Deoxyribose, nucleotides

Base X = H Nucleoside X = Ribose or Deoxyribose Nucleotide, Where X = Ribose Phosphate... 

Nucleosides (e. g. adenosine, cytidine, guanosine, pyrimidine, thymidine, uridine) consist of a nitrogenous purine or pyrimidine base linked to a 5-carbon sugar (ribose or deoxyribose). Nucleotides (adenine, cytosine, guanine, thymine, uracil), the phosphate esters of nucleotides, form the basis of RNA and DNA. As infectious viral nucleic acids, they are capable of penetrating the cells and using available enzyme systems for replication. 

Lok C N, Viazovkina E, et al. (2002). Potent gene-specific inhibitory properties of mixed-backbone antisense oligonucleotides comprised of 2 -deoxy-2 -fluoro-D-arabinose and 2 -deoxyribose nucleotides. Biochem. 41 3457-3467. 

Natural nucleoside bases can be one of five heterocycUc aromatic compounds and include adenine, guanine (the purines), cytosine, thymine and uracil (the pyrimidines). Nucleosides are composed of a base which is attached to a carbohydrate moiety through one of the aromatic ring nitrogen atoms. The specific carbohydrate distinguishes RNA (ribose) from DNA (deoxyribose). Nucleotides are phosphory-lated derivatives of nucleosides and contain one, two, three or (less commonly) four or more phosphate residues either at the 5 position or at the 3 position (Fig. 11.1.1). 

Draw the 2-deoxyribose nucleotide that will result if each of the following heterocycles is incorporated ... 

The conformation of the sugar largely determines the overall structure of the nucleic acid polymer. By convention, the carbons in the pentose sugar are numbered as Cl, C2, . .. C5, beginning with the carbon bearing the nitrogenous base. In DNA, the 2 -deoxyribose nucleotides tend to form the classic B-form double helix (Fig. 9.3a) with antiparallel strands, whose stabihty is determined primarily by the overlap of orbitals from adjacent aromatic nucleobases (ti-ti stacking interactions). In the B-form, each base pair is rotated by about 36 relative to the next, such that a... 

Nucleic Acid Polymer of deoxyribose nucleotides Polymer of ribose nucleotides... 

Any one nucleotide, the basic building block of a nucleic acid, is derived from a molecule of phosphoric acid, a molecule of a sugar (either deoxyribose or ribose), and a molecule of one of five nitrogen compounds (bases) cytosine (C), thymine (T), adenine (A), guanine (G), uracil (U). 

A chain of nucleotides containing only deoxyribose as the sugar is a DNA. Similarly, RNA possesses chains nucleotides having only ribose as the sugar and is therefore a ribonucleic acid. 

The primary stmcture of DNA is based on repeating nucleotide units, where each nucleotide is made up of the sugar, ie, 2 -deoxyribose, a phosphate, and a heterocycHc base, N. The most common DNA bases are the purines, adenine (A) and guanine (G), and the pyrimidines, thymine (T) and cytosine (C) (Fig. 1). The base, N, is bound at the I -position of the ribose unit through a heterocycHc nitrogen. 

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. 

The nucleic acids DNA (deoxyribonucleic acid) and RNA (ribonucleic acid) are biological polymers that act as chemical carriers of an organism s genetic information. Enzyme-catalyzed hydrolysis of nucleic acids yields nucleotides, the monomer units from which RNA and DNA are constructed. Further enzyme-catalyzed hydrolysis of the nucleotides yields nucleosides plus phosphate. Nucleosides, in turn, consist of a purine or pyrimidine base linked to Cl of an aldopentose sugar—ribose in RNA and 2-deoxyribose in DNA. The nucleotides are joined by phosphate links between the 5 phosphate of one nucleotide and the 3 hydroxyl on the sugar of another nucleotide. 

DNA and RNA are formed of nucleotides. Each nucleotide or nucleoside is composed of a purine or pyrimidine base linked to the 1-position of a ribose sugar in the case of RNA and a 2 -deoxyribose sugar in the case of DNA.155 The 5 position is phosphorylated in the case of a nucleotide, while the nucleoside is not phosphorylated therefore, nucleotides are nucleoside phosphates. Phosphorylation can include one, two, or three phosphate groups. The most familiar example of a phosphorylated nucleotide is phosphorylated adenosine, which occurs as the mono-, di-, and triphosphate (AMP, ADP, and ATP, respectively) and is a principal means of energy storage in biological systems. 

An analogous series of reactions is used to produce depyrimidinated DNA fragments. Hydrazine is used in these reactions, since both cytosine and thymine react with hydrazine. The bases are cleaved to yield urea and a pyrazole ring. The deoxyribose moiety is left as a hydrazone. Piperidine, which reacts with the hydrazone, is used to cleave the nucleotide chain. Cytosines react specifically with hydrazine in 5 mol/ L NaCl, but no specific reaction exists for thymines. Consequently, one aliquot yields labeled oligonu-cleotides 3 -terminated at cytosines, whereas a second aliquot contains nucleotides cleaved in the absence of NaCI at both cytosine and thymine residues. 

Deoxyribose nucleic acid (DNA) Comprises a backbone with four nucleotide bases, adenine, cytosine, guanine and thymine, bound to it. The genetic information in all cells is encoded in this genome of double-stranded DNA, comprising 3 billion base pairs located in the chromosomes. 

The actual building blocks for the nucleic acids are the nucleotides, which are formed in an esterification reaction between nucleosides and phosphate three OH functions of ribose, and two of deoxyribose, can undergo esterification ... 

Nucleotide A subunit of DNA or RNA consisting of a purine (adenine and guanine) or a pyrimidine base [thymine (DNA only), uracil (RNA only) and cytosine], a phosphate molecule, and a sugar molecule (deoxyribose in DNA and ribose in RNA). 

Figure 3.3 Chemical structure of (a) ribose and (b) 2 -deoxyribose, the nucleotide pentoses found in RNA and DNA respectively. The differences in chemical structure are highlighted by the dotted circles...

In nature, eight common nucleotides exist, four found in DNA and four in RNA. In the standard abbreviations for DNA nucleotides, a lowercase d specifies the presence of deoxyribose. RNA nucleotides lack this designation. Nucleosides have names of one word (e.g., deoxyadenosine, cytidine, and uridine). The ending monophosphate completes the nucleotide names. Table 16.1 lists correct names for all common nucleotides and nucleosides, and Figure 16.9 shows linkages and structures for all eight nucleotides. 

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). 

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