Exam 2 2010 - Biology 5357 Chemistry Physics of Biological...

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Biology 5357 Chemistry & Physics of Biological Molecules Examination #2 Nucleic Acids Membranes December 16, 2010
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1. The pre-Q riboswitch has the smallest known aptamer domain. Here, a schematic of the structural change that occurs upon preQ 1 binding is shown. It involves formation of a pseudoknot, in which a new stem (P2) is formed when the 3 ! tail base-pairs with the loop nucleotides. PreQ 1 forms a hydrogen-bonded interaction with C17. (Ap is an adenine analog that isn’t important here). Also shown is the imino proton spectrum of the aptamer with and without preQ 1 . [RNA] = 0.2 mM, [preQ 1 ] = 0.4 mM, [Mg 2+ ] = 2 mM, in 25 mM sodium cacodylate at pH 6.5 and 298 K. A. (5 points) You remember that when a base pair is stable, its imino proton(s) are observed. How do you interpret the two imino proton spectra shown? B. (10 points) The +preQ 1 spectrum includes both preQ 1 and Mg 2+ . Predict how the aptamer structure might or might not change in the presence of Mg 2+ but without preQ 1 . Explain your reasoning. C. (10 points) If Mg 2+ is required for preQ 1 to bind, what might you conclude about the aptamer structure?
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  • Fall '11
  • PONDER
  • Membranes, Proton, DSPC, Physics of Biological Molecules, lipid preparations

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