Double helix pairs

Initiation of transcription involves binding of the RNA polymerase to the promoter region. This sequence contains characteristic consensus nucleotide sequences that are highly conserved. These include the Pribnow box and the -35 sequence. Elongation involves RNA polymerase copying one strand of the DNA double helix, pairing C s with G s and A s (on the DNA template) with U s on the RNA transcript. Substrates are ribonucleoside triphosphates. Termination may be accomplished by the RNA polymerase alone, or may require p factor. 

The genetic code differs very little between species. By contrast, considerable differences occur between species in the anticodon translation system of tRNA, as evidenced by the mitochondrial tRNA system. In all systems the bases in the anticodon-codon complex run antiparallel, as in standard double-helix pairing, and in all cases only Watson-Cricklike base pairing occurs between the first two bases in the codon and the opposing bases in the anticodon segment of the tRNA. However, for the 3 base in the codon, the rules for pairing vary with the species and with the base in question. These rules, summarized in table 29.4, are as follows. 

DNA is composed of two antiparallel complementary strands, which build a double helix. Pairing of the bases, which grant stability to the helix, takes place via hydrogen bonds. The base pairs (bp) are A-T (two bonds) and G-C (three bonds), and constitute the inner side of the double helix (Scheme 1). The backbone of the helix is composed of the sugar-phosphate chain. Another important contribution to the stability of the helix comes from the base stacking of the aromatic rings of the... 

FIGURE 28 5 (a) Tube and (b) space filling models of a DNA double helix The carbohydrate-phosphate backbone is on the out side and can be roughly traced in (b) by the red oxygen atoms The blue atoms belong to the purine and pyrimidine bases and he on the inside The base pairing is more clearly seen in (a)... 

Section 28 8 The most common form of DNA is B DNA which exists as a right handed double helix The carbohydrate-phosphate backbone lies on the outside the punne and pyrimidine bases on the inside The double helix IS stabilized by complementary hydrogen bonding (base pairing) between adenine (A) and thymine (T) and guanine (G) and cytosine (C)... 

Genes are constructed from sets of deoxyribonucleic acids (DNA), which in turn consist of chains of nucleotides. These chains occur in matched pairs, twisted around each other (a double helix). 

Figure 7.1 Schematic drawing of B-DNA. Each atom of the sugar-phosphate backbones of the double helix is represented as connected circles within ribbons. The two sugar-phosphate backbones are highlighted by orange ribbons. The base pairs that are connected to the backbone are represented as blue planks.

Notice that in B-DNA the central axis of this double helix goes through the middle of the base pairs and that the base pairs are perpendicular to the axis. 

We have, so fai, described the structure of DNA as an extended double helix. The crystallographic evidence that gave rise to this picture was obtained on a sample of DNA removed from the cell that contained it. Within a cell—its native state—DNA almost always adopts some shape other than an extended chain. We can understand why by doing a little arithmetic. Each helix of B-DNA makes a complete turn every 3.4 X 10 m and there ar e about 10 base pair s per turn. A typical human DNA contains 10 base parr s. Therefore,... 

Double helix (Section 28.8) The form in which DNA normally occurs in living systems. Two complementary strands of DNA are associated with each other by hydrogen bonds between their base pairs, and each DNA strand adopts a helical shape. 

FIGURE 1.5 The DNA double helix. Two complementary polynucleotide chains running in opposite directions can pair through hydrogen bonding between their nitrogenous bases. Their complementary nucleotide sequences give rise to structural complementarity. 

The DNA isolated from different cells and viruses characteristically consists of two polynucleotide strands wound together to form a long, slender, helical molecule, the DNA double helix. The strands run in opposite directions that is, they are antiparallel and are held together in the double helical structure through interchain hydrogen bonds (Eigure 11.19). These H bonds pair the bases of nucleotides in one chain to complementary bases in the other, a phenomenon called base pairing. 

Because of the double helical nature of DNA molecules, their size can be represented in terms of the numbers of nucleotide base pairs they contain. For example, the E. coli chromosome consists of 4.64 X 10 base pairs (abbreviated bp) or 4.64 X 10 kilobase pairs (kbp). DNA is a threadlike molecule. The diameter of the DNA double helix is only 2 nm, but the length of the DNA molecule forming the E. coli chromosome is over 1.6 X 10 nm (1.6 mm). Because the long dimension of an E. coli cell is only 2000 nm (0.002 mm), its chromosome must be highly folded. Because of their long, threadlike nature, DNA molecules are easily sheared into shorter fragments during isolation procedures, and it is difficult to obtain intact chromosomes even from the simple cells of prokaryotes. 

An alternative form of the right-handed double helix is A-DNA. A-DNA molecules differ in a number of ways from B-DNA. The pitch, or distance required to complete one helical turn, is different. In B-DNA, it is 3.4 nm, whereas in A-DNA it is 2.46 nm. One turn in A-DNA requires 11 bp to complete. Depending on local sequence, 10 to 10.6 bp define one helical turn in B-form DNA. In A-DNA, the base pairs are no longer nearly perpendicular to the helix axis but instead are tilted 19° with respect to this axis. Successive base pairs occur every 0.23 nm along the axis, as opposed to 0.332 nm in B-DNA. The B-form of DNA is thus longer and thinner than the short, squat A-form, which has its base pairs displaced around, rather than centered on, the helix axis. Figure 12.13 shows the relevant structural characteristics of the A- and B-forms of DNA. (Z-DNA, another form of DNA to be discussed shortly, is also depicted in Figure 12.13.) A comparison of the structural properties of A-, B-, and Z-DNA is summarized in Table 12.1. 

Figure 3.10 Stniciural details of the bridging units between pairs of bases in separate strands of the double helix of DNA (a) the thymine-adenine pair (b) the cytosine-guanine pair.

DNA is made up ot two intertwined strands. A sugar-phosphate chain makes up the backbone of each, and the two strands are joined by way of hydrogen bonds betwen parrs of nucleotide bases, adenine, thymine, guanine and cytosine. Adenine may only pair with thymine and guanine with cytosine. The molecule adopts a helical structure (actually, a double helical stnrcture or double helix ). 

In 1953, James Watson and Francis Crick made their classic proposal for the secondary structure of DNA. According to the Watson-Crick model, DNA under physiological conditions consists of two polynucleotide strands, running in opposite directions and coiled around each other in a double helix like the handrails on a spiral staircase. The two strands are complementary rather than identical and are held together by hydrogen bonds between specific pairs of... 

The double helix model provides a simple explanation for cell division and reproduction. In the reproduction process, the two DNA chains unwind from each other. As this happens, a new matching chain of DNA is synthesized on each of the original ones, creating two double helices. Since the base pairs in each new double helix must match in the same way as in the original, the two new double helices must be identical to the original. Exact replication of genetic data is thereby accomplished, however complex that data may be. 

FIGURE 19.29 The bases in the DNA double helix fit together by virtue of the hydrogen bonds that they can form, as shown on the left. Once formed, the AT and CC pairs are almost identical in size and shape. As a result, the turns of the helix shown on the right are regular and consistent. 

Fic. 10.—Parallel packing arrangement of 6-fold, A-amylose (8) molecules, (a) A stereo side view of less than 2 turns of a pair of double helices 10.62 A (=al2) apart. The two strands in each helix are distinguished by open and filled bonds, and the helix axis is also drawn, for convenience. Note that atom 0-6 mediates both intra- and inter-double helix hydrogen bonds. 

---