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A Redesigned Undergraduate Biochemistry Lab
Author(s) -
Mills Jeffrey L.,
Hart Kaitlin,
Thurnherr Emily,
O'Handley Suzanne F.,
Bernstein Herbert J.,
Craig Paul A.
Publication year - 2016
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.30.1_supplement.880.8
Subject(s) - in silico , curriculum , undergraduate research , function (biology) , theme (computing) , computer science , computational biology , medical education , biochemistry , chemistry , biology , psychology , medicine , genetics , world wide web , pedagogy , gene
The need for a significant improvement in undergraduate STEM education has been broadly recognized. The primary purposes of this project are to (1) improve understanding of the process of training students to be effective scientists, (2) test the hypothesis that “undergraduate students can characterize proteins of unknown function as the central theme of their biochemistry teaching laboratory”, and (3) that actually doing hypothesis‐driven experimental science is a useful tool in training students to become an experimental scientist. We have incorporated authentic inquiry into an undergraduate biochemistry lab course. Students at RIT are combining computational ( in silico ) and wet lab ( in vitro ) techniques as they characterize proteins whose three‐dimensional structures are known but to which functional annotations have not been assigned. Following an initial pilot phase at RIT during the Fall 2015 semester, our curriculum will be implemented at five additional campuses (California Polytechnic, Hope, Oral Roberts, St. Mary's, and Ursinus). The feasibility of the proposed characterization protocols has already been successfully tested in an undergraduate research setting at RIT and Dowling College. Our students have used an internally developed program, ProMOL, to compare over 3000 PDB entries with “unknown function” against a library of known enzyme active site motif templates and have found 64 “good hits”. At the beginning of the semester, students selected one of these good hits and characterized it further with ProMOL and other well‐established in silico methods, such as DALI, Pfam, and BLAST. Following initial bioinformatics characterization, well‐established in vitro techniques for protein expression, purification, and validation of activity have been used. As this new curriculum is focused on research and discovery, it is reasonable to expect some of the students to produce novel results that will contribute to the field of structural biology, both as publications and as annotations to structural biology databases such as the Protein Data Bank. Support or Funding Information This project is supported by NSF IUSE 1503811.