Bi1_2011_PS2_v2

Bi1_2011_PS2_v2 - Bi1: The Biology and Biophysics of...

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Page 1 of 9 Bi1: The Biology and Biophysics of Viruses Spring 2011 Problem Set 2: Structural Biology Due Tuesday, April 12 at 4:00 P.M. in the Bi 1 closet Name: ___________________________________________________________ Section # : _________________________________________________________ Mail Code : ________________________________________________________ TA Names : ________________________________________________________ Date and Time turned in : ____________________________________________ Number of pages including this one : ___________________________________ AFTER YOU FINISH: How long did it take you to complete this problem set? __________________________ Go to the Bi1 moodle site at http://courses.caltech.edu/ and take the homework survey There are 2 questions with the second question as extra credit. The number of parts to each question is listed at the beginning of each; be sure to answer all the parts! Grade: Problem 1 __________ Problem 2 (Extra credit) __________ TOTAL: _________ HOMEWORK INSTRUCTIONS 1) Turn in your homework stapled to this cover page. 2) Use separate sheets of paper for your answers. 3) Write or type your answers neatly. 4) Put your name on each page of your answers. 5) Box your answers, please, so that the grader can find them. Points may be deducted if you don’t follow these instructions!
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Page 2 of 9 Required reading: PyMOL tutorial (posted with your problem set at: http://www.its.caltech.edu/~bi1/assignments.html ) Suggested reading: Biological Science 3 rd edition, pp. 43-58, 205-207 Problem 1: Structural analysis on some various fluorescent proteins (100 points, 14 parts) Be sure you go over the PyMOL tutorial before starting this set! Green fluorescent protein (GFP) was first purified from Aequorea victoria in the 1960’s by Osamu Shimomura. GFP was then further developed in the 1990s, and its usefulness in molecular biology made clear. Martin Chalfie’s group pioneered this work, and later Roger Tsien’s group further developed the protein, finding mutants that expressed more stably at 37°C (the temperature at which many biological experiments are carried out), exhibited better fluorescent efficiencies, and were shifted in absorption and emission spectra. The picture to the right shows a San Diego beach scene drawn with live bacteria expressing fluorescent proteins of different colors! Fluorescent proteins are now used by biologists in a myriad of different ways to keep track of the movements and reactions in cells and organisms. For example, fusion proteins can be created whereby the sequence of GFP is fused to the sequence of the protein of interest, and then one can track the movements of the fusion protein in real time within a living cell with a microscope. Another example is the use of FRET (fluorescence resonance energy transfer) assays to study protein-protein interactions (fluorescent energy is transferred from one fluorophore to a fluorophore in very close proximity, allowing close molecular interactions to
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Bi1_2011_PS2_v2 - Bi1: The Biology and Biophysics of...

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