mcb100A-sp09-mt1-Alber-soln - Name MCB 100A ChemC130 Mi...

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Name: __________________________________ 1/5 MCB 100A/ChemC130 Midterm 1 2009 Please write your name on the first page. 1. Find the letter below that best matches the following statements. Use a letter only once . (20 pts.) A. hydrogen bonds B. most important structural restraints determined using NMR C. wide and shallow in RNA duplex D. flips backbone into the structure E. reverses chain direction in 4 residues F. stacking G. Watson-Crick base pairs display different H-bonding pattern H. C3’ endo sugar pucker I. measure of quality of a sequence alignment J. genetic code K. measure of quality of a NMR structure L. all tRNAs M. depends on temperature, denaturant concentration and buried surface area N. ionic interaction O. often recognized by hydrogen bonds from side chains in a helix P. fold Q. extended protein strand R. measure of quality of a crystal structure i) __I___ E-value ii) __B__ through-space interactions iii) __J__ requires faithful charging of tRNAs with the correct amino acid iv) __M__ hydrophobic effect v) __ N __ falls off as 1/distance vi) __L___ cloverleaf secondary structure vii) __E___ ! -turn viii) __F___ metal-ion core ix) __P___ shared by homologous proteins x) __O___ major groove 2a. List three different advantages of a DNA genome compared to a RNA genome. (9 pts.) 1. More chemically stable 2. Made by error correcting polymerase (replicated more accurately). 3. U can be recognized as DNA damage. 4. Major grove of DNA is accessible for sequence specific recognition. 5. Can be longer (because of 1 and 2). Partial credit: -Describe DNA is B form but don’t explain the effect of this, i.e. larger major groove, larger P to P distance, etc. -Saying less error in DNA, but not being specific about DNA polymerase vs RNA polymerase or the ability to recognize DNA damage like U -NO points for just saying DNA is more stable -NO points for saying DNA is double helix because RNA can also adopt double helix structure
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Name: __________________________________ 2/5 2b. The A-minor motif occurs frequently in folded RNA structures. What is the general role of an A- minor motif? (5 pts.) It brings together three chains, two of which form a base pair. Partial credit: -Only mention 3 stands or 3 chains -To form/stabilize tertiary structure -Stabilization of RNA structure 2c. List two reasons that DNA strands could not form an A-minor motif. (4 pts.) 1. No 2’ OH in DNA for ribose H-bonding (in ribose zipper). 2. Minor groove in B DNA too narrow and deep to fit A base. Partial credit: -Describe DNA is B form but don’t explain consequences of this, i.e narrow minor groove 3. The sequence of part of a helix in the folded core of your favorite protein (YFP) is: RMELLKAAIEGD. 3a.
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mcb100A-sp09-mt1-Alber-soln - Name MCB 100A ChemC130 Mi...

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