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CHE 380: Principles of Biochemistry  

Last Updated: Mar 26, 2014 URL: Print Guide RSS Updates

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Protein Paper

Due date:  Friday, April 11 @ 5 PM

  • Upload to the course site.
  • Each day late is a 10% penalty!

Paper Requirements

  • Minimum 5 pages, double spaced.
  • Minimum three peer-reviewed research articles.
  • References:  ACS style (use EndNote and Cite While You Write).
  • Create three to five figures using PyMOL.
  • Refer to your assignment hand-out for more on:
    • Writing style
    • Figures
    • References

Assignment Handout


Paper Contents

What do you need to include in your paper?  Read the following carefully!

1. Background information on the protein.

·       What is the function of the protein? (What reaction does it catalyze?)

·       To which class of enzymes does your protein belong?  (Explore the 4 digit EC number for full classification.)

·       Why is the protein of interest?

·       Does this protein have uses beyond normal cellular function (laboratory technique, industrial catalyst, etc.)?


2. Structural information on the protein from the PDB entry

·       Discuss important elements of the 1°, 2°, 3°, and 4° structure. (In some cases, you may need to state that your protein has no 4° structure.)

·       Are ligands a part of the structure? What is their function?

·       Incorporate the primary reference from PDB page into your report in your discussion of the protein structure.

·       Is there more than one entry for your protein in PDB? Why? How do they differ from the entry you were assigned?


3. What is the relationship of the molecular structure to the function of the protein?

·       Describe specific molecular interactions (hydrogen bonds, electrostatic bonds, hydrophobic interactions) that are important for the protein’s function. Show figures of these interesting interactions with PyMOL figures.

·       Clearly articulate the importance of the interactions for the protein’s function.


4. What current research is being done on your assigned protein? 

·       What have mutagenesis studies revealed about your protein’s function?

·       Have there been any in vivo studies?  What is their significance?

Subject Guide

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