Molecular Visualizations in the High School Biology Classroom

Molecular Visualizations in the High School Biology Classroom

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.

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

1. “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.

2. “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.

3. “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.

The Lessons

Cholera Toxin

Instructions for Students

Protein Data Bank: Molecule of the Month

Over 100 Proteins With Detailed Descriptions!

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.

VMD Model

Example 1: Cholera Toxin, Danville High School biology student, 2006

Physical Model

Example 2: Dihydrofolate Reductase, Neuqua Valley High biology student, 2007

VMD Model Physical Model

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

VMD Model Physical Model

Example 4: Transcribing T7 RNA Polymerase, Neuqua Valley High biology student, 2007

VMD Model Physical Model

Example 5: Luciferase, Neuqua Valley High biology student, 2007

VMD Model

Physical Model

Example 6: Growth Hormone, Danville High biology student, 2008

VMD Model Physical Model

Example 7: ATP Synthase, Neuqua Valley High biology student, 2007

VMD Model Physical Model

VMD Model

Physical Model

Example 8: Alcohol Dehydrogenase, Danville High biology student, 2008

Example 9: Hemoglobin, Danville High biology student, 2008

VMD Model Physical Model

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.

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