This project was prepared as part of a BioQUEST faculty development workshop entitled BioQUEST 2004 Summer Workshop for Undergraduate Faculty: Systems Biology at Beloit College in June 2004. The BioQUEST Curriculum Consortium is committed to the reform of undergraduate biology instruction through an emphasis on engaging students in realistic scientific practices. This approach is sometimes characterized as an inquiry driven approach and is captured in BioQUEST's three P's (problem-posing, problem-solving, and peer-persuasion). As part of this workshop groups of faculty were encouraged to initiate innovative curricular projects. We are sharing these works in progress in the hope that they will stimulate further exploration, collaboration and development. Please see the following links for additional information:
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Tools presented in the problem space can be used for in-class projects in introductory biology classes. More complex questions could be carried from introductory biology to more advanced biochemistry, molecular biology and evolution classes. Undergraduate students could also use this as a starting point to develop independent research projects.
Prions are infectious protein particles associated with various neurodegenerative diseases in humans and animals. This problem space introduces basic skills in protein structure and sequence exploration that can be used to analyze some unusual properties of prions, and develop testable hypotheses that can be explored through these tools. Students will be challenged to use a systems-biology approach to link structure, evolution and function of proteins.
Power Point Presentation: Prion Problem Space: Mad cows, itchy sheep and protein structure?
1. GeneDoc software for sequence analysis from http://www.psc.edu/biomed/genedoc/
2. CN3D structure visualization and analysis software from NCBI http://ncbi.nih.gov/Structure/CN3D/cn3d/shtml
3. ProParam tool for calculation physical parameters of protein sequences http://ca.expasy.org/cgi-bin/protparam.
4. http://www.mad-cow.org - online collection of various experimental results, visualization models, and stories about BSE (NOT peer-reviewed, but with links to many published articles. Also not updated since April 2001.)
5.http://www.cyber-dyne.com/~tom/yeast.html Abstracts and references for articles about yeast prions.
6.Helical wheel creation software http://bioinf.man.ac.uk/%7Egibson/HelixDraw/helixdraw.html
7.PrP and Doppel sequences http://receptors.ucsf.edu/Prion/seq/002/002.SEQ.html.
8.List of some (Q/N) repeat-rich proteins http://receptors.ucsf.edu/Prion/seq/003/003.html
We plan to impliment this activity in two classrooms this academic year.