Biology 63, Molecular Biology..... About the Molecular Tutorial Assignment

For a description of the course, back to syllabus

For a schedule of lectures and assignments, back to course outline

To be turned in on October 7:
  1. A proposal describing the macromolecule/s that are to be the subject of your tutorial. The proposal should be ~1 page in length, and should describe the interesting features of the system you wish to build your tutorial on. Relevant references should be included!
  2. One or more *.pdb files in your pdbs folder in the p:\class\biology\biology63\yourname\folder. The *.pdb file/s should contain the atomic coordinates of the molecule/s that are the subject of the proposal in 1.
  3. One or more RasMol/Chime scripts that affect the pdb/s in 2. The script/s should be suitable for inserting into a tutorial. The script/s should include a move command, a select command, commands that highlights particular structures, and a rotate command, at a minimum.

Weeks of November 9th and 16th: individual meetings with DM
During these weeks, you must make one appointment for a 1/2 hour conference with me to go over your progress to date. You should use this opportunity to ask me questions, discuss problems, and to present a rough draft of your tutorial, even if this is only an outline with ideas for important scripts. You may see the schedule for appointments by visiting the appointment page, picking a time, and e-mailing DM an appointment time (username: marcey). First-come, first-served!

To be turned in on December 19 (by 4:30 PM!):

  1. Copies of all primary research papers used in tutorial construction, with relevant passages underlined or highlighted.
  2. A folder in the bio63 directory (p:\class\biology\biol63\) with your name on it that contains a fully-functioning tutorial.
  3. A copy of the above folder on a floppy disc/s.

This assignment involves the construction of a web page to illustrate aspects of the structure-function relationships for a particular central dogma molecule of your choice. In creating a tutorial to teach your colleagues about the structural intricacies of a particular molecule, you will learn alot (the goal of this assignment), not only about the molecule you have chosen, but also about general principles of macromolucular structure. Your tutorial must include at least one reference from the primary research literature describing the structure of the molecule at high resolution (< 3 angstroms). Good source journals in the Olin library for papers describing macromolecular structure are Nature, Science, Nature Structural Biology, Cell. Other recommended journals include Protein Science, RNA, ect.

The Brookhaven National Laboratory's Protein Data Base (PDB) contains a comprehensive collection of molecules for which structural data is available. The downloadable *.pdb files are text files containing the atomic coordinates of particular molecules. You may search this database at:

To produce a desired tutorial, you must learn three skills:

To view an example of a tutorial of this type, visit the pol III beta tutorial at http://www.kenyon.edu/depts/bmb/chime/poliiib.htm. This is an assignment you should start early in the semester.

DM will holdtwo hands on demonstrations of the techniques used to build the tutorials (9/22 & 10/1 - common hour, Crawford). In addition, those wishing one-on-one instruction will be able to make appointments to begin learning the necessary scripting commands. If you have no HTML experience, it is strongly advised that you attend several of the PILR workshops on HTML held at the library. Please stop by the library for PILR workshop schedules.

The following links will help you learn and use each of the three tools needed to build a macromolecular tutorial: