Deoxyribonucleotide, structures

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. 

Figure 28.1 Structures of the four deoxyribonucleotides and the four ribonucleotides.

Draw the complete structure of the deoxyribonucleotide sequence from which the mRNA codon in Problem 28.24 was transcribed. 

Sequences of more than 350 bases can be obtained from some gels. The sequence of the complementary DNA strand is often determined as a check on accuracy of the first analysis. The primary structure of thousands of deoxyribonucleotides can be deduced by the analysis of... 

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. 

Figure 8-4 gives the structures and names of the four major deoxyribonucleotides (deoxyribonucleo-side 5 -monophosphates), the structural units of DNAs, and the four major ribonucleotides (ribonucleoside 5 -monophosphates), the structural units of RNAs. Specific... 

The enzyme is very sensitive to the secondary structure of the substrate. Native calf thymus DNA is quite resistant to enzymic attack by spleen exonuclease, being split at less than 4% the rate at which alkali-denatured DNA is split (11). Long deoxyribonucleotides (average chain length 20-50), which still have complementary double-stranded structure, are rather resistant to the enzyme (26). Some limited results obtained with synthetic polyribonucleotides (11) are rather puzzling since poly C was found to be completely resistant, whereas poly A, poly I, and poly U were degraded at comparable rates. In the solvent used (0.15 M acetate buffer-0.01 M EDTA, pH 5.0), poly A and poly C are believed to have... 

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.)... 

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... 

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 structure of a deoxyribonucleotide. Drawn in abbreviated form at lower left. The illustrated structure is written pTpApCpG. 

Draw the complete structure of deoxycytidine 5 -phosphate, one of the four deoxyribonucleotides. 

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. 

Write the structures of (a) the ribonucleotide containing adenine and (b) the deoxyribonucleotide containing thymine. 

Extensive studies were performed to determine the minimum lengths of oligo(deoxyribonucleotides) that could be joined,269,270 and it was found that a tetramer can act as the 5 -phosphorylated donor molecule. An example of the potential difficulties in the joining-reaction is found at the 5 -end of the structure gene for271 a tRNAAla, as shown in formula 6. If segment 3 is 5 -phosphorylated, a dimerization... 

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