The following is a problem set. Some of these problems are representative of the type that will be on your exam (more integrated "thought-type" questions); others point out the level of understanding and factual knowledge I would like you to have. I have included suggested sentence limits for the answers-similar limits will be present on your exam. These guides are given to encourage you to provide a clear, concise and incisive answer to the question.
 
 

Suggested Questions/Lecture

Lecture 2 Ques. 1 & 2

Lecture 3 & 4 Ques. 3-8

Lecture 5 Ques. 10 & 11

Lecture 6 Ques. 12 & 13
 
 

1. The composition, in mole fraction units, of one strand of double helical DNA is [A]=0.3 and [G]=0.24. a)What can you say about the mole fraction of [T] and [C] on that strand ? (1 sentence) b) What can you say about the mole fraction of A,G,T,C on the complimentary strand? (2 sentences). [Answer]

 

 

2. Name the two driving forces that stabilize base stacking and describe how they contribute to the cooperativity of helix formation. (4 sentences). [Answer]

 

 

3. What is the repeating unit of B-DNA? Justify your answer (3 sentences). [Answer]

 

 

4. Griffith used heat-killed S pneumococci to transform R mutants. Studies show that double stranded DNA is needed for efficient transformation. Given your knowledge of denaturation-renaturation phenomena, why is it not surprising that his experiments worked. Illustrate your answer. (4 sentences). [Answer]

 

 

5. Describe why T_m of "normal" DNA is affected by salt. Speculate why the T_m of DNA which contains phosphates that have been modified to render them uncharged is not. (4 sentences). [Answer]

 

 

6. Consider the transition of a poly dA-dT^.poly dA-dT from the B-form DNA to the Z-form. By a rapid sampling technique we determine that about half the sugar configurations do not change while half of the sugars intermediates in the B->Z transition display a range of conformations. a) Why? We observe that approximately half the possible configurations available to the sugar that change configurations are not observed. b) Why? (3 sentences). [Answer]

 

 

7. The configuration of the sugars attached to the guanine base in poly dG-dC^.poly dG-dC in Z-DNA are in the C3' endo. Why? (3 sentences). [Answer]

 

 

8. DNase I is an enzyme which binds to the minor groove and cleaves DNA. In order to cut DNA, the minor groove width should be near ~5.7 A. Would you expect DNase I to cleave Z-DNA? Why? (3 sentences) [Answer]

 

 

9. An excited graduate student comes to you and says that the regulatory protein he is studying binds in the minor groove of B-form DNA. Why is he probably wrong? (2 sentences) Speculate on how he might possibly be right? (2-3 sentences) [Answer]

 

 

10. Draw the curve which would describe the ring closure probabilities vs. chain length for DNA modeled as (a) a completely flexible chain, (b) a rigid rod, and (c) a worm-like coil having persistence length of 250 bp. [Answer]

 

 

11. Would you expect salt concentration to affect the persistence length of DNA? Why or why not? (3 sentences) [Answer]

 

 

12. An archebacterium found in living in a hot spring (~95^oC), is found to have an enzyme that introduces positive supercoils into DNA. Why is this an advantage for this organism? (3 sentences) [Answer]

 

 

13. Suppose that one turn of B-DNA in a circular DNA with L_k=100, T_w=104 and W_r=-4 becomes a turn of Z-DNA. What are the values of L_k, W_r and T_w after the transition? How does this transition alter the mobility of this DNA in an agarose gel? If Z-DNA is a higher energy form of DNA, why is it then favored by supercoiling? (3 sentences) [Answer]