Students often struggle to understand protein folding and the biochemical interactions that lead to the different levels of protein structure. In order to make this concept more concrete for students, the free program called Jmol can be used to visualize the 3D structure of a protein.
By guiding students step-by-step though the commands necessary to highlight important features of protein structure, they will be able to use this powerful tool without any background knowledge of the Jmol program or its commands. Teachers are encouraged to look into the various capabilities of the program in order to troubleshoot student questions; there are several reference pages online that can be found fairly easily with a Google search. However, the assignment includes all commands necessary to view the proteins.
Jmol can be downloaded for free at www.jmol.org and does not require installation. For use in the classroom, downloading the program to a network drive that students can access is an easy way to get everyone working.
This assignment includes an exploration of primary, secondary, tertiary, and quaternary levels of protein structure, with an optional extension activity that focuses specifically on enzymes. It was designed for a freshman-level honors biology class, but would also be helpful as a refresher for AP/IB Biology.
This activity can be completed in 2-3 50 minute class periods.