Phosphate groups nucleotides

Nucleotides. Phosphate groups may be attached to the ribose group of uridine at the 2, 3, or 5 positions to give 2, 3, or 5 -uridylic acid (UMP). The ionizable groups in 3 -UMP are shown in Figure 3. These... 

In this investigation, clusters of 5 -dTMP and 5 -dCMP were examined which contain Na" " and 5 H2O molecules, where the Na ion is partially solvated and bound to the nucleotide phosphate group. Similar geometries were previously examined in clusters of 5 -dGMP and 5 -dAMP (20, 21, 33). The structures of the 5 -dTMP and... 

The nucleotides are linked together via the phosphate groups, which connect the 5 -hydroxyl group of one nucleotide and the 3 -hydroxyl group of the next to form a polynucleotide chain (Fig. la). DNA is not a rigid or static molecule rather, it can adopt a variety of hehcal motifs. 

Another class of DNA-binding proteins are the polymerases. These have a nonspecific interaction with DNA because the same protein acts on all DNA sequences. DNA polymerase performs the dual function of DNA repHcation, in which nucleotides are added to a growing strand of DNA, and acts as a nuclease to remove mismatched nucleotides. The domain that performs the nuclease activity has an a/P-stmcture, a deep cleft that can accommodate double-stranded DNA, and a positively charged surface complementary to the phosphate groups of DNA. The smaller domain contains the exonuclease active site at a smaller cleft on the surface which can accommodate a single nucleotide. 

Polymerization of nucleotides occurs through the sugar and phosphate groups so that the polymers consist of a sugar-phosphate backbone having pendent bases. 

Just as proteins are biopolymers made of amino acids, nucleic acids are biopolv-mers made of nucleotides joined together to form a long chain. Each nucleotide is composed of a nucleoside bonded to a phosphate group, and each nucleoside is composed of an aldopentose sugar linked through its anomeric carbon to the nitrogen atom of a heterocyclic purine or pyrimidine base. 

Although the 3 - and 5 -polyphosphate derivatives mentioned above exhibit exquisite inhibitory potency these compounds are not cell permeable. To take advantage ofthepotency of such derivatives for studies with intact cells and tissues, there are two possibilities. One is chemically to protect the phosphate groups from exonucleotidases that also allows the compound to transit the membrane intact. The other is to provide a precursor molecule that is cell permeable and is then metabolized into an inhibitor by intracellular enzymes. The general term for such a compound is prodrug nucleotide precursors are also referred to as pronucleotides. Families of protected monophosphate derivatives were synthesized, based on (3-L- and 3-D-2, 5 -dd-3 -AMP, 3-L-2, 3 -dd-5 -AMP, and the acyclic 9-substituted adenines, PMEA and PMPA. Protective substituents were (i) -( -pivaloyl-2-thioethyl) ... 

An enzyme on the cell surface that metabolizes nucleotide derivatives by hydrolytically cleaving one or more phosphate groups. 

The DNA monomers are each completed by a phosphate group, —O—P032, covalently bonded to carbon atom 5 of the ribose unit to give a compound called a nucleotide (28). Because there are four possible nucleoside monomers (one for each base), there are four possible nucleotides in each type of nucleic acid. 

Molecules of DNA and RNA are polynucleotides, polymeric species built from nucleotide units. Polymerization takes place when the phosphate group of one nucleotide (which is the conjugate base of an organic phosphoric acid) condenses... 

The DNA double heUx illustrates the contribution of multiple forces to the structure of biomolecules. While each individual DNA strand is held together by covalent bonds, the two strands of the helix are held together exclusively by noncovalent interactions. These noncovalent interactions include hydrogen bonds between nucleotide bases (Watson-Crick base pairing) and van der Waals interactions between the stacked purine and pyrimidine bases. The hehx presents the charged phosphate groups and polar ribose sugars of... 

The UMP nucleotide contains uracil, ribose, and one phosphate group. The structure of uracil and the hydrogen eliminated during the condensation appear in Figure 13-22. Here are the component parts, drawn in position to eliminate water molecules and link ... 

A nucleic acid polymer contains nucleotide chains in which the phosphate group of one nucleotide links to the sugar ring of a second. The resulting backbone is an alternating sequence of sugars and phosphates, as shown in... 

C13-0024. Nucleotides can contain more than one phosphate group. One example is energy-storing adenosine triphosphate (ATP), which is discussed in Chapter 14. An ATP molecule is formed in two sequential condensation reactions between phosphoric acid and the phosphate group of AMP ... 

The association between RNase A and 3 -UMP or 3 -dUMP has been studied by P n.m.r. and kinetic methods, respectively. In both cases the participation of two dissociable groups at the active site of the enzyme was demonstrated, in agreement with n.m.r. and A -ray - studies on the binding of 3 -CMP to RNase. In the binding of Tj RNase to purine nucleotide monophosphates, the phosphate group appears to have an important effect while the ribose ring is relatively unimportant. ... 

DNA and RNA are formed of nucleotides. Each nucleotide or nucleoside is composed of a purine or pyrimidine base linked to the 1-position of a ribose sugar in the case of RNA and a 2 -deoxyribose sugar in the case of DNA.155 The 5 position is phosphorylated in the case of a nucleotide, while the nucleoside is not phosphorylated therefore, nucleotides are nucleoside phosphates. Phosphorylation can include one, two, or three phosphate groups. The most familiar example of a phosphorylated nucleotide is phosphorylated adenosine, which occurs as the mono-, di-, and triphosphate (AMP, ADP, and ATP, respectively) and is a principal means of energy storage in biological systems. 

Nucleoside reverse transcriptase inhibitor (NRTI)/nucleotide reverse transcriptase inhibitor (NtRI) A modified version of a naturally-occurring nucleoside or nucleotide that prevents human immunodeficiency virus (HIV) replication by interfering with the function of the viral reverse transcriptase enzyme. The nucleoside/nucleotide analog causes early termination of the proviral DNA chain. For activity, an NRTI requires three phosphorylation steps once inside the cell, whereas an NtRI has a phosphate group attached and needs only two phosphorylation steps inside the cell for activity. 

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