Adapting a Course-Based Undergraduate Research Experience into Independent Student Research Projects at a Small Liberal Arts College

Abstract

The Biochemistry Authentic Scientific Inquiry Lab (BASIL) project is a Course-Based Undergraduate Research Experience (CURE) deployed at multiple colleges and universities throughout the United States. This biochemistry laboratory curriculum has students use bioinformatics and biochemical techniques to determine the function of a given protein structure. Due to the needs of my particular institution, I am implementing this experience as independent student research projects instead. In this curriculum, students focus on a specific protein structure in the Protein Data Bank without an assigned function. They visualize the proteins with PyMOL, perform sequence and structural alignments with BLAST, Pfam, Dali, and ProMOL, and explore potential substrates with PyRX and Autodock Vina. A putative enzyme function is then established and potential substrates are identified. After purification and expression of the protein, students use p-nitrophenyl substituted substrate analogues to perform colorimetric enzyme assays; enzymatic hydrolysis of the substrate analogue liberates p-nitrophenol, which can be monitored using spectroscopy. Adapting this curriculum into independent student research projects has been a successful means of bringing collaborative bioinformatics research to a small, primarily undergraduate liberal arts college. A CURE requires that the laboratory experiences, while authentic, can be undertaken by undergraduate students who can only devote a few hours a week to the project. These requirements line up well with the research activities possible at a small college. The BASIL modules have been utilized with the research students similarly to their use by course-based students, and we seek to also assess research students’ learning. The BASIL project aims to provide both consistency in curricular materials and flexibility in implementation style for different institutions. Feedback about interest in using or adapting this curriculum is welcomed and encouraged.