MT2_F09_answers

MT2_F09_answers - MCB124 Fall 2009 MIDTERM 2 page 3 NAME I....

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MCB124 Fall 2009 MIDTERM 2 page 3 NAME I. STRUCTURE DETERMINATION (20 pts) For the following questions, indicate the techinique(s) that are appropriately described by the sentence. ( 1 pt each ) Key: AFM Atomic Force Microscopy XRAY 3-D Xray crystallography EX 2-D Electron crystallography CRYO Single Particle CryoEM with image averaging NMR Nuclear magnetic resonance NONE none of these 1. ________XRAY _____ Yield(s) the atomic coordinates of atom to accuracies of < 0.5 Å 2. ___CRYO,AFM__ Require(s) only small amounts of sample (< 1mg) 3. _______NMR________ Can be used the measure the pKa of amino acid side chains in solution 4. XRAY, EX, CRYO Provide(s) an actual image of the molecule 5. _______NMR________ Provide(s) information on dynamic molecular motion in solution 6. ________XRAY (EX)_ Can yield the atomic-resolution structures of viruses and ribosomes 7. ________XRAY, EX _ Require(s) crystals 8. CRYO (EX) Routinely provide(s) the overall 3-D molecular shape to 10-20 Å resolution 9. _______NMR________ Limited to molecules of less than 40 kD in size 10 . XRAY, EX, NMR (CRYO) Use(s) Fourier Transform mathematics for structure solution 11 . EX Determine membrane protein structure in a lipid bilayer 12 . _______NMR________ 3-D structures are calculated from atom-atom distances of less than 5 Å 13 _______AFM________ Provides a ”topographic” map at vertical resolution of < 1Å 14 ._____NONE______ For visualizing the interior surfaces of cellular and organellular membranes 15. _______AFM (CRYO)_ Can be used to visualize large DNA strands as “strings” 16/17. An acceptable atomic resolution X-ray crystal structure has a resolution of higher than 3.0 Å and an R-factor of less than 25 %. ( 1pt each ) 18. Spin-energy transfer gives rise to Crosspeaks in a 2-D NMR spectrum. ( 1 pt ) 19. What NMR experiment assigns particular resonances to protons in specific residues? COSY ( 1 pt ) 20. What NMR experiment yields 3-D information for structure solution ? NOESY ( 1 pt ) II. COMPUTATIONAL STRUCTURAL BIOLOGY (10 pts) A. All computational approaches to predicting structures involve two fundamental tasks that must be accomplished. Briefly in the SMALL space provided (NO MORE), explain these tasks. (1 pt each) 1 . SEARCH : Generation of reasonable candidate structures that fit the data 2. . SCORING : Evaluate the candidate structures in order to rank their likelihood 3. Energy minimization methods generate two results at the end of the experiment. They are The nearest low energy structure to the starting model and its energy . (1 pt each)
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MCB124 Fall 2009 MIDTERM 2 page 4 NAME B. At the heart of most computational approaches to structure is calculating the relative energies of complex biomolecules, which is typically done by summing the energies of individual atomic interactions . BRIEFLY describe THREE of these energetic terms. (1 pt each) Any three of the following Bond energies : the energy of covalent bonds based on their length
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MT2_F09_answers - MCB124 Fall 2009 MIDTERM 2 page 3 NAME I....

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