Nucleic acids nucleotide transfer

Transfer RNA (tRNA) Transfer RNAs are relatively small nucleic acids containing only about 70 nucleotides They get their name because they transfer ammo acids to the ribosome for incorporation into a polypeptide Although 20 ammo acids need to be transferred there are 50-60 tRNAs some of which transfer the same ammo acids Figure 28 11 shows the structure of phenylalanine tRNA (tRNA ) Like all tRNAs it IS composed of a single strand with a characteristic shape that results from the presence of paired bases m some regions and their absence m others... 

Ribulose 5-phosphate is the substrate for two enzymes. Ribulose 5-phosphate 3-epimerase alters the configuration about carbon 3, forming another ketopentose, xylulose 5-phosphate. Ribose 5-phosphate ketoisom-erase converts ribulose 5-phosphate to the corresponding aldopentose, ribose 5-phosphate, which is the precursor of the ribose required for nucleotide and nucleic acid synthesis. Transketolase transfers the two-carbon... 

Not all the cellular DNA is in the nucleus some is found in the mitochondria. In addition, mitochondria contain RNA as well as several enzymes used for protein synthesis. Interestingly, mitochond-rial RNA and DNA bear a closer resemblance to the nucleic acid of bacterial cells than they do to animal cells. For example, the rather small DNA molecule of the mitochondrion is circular and does not form nucleosomes. Its information is contained in approximately 16,500 nucleotides that func-tion in the synthesis of two ribosomal and 22 transfer RNAs (tRNAs). In addition, mitochondrial DNA codes for the synthesis of 13 proteins, all components of the respiratory chain and the oxidative phosphorylation system. Still, mitochondrial DNA does not contain sufficient information for the synthesis of all mitochondrial proteins most are coded by nuclear genes. Most mitochondrial proteins are synthesized in the cytosol from nuclear-derived messenger RNAs (mRNAs) and then transported into the mito-chondria, where they contribute to both the structural and the functional elements of this organelle. Because mitochondria are inherited cytoplasmically, an individual does not necessarily receive mitochondrial nucleic acid equally from each parent. In fact, mito-chondria are inherited maternally. 

Figure 10.13 Phosphoryl-transfer reactions. The figure shows (a) nucleotide polymerization, (b) nucleic acid hydrolysis, (c) first cleavage of an exon-intron junction by group I ribozyme (d) and by a group II ribozyme, (e) strand transfer during transposition and (f) exon ligation during RNA splicing. (From Yang et al., 2006. Copyright 2006, with permission from Elsevier.)...

Nucleic acid Either of two types of macromolecule (DNA or RNA) formed by polymerization of nucleotides. Nudeic adds are found in all living cells and contain the information (genetic code) for the transfer of genetic information from one generation to the next. [NIH]... 

The kinetics and mechanisms of the oxidation of DNA, nucleic acid sugars, and nucleotides by [Ru(0)(tpy)(bpy)] and its derivatives have been reported. " The Ru =0 species is an efficient DNA cleavage agent it cleaves DNA by sugar oxidation at the 1 position, which is indicated by the termini formed with and without piperidine treatment and by the production of free bases and 5-methylene-2(5//)-furanone. Kinetic studies show that the I -C— activation is rate determining and a hydride transfer mechanism is proposed. The Ru =0 species also oxidizes guanine bases via an 0x0 transfer mechanism to produce piperidine-labile cleavages. 

The transfer of genetic information from the level of the nucleic acid sequence of a gene to the level of the amino acid sequence of a protein or to the nucleotide sequence of RNA is termed gene expression. The entire process of gene expression in eucaryotes includes the following steps ... 

The translating of a sequence of DNA nucleotides into a sequence of amino acids—in other words, into the manufacture of a protein—involves many intricate cellular mechanisms that are still the subject of much research. The overall process, however, is conceptually straightforward, involving two steps— transcription followed by translation. These steps are mediated by the other major nucleic acid, RNA, of which there are three forms—messenger RNA (rnRNA), ribosomal RNA (rRNA), and transfer RNA (tRNA). 

To avoid too fast an energy transfer and enhance the selectivity of the laser excitation of the chosen sites in large biomolecules, it seems very promising to use their chemical labeling. This is especially important in the mapping of the sequences of DNA nucleotide bases having very close spectral properties. The first experiments on the MPI of dye-labeled nucleic acid bases were quite a success [11]. 

In 1950, when the study of ribosomes began, no methods for determining the sequences of amino acids in proteins or of nucleotides in nucleic acids existed.11 Sanger published the sequences of the two short chains of insulin in 1953, and the first transfer RNA sequence was published by Holley in 1965.21 Never-... 

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 biological functions of the nucleic acids involve the participation of metal ions. In particular K+ and Mgr+ stabilize the active nucleic acid conformations. Mg2+ also activates enzymes which are involved in phosphate transfer reactions and in nucleotide transfer. The monomeric nucleotides are also involved in a number of metabolic processes and here again metal ions are implicated. Consequently, there has been considerable attention focussed on the coordination properties of these molecules as a means of understanding the mechanism of the metal ion involvements. A number of reviews are available which cover the studies on metal interactions.113 117... 

Nucleotides play important roles in all major aspects of metabolism. ATP, an adenine nucleotide, is the major substance used by all organisms for the transfer of chemical energy from energy-yielding reactions to energy-requiring reactions such as biosynthesis. Other nucleotides are activated intermediates in the synthesis of carbohydrates, lipids, proteins, and nucleic acids. Adenine nucleotides are components of many major coenzymes, such as NAD+, NADP+, FAD, and CoA. (See chapter 10 for structures of these coenzymes.)... 

Polynucleotide polymerases, or nucleotidyl transferases, are enzymes that catalyze the template-instructed polymerization of deoxyribo- or ribonu-cleoside triphosphates into polymeric nucleic acid - DNA or RNA. Depending on their substrate specificity, polymerases are classed as RNA- or DNA-dependent polymerases which copy their templates into RNA or DNA (all combinations of substrates are possible). Polymerization, or nucleotidyl transfer, involves formation of a phosphodiester bond that results from nucleophilic attack of the 3 -OH of primer-template on the a-phosphate group of the incoming nucleoside triphosphate. Although substantial diversity of sequence and function is observed for natural polymerases, there is evidence that many employ the same mechanism for DNA or RNA synthesis. On the basis of the crystal structures of polymerase replication complexes, a two-metal-ion mechanism of nucleotide addition was proposed [1] during this two divalent metal ions stabilize the structure and charge of the expected pentacovalent transition state (Figure B.16.1). 

The base-pairing of complementary nucleotides gives the secondary structure of a nucleic acid. In a double-stranded DNA or RNA, this refers to the Watson-Crick pairing of complementary strands. In a single-stranded RNA or DNA, the intramolecular base pairs between complementary base pairs determines the secondary structure of the molecule. For example, the cloverleaf structure of Figure 8-2a gives the secondary structure of transfer RNAs. 

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