What is the distinction between the two classes of Topoisomerases (Topo-I and Topo-II). Write the schematic mechanism (as shown in the slides) for the two types of Topoisomerases that accounts for this distinction? Which class of Topoisomerase requires ATP and why?
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43. What is the distinction between the two classes of Topoisomerases (Topo-I and Topo-II). Write the schematic mechanism (as shown in the slides) for the two types of Topoisomerases that accounts for this distinction? Which class of Topoisomerase requires ATP and why? What is (usually) the nucleophile in the topoisomerase reaction and how does it preserve the phosphotransfer potential of the cleaved DNA strand? Is there a eukaryotic Topoisomerase that adds negative supercoils to DNA? How does eukaryotic DNA obtain negative supercoils?
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- Quinolone antibiotics treat bacterial infections by blocking the activity of topoisomerase. Why does this treatment work? Explain what occurs at the molecular level.45. Why are topoisomerase inhibitors excellent drugs? How is it possible to use agents that block the action of topoisomerase as antibacterial antibiotics?Telomerase activity has been found to be 10 to 20 times more active in cancer cells than in normal somatic cells. What is the significance of this circumstance?
- What distinguishes topoisomerase type I from topoisomerase type II (“gyrase”) in E. coli bacteria? Both types of topoisomerases participate in the formation of nucleosomes. Topoisomerase type I cleaves one strand of a DNA duplex to remove DNA supercoils, and topoisomerase type II cleaves both strands of the DNA duplex when introducing negative supercoils into the molecule. Topoisomerase type I works to replicate DNA and topoisomerase type II works to transcribe RNA. Topoisomerase type I works on double-stranded DNA, and topoisomerase type II ("gyrase") works on single-stranded DNA. Topoisomerase type I adds negative DNA supercoils, and topoisomerase type II removes them.DNA polymerase I, DNA ligase, and topoisomerase I catalyze the formation of phosphodiester bonds. What is the activated intermediate in the linkage reaction catalyzed by each of these enzymes? What is the leaving group?Budding yeasts such as S. cerevisiae exhibit telomerase activity throughout their life cycles, whereas human somatic cells do not exhibit telomerase activity. Suggest why this is so.
- What is the velocity of movement (in micrometers per second) of DNA polymerase III holoenzyme relative to the template?DNA topoisomerases play important roles in DNA replication and in supercoiling . These enzymes are also the targets for certain anticancer drugs (see the introduction to this chapter). Eric Nelson and his colleagues studied m-AMSA, one of the anticancer compounds that acts on topoisomerase (E. M. Nelson, K. M. Tewey, and L. F. Liu. 1984. Proceedings of the National Academy of Sciences of the United States of America 81:1361–1365). They found that m-AMSA stabilizes an intermediate produced in the course of topoisomerase action. The intermediate consists of topoisomerase bound to the broken ends of the DNA. Breaks in DNA that are produced by anticancer compounds such as m-AMSA inhibit the replication of the cellular DNA and thus stop cancer cells from proliferating. Explain how m-AMSA and other anticancer agents that target topoisomerase enzymes taking part in replication might lead to DNA breaks and chromosome rearrangements.51. In 1973, Cohen and Boyer created the first chimera by successfully incorporating the frog rRNA into bacteria. The restriction endonuclease EcoRI was used to cut the frog DNA that contained the rRNA gene and the vector plasmid pSC101. The DNA fragments and the vector plasmid pSC101 were combined and transferred to E. coli bacteria.The frog DNA fragment and pSC101 were able to combine when Select one: a. a pyrimidine base in the sticky end of the DNA fragment came in contact with a pyrimidine base in pSC101 b. a nucleotide in the sticky end of the DNA fragment came in contact with a complementary base in pSC101 c. a nucleotide in the sticky end of the DNA fragment came in contact with the same base in pSC101 d. a purine base in the sticky end of the DNA fragment came in contact with a purine base in pSC101
- In the traditional alkaline lysis method of Solution 1, what is the purpose of RNAse A?Supercoiled DNA is slightly unwound compared to relaxed DNA and this enables it to assume a more compact structure with enhanced physical stability. Describe the enzymes that control the number of supercoils present in the E. coli chromosome. How much would you have to reduce the linking number to increase the number of supercoils by five?What is the signifi cance of the different DNA-binding properties of prokaryotic RNA polymerase core enzyme and holoenzyme?