A 13‐week research‐based biochemistry laboratory curriculum

Abstract

Here, we present a 13-week research-based biochemistry laboratory curriculum designed to provide the students with the experience of engaging in original research while introducing foundational biochemistry laboratory techniques. The laboratory experience has been developed around the directed evolution of an enzyme chosen by the instructor, with mutations designed by the students. Ideal enzymes for this curriculum are able to be structurally modeled, solubly expressed, and monitored for activity by UV/Vis spectroscopy, and an example curriculum for haloalkane dehalogenase is given. Unique to this curriculum is a successful implementation of saturation mutagenesis and high-throughput screening of enzyme function, along with bioinformatics analysis, homology modeling, structural analysis, protein expression and purification, polyacrylamide gel electrophoresis, UV/Vis spectroscopy, and enzyme kinetics. Each of these techniques is carried out using a novel student-designed mutant library or enzyme variant unique to the lab team and, importantly, not described previously in the literature. Use of a well-established set of protocols promotes student data quality. Publication may result from the original student-generated hypotheses and data, either from the class as a whole or individual students that continue their independent projects upon course completion. © 2017 by The International Union of Biochemistry and Molecular Biology, 45(5):437-448, 2017.

Student Perceptions of Their Gains in Course-Based Undergraduate Research Abilities Identified as the Anticipated Learning Outcomes for a Biochemistry CURE

“…The findings of this study have shown that the PPI is an effective instrument for revealing changes in students’ perceived KEC with respect to key ALOs that focus on research abilities developed during the BASIL CURE. These are novel findings that complement other perception metrics (e.g., refs , , − , − , ) used to study CUREs that focus on general lab-related abilities rather than research abilities such as discovery and problem-solving. This is because the PPI survey reported here provides no information about students’ identity as a scientist, their satisfaction with the research experience, , their feelings of project ownership and perceptions of collaboration, their experiences with mentorship and resulting interest in research, , or their experience with communicating their findings .…”

“…[3][4][5]10 In this regard, when scientists explain mechanisms such as how proteins function, they use scientific reasoning about research methods and data to characterize what is known about the mechanism and how it works. 20,21 Thus, the current study could not be done using any of the methods reported in other published work such as to determine whether students selfidentify as a scientist, 22 if students were confident with laboratory techniques, 7,23 or if they are satisfied and benefit according to items ranging from "lab reports" to "knowledge of basic modern biochemistry laboratory techniques". 23 It was not our goal to compare student experiences between computational and wet-lab CUREs in terms of course satisfaction, 7,24 interest in research project, 16−18 or sense of achievement.…”

“…20,21 Thus, the current study could not be done using any of the methods reported in other published work such as to determine whether students selfidentify as a scientist, 22 if students were confident with laboratory techniques, 7,23 or if they are satisfied and benefit according to items ranging from "lab reports" to "knowledge of basic modern biochemistry laboratory techniques". 23 It was not our goal to compare student experiences between computational and wet-lab CUREs in terms of course satisfaction, 7,24 interest in research project, 16−18 or sense of achievement. 24 Nor was our study intended to measure differences between CURE and non-CURE lab courses based on students' perceived degree of project ownership, 25 or perceptions of collaboration, discovery and relevance, and iteration.…”

“…In the past, CURE curricula have primarily been evaluated by using various Likert-scale self-reported (perception) survey data as a rough indicator of CURE success. However, whereas typical survey items measure affective things like satisfaction, , interest, − experiences with mentorship, , communicating science, and general feelings of confidence, , our PPI study is instead focused on measuring students’ perceptions of their development of the scientific skepticism typically practiced when using data from research methods to make original claims about, in this case of BASIL, the function of proteins. − , In this regard, when scientists explain mechanisms such as how proteins function, they use scientific reasoning about research methods and data to characterize what is known about the mechanism and how it works. , Thus, the current study could not be done using any of the methods reported in other published work such as to determine whether students self-identify as a scientist, if students were confident with laboratory techniques, , or if they are satisfied and benefit according to items ranging from “lab reports” to “knowledge of basic modern biochemistry laboratory techniques” . It was not our goal to compare student experiences between computational and wet-lab CUREs in terms of course satisfaction, , interest in research project, − or sense of achievement .…”

A course‐based undergraduate research experience investigating the consequences of nonconserved mutations in lactate dehydrogenase

“…We plan to address this by maintaining a database of previous results and then providing this information at the outset of the CURE project for students to use as a starting point for their planned mutagenesis. In the future, classroom laboratories could focus on mutating a single nonconserved position to all amino acids using saturation mutagenesis and high‐throughput screening as illustrated by Lefurgy and Mundorff . Alternatively, this CURE could be adapted to approach a variety of different hypothesis‐driven avenues, such as exploring co‐evolving positions or potential allosteric sties in LDH or any other enzyme.…”