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Nucleotide

(at center), a nitrogenous base called adenine (upper right), and one phosphate group (left). The deoxyribose sugar joined only to the nitrogenous base forms a Deoxyribonucleoside called deoxyadenosine, whereas the whole structure along with the phosphate group is a nucleotide, a constituent of DNA with the name deoxyadenosine monophosphate.]] Nucleotides are organic molecules that serve as the monomer units for forming the nucleic acid polymers deoxyribonucleic acid (DNA) and ribonucleic acid (RNA), both of which are essential biomolecules in all life-forms on Earth. Nucleotides are the building blocks of nucleic acids; they are composed of three subunit molecules: a nitrogenous base, a five-carbon sugar ( ribose or deoxyribose), and at least one phosphate group. They are also known as phosphate nucleotides. A nucleoside is a nitrogenous base and a 5-carbon sugar. Thus a nucleoside plus a phosphate group yields a nucleotide. Nucleotides also play a central role in life-form metabolism at the fundamental, cellular level. They carry packets of chemical energy—in the form of the nucleoside triphosphates ATP, GTP, CTP and UTP—throughout the cell to the many cellular functions that demand energy, which include synthesizing amino acids, proteins and cell membranes and parts; moving the cell and moving cell parts, both internally and intercellularly; dividing the cell, etc.Alberts B, Johnson A, Lewis J, Raff M, Roberts K & Walter P (2002). Molecular Biology of the Cell (4th ed.). Garland Science. . pp. 120–121. In addition, nucleotides participate in cell signaling ( cGMP and cAMP), and are incorporated into important cofactors of enzymatic reactions (e.g. coenzyme A, FAD, FMN, NAD, and NADP+). In experimental biochemistry, nucleotides can be radiolabeled with radionuclides to yield radionucleotides.

Structure

) of a nucleic acid, shown at upper left.]] A nucleotide is composed of three distinctive chemical sub-units: a five-carbon sugar molecule, a nitrogenous base—which two together are called a nucleoside—and one phosphate group. With all three joined, a nucleotide is also termed a "nucleoside monophosphate". The chemistry sources ACS Style Guide and IUPAC Gold Book prescribe that a nucleotide should contain only one phosphate group, but common usage in molecular biology textbooks often extends the definition to include molecules with two, or with three, phosphates. Thus, the terms "nucleoside diphosphate" or "nucleoside triphosphate" may also indicate nucleotides. Nucleotides contain either a purine or a pyrimidine base—i.e., the nitrogenous base molecule, also known as a nucleobase—and are termed ribonucleotides if the sugar is ribose, or deoxyribonucleotides if the sugar is deoxyribose. Individual phosphate molecules repetitively connect the sugar-ring molecules in two adjacent nucleotide monomers, thereby connecting the nucleotide monomers of a nucleic acid end-to-end into a long chain. These chain-joins of sugar and phosphate molecules create a 'backbone' strand for a single- or double helix. In any one strand, the chemical orientation ( directionality) of the chain-joins runs from the 5'-end to the 3'-end (read: 5 prime-end to 3 prime-end)—referring to the five carbon sites on sugar molecules in adjacent nucleotides. In a double helix, the two strands are oriented in opposite directions, which permits base pairing and complementarity between the base-pairs, all which is essential for replicating or transcribing the encoded information found in DNA. Unlike in nucleic acid nucleotides, singular cyclic nucleotides are formed when the phosphate group is bound twice to the same sugar molecule, i.e., at the corners of the sugar hydroxyl groups. These individual nucleotides function in cell metabolism rather than the nucleic acid structures of long-chain molecules. Nucleic acids then are polymeric macromolecules assembled from nucleotides, the monomer-units of nucleic acids. The purine bases adenine and guanine and pyrimidine base cytosine occur in both DNA and RNA, while the pyrimidine bases thymine (in DNA) and uracil (in RNA) in just one. Adenine forms a base pair with thymine with two hydrogen bonds, while guanine pairs with cytosine with three hydrogen bonds. ) is indicated by "Base" and " glycosidic bond" (sugar bond). All five primary, or canonical, bases—the purines and pyrimidines—are sketched at right (in blue).]]

Synthesis

Nucleotides can be synthesized by a variety of means both in vitro and in vivo. In vivo, nucleotides can be synthesized de novo or recycled through salvage pathways.{{cite journal | last = Zaharevitz | first = DW |author2=Anerson, LW |author3=Manlinowski, NM |author4=Hyman, R |author5=Strong, JM |author6= Cysyk, RL | title = Contribution of de-novo and salvage synthesis to the uracil nucleotide pool in mouse tissues and tumors in vivo }} The components used in de novo nucleotide synthesis are derived from biosynthetic precursors of carbohydrate and amino acid metabolism, and from ammonia and carbon dioxide. The liver is the major organ of de novo synthesis of all four nucleotides. De novo synthesis of pyrimidines and purines follows two different pathways. Pyrimidines are synthesized first from aspartate and carbamoyl-phosphate in the cytoplasm to the common precursor ring structure orotic acid, onto which a phosphorylated ribosyl unit is covalently linked. Purines, however, are first synthesized from the sugar template onto which the ring synthesis occurs. For reference, the syntheses of the purine and pyrimidine nucleotides are carried out by several enzymes in the cytoplasm of the cell, not within a specific organelle. Nucleotides undergo breakdown such that useful parts can be reused in synthesis reactions to create new nucleotides. In vitro, protecting groups may be used during laboratory production of nucleotides. A purified nucleoside is protected to create a phosphoramidite, which can then be used to obtain analogues not found in nature and/or to synthesize an oligonucleotide.

Pyrimidine ribonucleotide synthesis

.The color scheme is as follows: enzymes, coenzymes, substrate names, inorganic molecules ]] The synthesis of the pyrimidines CTP and UTP occurs in the cytoplasm and starts with the formation of carbamoyl phosphate from glutamine and CO2. Next, aspartate carbamoyltransferase catalyzes a condensation reaction between aspartate and carbamoyl phosphate to form carbamoyl aspartic acid, which is cyclized into 4,5-dihydroorotic acid by dihydroorotase. The latter is converted to orotate by dihydroorotate oxidase. The net reaction is: (S)-Dihydroorotate + O2 → Orotate + H2O2 Orotate is covalently linked with a phosphorylated ribosyl unit. The covalent linkage between the ribose and pyrimidine occurs at position C1See IUPAC nomenclature of organic chemistry for details on carbon residue numbering of the ribose unit, which contains a pyrophosphate, and N1 of the pyrimidine ring. Orotate phosphoribosyltransferase (PRPP transferase) catalyzes the net reaction yielding orotidine monophosphate (OMP): Orotate + 5-Phospho-α-D-ribose 1-diphosphate (PRPP) → Orotidine 5'-phosphate + Pyrophosphate Orotidine 5'-monophosphate is decarboxylated by orotidine-5'-phosphate decarboxylase to form uridine monophosphate (UMP). PRPP transferase catalyzes both the ribosylation and decarboxylation reactions, forming UMP from orotic acid in the presence of PRPP. It is from UMP that other pyrimidine nucleotides are derived. UMP is phosphorylated by two kinases to uridine triphosphate (UTP) via two sequential reactions with ATP. First the diphosphate form UDP is produced, which in turn is phosphorylated to UTP. Both steps are fueled by ATP hydrolysis: ATP + UMP → ADP + UDP UDP + ATP → UTP + ADP CTP is subsequently formed by amination of UTP by the catalytic activity of CTP synthetase. Glutamine is the NH3 donor and the reaction is fueled by ATP hydrolysis, too: UTP + Glutamine + ATP + H2O → CTP + ADP + Pi Cytidine monophosphate (CMP) is derived from cytidine triphosphate (CTP) with subsequent loss of two phosphates.{{cite journal | last = Jones | first = M. E. | title = Pyrimidine nucleotide biosynthesis in animals: Genes, enzymes, and regulation of UMP biosynthesis | journal = Annu. Rev. Biochem. | volume = 49 | issue = 1| pages = 253–79 | date = 1980 | doi = 10.1146/annurev.bi.49.070180.001345 | pmid = 6105839 }}
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This article based upon the http://en.wikipedia.org/wiki/Nucleotide, the free encyclopaedia Wikipedia and is licensed under the GNU Free Documentation License.
Further informations available on the list of authors and history: http://en.wikipedia.org/w/index.php?title=Nucleotide&action=history
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