PA Faculty Mini-Grant Submitted by John A. Means, Ph.D. Assistant Professor of Chemistry University of Rio Grande School of Sciences P. O. Box 500 Rio Grande, OH 45674 voice: 740-245-7165 fax: 740-245-7172 e-mail: jmeans@rio.edu

Purpose of this Proposal:

Many chemistry students have difficulty visualizing the structure of matter on the molecular level1 and in translating between three levels of thought – the macroscopic (the observable), the submicroscopic (the unobservable), and the symbolic (the chemical formulas that represent the submicroscopic).2,3 This is likely related to the abstract nature of the material. In order for students to make the connections between these three levels, it is necessary to employ stylized artwork in textbooks, models, and computer graphics. Studies have shown, for both high school chemistry and college General Chemistry students, that the use of computer-based molecular visualization can improve student spatial ability (the ability to visualize three-dimensional tasks when presented with a two-dimensional representation) and the learning of chemistry topics that are related to three-dimensional structures.4-6 In Biochemistry, the lack of spatial ability is even more debilitating to students because of the additional complexity of biological macromolecules, such as proteins and nucleic acids. Physical, three-dimensional models of large biological molecules have been incorporated into the discussion of proteins and nucleic acids in the Biochemistry class.7 There are obvious limitations with this method. First, the number/variety of molecules provided for the students' study would be limited. Second, the students would experience difficulty when attempting to closely inspect regions inside the structure of the molecules. Finally, physical models do not always present the most accurate picture of what is reality at the submicroscopic level. A number of computer visualization projects have been proposed for use in Biochemistry lecture and lab.8-16 These reports are all similar in that, at the termination of the project or course, the students were asked if the computer exercises improved their understanding of the material. In all of these cases, the students responded positively to these projects. However, none of these reports presented quantitative data to assess the contribution of the projects to student learning of the course content. The intention of this grant proposal is two-fold. The first objective is to obtain quantitative data to assess the contribution of computer-assisted molecular visualization to the students' understanding of biochemical structure. The second objective is to additionally obtain qualitative data (student questionnaires/surveys) in an attempt to correlate the students' responses with the quantitative data. In order to achieve these objectives, this grant proposes to purchase a customized Linux workstation on which free/open source visualization software will be installed for the biochemistry students to visually explore the structures of biological macromolecules. A customized Linux workstation will allow the students to maximize their visualization experience because of the breadth of molecular visualization software that is available for the Linux operating system and because of the hardware requirements for this software. In addition, a Linux workstation would play a key role in future undergraduate research opportunities involving computational chemistry/molecular modeling projects.

Investigative Process:

Employing molecular visualization projects that will be designed by the Biochemistry instructor, students will be guided through the investigation of three classes of molecules that are of structural interest in biochemistry – proteins, nucleic acids, and carbohydrates. Three different molecular visualization projects will be designed by the instructor, one project for each of the three classes of molecules. Prior to the introduction of protein structure in the class, students will be given a pre-test to determine their initial understanding of protein structure. The topic of protein structure will then be covered in class, followed by a post-test to measure student learning from the class presentation. Following this post-test, half of the students in the class will be assigned a molecular visualization project to further investigate the nuances of protein three-dimensional structure. Following this project, all of the students in the class will take a second post-test to determine what effect the project may have had on student learning pertaining to protein structure. In accordance with a previously reported approach, none of the questions on these tests will be identical, but the questions will be very similar such that they are of equivalent difficulty.4 Data will then be analyzed statistically to determine the effect of the molecular visualization project on student learning. After the second post-test, the protein structure project will be assigned for the remaining half of the students who did not initially participate in the project, so that all of the students have the opportunity to benefit from the molecular visualization experience. Molecular visualization projects will then be assigned for nucleic acids and carbohydrates, as each of those topics arise in the class. The effectiveness of the protein project for the remaining half of the class and of the nucleic acids and carbohydrates projects will only be evaluated based on the questionnaire/survey results. At the end of the semester, students will be given a questionnaire/survey to rate the effectiveness of all three of the projects and gain feedback for future improvements. As mentioned above, other projects involving proteins have already been reported.9,11-14 Aspects of each of these projects will be utilized in designing the project concerning protein structure, so that questionnaire/survey results can be directly compared with those previous reports. It will be necessary for novel projects to be developed by the instructor for the nucleic acids and carbohydrates topics, as no previous projects have been found for comparison. At the conclusion of the grant activities, the collected data – quantitative and qualitative – will be compiled and analyzed to determine viability for publication in an appropriate journal. The number of students enrolled in the class will be the primary consideration for publication viability. Regardless of the publication status, a summary of the findings will be submitted to SEOCEMS for inclusion on the website.

Phase I -Summary of Activities:

November 2008 • order Linux workstation December 2008/January 2009 • install molecular visualization software • develop molecular visualization projects for proteins, nucleic acids, and carbohydrates Winter semester 2009 • assign visualization projects • administer pre-/post-tests • distribute questionnaires/surveys May 2009 • analyze data collected from pre-/post-tests and questionnaires/surveys • determine viability for publication • submit written summary of findings to SEOCEMS

SEOCEMS Faculty Mini-Grant, $5,000

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Project Report and Conclusions