Molecular Visualizations in the High School Biology Classroom

1. Molecular Visualizations in the High School Biology Classroom Sharlene Denos1, Matthew Kirkpatrick2 , Kathryn Hafner3, and Shelley Barker3 1) Center for Biophysics & Computational Biology, University of Illinois at Urbana-Champaign, Urbana, IL. 2) Neuqua Valley High School, Naperville, IL. 3) Danville High School, Danville, IL What: Lessons which employ the powerful research tool VMD to teach high school students about biopolymers, protein structure and function, and molecular evolution. Where: Honors, regular and AP biology classes at public high schools in both high and low income districts Illinois. How: A UIUC graduate student, funded by an NSF fellowship, worked with local teachers to develop lessons relevant to her research and the course curricula.

2. The Lessons • “Visualizing Biopolymers & Their Building Blocks” • Students work in groups to answer questions about biopolymers and their building blocks by looking at their structures in VMD. • This is similar to what is commonly done with physical models in organic chemistry classes, but without the considerable cost of such models. • “Discovering the Structure of Your Favorite Protein” • Students choose a protein from the Protein Data Bank’s “Molecule of the Month” feature and learn about its structure and function. • Students load the molecule into VMD and use the “representations” menu to highlight features of their protein which are important for stability and function. • Students use their VMD model to build a 3-dimensional physical model from materials of their choice. • Students use their VMD and physical models to teach their class-mates and teacher about their protein. • “Proteins as Molecular Clocks” • Students choose a group of taxonomically related organisms (i.e. canines, trees, archeabacteria, etc.) and 3 proteins known to be present in all of the organisms (i.e. hemoglobin in higher animals, cytochrome C in bacteria, etc.). • Students use Multiseq to align protein sequences in the chosen organisms and build phylogenetic trees based on this alignment.

3. Instructions for Students Cholera Toxin

4. Protein Data Bank: Molecule of the Month

5. Over 100 Proteins With Detailed Descriptions!

6. Building a Protein Representation in VMD RNA Polymerase protein initially looks like this Students must build a representation like this, where the nascent mRNA, 2 DNA strands, and the protein are easy to distinguish.

7. Example 1: Cholera Toxin, Danville High School biology student, 2006 Physical Model VMD Model

8. Example 2: Dihydrofolate Reductase, Neuqua Valley High biology student, 2007 Physical Model VMD Model

9. Example 3: Green Fluorescent Protein (2 copies in one PDB file), Neuqua Valley High biology student, 2007 Physical Model VMD Model

10. Example 4: Transcribing T7 RNA Polymerase, Neuqua Valley High biology student, 2007 Physical Model VMD Model

11. Example 5: Luciferase, Neuqua Valley High biology student, 2007 VMD Model Physical Model

12. Example 6: Growth Hormone, Danville High biology student, 2008 VMD Model Physical Model

13. Example 7: ATP Synthase, Neuqua Valley High biology student, 2007 VMD Model Physical Model

14. Example 8: Alcohol Dehydrogenase, Danville High biology student, 2008 VMD Model Physical Model

15. Example 9: Hemoglobin, Danville High biology student, 2008 Physical Model VMD Model

16. Conclusions • Molecular visualizations can be integrated into the current high school biology curriculum • High school teachers and students are capable of manipulating molecules using VMD • VMD lessons help students “relate” better to biomolecules and provide a means for inquiry learning in classes typically dominated by lectures, memorization and multiple choice testing.

17. Acknowledgements • Shelley Barker, Kathy Hafner and the Danville High School biology students • Matt Kirkpatrick and the Neuqua Valley High School biology students • The National Science Foundation GK-12 Program • Klaus Schulten and the NIH Resource for Macromolecular Modeling & Bioinformatics at UIUC