2-Deoxyribonucleotides, common

FIGURE 8-4 Deoxyribonucleotides and ribonucleotides of nucleic acids All nucleotides are shown in their free form at pH 7.0. The nucleotide units of DNA (a) are usually symbolized as A, G, T, and C, sometimes as dA, dG, dT, and dC those of RNA (b) as A, G, U, and C. In their free form the deoxyribonucleotides are commonly abbreviated dAMR dGMR dTMR and dCMP the ribonucleotides, AMR... 

Note Nucleoside and nucleotide are generic terns that include both ribo- and deoxyribo- fonns. Aso, ribonucleosides and ribonucleotides are here designated sinply as nucleosides and nucleotides (e.g., ribo-adenosine as adenosine), and deoxyribo-nucleosides and deoxyribonucleotides as deoxynucleosides and deoxynucleotides (e.g, deoxyribo adenosine as deoxyadeno-sine). Both fonns of nailing are acceptable, but the shortened names are more commonly used Ttynine is an exception ribotlynidine is used to describe its unusual occurrence in RNfY... 

FIGURE 8-10 Absorption spectra of the common nucleotides The spectra are shown as the variation in molar extinction coefficient with wavelength. The molar extinction coefficients at 260 nm and pH 7.0 (e26o) are listed in the table. The spectra of corresponding ribonucleotides and deoxyribonucleotides, as well as the nucleosides, are essentially identical. For mixtures of nucleotides, a wavelength of 260 nm (dashed vertical line) is used for absorption measurements. 

Structures of three common ribonucleotides (a) and four common deoxyribonucleotides (b). See Table 23.1 for alternative names and for names of the corresponding bases and nucleosides. The ribonucleotides contain a ribose sugar, whereas the deoxyribonucleotides have a deoxyribose that lacks a hydroxyl group at C-2 of the pentose. In all cases the phosphoryl group is attached... 

Recognize the structures of DNA and RNA, and draw the structures of the common ribonucleotides and deoxyribonucleotides. 

These four bases are incorporated into deoxyribonucleosides and deoxyribonucleotides similar to the bases in ribonucleosides and ribonucleotides. The following structures show the common nucleosides that make up DNA. The corresponding nucleotides are simply the same structures with phosphate groups at the 5 positions. 

Ribonucleotide reductase catalyses the reduction of the four common ribonucleotides to their corresponding deoxyribonucleotides, an essential step in DNA synthesis. All four ribonucleotides are reduced by the same enzyme [77], The enzyme (250 000 mol. wt.) is a complex of two proteins Mi which contains substrate and redox-active sulphydryl groups and M2 which contains both a (x-oxo-bridged binuclear iron centre (Fig. 5) [77] and a tyrosine moiety sidechain which exists as a free radical stabilised by the iron centre [78], This radical, which is only 5.3 A away from iron centre 1, has access to the substrate-binding pocket and is essential for enzyme activity. Electrons for the reduction reaction are supplied from NADPH via thioredoxin, a small redox-active protein. 

We turn now to the synthesis of deoxyribonucleotides. These precursors of DNA arc formed by the reduction ot ribonucleotides specifically the 2 -hydroxyl group on the ribose moiety is replaced by a hydrogen atom. The substrates are ribonucleoside diphosphates, and the ultimate reduclant is NADPH. The enzyme ribonucleotide reductase is responsible for the reduction reaction for all four ribonucleotides. The ribonucleotide reductases of different organisms are a remarkably diverse set of enzymes. Yet detailed studies have revealed that they have a common reaction mechanism, and their three-dimensional structural features indicate that these enzymes are homologous. We will focus on the best understood of these enzymes, that of E. coli living aerobically. 

Structures, names, and common abbreviations of four deoxyribonucleotides or deoxyribonucleotide-5 -phosphates. 

FIGURE 1-31 DNA to RNA to protein. Linear sequences of deoxyribonucleotides in DNA, arranged into units known as genes, are transcribed into ribonucleic acid (RNA) molecules with complementary ribonucleotide sequences. The RNA sequences are then translated into linear protein chains, which fold into their native three-dimensional shapes, often aided by molecular chaperones. Individual proteins commonly associate with other proteins to form supramolecular complexes, stabilized by numerous weak interactions. 

S Additional information <3, 7> (<3> enzyme exists in different conformational states with different substrate kinetic properties [9] <3> presumably one common nucleoside acceptor site [15] <3> purine deoxynucleo-side activity inseparably associated with deoxycytidine kinase protein [16] <3> several isozymes cytosolic deoxycytidine kinase I and II, plus mitochondrial isozyme [10] <3> multisubstrate enzyme, that also phos-phorylates purine deoxyribonucleotides [9] <7> enzyme has two separate active sites for deoxycytidine and deoxyadenosine activity [22] <3> reacts with both enantiomers of -deoxycytidine, -deoxyguanidine, -deoxyadenosine, and a-D-deoxycytidine is also substrate [31] <3> reacts with both enantiomers of jS-deoxyadenosine, j3-arabinofuranosyl-adenine and jd-deoxyguanine ]34] <3> remarkably relaxed enantioselectivity with respect to cytidine derivatives in p configuration [36] <3> lack of enantioselectivity for D- and L-analogues of cytidine and adenosine [43]) [9, 10, 15, 16, 22, 31, 34, 43]... 

The fermentative bacteria, Lactobacillus leichmannii probably possess the most simple of all ribonucleotide reductases, but the protein does require the most complex coenzyme known, 5 -deoxyadenosylcobalamin (Fig. 1). This corrinoid coenzyme catalyzes but few enzymatic reactions, usually involving an intramolecular 1,2-hydrogen shift as found in the common methylmalonylCoA succinylCoA isomerase reaction. Participation in deoxyribonucleotide formation, where hydrogen transfer occurs intermolecularly (Eq. I), was first implicated by the nutritional requirement of lactobacilli for vitamin B12 during DNA synthesis, and was verified in cell-free extracts by Blakley and H. A. Barker in 1964 The reaction has been studied in great detail in the laboratories of Beck Blakley and Hogenkamp ... 

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 ... 

Although it is outside the scope of this chapter to even begin to expose the wealth of information concerning the formation of polymeric DNA and RNA beyond that which has already been mentioned, it is, nonetheless, important to recognize that the overall reaction catalyzed by DNA polymerase enzymes is to take a growing deoxyribonucleotide monophosphate polymer and to add to it a deoxyribonucleo-tide triphosphate and to eliminate two linked phosphate units, that is, PiO or its equivalent (commonly written as PP). Further, it is important to note that in principle and in practice, the polymerization process is reversible. And, both in principle and in practice, it is common to find the phosphate units scrambled. Indeed, it is presumed that this is one of the ways of introducing radioactive phosphate into deoxyribonucleotide triphosphates. ... 

The number of bound phosphates can vary in a nucleotide. When phosphate is absent, the molecule is referred to as a nucleoside or a deoxynucleoside, depending on the hydroxylation-state of the sugar. Up to three phosphate groups can be present. When one or more phosphates are present, the compound is commonly referred to by the base present, how many phosphates are present, and whether the deoxy-form of the sugar is used. For example, when the base adenine is present and there are two phosphates, the corresponding deoxyribonucleotide and ribonucleotide are typically referred to by the abbreviations, dADP and ADR The former and latter abbreviations indicate deoxy-adenine diphosphate and... 

---