1. Define the relationship between twist, writhe and linking number. Are the twist and writhe topological properties or geometric properties? Why is this significant? What is the twist and writhe of relaxed (but not broken) circular DNA?
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41. Define the relationship between twist, writhe and linking number. Are the twist and writhe topological properties or geometric properties? Why is this significant? What is the twist and writhe of relaxed (but not broken) circular DNA?
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- 46. What are SMC proteins? Describe the function of SMC proteins and explain how they might contribute to creating and maintain the compacted structure of DNA inside of cells. Describe the basic functions of condensins and cohesins.. In a supercoiled DNA, a stretch of about 20 base pairs changes from the B form to the Z form. What is the change in (a) T, (b) L, and (c) W?34. Draw double-stranded DNA (two basepairs long with one AT basepair and one GC basepair). Your drawing should be flat; do not draw the twist of the helix. Be sure to include the 5’-P, 3’- OH, deoxyribose sugar rings (with carbons 1’-5’ and the O indicated), and a simplified phosphodiester bond (O-P-O). Show purines as two differently-sized rings and pyrimidines as one ring and show the correct number of hydrogen bonds between bases. The dsDNA must be antiparallel. Drawing a simplified version of dsDNA will help you gain a better understanding of the concepts underlying dsDNA structure. It will most likely take a couple of tries to get a clear figure.
- 29.) equalities now called Chargaff's rule. Biochemist Erwin Chargaff was the first to note that, in DNA, [A]=[T] and [G]=[C], A) Using this rule, determine the percentages of all the bases in DNA that is 20% thymine. [A] = [C] = [G] [T] = 20% %3D - B) If a single strand of RNA is 20% uracil, what can you predict about the percentages of the remaining bases and why?The A and G compositions (mole percent) of one of the strands of a duplex DNA is A = 27 and G = 30. (a) What would be the T and C compositions of the complementary strand? (b) What can be said about the A and G compositions of its complementary strand?For some DNAs, it is possible to separate the two strands, after denaturation,in a CsCl gradient.(a) What property of any DNA determines where it will band in a CsClgradient?(b) What kind of DNA might have two strands that differ sufficiently in thisproperty that they could be separated after denaturation?
- The base composition of one of the DNA chains of a DNA double helix contains 18 mol-%A, 35 mol-%T, 26 mol-%C, and 21 mol-%G (a) What is the base composition of the complementary DNA chain? (b) Is the total amount of purine bases equal to the total amount of pyrimidine bases for the DNA double helix?The double helical structure of DNA is intrinsically unstable and easily dissociates to form two separate strands. Why? How does this affect the two key biological functions of chromosomal DNA? What would happen if the DNA helices were too stable?For some DNAS it is possible to separate the two strands, after denaturation, in a CsCl gradient. (a) What property of any DNA determines where it will band in a CsCI gradient? (b) What kind of DNA might have two strands that differ sufficiently in this property that they could be separated after denaturation?
- When the helix axis of a closed circular duplex DNA of 2310 bp is constrained to lie in a plane, the DNA has a twist (T) of 207. When released, the DNA takes up its normal twist of 10.5 bp per turn. Indicate the values of the linking number (L), writhing number (W), and twist for both the constrained and unconstrained conformational states of this DNA circle. What is the superhelix density, σ = W/T, of both the constrained and unconstrained DNA circles?47. Define, in the context of DNA structure, "topological bonds."7 a-d. i. ii. Draw the following base pair arrangements in B-DNA if you were looking down the barrel of the helix. Draw the Hydrogen bonds between the base pairs and label the atoms that participate in these bonds as hydrogen bond donors with a D and hydrogen bond acceptors with an A. Draw a thicker line leaving the atoms that participate in the glycosidic bonds. iii. iv. Label the major and minor groove on the common pairings, shown in "a" and "c". a. Adenine-Thymine Base Pair b. Adenine (rare form)- Cytosine c. Guanine-Cytosine Base Pair d. Guanine (rare form) - Thymine 7e. On your picture in question "a", highlight or circle the proton that shifts when Adenine tautomerizes to its rare imino form. Draw an arrow pointing to the atom it moves to. 7f. On your picture in question "c", highlight or circle the proton that shifts when Guanine tautomerizes to its rare enol form. Draw an arrow pointing to the atom it moves to.