Download Protein Structure Determination and Design

Empowering Teachers Through Modeling
Assignment 3: Protein Structure Determination and Design
Name:
Date:
Answer each of the following questions below.
Part I: Protein Structure Determination Methods.
1. What are the four steps of X-ray crystallography as identified by the video found at the following
link:
http://pdb101.rcsb.org/teach/biomolecular-structures-and-models/learning-materials
1. ______________________________________________________________
2. _______________________________________________________________
3. _______________________________________________________________
4. _______________________________________________________________
2. How is cryo-EM different from X-ray crystallography? Why would you use this method?
3. Go to the PHET simulation for NMR at the following link:
http://phet.colorado.edu/en/simulation/mri
What frequency setting is used to get the following elements to emit if the field is set at 2.50 Tesla
and the power is at 50%?
Carbon-13 ______
Hydrogen ______
4. What is the advantage of NMR over cryo-EM or X-ray crystallography?
Nitrogen ______
Part II: Model Design Practice.
1. Open one of your selected PDB file structures in Jmol.
2. Change the background color to white.
3. Display and color the alpha carbon backbone of your protein model.
4. Highlight the secondary structures in your protein model.
5. Practice saving your model as a JPG.
6. Practice saving your script file.
7. If time allows, practice with your other two selected PDB files.
Reading Assignment:
Teaching for Conceptual Understanding in Science
Chapter 3: pages 39-54
Choose one “golden line” from the reading (a statement that really resonates with you). Identify the
page number and write the statement below. Be prepared to explain why you chose it.
Page Number:
Golden Line: