ps2s_05

ps2s_05 - MIT Department of Biology 7.014 Introductory...

Info iconThis preview shows pages 1–3. Sign up to view the full content.

View Full Document Right Arrow Icon
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.
Background image of page 1

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
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.
Background image of page 2
Image of page 3
This is the end of the preview. Sign up to access the rest of the document.

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.

Page1 / 8

ps2s_05 - MIT Department of Biology 7.014 Introductory...

This preview shows document pages 1 - 3. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online