2.  (10 points).  Describe how fluorescence polarization (or…

2.  (10 points).  Describe how fluorescence polarization (or anisotropy) measurements can be used to measure a macromolecule/ligand interaction. Assume the small molecule ligand can emit fluorescence in this example. a.    (4 points). What property of the light does one take advantage of to assess the binding reaction? Describe how this property leads to the ability to distinguish free from bound ligand. b.    (3 points). What property of the fluorophore should one consider when designing these experiments (and why)? c.    (3 points). In the case that the ligand is not fluorescent, one might chemically attach a fluorophore to the ligand. What would happen to the measured polarization if the fluorophore was linked to the ligand by a relatively long linker compared to very short linker?  

7.  The figure below shows the Kratky plots of an RNA molecu…

7.  The figure below shows the Kratky plots of an RNA molecule, the regulatory domain of the Lys riboswitch, both in the absence and in the presence of 5 mM MgCl2 (all other buffer conditions are identical). What is the explanation for the different curve shapes?

5.  (10 points).  In class we talked about the steps require…

5.  (10 points).  In class we talked about the steps required for determining a structure using X-ray diffraction. Answer the questions below about X-ray structure determination. a.    (2 points). Why are crystals used for diffraction experiments rather than a single molecule, which in principle could diffract an X-ray? b.    (2 points). Describe Bragg’s law and why it allows for one to see reflections (i.e., a diffraction pattern). c.    (2 points). Why are Miller indices useful for describing an X-ray diffraction experiment? d.    (2 points). Describe the setup for an X-ray diffraction experiment and how one would collect data. e.    (2 points). What is the “phase problem” in X-ray crystallography and describe one method that allows one to solve the phase problem.