Nucleotide residues

Figure 38-5. Examples of the effects of deletions and insertions in a gene on the sequence of the mRNA transcript and of the polypeptide chain translated therefrom. The arrows indicate the sites of deletions or insertions, and the numbers in the ovals indicate the number of nucleotide residues deleted or inserted. Blue type indicates amino acids in correct order.

A method has been developed which is designed to remove nucleotide residues singly from a polynucleotide chain, and it is anticipated that more precise information will shortly be forthcoming regarding the order in which the nucleotides are linked.220 The method is based on the fact that esters of 3-oxo alcohols are unstable toward alkali. In agreement with this, it is found that the products of the action of periodate on adenosine 5-phosphate (XXX) or adenosine 5-(benzyl hydrogen phosphate) are hydrolyzed under very mild conditions. Thus, after removal of terminal, singly-esterified phosphoryl residues from a polynucleotide chain, it is anticipated that periodate oxidation and hydrolysis will result in the removal of the... 

R = carbohydrate, nucleoside, or nucleotide residue Scheme 25.—Proposed Mechanism for Photochemical Reaction of o-Nitrobenzyl Compounds. 

Site-directed mutagenesis Induced change in the nucleotide sequence of DNA aimed at particular nucleotide residues, usually in order to test their function. 

The ion-exchange separation usually affords individual fractions of structurally related glycosyl esters of nucleoside pyrophosphates, containing the same nucleotide residue, but differing in the structure of the glycosyl groups. Separation of the esters of N-acetylhexos-amines, uronic acids, and neutral monosaccharides from one another is also usually achieved. 

It remains unclear whether or not the rate of cleavage of the gly-cosyl bond in sugar nucleotides depends upon the structure of the nucleotide residue, and the same uncertainty is true for other reactions that affect the glycosyl group no systematic kinetic studies have been reported. However, it may be noted that there appears to be no essential difference between the rates of acidic hydrolysis of the 5 -(a-D-glucopyranosyl pyrophosphates) of uridine and N3-methyluridine, 331... 

The possible backbone phosphodiester conformations in a dinucleotide monophosphate and a dinucleotide triphosphate are investigated by semiempirical energy calculations. Conformational energies are computed as a function of the rotations o and <0 about the internucleotide P-0(3 ) and P-015 1 linkages, with the nucleotide residues themselves assumed to be in one of the preferred [C(3 )-e/K/o) conformations. 

Adds a phosphate to the 5 -0H end of a polynucleotide to label it or permit ligation Adds homopolymer tails to the 3 -0H ends of a linear duplex Removes nucleotide residues from the 3 ends of a DNA strand Removes nucleotides from the 5 ends of a duplex to expose single-stranded 3 ends Removes terminal phosphates from either the 5 or 3 end (or both)... 

By the 1960s it had long been apparent that at least three nucleotide residues of DNA are necessary to encode each amino acid. The four code letters of DNA (A, T, G, and C) in groups of two can yield only 42 = 16 different combinations, insufficient to encode 20 amino acids. Groups of three, however, yield 43 = 64 different combinations. 

Yeast alanine tRNA (tRNA 3), the first nucleic acid to be completely sequenced (Fig. 27-11), contains 76 nucleotide residues, 10 of which have modified bases. Comparisons of tRNAs from various species have revealed many common denominators of structure (Fig. 27-12). Eight or more of the nucleotide residues have modified bases and sugars, many of which are methylated derivatives of the principal bases. Most tRNAs have a guanylate (pG) residue at the 5 end, and all have the trinucleotide sequence CCA(3 ) at the 3 end. When... 

Transfer RNAs have 73 to 93 nucleotide residues, some of which have modified bases. 

In accordance with coding requirements each site is actually a triplet of nucleotide residues, but this feature need not concern us here. 

Transfer RNAs (tRNAs), the smallest of the three major species of RNA molecules (4S), have between 74 and 95 nucleotide residues. There is at least one specific type of tRNA molecule for each of the twenty amino acids commonly found in proteins. Together, tRNAs make up about fifteen percent of the total RNA in the cell. The tRNA molecules contain unusual bases (for example, pseudouracil, see Figure 22.2, p. 290) and have extensive intrachain base-pairing (Figure 30.3). Each tRNA serves as an "adaptor molecule that carries its specific amino acid—covalently attached to its 3-end—to the site of protein synthesis. There it recognizes the genetic code word on an mRNA, which specifies the addition of its amino acid to the growing peptide chain (see p. 429). 

Because of their relatively low molecular weight (70 to 90 nucleotide residues), transfer ribonucleic acids are of special interest for 13C NMR investigations [769, 778, 782-784] of nucleic acids. Using a tube of 20 mm o.d., a sample of thermally denatured yeast... 

The phosphodiester bonds of xanthylic acid in deaminated RNA were scarcely split by RNase U2 (30). The susceptibility of purine nucleotide residues to RNase U2 decreases in the order of A>G>I X, indicating that the phosphodiester bonds of adenylic acid and inosinic acid without a keto group at the position of purine base are more sensitive to RNase U2 than those of guanylic acid and xanthylic acid. The resistance of TNP-RNA to RNase U2 may be also attributed to the steric hindrance by a larger substituent at 2-amino groups of guanylyl residues, as with RNase T, (SO). 

During the past three years endonucleases have been discovered which possess a specificity which is considerably more refined than that shown by the nucleases considered thus far. Typically, these enzymes catalyze the cleavage of one or, at most, a few phosphodiester bonds in a DNA molecule composed of many thousands of nucleotide residues. In no instance has the basis for this remarkable specificity been established. However, in the case of the E. coli restriction enzymes the presence or absence of a methyl group on a specific deoxyadenylate or deoxycyti-dylate residue may be involved. 

The processing steps of E. coli tyrosine tRNATyr are diagrammed in figure 28.15. The initial transcript has, in addition to the 85 nucleotide residues of the final product, 41 residues at the 5 end and 225 residues at the 3 end it probably folds to form the typical cloverleaf structure of the mature tRNA prior to processing. Processing begins when a specific endonuclease called RNaseF cleaves the precursor... 

Phosphodiester. A molecule containing two alcohols esterified to a single molecule of phosphate. For example, the backbone of nucleic acids is connected by 5 -3 phosphodiester linkages between the adjacent individual nucleotide residues. 

Being able to record only low resolution data also implies that these are relatively few in number. Here some relief is provided by the high symmetry of regular helical molecules. Many helical polyncleotides, for example, provide 100-200 independent X-ray reflections that can be used to determine the molecular geometry of the one nucleotide residue from which all the others can be generated by symmetry operations. A comparable data set... 

Usually the asymmetric unit of a helical polynucleotide chain is effectively one nucleotide residue. To date, over two dozen nucleic acid structures of this kind—both native and synthetic and of varying base composition and sequence have been defined accurately and in most cases refined extensively. 

A histidine residue localized in the active site of the proteinoid may be the primary acceptor of the nucleotide. The nucleotide residue bound to the proteinoid would then transfer to the final acceptor. The metal ion may work as a transfer catalyst. 

Figure 7.1. Molecular structure of RNA. The single-stranded RNA molecule consists of ribo-nucleoside residues linked to each other via phosphodiester bonds. The four nitrogenous bases in RNA are shown with their linkage at the Q position of ribose. The RNA chain elongates from the 5 to the 3 direction as the new nucleotide residues are added at the 3 -OH end of the chain during RNA synthesis in a cell. (Adapted from Textbook of Biochemistry with Clinical Correlations, T. M. Devlin, ed., Wiley, New York, 1982.)...

Figure 14.11. Construction of biopolymer with HyperChem. Two menus are available for creating 3D structure models in HyperChem. The Build menu provides tools for creating organic molecules. Use the Drawing tool to sketch atoms in a molecule and connect them with covalent bonds. Invoke the Model builder to create a 3D structure from the 2D sketch. The Databases menu offers tools for creating biopolymers from residues with user specified linkages and conformations—that is, polysaccharides from monosaccharides, polypeptides form amino acids, and polynucleotides from nucleotides. A double-stranded DNA chain, for example, is constructed from nucleotide residues in a desired conformation (the inset).

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