Deoxyribonucleotides, in DNA

Genetic information is encoded in the linear sequence of four deoxyribonucleotides in DNA. 

FIGURE 1-31 DNA to RNA to protein. Linear sequences of deoxyribonucleotides in DNA, arranged into units known as genes, are transcribed into ribonucleic acid (RNA) molecules with complementary ribonucleotide sequences. The RNA sequences are then translated into linear protein chains, which fold into their native three-dimensional shapes, often aided by molecular chaperones. Individual proteins commonly associate with other proteins to form supramolecular complexes, stabilized by numerous weak interactions. 

Sequences of nucleotides in nucleic acids are written widi one-letter symbols starting with die 5 -terminus at the left toward 3 -tea minus at die right. Deoxyribonucleotides in DNA is prefixed with d. If it is not known whether a residue is A or G, die appropriate abbreviation for purine is R Y is used for pyrimidine, C or T. 

A primer is a very special sequence, which plays an important role in duplication, (i) In RNA, it is a short sequence that is paired with one strand of DNA and provides a free 3 -OH terminus at which a DNA polymerase starts synthesis of a deoxyribonucleotide chain, (ii) In DNA, it is another short sequence, which is complementary to a sequence of messenger RNA and allows reverse transcriptase to start copying the adjacent sequences of mRNA. (iii) In retroviruses, it is a cellular transfer RNA whose elongation initiates RNA-directed DNA synthesis by the DNA polymerase. 

As already mentioned, RNR is the metalloenzyme in which the first definitively characterized stable amino acid radical (1), later identified as a tyrosyl radical, was found in 1972. The RNR enzymes catalyse the reduction of ribonucleotides to their corresponding deoxyribonucleotides utilized in DNA biosynthesis. There are three unique classes of this enzyme, differing in composition and cofactor requirements all of them, however, make use of metal ions and free radical chemistry. Excellent reviews on RNRs are available (60, 61, 70, 89-97). 

Initial insight of the role of CSN in cell-cycle control came from the finding that csnl and csn2 deletion S. pomhe strains have an S-phase delay [52]. Interestingly, this effect did not occur in strains missing other CSN subunits. The S-phase delay was caused by the accumulation of the cell-cycle inhibitor Spdl (S-phase delayed 1), which is involved in the misregulation of the ribonucleotide reductase (RNR). RNR catalyzes the production of deoxyribonucleotides for DNA synthesis and... 

Ribonucleotide reductase is required for the formation of the deoxyribonucleotides for DNA synthesis. Figure 1-18-2 shows its role in dTMP synthesis, and Figure 1-18-3 shows all four nucleotide substrates ... 

Methylated bases occur in small amounts in deoxyribonucleotides. The role of methylation, especially of cytosine in DNA, is discussed below and in Chapter 15. 

The two classes of nucleotide that must be synthesised are the pyrimidine and purine ribonucleotides for RNA synthesis and the deoxyribonucleotides for DNA synthesis. For the original sources of the nitrogen atoms in the bases of the pyrimidine and purine nucleotides, see Figure 20.7. The pathway for the synthesis of the pyrimidine nucleotides is... 

DNA is a linear polymer of deoxyribonucleotides in which the sequence of purine and pyrimidine bases encodes cellular RNA and protein molecules. 

The deoxyribonucleotides in the DNA polymer are connected by phosphodi-ester bonds between the 5 -phosphate group attached to one deoxyribose sugar and the 3 -hydroxyl group of the next sugar. 

The sugar component in RNA is ribose, whereas in DNA it is 2-dexoyribose. In deoxyribonucleotides, the heterocyclic bases are purine bases, adenine and guanine, and pyrimidine bases, cytosine and thymine. In ribonucleotides, adenine, guanine and cytosine are present, but not thymine, which is replaced by uracil, another pyrimidine base. 

The information in DNA is encoded in its linear (onedimensional) sequence of deoxyribonucleotide subunits, but the expression of this information results in... 

DNA is a linear polymer of covalently joined deoxyribonucleotides, of four types deoxyadenylate (A), deoxyguanylate (G), deoxycytidy-late (C), and deoxythymidylate (T). Each nucleotide, with its unique three-dimensional structure, can associate very specifically but non-covalently with one other nucleotide in the complementary chain A always associates with T, and G with C. Thus, in the double-stranded DNA molecule, the entire sequence of nucleotides in one strand is complementary to the sequence in the other. The two strands, held together by hydrogen bonds (represented here by vertical blue lines) between each pair of complementary nucleotides, twist about each other to form the DNA double helix. In DNA replication, the two strands separate and two new strands are synthesized, each with a sequence complementary to one of the original strands. The result is two double-helical molecules, each identical to the original DNA. 

Disulfide bridge. A covalent linkage formed by oxidation between two SH groups either in the same polypeptide chain or in different polypeptide chains. DNA. Deoxyribonucleic acid. A poly-deoxyribonucleotide in which the sugar is deoxyribose the main repository of genetic information in all cells and most viruses. 

As much of the terminology used in molecular biology may be unfamiliar to some readers, it is appropriate to define some of the vocabulary and this is given in an appendix to this chapter. There are two types of nucleic acids, the ribonucleic acids (RNA) and the deoxyribonucleic acids (DNA). Genetic information is carried in the linear sequence of nucleotides in DNA. Each molecule of DNA contains two complementary strands of deoxyribonucleotides which contain the purine bases, adenine and guanine and the pyrimidines, cytosine and thymine. RNA is single-stranded, being composed of a linear sequence of ribonucleotides the bases are the same as in DNA with the exception that thymine is replaced by the closely related base uracil. DNA replication occurs by the polymerisation of a new complementary strand on to each of the old strands. 

Genetic Information in E. Coli DNA The genetic information contained in DNA consists of a linear sequence of coding units, known as codons. Each codon is a specific sequence of three deoxyri-bonucleotides (three deoxyribonucleotide pairs in double-stranded DNA), and each codon codes for a single amino acid unit in a protein. The molecular weight of an E. coli DNA molecule is about... 

SPECIFICITY. Restriction endonucleases are highly specific in hydrolyzing doubled-stranded DNA. Not only do they recognize a specific sequence of four to six base pairs (up to 11 base pairs in case of Bgl I see Table II) but the base pairs must be patind/iomic in the two strands of DNA. The cleavage sites possess twofold rotational symmetry as shown in Scheme I for restriction endonuclease Aat II from AcdtobacXdA OUddtL (Table II A, T, G, C indicate deoxyribonucleotides in this paper). In this example, the T-C phosphodiester bond in each strand two residues distal to the symmetry axis is cleaved by restriction endonuclease Aat II. 

Ribonucleotide reductase catalyses the reduction of the four common ribonucleotides to their corresponding deoxyribonucleotides, an essential step in DNA synthesis. All four ribonucleotides are reduced by the same enzyme [77], The enzyme (250 000 mol. wt.) is a complex of two proteins Mi which contains substrate and redox-active sulphydryl groups and M2 which contains both a (x-oxo-bridged binuclear iron centre (Fig. 5) [77] and a tyrosine moiety sidechain which exists as a free radical stabilised by the iron centre [78], This radical, which is only 5.3 A away from iron centre 1, has access to the substrate-binding pocket and is essential for enzyme activity. Electrons for the reduction reaction are supplied from NADPH via thioredoxin, a small redox-active protein. 

RNRs catalyze the reduction of ribonucleotides to deoxyribonucleotides, which represents the first committed step in DNA biosynthesis and repair.These enzymes are therefore required for all known life forms. Three classes of RNRs have been identified, all of which turn out to be metalloenzymes. The so-called class I RNRs contain a diiron site (see Cobalt Bn Enzymes Coenzymes and Iron-Sulfur Proteins for the other two types of RNRs). As diagrammed in Figure 5, these enzymes generate first a tyrosyl radical proximal to the diiron site in the protein subunit labeled R2, and then a thiyl radical in an adjacent subunit (Rl) that ultimately abstracts a hydrogen atom from the ribonucleotide substrate. This controlled tyrosine/thiol radical transfer must occur over an estimated distance of 35 A, and a highly choreographed proton-coupled electron transfer (PCET) mechanism across intervening aromatic residues has been proposed. Perhaps, even more remarkably,... 

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