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. 2005 Fall;4(3):207-20.
doi: 10.1187/cbe.04-07-0044.

An inquiry into protein structure and genetic disease: introducing undergraduates to bioinformatics in a large introductory course

April E Bednarski  1 , Sarah C R Elgin, Himadri B Pakrasi
Affiliations

An inquiry into protein structure and genetic disease: introducing undergraduates to bioinformatics in a large introductory course

April E Bednarski et al. Cell Biol Educ. 2005 Fall.

Abstract

This inquiry-based lab is designed around genetic diseases with a focus on protein structure and function. To allow students to work on their own investigatory projects, 10 projects on 10 different proteins were developed. Students are grouped in sections of 20 and work in pairs on each of the projects. To begin their investigation, students are given a cDNA sequence that translates into a human protein with a single mutation. Each case results in a genetic disease that has been studied and recorded in the Online Mendelian Inheritance in Man (OMIM) database. Students use bioinformatics tools to investigate their proteins and form a hypothesis for the effect of the mutation on protein function. They are also asked to predict the impact of the mutation on human physiology and present their findings in the form of an oral report. Over five laboratory sessions, students use tools on the National Center for Biotechnology Information (NCBI) Web site (BLAST, LocusLink, OMIM, GenBank, and PubMed) as well as ExPasy, Protein Data Bank, ClustalW, the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, and the structure-viewing program DeepView. Assessment results showed that students gained an understanding of the Web-based databases and tools and enjoyed the investigatory nature of the lab.

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Figures

Figure 1
Figure 1. Distribution of student majors in the Bioinformatics lab Spring 2004. *No response
Figure 2
Figure 2. Students working in the Bioinformatics computer lab
Figure 3
Figure 3. Students presenting their oral reports
See this image and copyright information in PMC

References

    1. Altschul S.F, Madden T.L, Schäffer A.A, Zhang J, Zhang Z, Miller W, Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. (1997).;25:3389–3402. - PMC - PubMed
    1. Andersen O.A, Flatmark T, Hough E. Crystal structure of the ternary complex of the catalytic domain of human phenylalanine hydroxylase with tetrahydrobiopterin and 3-(2-thienyl)-L-alanine, and its implications for the mechanism of catalysis and substrate activation. J. Mol. Biol. (2002).;320:1095–1108. - PubMed
    1. Anderson A, Basilevsky A, Hum D. Measurement: theory and techniques. In: Rossi P, Wright J, Anderson A, editors. Handbook of Survey Research. New York: Academic Press; (1983).. pp. 231–287. In:
    1. Bednarski A, Heyse D, Pakrasi H. The course webpage for Biology 3055 at Washington University in St. Louis. (2004).. http://www.nslc.wustl.edu/courses/Bio3050/bio3055.html (accessed 2 May 2005).
    1. Berg J, Tymoczko J, Stryer L. Biochemistry. New York: WH Freeman and Company; (2002)..

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