Nucleotide deoxyribonucleotide

Cytosine was isolated from hydrolysis of calf thymus in 1894 and by 1903 its structure was known and it had been synthesized from 2-ethylthiopyrimidin-4(3H)-one. The acid hydrolysis of ribonucleic acid gives nucleotides, among which are two cytidylic acids, 2 -and 3 -phosphates of cytidine further hydrolysis gives cytidine itself, i.e. the 1-/3-D-ribofuranoside of cytosine, and thence cytosine. The deoxyribonucleic acids likewise yield deoxyribonucleotides, including cytosine deoxyribose-5 -phosphate, from which the phosphate may be removed to give cytosine deoxyriboside and thence cytosine. 

Methylcytosine (964 X = O) was synthesized in 1901 and its isolation from hydrolyzates of tubercule bacilli was reported in 1925. However, this was later shown to be incorrect and only about 1950 was it isolated by hydrolysis of the deoxyribonucleotide fractions from thymus, wheat germ and other sources (50MI21302). Nucleotides and a nucleoside of 5-methylcytosine are known. 

The most conspicuous use of iron in biological systems is in our blood, where the erythrocytes are filled with the oxygen-binding protein hemoglobin. The red color of blood is due to the iron atom bound to the heme group in hemoglobin. Similar heme-bound iron atoms are present in a number of proteins involved in electron-transfer reactions, notably cytochromes. A chemically more sophisticated use of iron is found in an enzyme, ribo nucleotide reductase, that catalyzes the conversion of ribonucleotides to deoxyribonucleotides, an important step in the synthesis of the building blocks of DNA. 

Nucleic acids are linear polymers of nucleotides linked 3 to 5 by phosphodi-ester bridges (Figure 11.17). They are formed as 5 -nucleoside monophosphates are successively added to the 3 -OH group of the preceding nucleotide, a process that gives the polymer a directional sense. Polymers of ribonucleotides are named ribonucleic acid, or RNA. Deoxyribonucleotide polymers are called deoxyribonucleic acid, or DNA. Because C-1 and C-4 in deoxyribonucleotides are involved in furanose ring formation and because there is no 2 -OH, only... 

Using method a, oligodeoxyribonucleotides were synthesized from di- to deca-deoxyribonucleotides by means of mesitylenesulfonylimidazole and mesitylenesulfonyl-1,2,4-triazole. With triisoproylbenzenesulfonylimidazole die condensation took place more slowly.11121 Compared widi the corresponding arylsulfonyl chlorides, imidazolides induced intemucleotide condensation much more slowly, but caused no darkening of the reaction mixture, did not affect acid-sensitive bonds in trityl protected nucleotides, and did not sulfonate the 3 -hydroxy groups.11111 The reaction conditions were room temperature, 5—6 days, and pyridine as solvent.11111... 

Fluorescein-labelled deoxyribonucleotide triphosphates may be used in place of those labelled with 32P. Once the DNA sequences are separated by electrophoresis, the resulting DNA bands fluoresce and are analysed by a flu-orogram imager, which produces a picture of the fluorescent bands similar to the autoradiography produced when using 32P-labelled nucleotides. 

Ribonucleotide reductase is required for the formation of the deoxyribonucleotides for DNA synthesis. Figure 1-18-2 shows its role in dTMP synthesis, and Figure 1-18-3 shows all four nucleotide substrates ... 

Figure 20.5 Nucleotides that are required for RNA or DNA synthesis. Note that the ribonucleotide diphosphates are the precursors for the formation of deoxyribonucleotides. It is the triphosphates that are required for polymerisation to form either RNA or DNA (see text).

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... 

These enzymes use DNA as a template and the ribonucleotide substrates must be present in the nucleus, i.e. ATP, GTP, CTP and UTP. Similarly, for the synthesis of DNA, the deoxyribonucleotides dATP, dGTP, dCTP and dTTP must be present in the nucleus. In addition, since the ribonucleoside diphosphates are required for synthesis of deoxyribonucleotides, these diphosphates must also be present. The concentrations of these various nucleotides have not been measured in the nucleus but it may be assumed that the concentrations of the ribonucleotides will be similar in the nucleus to those in the cytosol. 

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... 

The biosynthetic pathways for the pyrimidine nucleotides (2) are more complicated. The first product, UMP, is phosphorylated first to the diphosphate and then to the triphosphate, UTP. CTP synthase then converts UTP into CTP. Since pyrimidine nucleotides are also reduced to deoxyribonucleotides at the diphosphate level, CTP first has to be hydrolyzed by a phosphatase to yield CDP before dCDP and dCTP can be produced. 

DNA ligase (NAD+) [EC 6.5.1.2] (also referred to as polydeoxyribonucleotide synthase (NAD+), polynucleotide ligase (NAD+), DNA repair enzyme, and DNA join-ase) catalyzes the reaction of NAD+ with (deoxyribo-nucleotide) and (deoxyribonucleotide) to produce AMP, nicotinamide nucleotide, and (deoxyribonucleo-tide)( +m). This forms a phosphodiester at the site of a single-strand break in duplex DNA. RNA can also act as substrate to some extent. 

DNA is a linear polymer of covalently joined deoxyribonucleotides, of four types deoxyadenylate (A), deoxyguanylate (G), deoxycytidy-late (C), and deoxythymidylate (T). Each nucleotide, with its unique three-dimensional structure, can associate very specifically but non-covalently with one other nucleotide in the complementary chain A always associates with T, and G with C. Thus, in the double-stranded DNA molecule, the entire sequence of nucleotides in one strand is complementary to the sequence in the other. The two strands, held together by hydrogen bonds (represented here by vertical blue lines) between each pair of complementary nucleotides, twist about each other to form the DNA double helix. In DNA replication, the two strands separate and two new strands are synthesized, each with a sequence complementary to one of the original strands. The result is two double-helical molecules, each identical to the original DNA. 

Nucleic acids have two kinds of pentoses. The recurring deoxyribonucleotide units of DNA contain 2 -deoxy-D-ribose, and the ribonucleotide units of RNA contain D-ribose. In nucleotides, both types of pentoses are in their j3-furanose (closed five-membered ring) form. As Figure 8-3 shows, the pentose ring is not planar but occurs in one of a variety of conformations generally described as puckered. ... 

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. 

Nucleoside monophosphates are converted to their triphosphates by enzymatic phosphorylation reactions. Ribonucleotides are converted to deoxyribonucleotides by ribonucleotide reductase, an enzyme with novel mechanistic and regulatory characteristics. The thymine nucleotides are derived from dCDP and dUMP. 

The nucleotides described thus far in this chapter all contain ribose (ribonucleotides). The nucleotides required for DNA synthesis, however, are 2 -deoxyribonucleotides, which are produced from ribonucleoside diphosphates by the enzyme ribonucleotide reductase. 

Prokaryotic and eukaryotic DNA polymerases elongate a new ChA strand by adding deoxyribonucleotides, one at a time, to the 3-end of the growing chain (see Figure 29.16). The sequence of nucleotides that are added is dictated by the base sequence of fie Figure 29.15 template strand with which the incoming nucleotides are paired. 

Differences between 5 - 3 and 3 - 5 exonucleases The 5 - 3 exonuclease activity of DNA polymerase I differs from the 3 - 5 exonuclease used by both DNA polymerase I and III in two important ways. First, 5 3 exonuclease can remove one nucleotide at a time from a region of DNA that is properly base-paired. The nucleotides it removes can be either ribonucleotides or deoxyribonucleotides. Second, 5 —>3 exonuclease can also remove groups of altered nucleotides in the 5 —>3 direction, removing from one to ten nucleotides at a time. This ability is important in the repair of some types of damaged DNA. 

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