Nucleotides definition

FIGURE 11.33 Restricdon mapping of a DNA molecule as determined by an analysis of the electrophoretic pattern obtained for different restriction endonuclease digests. (Keep in mind that a dsDNA molecule has a unique nucleotide sequence and therefore a definite polarity thus, fragments from one end are distinctly different from fragments derived from the other end.)... 

The major advantage of the tandem mass spectrometry approach compared to MALDI peptide fingerprinting, is that the sequence information obtained from the peptides is more specific for the identification of a protein than simply determining the mass of the peptides. This permits a search of expressed sequence tag nucleotide databases to discover new human genes based upon identification of the protein. This is a useful approach because, by definition, the genes identified actually express a protein. 

Although tremendous progress has been made in characterizing the enzymes that control the synthesis and metabolism of cyclic nucleotides in the nervous system, our understanding of the regulation and interaction of these systems is far from complete. Work is now needed to definitively characterize, for each of these enzyme sub-types, its unique distribution pattern in the brain as well as its distinct functional and regulatory properties. 

The conformations of the furanose ring in 250 nucleoside and nucleotide structures were analysed by Bartenev et al. (1987). These authors made the assumption, referred to above, that intermolecular interactions have a random effect on the structure in the crystal, and that the probability JVg of a structure crystallizing in a non-ground-state conformation is the same as the probability of it arising in thermal equilibrium at ambient temperature T in solution (6). (A difficulty arises immediately with the definition of the temperature, because structural parameters for molecules in crystals are... 

Clearly, the results emerging suggested that at least two nucleotides were modified, the absolute sequence position within the tRNA had yet to be established. Ching etalP showed that a Se U residue was present in the wobble position of the tRNA " from C. sticklandii. This study confirmed a notion that the modification probably affects the translation efficiency of certain transcripts, based on the level of modification by selenium. The authors speculated that the modification to seleno-tRNA (GAG) allowed for more efficient use of this tRNA species as compared to the tRNA (GAA). Even today, no definitive data exist to show that this modification alters the translation efficiency in these bacterial model systems. Nonetheless, these studies had established the chemical forms of Se U and mnm Se U, and established that they were derived from modifications to nucleotides that first required sulfur (S U and mnm S U), the mechanism by which selenium was inserted into the tRNA would not be definitively answered until many years later. 

All the phosphodiester linkages have the same orientation along the chain (Fig. 8-7), giving each linear nucleic acid strand a specific polarity and distinct 5 and 3 ends. By definition, the 5 end lacks a nucleotide at the 5 position and the 3 end lacks a nucleotide at the 3 position. Other groups (most often one or more phosphates) may be present on one or both ends. 

A short nucleic acid is referred to as an oligonucleotide. The definition of short is somewhat arbitrary, but polymers containing 50 or fewer nucleotides are generally called oligonucleotides. A longer nucleic acid is called a polynucleotide. 

It would be expected to occur by chance in about 1 /45 nucleotides. Many binding sites for RNA polymerase, the so called promoters (Chapter 28) contain the consensus sequence TAtAaT, at position -10, ahead of the 5 end of the sequence that is transcribed into mRNA. The lower case t and a used here imply that other nucleotides may often replace T or A at these positions. There are many promoters and over 70% of those described have this consensus sequence. All have the less restricted sequence TAxxxT, where x may be any nucleotide. Our definition of consensus sequence is somewhat arbitrary. Now consider the problem of locating a -35 site whose consensus sequence is TTGACA but which may, for different genes, be shifted backward or forward by a nucleotide or two. This is a consensus sequence. Therefore, in many cases one or more substitutions in the sequence will have been made. The result is that the sequence of nucleotides in... 

In fact, kinetic studies of the GTP-dependent avian mitochondrial enzyme indicate two metal-binding sites, one on the polyphosphate group of the bound GTP and one on carboxylate side chains of the protein.252 255 The three-dimensional structure of the ATP-dependent E. coli enzyme reveals a nucleotide binding site similar to the ATP site of adenylate kinase (Fig. 12-30).256 A definite binding site for C02 is also present in the enzyme.257... 

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