Biochemistry Exam I - October 3, 2006: Nucleic Acids and Hybridization - Prof. Jason D. Ka, Exams of Biology

Download Biochemistry Exam I - October 3, 2006: Nucleic Acids and Hybridization - Prof. Jason D. Ka and more Exams Biology in PDF only on Docsity! Score for the page Biochemistry 674 Your Name: Nucleic Acids Prof. Jason Kahn Exam I (100 points total) October 3, 2006 You have 80 minutes for this exam. Exams written in pencil or erasable ink will not be re-graded under any circumstances. Explanations should be concise and clear. I have given you more space than you should need. There is a extra space on the last page if you need it. You do not need a calculator for this exam, and no other study aids or materials are permitted. Generous partial credit will be given, i.e., if you don’t know, guess. Honor Pledge: At the end of the examination time , please write out the following sentence and sign it, or talk to me about it: “I pledge on my honor that I have not given or received any unauthorized assistance on this examination.” 1. DNA Structure and Stability (30 pts): There are a lot of deviations from Watson Crick base pairing and the WC helix, both from nature and from synthesis. Eric Kool of Stanford has been particularly active in the latter field. (a; 10 pts) Draw two G:A base pairs: (1) a structure in which the Watson-Crick H-bonding faces of G and A interact with each other. (2) Freeform H-bonding of your choice, with at least two H-bonds formed, different from (1). An example might be the G:A pair seen in the tetraloop. You do not need to draw out sugars. Biochemistry 674 Exam I, 10/3/06 2/8 Score for the page (b; 3 pts) We have emphasized over and over what it is that makes the WC base pairs special. What is it? (c; 3 pts) G:A base pair # 1 from part (a) destabilizes B-form DNA. Why? It stacks and H-bonds well. Kool’s group has synthesized the extended adenine at the right (xA) and incorporated the xA:T base pair into DNA oligonucleotides. (d; 3 pts) Why did they choose to make the xA shown instead of “Not xA” shown below xA? (e; 3 pts) It is observed that the structure and backbone of the extended DNA (with an extendabase in each pair) is essentially a thick B-form, as shown below. This was somewhat surprising, at least to me. Why is it surprising? (Consider the limit of including more benzene “extenders.”) Biochemistry 674 Exam I, 10/3/06 5/8 Score for the page (c; 9 pts) Why 25mers? Why do much longer probes not work well for identifying SNPs? On the other hand, why not make the probes much shorter, so that synthesis would be easier? In general, what two somewhat conflicting goals do we have in any hybridization experiment? 3. RNA Structure (20 pts): (a; 10 pts) Sketch base-catalyzed hydrolysis of the RNA phosphodiester backbone. Why are there no large RNA genomes? Biochemistry 674 Exam I, 10/3/06 6/8 Score for the page The essential RNA (i) below was proposed to form the structure shown based on computer modeling. Then homologous sequences (ii) and (iii) were discovered. The bases that differ from RNA (i) are indicated in bold. The underlines are hints. (b; 4 pts) Explain the notion of correlated invariants in phylogenetic studies of RNA structure. (c; 6 pts) The sequences (ii) and (iii) support a structure different from the one shown. Draw the structure, for sequence (i). Why is this structure unexpected? Biochemistry 674 Exam I, 10/3/06 7/8 Score for the page 4. DNA Topology (20 pts): (a; 15 pts) Sketch the three main ways in which negative supercoiling is manifested (one has ΔTw < 0 and the other two are writhed). Identify the thermodynamically stable form for typical supercoiled B-DNA in the absence of proteins. Give one biological function for each of the two writhed forms.