Study Questions for Exam 1

Study Question Set 3
Proteins 1 - Protein Secondary Structure


Chapter 6


1, 2, 4, 6a


Chapter 5




Chapter 6


1 - 6, 8, 10 - 14, 18



1, 2, 4 - 8, 12




"Topics" = "Topics for Discussion"
"Facts"     = "Do you know the facts?"
"Applying" = "Applying What You Know"

Additional Questions

  1. Do the "Biochemistry on the Internet" problem from Chapter 6 of Osgood and Ocorr (Problem 10). Familiarize yourself with the various protein databases available for determining protein sequence similarities (and hence possible homologies).
  2. What types of interaction(s) stabilize alpha helices?   Be complete.
  3. What types of interaction(s) stabilize beta sheets?   Be complete.
  4. In what ways might charged amino acyl residues affect alpha helix stability?
  5. Why are asparagine and serine found less frequently than methionine and glutamate in alpha helices?
  6. Why do valine and isoleucine occur more frequently in beta strands than in alpha helices?
  7. Explain why glycine would not occur frequently in alpha helical regions.
  8. Explain why proline would not occur frequently in alpha helical regions.
  9. Explain why proline would not occur frequently in beta strands.
  10. Explain why proline and glycine occur frequently in beta turns.   Be specific.
  11. Indicate the features that make the structure of collagen unusual.
  12. Try the following internet links for studying protein structure. These links require the "Chime" browser plug-in.   (See information about downloading Chime at home.)
    • Go to Professsor William McClure's tutoral at Carnegie Mellon University to examine various features of protein secondary structures at   You can select the various features you want to study by scrolling through the menu in the upper frame, or you can work through the turtorial on the right side of the lower frame.
    • You might also follow Professor McClure's link to a chime presentation of the collagen triple helix at .
    • Try some of the questions on protein structure at Professor McClure's website. I recommend Questions 1 - 4 of "Overall Architecture", Questions 1 - 7 of "Secondary Structure", and Question 7 of "Tertiary Structure & Side chains".
    • Professor Jason Kahn, at the University of Maryland, has provided two interesting web pages in Chime.
    • Professor Sears at the University of Californmia, Santa Barbara has some excellent tutorials, including this one on an alpha-helix in hemoglobin and other features of protein structure. Once you reach his web page at, select the Proteins tab.

Go to Study Question Set 4 - Proteins 2

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Last updated 1/17/2004


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