1 of the pentose in the /3 configuration. This means that the base is cis relative to C-5 —OH and trans relative to the C-3 —OH. The major function of deoxyribonucleotides (those that have 2-deoxyribose as the pentose) is to serve as building blocks for DNA. Although ribonucleotides similarly serve as the units for RNA synthesis, they also have a multitude of other functions in cell metabolism. In some synthetic nucleosides with therapeutic properties, other pentose components such as arabinose are present. (See fig. 12.2 for the structure of arabinose.)... 

The two classes of nucleotide that must be synthesised are the pyrimidine and purine ribonucleotides for RNA synthesis and the deoxyribonucleotides for DNA synthesis. For the original sources of the nitrogen atoms in the bases of the pyrimidine and purine nucleotides, see Figure 20.7. The pathway for the synthesis of the pyrimidine nucleotides is... 

Hydroxyurea interferes with the synthesis of both pyrimidine and purine nucleotides (see table 23.3). It interferes with the synthesis of deoxyribonucleotides by inhibiting ribonucleotide reductase of mammalian cells, an enzyme that is crucial and probably rate-limiting in the biosynthesis of DNA. It probably acts by disrupting the iron-tyrosyl radical structure at the active site of the reductase. Hydroxyurea is in clinical use as an anticancer agent. 

The nucleotides of DNA are called deoxyribonucleotides, since they contain the sugar deoxyribose, whereas, those of RNA are called nbonucleotides since they contain nbose instead. Each nucleotide contains both a specific and a nonspecific region. The phosphate and sugar groups are the nonspecific portion of the nucleotide, while the purine and pyrimidine bases make up the specific portion. 

As much of the terminology used in molecular biology may be unfamiliar to some readers, it is appropriate to define some of the vocabulary and this is given in an appendix to this chapter. There are two types of nucleic acids, the ribonucleic acids (RNA) and the deoxyribonucleic acids (DNA). Genetic information is carried in the linear sequence of nucleotides in DNA. Each molecule of DNA contains two complementary strands of deoxyribonucleotides which contain the purine bases, adenine and guanine and the pyrimidines, cytosine and thymine. RNA is single-stranded, being composed of a linear sequence of ribonucleotides the bases are the same as in DNA with the exception that thymine is replaced by the closely related base uracil. DNA replication occurs by the polymerisation of a new complementary strand on to each of the old strands. 

Understand the purine and pyrmidine de novo biosynthetic pathways, with special attention to enzymes controlling pathway rates and the properties of such enzymes the positive and negative effectors steps inhibited by the various antitumor agents and their mechanisms final products of the de novo pathways and how the various nucleotides are generated from them and the biosynthesis of deoxyribonucleotides and the attendant mechanisms. 

DNA is a polymer of deoxyribonucleotide units. A nucleotide consists of a nitrogenous base, a sugar and one or more phosphate groups. The sugar in a deoxyribonucleotide is deoxyribose. The base is a purine or pyrimidine. The purines in DNA are adenine (A) and guanine (G) and the pyrimidines are thymine (T) and cytosine (C) (figure 3.17). 

See also De Novo Biosynthesis of Purine Nucleotides, Purine Degradation, Excessive Uric Acid in Purine Degradation, Salvage Routes to Deoxyribonucleotide Synthesis, Nucleotide Analogs in Selection... 

See also De Novo Biosynthesis of Purine Nucleotides, Salvage Routes to Deoxyribonucleotide Synthesis... 

Two reactions that are required to form the precursors of DNA are described in detail ribonucleotide reductase converts ribonucleotides to deoxyribonucleotides, and thymidylate synthase methylates dUMP to form dTMP. The authors present the mechanisms and cofactors of these enzymes and explain how some anticancer drugs and antibiotics function by inhibition of dTMP synthesis and thus the growth of cells. Nucleotides also serve important roles as constituents of NAD", NADP, FAD, and coenzyme A (CoA), so the syntheses of these cofactors are described briefly. The chapter concludes with an explanation of how the purines are catabolized and some of the pathological conditions that arise from defects in the catabolic pathway of the purines. 

It should be realized at the outset that all organisms have to possess the capacity to make deoxyribonucleotides firom ribonucleotides. This is the only process which permits the cell to utilize one fraction of the total nucleotides formed de novo in pyrimidine and purine biosynthesis for DNA replication there is no alternative biochemical route producing 2-deoxyribose, its phosphates, or N-glycosides from other molecules (Scheme II). 

Table 5 contains ribonucleotides with the common amino and carbonyl structures, with extra substituents, and with totally unsubstituted bases like purine or benzimidazole. Apparent values and velocities do not vary more than about tenfold in the presence of specific effector deoxyribonucleotides. Guanine and cytosine nucleotides have usually fastest and compounds with fewer base substituents show decreased reaction rates. Loss of substrate activity is only observed in syn-oriented nucleotides where the nucleobase is rotated about the glycosidic bond like in 8-bromo-ADP or -ATP. Molecular conformation-enzyme activity relationships have been discussed in detail ... 

The enzyme studies described above are also compatible with a number of experiments in which incorporation of ribonucleotides into DNA has been shown to be more efficient than incorporation of deoxyribonucleotides Functional compartmentation of DNA precursors is also observed in the utilization of deoxyuridine or thymidine for DNA which in E. coli or in eukaryotic cells occurs without prior equilibration with the free dTTP pool On the other hand, in thymocytes purine deoxyribonucleosides are converted to nucleotides but are not utilized for DNA replication however here they allosterically inhibit ribonucleotide reduction . All these data agree with the existence of two different deoxyribonucleotide pools, one associated with the replitase complex and another independent pool of free deoxyribonucleotides. 

In ribonucleotides, the pentose is the o-ribose while in deoxyribonucleotides, the sugar is 2 -deoxy-D-ribose. The nitrogen base of the planar, heterocyclic molecule derived from purine or pyrimidine is linked to Cl of the sugar residue. The phosphate group may be bonded to the C3 or C5 of a pentose to form its 3 -nucleotide or its 5 -nucleotide respectively. In nucleic acids, the purine and pyrimidine bases of nucleotides serve solely as information symbols for the coding of genetic information. 

Sequences of nucleotides in nucleic acids are written widi one-letter symbols starting with die 5 -terminus at the left toward 3 -tea minus at die right. Deoxyribonucleotides in DNA is prefixed with d. If it is not known whether a residue is A or G, die appropriate abbreviation for purine is R Y is used for pyrimidine, C or T. 

It is as nucleotides, i.e., ribosyl phosphate derivatives, that most of the reactions of purines and pyrimidines take place, and the origin of the ribosyl phosphate moiety must therefore be discussed. The deoxyribosyl phosphate moiety of deoxyribonucleotides is synthesized by way of ribonucleotides, and this process will be discussed in Chapter 16. The pertinent literature through 1962 has been reviewed in the English edition of Hollman s book (I) references given there will not usually be repeated here. 

Stadtman 65) and Blakley and Vitols 66) have reviewed studies of the inhibition and stimulation of the purine phosphoribo ltransferases by purine ribo- and deoxyribonucleotides. At relatively high concentrations, a variety of nucleotides inhibit these enzymes, while a few increase these activities at low concentrations. Studies by Henderson et al. 67) have shown that inhibitors bind to several kinetically significant forms of adenine phosphoribosyltransferase and that there are probably several different inhibitor binding sites which are not the same as those to which substrates and products bind. It must be emphasized, however, that the physiological significance of the studies conducted so far is unclear. Attempts to study the control of these reactions in intact cells have merely emphasized the complexity of this control. Under some conditions the availability of PP-ribose-P may limit the rate of these reactions. 

So far as is known, pyrimidine ribo- and deoxyribonucleotides are de-phosphorylated by the nucleotidases and phosphatases described in Chapter 10 as acting on purine nucleotides. Although a number of potential de-phosphorylating enzymes may be avaUable in most cells, the relative quantitative importance of each is not known. 

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