Nucleotides components

Once the broad outlines of DNA replication and protein biosynthesis were established scien tists speculated about how these outlines af fected various origins of life scenarios A key question concerned the fact that proteins are re quired for the synthesis of DNA yet the synthesis of these proteins is coded for by DNA Which came first DNA or proteins How could DNA store genetic infor mation if there were no enzymes to catalyze the polymerization of its nucleotide components How could there be proteins if there were no DNA to code for them ... 

The nucleic acids play a central role in the storage and expression of genetic information (see p. 236). They are divided into two major classes deoxyribonucleic acid (DNA) functions solely in information storage, while ribonucleic acids (RNAs) are involved in most steps of gene expression and protein biosynthesis. All nucleic acids are made up from nucleotide components, which in turn consist of a base, a sugar, and a phosphate residue. DNA and RNA differ from one another in the type of the sugar and in one of the bases that they contain. 

RNA molecules are unable to form extended double helices, and are therefore less highly ordered than DNA molecules. Nevertheless, they have defined secondary and tertiary structures, and a large proportion of the nucleotide components enter into base pairings with other nucleotides. The examples shown here are 5S-rRNA (see p. 242), which occurs as a structural component in ribosomes, and a tRNA molecule from yeast (see p.82) that is specific for phenylalanine. 

ATP and the other nucleoside triphosphate coenzymes not only transfer phosphate residues, but also provide the nucleotide components for this type of activation reaction. On this page, we discuss metabolites or groups that are activated in the metabolism by bonding with nucleosides or nucleotides. Intermediates of this type are mainly found in the metabolism of complex carbohydrates and lipids. 

The nucleotide components required for transcription and replication have to be imported into the nucleus from the cytoplasm, incorporation of these components into RNA leads to primary products, which are then altered by cleavage, excision of introns, and the addition of extra nucleotides (RNA maturation see p. 242). it is only once these process have been completed that the RNA molecules formed in the nucleus can be exported into the cytoplasm for protein synthesis (translation see p. 250). 

Fig. 21. Nucleotide components in substances tested as substrates or inhibitors (a) sugar components, (b) pyrimidine base components, and (c) phosphate components.

Nucleotide Components A Phosphoryl Group, a Pentose, and a Base... 

Degeneracy of the code is very obvious from an examination of the codon assignments shown in Tabic 17.1. For example, there are six codons for leucine. It should be noted that the nucleotide components of each triplet... 

Nucleosides and Nucleotides occur in a limited number of preferred conformations. Except for the planar purine or pyrimidine base, the nucleotide component of the nucleic acids contains only single bonds (see Fig. 17.1). Rotation about bonds is restrained by the requirements of the furanose ring closure, and for the acyclic bonds, rotation is restricted by electronic factors and is limited by intramolecular interactions. Therefore only a few conformations have to be considered if nucleosides and nucleotides are described in their three-dimensional shapes. 

Another variable is the relative amounts of nucleotide component and condensing agent in joining-reactions. The occurrence of side reactions catalyzed by DCC is minor, so a large (5-10-fold) excess of the reagent is routinely used to optimize yields and minimize reaction times. However, after prolonged reaction in pyridine, byproducts... 

It follows from the above that, if highly specific oligosaccharides need to be synthesized, glycosyltransferases [21] of the Leloir type [22] should be the enzymes of choice. These enzymes connect sugars via the activated nucleotide components with high stereo- and regioselectivity. They are substrate-specific, but, in vitro, with solubilized enzymes, it becomes possible to transfer modified donors to modified acceptors and thus broaden the scope of the synthetic applicability. 

Many schemes for fractionating nucleotides, nucleosides and bases on sulphonated polystyrene resins have been published. The main difficulty with these methods is variation between resin batches (e.g. Anderson et al. 1963). Nucleotide separations can be achieved on DEAE-cellulose (Whatman Data Sheet 13, 1967) and DEAE-Sephadex (Piers et al. 1965b) but these media do not seem to be widely used. Gel filtration columns will separate some nucleotide components. Ligand exchange chromatography and partition chromatography of nucleosides are useful for minor components. 

Neither of the ADH enzymes is isolated as DPN complexes, but each has a strong and characteristic affinity for the reduced and oxidized forms of the coenzyme (Velick, 1954). The O.D. 280/260 ratio measures protein and nucleotide components of a particular ADH preparation, and a high ratio of a pure protein denotes removal of DPN or DPNH from the apoen-zyme. 

Many unusual nucleotides have been found as minor components of nucleic acids, especially in the soluble or transfer ribonucleic acids. Most of these minor components contain methylated aglycons in their structure. A review of these nucleotides has been presented by Dekker, and general techniques for their isolation as nucleosides have been reported by Hall. In addition, 5,6-dihydrouridylic acid (34) has been isolated by enzymic hydrolysis of certain transfer ribonucleic acids from yeast, and 4-thiouridylic acid (35) was obtained from the alkaline hydrolyzate of transfer ribonucleic acid from Escherichia coli. A nucleotide whose ultraviolet absorption spectrum was very similar to that of 2-thiouridine has been reported to be present in transfer ribonucleic acid. Although the a anomer (36) of cytidylic acid has been detected (and identified) in a yeast ribonucleic acid hydrolyzate, it is not certain whether this -cytidylic acid is a minor component of ribonucleic acid or an artifact produced during the alkaline hydrolysis. Among the minor nucleotide components of transfer ribonucleic acid, pseudouridylic acid (37)89-98 jg unique, in that the D-ribosyl moiety is linked to the aglycon... 

Note that the nucleotide components of each triplet are written in terms of the ribonucleotides A, U, C, G, which are present in... 

A Seg set contains a segmented Bioseq and a Parts Bioseq-set, which in turn contains the raw Bioseqs that are referenced by the segmented Bioseq. This may constitute the nucleotide component of a Nuc-prot set. 

Various minor or unusual bases occur in DNA and (to a greater extent) in RNA samples from natural sources. These additional nucleotide components are mostly simple derivatives of the main bases and occur only to the extent of 1 or 2%, for example. Table 10.17. Their significance is not yet fully understood but they do contribute to irregularities of structure and behaviour (Chapter 11.5). 

Gas-phase appearance potentials for nucleotide bases were measured in early mass spectrometry experiments (8). In the first photoelectron (PE) probe of a nucleotide component, ionization potentials (IPs) of the valence manifold of ir and lone-pair orbitals of uracil were measured (9). This was followed by numerous photoelectron... 

Theoretical and Experimental Ionization Potentials of Nucleotide Components... 

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