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Problem Set #2

Problem Set #2 - 6 Are hydrophobic interactions important...

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Biology 100 Fall, 2009 Problem Set #2 due: October 12, 2009 The Protein Data Bank homepage on the World Wide Web is the epicenter of all things protein. First, visit MolVis.org and choose the Hemoglobin J-mol tutorial. When you’re ready, go to the MolVis homepage and load the Protein Data Bank file: 1D66. Take the Introduction tour to familiarize yourself with Jmol; click on the image, then try using your mouse wheel. (Optionally, you may download Protein Data Bank datafiles and view them with the standalone program RasMol or [for PCs RasTop ].) 1. What is described in the PDB datafile locator 1D66? (Be detailed and explicit.) 2. Does this structural file offer an example of quaternary structure? Why or why not? 3. How many primary polypeptide chains are present? What are the lengths of these chains in amino acid residues? 4. What protein secondary structural elements are present? How many of each? 5. What other biological macromolecule is present in this structure?
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Unformatted text preview: 6. Are hydrophobic interactions important for the protein’s structure? Where are these abundant? 7. Is the 1D66 protein an acidic protein, a neutral protein, or a basic protein? Why? (Try ‘Charge’ representation to help visualize this problem.) 8. Compare primary amino acid sequences for the proteins involved. What do you note? 9. Does this structure show ordered water molecules? How many? Where are they located? 10. Do the protein(s) involved have a prosthetic group(s)? If so, what? How much? 11. Are hydrophobic interactions important for anchoring this prosthetic group(s) to the host protein (also known as the apoprotein)? Please explain your conclusion. 12. Use your mouse wheel to zoom in. Which amino acid R-groups form a ‘coordination cage’ around these prosthetic group(s)? Number their positions in polypeptide chain(s)....
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