Nucleosides and nucleotide naming

Table 27-1 gives the nomenclature of purine and pyrimidine nucleosides and nucleotides. Names of purine nucleosides end in -osine, whereas those of pyrimidine nucleosides end in -idine guanine nucleoside is guanosine and should not be confused with guanidine, which is not a nucleic acid base thymidine is a deoxyriboside. 

See also Nucleic Acids, Nucleoside and Nucleotide Naming, Phosphodiester Bonds, RNA, Proteins... 

See also Nucleoside and Nucleotide Naming, mRNA, Background on Transcription (from Chapter... 

The nomenclature for the commonly found bases, nucleosides, and nucleotides is shown in Tables I-l-2a and -2b. Note that the deoxy part of the names deoxythymidine, dTMP, etc., is sometimes understood, and not expressly stated, because thymine is almost always found attached to deoxyribose. 

Cytosine, thymine, and uracil are pyrimidines along with adenine and guanine they account for the five nucleic acid bases. Pyrimidines are heterocyclic single-ringed compounds based on the structure of pyrimidine. Cytosine, thymine, and uracil, like adenine and guanine, form nucleosides and nucleotides in RNA and DNA. When the bases combine with ribose, a ribo-nucleoside forms and when it attaches to deoxyribose, a deoxyribosenucleoside is formed. Names of the nucleoside are summarized in Table 29.1. These in turn combine with phospho-ryl groups, in a process called phosphorylation, to form their respective nucleotides that form nucleic acids. The nucleotides can be tri, di, and mono phosphate nucleotides similar to the way in which adenine forms ATP, ADP, and AMP. 

Adenosine nucleosides and nucleotides exert a variety of effects through the activation of specific membrane receptors which are generally referred to as puri no receptors. Burnstock defined two major classes of purinoreceptors named P1 and P2 (Burnstock, 1978). It was found that P1 purinoreceptors (adenosine receptors) are more responsive to adenosine. Adenosine receptors are the only extracellular nucleoside membrane receptors that have been described so far. P2 purinoreceptors (ATP-receptors) are more responsive to ATP and ADP as physiological agonists (Muller, 1996 Baraldi etal., 1999). 

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... 

Nucleotides are nucleosides that have been phosphorylated on the 5 -hydroxyl group. One, two, or three phosphates can be added. Nucleotides are generally named by appending monophosphate, diphosphate, or triphosphate to the end of the name of the corresponding nucleoside, and the names are typically abbreviated. The suffixes -MP, -DP, and -TP correspond to mono-, di-, and triphosphate, respectively. Examples of 2 -deoxyadenosine 5 -diphosphate or ADP (6.13) and uridine 5 -monophosphate or UMP (6.14) are shown in Figure 6.5. 

The nomenclature of nucleotides and their constituent units was presented earlier (Section 5.1.2). Recall that a nucleoside consists of a purine or pyrimidine base linked to a sugar and that a nucleotide is a phosphate ester of a nucleoside. The names of the major bases of RNA and DNA, and of their nucleoside and nucleotide derivatives, are... 

The terms nucleoside and nucleotide are used to refer generically to these molecules. Nucleosides containing the sugar ribose are referred to precisely as ribonucleosides. Similarly, nucleotides containing the sugar ribose are called ribonucleotides. If the sugar present is deoxyribose, the precise names are deoxyribonucleosides and deoxyribonucleotides. 

Fio. 1. Important compounds in purine metabolism. Nucleosides of the purine bases are joined in 0-glycosidic linkage from the first carbon of ribose to the nitrogen of position 9 of the ring. The nucleotides are phosphoric acid esters of the nucleosides, usually substituted at carbon 5 of the ribose. The proper chemical names for the nucleoside and nucleotide of adenine are 9- 8-D-ribofuranosyladenine (adenosine) and 9-/3-D-6 -phospho-D-ribosyladenine (6 -adenylic acid), respectively. 

The name of a nucleoside that contains a purine ends with osine, whereas a nucleoside that contains a pyrimidine ends with idine. The names of the nucleosides of DNA add deoxy to the beginning of their names. The corresponding nucleotides in RNA and DNA are named by adding -5 -monophosphate. Although the letters A, G, C, U, and T represent the bases, they are often used in the abbreviations of the respective nucleosides and nucleotides. The names and abbreviations of the bases, nucleosides, and nucleotides in DNA and RNA are listed in Table 17.2. 

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. 

Be sure to note on each spectrum the name of the nucleoside or nucleotide and the wavelength of maximun absorption. 

Two types of heterocyclic N bases are found the pyrimidine bases (31), (32) and (33), and the purine bases (34) and (35). The pKt values are given in Table 10 as are the names of the compounds derived from the bases. One other difference between DNA and RNA is that the former is found to contain thymine, while the latter contains uracil. The average cell contains 2-5% of its dry weight as nucleic acids and nucleotides neither the heterocyclic bases nor the nucleosides occur as such in cells. 

Names of Pyrimidine and Purine Bases, Nucleosides, and 5 -Nucleotides ... 

The separation of nucleotides and deoxynucleotides, previously a formidable task involving the fractional crystallization of heavy metal and alkaloid salts 102) has been made much easier by developments in analytical techniques. Ion-exchange methods may be used for the purification, isolation, and identification of both classes of nucleotides from hydrolysis mixtures 103), Countercurrent distribution 104) and starch 106) and cellulose-column 106) as well as paper-strip chromatography 107) have also proved to be useful in separating nucleotides from natural sources. Spectro-photometric procedures based on the characteristic ultraviolet absorption spectra of the purines and pyrimidines have been the most convenient method to locate, estimate, and identify the fractions obtained in the previous separations. Since the nucleotides are acid in nature, they are often named as acids, e.g., adenylic acid, cytidylic acid. The general constitution of the purine nucleotides (and by analogy the pyrimidine nucleotides) is demonstrated by their hydrolysis by acids to a purine and ribose (or 2-deoxyribose) monophosphate and by alkalies to the nucleosides and phosphoric acid. The order of the constituents in a purine nucleotide must, therefore, be ... 

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