Bio 3055 Bioinformatics Lab
About Bio 3055
This curriculum was created to accompany an introductory biochemistry course for sophomore undergraduate students. The entire computer activity takes approximately 10 hours of student time and was written to span five 2-hour sessions.
Accompanying lectures should include explanations of amino acid structure and the one-letter code, protein sequence alignments, BLAST searches, protein structure, and X-ray crystallography.
At Washington University, students using this curriculum have already studied molecular biology (DNA → RNA → protein) and Mendelian genetics. The activity is designed to help students to understand the link between genotype and phenotype, and to develop an appreciation of 3-D protein structure, while gaining an introduction to bioinformatics tools.
Funding provided by Howard Hughes Medical Institute. © 2005 Washington University in St. Louis.
Principles of Biology III Bioinformatics Lab
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, ten projects on ten 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 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 NCBI website (BLAST, LocusLink, OMIM, GenBank, and PubMed) as well as ExPasy, Protein Data Bank, ClustalW, the 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.
Although the goal of providing an inquiry-based experience for students is difficult to assess, the comments on our post-course survey showed that many students felt the lab gave them a better idea about the ways in which scientists approach problems and share information through literature and web-based databases. The independent projects succeeded in helping students focus on a single research problem and develop an interest in that problem. The oral and written reports gave students a chance to practice their skills in communicating scientific information. Finally, the collaborative nature and group work in the lab gave students opportunities to both defend their ideas and learn from their peers.
The pre/post test and questionnaire results showed that students gained substantial knowledge about accessing and using web-based tools and databases. It is important to note that these tools were presented and used at a basic level in this lab in order to facilitate introduction of several types of commonly used databases and tools in a short amount of time. After taking this lab, students have a general understanding of the vast amount of genetic information that is freely available on the web, and we hope that this lab experience will encourage students to seek opportunities in upper-level courses to learn more about this new area in biology. There are several small, upper-level biology courses at WU for students to choose from that provide a more advanced use of bioinformatics tools.
1 Bednarski, A.E., Elgin, S.C.R., and Pakrasi, H.B. An Inquiry into Protein Structure and Genetic Disease: Introducing Undergraduates to Bioinformatics in a Large Introductory Course, Cell Biol. Edu, fall 2005.