ps2s_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: The secondary structure is described as α -helical or β -sheet. Secondary structure is controlled by backbone hydrogen bonds between amino acids. H γ D-Crys is primarily - sheet, but has two small -helices; one at the top of each domain. ii. Quaternary (Hint: Use the “Color Ribbon by Protein Subunit” button): The quaternary structure of a protein created by a number of distinct interacting amino acid chains. If we color H D-Crys by chain we find there is only one amino acid chain and, therefore, no quaternary structure. There are two -sheet domains in the protein, but they are both from one amino acid chain. b) Does there appear to be a gap between the two protein domains in the ribbon and spacefill structure representations? Ribbon: Yes Spacefill: No c) Which of the two representations (spacefill or ribbon) more accurately represents the actual structure of H γ D-Crys in the cell? Why? The spacefill model is a more accurate representation of what H D-Crys looks like in the cell. The spacefill representation shows the van der Waal radius or electron density clouds of all non-hydrogen atoms in the protein. The ribbon structure simply shows a trace of the polypeptide backbone without showing any amino acid side chain atoms. 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!) The interaction involves a methionine, a phenylalanine, two valines, an isoleucine, and a leucine.
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Question 1, continued ii. The central cluster is composed of what type of amino acids (acidic, basic, hydrophobic, or polar)? All of the residues are hydrophobic amino acids.
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This note was uploaded on 11/11/2011 for the course BIO 7.012 taught by Professor Lander during the Fall '10 term at MIT.

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ps2s_05 - MIT Department of Biology 7.014 Introductory...

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