Chapter 11. Structure of Nucleic Acids Biochemistry by Reginald Garrett and Charles Grisham. Essential Question. What is the higher-order structure of DNA and RNA, and what methodologies have allowed scientists to probe these structures and the functions that derive from them?. Outline.
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Structure of Nucleic Acids
Reginald Garrett and Charles Grisham
Sequencing Nucleic Acids
Based on DNA polymerase reaction
See Figure 11.7
Factors for stablizing the DNA helix structure:
from polar atoms in the sugar-phosphate backbone with surrounding water.
See Figures 11.7, 11.8
Figure 11.9Helical twist and propeller twist in DNA.(a) Successive base pairs in B-DNA show a rotation with respect to each other (so-called helical twist) of 36° or so, as viewed down the cylindrical axis of the DNA. (b) Rotation in a different dimension—propellertwist—allows the hydrophobic surfaces of bases to overlap better. The view here is edge-on to two successive bases in one DNA strand (as if the two bases on the right-hand strand of DNA in (a) were viewed from the right-hand margin of the page; dots represent end-on views down the glycosidic bonds). Clockwise rotation (as shown here) has a positive sign. (c) The two bases on the left-hand strand of DNA in (a) also show positive propeller twist (a clockwise rotation of the two bases in (a) as viewed from the left-hand margin of the paper).
See Table 11.1
Discovered by Alex Rich
See Figure 11.17
Figure 11.17These c0t curves show the rates of reassociation of denatured DNA from various sources and illustrate how the rate of reassociation is inversely proportional to genome complexity. The DNA sources are as follows: poly A+poly U, a synthetic DNA duplex of poly A and poly U polynucleotide chains; mouse satellite DNA, a fraction of mouse DNA in which the same sequence is repeated many thousands of times; MS-2 dsRNA, the double-stranded form of RNA found during replication of MS-2, a simple bacteriophage;
C0: concentration of completely denatured DNA at t= 0
t1/2: the time for half of the DNA to renature
C0t1/2 = 1/k2
T4 DNA, theDNA of a more complex bacteriophage; E. coli DNA, bacterial DNA; calf DNA (nonrepetitive fraction), mammalian DNA (calf) from which the highly repetitive DNA fraction (satellite DNA) has been removed. Arrows indicate the genome size (in bp) of the various DNAs.
Nucleic acid hybridization: Different DNA strands of similar sequence can form hybrid duplexes
FIGURE 11.18 Solutions of human DNA (red) and mouse DNA (blue) are mixed and denatured, and the single strands are allowed to reanneal. About 25% of the human DNA strands form hybrid duplexes (one red and one blue strand) with mouse DNA.
Fig. 11-18, p.352
Density gradient centrifugation is a common method of separating macromolecules, particularly nucleic acids, in solution. A cell extract is mixed with a solution of CsCl to a final density of about 1.7 g/cm3 and centrifuged at high speed (40,000 rpm, giving relative centrifugal forces of about 200,000 g). The biological macromolecules in the extract will move to equilibrium positions in the CsCl gradient that reflect their buoyant densities.
Fig. 11A-1, p.374
Telomerase, a RNA-containing DNA polymerase, maintain the integrity of chromosome against degradation. Most normal somatic cells lack telomerase. They lose 50 nucleotides per cell cycle and eventually lead to chromosome instability and cell death.
10001700 repeats in human germline cells
20 different types of cancer cells were found to contain telomerase activity.
Telomerase RNA serves as the template for the DNA polymerase activity.
Ribosomes synthesize proteins