Nucleic acids phosphodiester link

In RNA, the base T found in DNA is replaced by uracil, which is similar in structure to T, but lacks the methyl group. The nucleotides in nucleic acids are linked by phosphodiester bonds between the 3 -hydroxyl of one nucleoside and the 5 -hydroxyl of the sugar of its neighbour in the sequence, as was first shown by Alexander Todd3 in 1952 (Figure 4.13). 

Now that we have the monomers, which are pretty complex in this case, it remains to define how they are joined together to create the polymer. The amino acids in proteins are linked by peptide bonds. The nucleotides in nucleic acids are linked by phosphodiester bonds, as is shown in figure 12.2. These DNA phosphodiester bonds are very stable. Indeed, samples of largely intact DNA can be recovered from organisms that have been extinct for thousands of years. This remarkable stability should not come as a surprise the central importance of DNA in all forms of life requires that it be stable to various sorts of insults. 

Nucleic acids are polymers of nucleotides joined by 3, 5 -phosphodiester bonds that is, a phosphate group links the 3 carbon of a sugar to the 5 carbon of the next sugar in the chain. Each strand has a distinct 5 end and 3 end, and thus has polarity. A phosphate group is often found at the 5 end, and a hydroxyl group is often found at the 3 end. 

A nucleotide consists of a heterocyclic base linked to a sugar (ribose or deoxyribose) and a phosphate group also linked to the sugar (Figure 10.6). Nucleic acids are polymers of nucleotides linked together by phosphodiester bonds (Figure 10.7). The enzymes that catalyse the breakdown of nucleic acids to nucleotides are nucleases. 

Phosphodiester Bonds Link Successive Nucleotides in Nucleic Acids... 

FIGURE 8-7 Phosphodiester linkages in the covalent backbone of DNA and RNA. The phosphodiester bonds (one of which is shaded in the DNA) link successive nucleotide units. The backbone of alternating pentose and phosphate groups in both types of nucleic acid is highly polar. The 5 end of the macromolecule lacks a nucleotide at the 5 position, and the 3 end lacks a nucleotide at the 3 position. 

Nucleotides are the building blocks of nucleic acids their structures and biochemistry were discussed in chapter 23. When a 5 -phosphomononucleotide is joined by a phosphodiester bond to the 3 -OH group of another mononucleotide, a dinucleotide is formed. The 3 -5 -linked phosphodiester intemucleotide structure of nucleic acids was firmly established by Lord Alexander Todd in 1951. Repetition of this linkage leads to the formation of polydeoxyribonucleotides in DNA or polyribonucleotides in RNA. The structure of a short polydeoxyribonucleotide is shown in figure 25.3. The polymeric structure consists of a sugar phosphate diester backbone with bases attached as distinctive side chains to the sugars. 

Phosphate Esters. An ester is formed by elimination of H20 and formation of a linkage between an acid and an alcohol (or phenol) (Fig. III-22). Phosphomonoesters, especially of monosaccharides, are very common (Fig. ffl-23). Because phosphoric acid is a tribasic acid, it can also form di- and triesters (Fig. III-24). Phosphotriesters are rarely found in nature, but diesters are extremely important, particularly as the fundamental linkage of the nucleic acid polymers, which are sequences of ri-bose (or deoxyribose) units linked by 3 —> 5 phos-phodiester bonds (see Fig. III-25). Like phosphoric acid, which has three dissociable protons (Fig. III-26), phosphomono- and phosphodiesters are acidic and typically ionize as shown in Fig. HI-27. Note the similarities between the pvalues for... 

Nucleic acids have a phosphodiester backbone that includes a ribose or deoxyri-bose group that is bound to a base (G, A, C, U, or T). The furanose sugar can adopt different conformations, and the link of the sugar to the base may have various torsion angles. 

Nucleic acids are biopolymers present in every living cell, with monomeric units consisting of a carbohydrate linked via a p-D-glycosidic bond to a heterocyclic base and interconnected by phosphodiester bonds at positions C-3 and C-5. The monomeric units of nucleic acids can be considered the nucleotides that are formed from a carbohydrate residue connected to the base by the p-D-glycosidic bond and to a phosphate group at C-5. The molecules derived from nucleotides by removing the phosphate group are the nucleosides. 

The existence of a phosphodiester bond between proteins and nucleic acids is by no means unique to topoisomerases. For example, the covalent bond formed between the poliovirus RNA-linked protein (VPg) and the 5 terminus of the poliovirus RNA has been determined to be a phosphoryl-tyrosine linkage (Ambros and Baltimore, 1978). Proteins are found covalently attached to the 5 termini of the genomes of phage 29 and adenovirus via a phosphoryl-serine bond (Hermoso and Salas, 1980 Desiderio and Kelly, 1981). It seems, therefore, that a phosphodiester bond between DNA and either serine or tyrosine residues in proteins may be a common feature of many proteins involved in DNA metabolism. 

Nucleic acids consist of three classes of compounds linked to each other in a specific way one of four nucleobases, a carbohydrate, and phosphodiester. The basic building block consists of one of four nucleobases covalently linked to a ribofuranose sugar residue linked in turn via a bridge of a 3 -5 -phosphodiester to the next carbohydrate, see Chap. 8. 

Three major biopolymers are present in cells proteins, composed of amino acids linked by peptide bonds nucleic acids, composed of nucleotides linked by phosphodiester bonds and polysaccharides, composed of monosaccharides (sugars) linked by glycosidic bonds (see Figure 2-11). 

The linear sequence of nucleotides linked by phosphodiester bonds constitutes the primary structure of nucleic acids. Like polypeptides, polynucleotides can twist and fold Into three-dimensional conformations stabilized by noncovalent bonds. Although the primary structures of DNA and RNA are generally similar, their three-dimensional conformations are quite different. These structural differences are critical to the different functions of the two types of nucleic acids. 

DNA (DeoxyriboNucleic Acid) is called the genetic material because it contains the genetic information for every cell and tissue in an organism. DNA is a component of the chromosomes (proteins are the other component). DNA is one of two types of nucleic acid. Ribonucleic acid (RNA) is the other. As such, DNA is a polymer of deoxyribonucleotides linked through phosphodiester bonds (Figure 4,1). 

Phosphoric acid links the sugars in both RNA and DNA. The acid has three dissociable OH groups with pA a values of 1.9, 6.7, and 12.4. Each of the OH groups can react with an alcohol to form a phosphomonoester, a phosphodiester, or a phosphotriester. In nucleic acids the phosphate group is a phosphodiester. 

Figure 1.61 Conformational freedom is heavily restricted in nucleic acids owing to lack of free rotation about 0 —P and P—0 bonds, (a) Nucleic acid equivalent of the Ramachandran plot illustrating the theoretically allowed angles of C and a. (b) Free rotation is primarily damped owing to the gauche effect in which lone-pair-o- orbital overlaps in phosphodiester links generate double bond character in 0—P bonds that restrict free rotation (adapted from Govil, 1976 [Wiley]).

---