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.
The Lessons
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.
Instructions for Students
Cholera Toxin
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.
Example 1: Cholera Toxin, Danville High School
biology student, 2006
VMD Model
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
Example 8: Alcohol Dehydrogenase, Danville
High biology student, 2008
VMD Model
Physical Model
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