ps2q_05

ps2q_05 - MIT Department of Biology 7.014 Introductory...

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MIT Department of Biology 7.014 Introductory Biology, Spring 2005 Name:______________________________________ Section :______ 7.014 Problem Set 2 Answers to this problem set are to be turned in. Problem sets will not be accepted late. Solutions will be posted on the web. Question 1 Open the Human γ D crystallin (H γ D-Crys) structure html file by clicking on the link on the Problem Sets page. Rotate the molecule and get an idea of the three dimensional structure of (H γ D-Crys). H γ D-Crys is a soluble human eye lens protein. I. The true 3-dimensional structure of H γ D-Crys can be observed using the “Show Spacefill” button, and a trace of the peptide backbone can be observed using the “Show Ribbon” button. a) If possible/applicable, describe the following types of structural features of H γ D-Crys: i. Secondary: ii. Quaternary (Hint: Use the “Color Ribbon by Protein Subunit” button): b) Does there appear to be a gap between the two protein domains in the ribbon and spacefill structure representations? Ribbon: Spacefill: c) Which of the two representations (spacefill or ribbon) more accurately represents the actual structure of H γ D-Crys in the cell? Why? II. We will now look at some interactions important in maintaining the tertiary structure of H γ D- Crys. d) Choose “Central Interaction” i. What are the names of the amino acids involved in this interaction? (Hint: It may help to change the representation of the residues to ball and stick by clicking in the box labeled “Ball and Stick on/off” below the 3D window. Keep in mind that in cpk coloring, gray is carbon, blue is nitrogen, and red is oxygen. Hydrogen is not shown!)
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Question 1, continued ii. The central cluster is composed of what type of amino acids (acidic, basic, hydrophobic, or polar)? iii. What type(s) of interaction(s) are formed between residues in this cluster? iv. Select “ Central Interaction with All Atoms Shown.” This view shows all the atoms of H γ D-Crys (not including hydrogens) as transparent dots. Is the central interaction located on the inside or the outside of the protein? Why is this reasonable given that H γ D-Crys is a soluble protein? e)
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ps2q_05 - MIT Department of Biology 7.014 Introductory...

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