BIOCHEMISTRY - L. Stryer - 1984

VOLUME 3

Part IV INFORMATION

CHAPTER 24 DNA: THE GENETIC ROLE, STRUCTURE, AND REPLICATION

24.3. The Genes of Some Viruses Consist of RNA

While the genes of all prokaryotic and eukaryotic organisms are made of DNA, viral genes may consist of either DNA or RNA. The tobacco mosaic virus, which infects the leaves

of tobacco plants, is one of the most thoroughly studied Introduction/7.html">RNA-containing Viruses. It is composed of a single RNA molecule surrounded by a protein coat made up of 2,130 identical subunits (for a Structure/133.html">Discussion of virus structure and assembly, see Ch. 30). Treatment of the virus with phenol separates the protein from the RNA. Isolated viral RNA is infectious, whereas the isolated protein is not. The Use of synthetic hybrid virus particles further demonstrated that the genetic Specificity of a virus resides solely in its RNA. Numerous strains of the tobacco mosaic virus exist. A synthetic hybrid virus was prepared from the RNA of strain 1 and the protein of strain 2. Another such virus was constructed using the RNA of strain 2 and the protein of strain 1. Upon infection of a Cell with these hybrid viruses, the viral progeny always consisted of RNA and Protein corresponding to the Specificity of the RNA of the hybrid virus used for infection.

24.4. The Watson-Crick DNA Double Helix

In 1953, James Watson and Francis Crick deduced the three-dimensional structure of DNA and immediately proposed a plausible mechanism for its Replication. This brilliant achievement stands as one of the most momentous Milestones in the history of biology, as it paved the way for understanding Gene function at THE MOLECULAR LEVEL. Watson and Crick analyzed X-Ray Diffraction patterns of DNA fibers (Fig. 24.6) obtained by Rosalind Franklin and Maurice Wilkins, and proposed a structural model that proved correct in its main features. The key characteristics of this model are as follows.

1. Two helical polynucleotide chains are coiled around a common axis. The chains run in opposite directions (Fig. 24.7).

2. The purine and pyrimidine bases are located on the inside of the helix, while the phosphate and deoxyribose residues are on the outside (Fig. 24.8). The planes of the bases are perpendicular to the helix axis, whereas the planes of the sugar residues are positioned at almost a right angle to the bases.

3. The diameter of the helix is 20 A. The distance

between adjacent bases along the helix axis is 3.4 A, and they are rotated relative to each other by 36°. Thus, each turn of the helix in each chain contains 10 NUCLEOTIDES, which corresponds to 34 A.

4. The two chains are held together by Hydrogen Bonds between Base Pairs. Adenine always pairs with thymine, and guanine with cytosine (Figs. 24.9 and 24.10).

5. There are no restrictions on The sequence of bases along a polynucleotide chain. A specific sequence of bases encodes precise Genetic information.

Class="center">Fig. 24.6. X-ray diffraction photograph of a hydrated DNA fiber (B-form). The cross in the center of the pattern is characteristic of a helical structure. Intense meridional reflections arise from diffraction by a stack of base pairs spaced 3.4 A apart from one another

Fig. 24.7. Schematic diagram of the DNA double-helix model. The entire structure repeats every 34 A, corresponding to 10 residues per chain

Fig. 24.8. Schematic diagram of one of the chains of the DNA double helix (viewed down the helix axis). The bases—in this case exclusively Pyrimidines—are located on the interior, and the sugar-phosphate backbone is on the exterior. It is clearly visible that the structure possesses a tenfold axis of Symmetry. The bases are shown in green, and the sugars in red

A crucial property of The Double Helix is the specificity of base pairing. Based on Steric constraints and hydrogen-bonding capabilities, Watson and Crick postulated that adenine must pair with thymine, and guanine with cytosine. The steric limitations on base positioning arise from the regular repeating STRUCTURE OF THE sugar-phosphate backbones of both polynucleotide chains. The glycosidic bonds linking a base pair to the backbone are separated by a distance of 10.85 A (Fig. 24.11). A pyrimidine-purine pair fits neatly into this space. Conversely, this distance is insufficient for two Purines. For two pyrimidines, there is more than enough room, but they would be too far apart to form hydrogen bonds. Consequently, one base in a pair within the DNA double helix must always be a purine, and the other a pyrimidine. Furthermore, base pairing is strictly constrained by the rules of Hydrogen bond formation. The hydrogen atoms in purine and pyrimidine bases occupy very specific positions. Adenine cannot pair with cytosine because this would place two hydrogen atoms in THE POSITION OF one bond and none in THE PLACE OF the other. Similarly, guanine cannot bind to thymine. Instead, adenine forms two hydrogen bonds with thymine, and guanine forms three hydrogen bonds with cytosine (Figs. 24.9 and 24.10). The orientation of these Hydrogen bonds and the distance between them are optimal for strong interaction between the bases.

Fig. 24.9. Model of the adenine-thymine base pair

Fig. 24.10. Model of the guanine-cytosine base pair

Fig. 24.11. Overlapping of an AT base pair (highlighted in yellow) on a GC base pair (highlighted in blue). Note that the positions of the glycosidic bonds and the C'-1 atom of deoxyribose (highlighted in green) are nearly identical in both types of base pairs.

DNA forms —

A-form DNA: a double-stranded DNA containing approximately 11 residues per helical turn. In this right-handed helix, the base-pair planes are tilted by about 20° relative to the perpendicular to the helical axis. It forms upon dehydration of B-form DNA.

B-form DNA: the classic Watson-Crick double helix containing approximately 10 residues per helical turn. In this right-handed helix, the base-pair planes are perpendicular to the helical axis.

Z-form DNA: a left-handed double-stranded form of DNA containing about 12 residues per turn. This structure was proposed by Alexander Rich and his colleagues based on studies of the crystal structure of d(CG)₃.

This base-pairing scheme received compelling confirmation from earlier studies on the Nucleotide Composition of DNA across various species. In the 1950s, Erwin Chargaff discovered that the ratios of adenine to thymine and guanine to cytosine were close to 1 in all species examined. The Significance of this finding remained unclear until the Watson-Crick model was proposed (Figs. 24.12 and 24.13). Only then did it become evident that this regularity reflects a fundamental property of DNA Structure and function — the specificity of base pairing.

Fig. 24.12. Model of the double-stranded DNA molecule, showing three base pairs. Note that the two strands run in opposite directions.

Fig. 24.13. Three-dimensional model of the DNA double helix. The major groove (shown in red) and minor groove (shown in blue) are clearly visible. Note that a portion of each base remains accessible for interaction with other molecules.