30 Oct 2014

Bio-Organic Reaction Animations (BioORA)

Web Resources and Apps

Submitted by Steven A. Fleming, Temple University
Categories
Description: 

 

Bio-Organic Reaction Animations (BioORA) can be used as a teaching tool for bio-inorganic courses. BioORA illustrates large biomolecules obtained from crystal structures in the Protein Data Bank using Jmol. The student can manipulate this structure, which is shown on the right-hand side of the screen of BioORA. On the left-hand side of the screen a stripped-down view of the binding site is shown. This stripped down representation can also be manipulated and has three viewing options: ball and stick, tube, and space-filling. The software helps students visualize the three-dimensional aspects of enzyme chemistry. There are more than 25 animations and several of them have coordinating metals involved in the reaction mechanisms that are illustrated.

 

Learning Goals: 

 

BioORA is a visualization program for biochemistry that will focus on molecular events.  The natural tendency has been to substitute acronyms for the biomacromolecules.  This is an understandable result in light of the size of the relevant structures.  However, we have shown that computer imaging technology is sufficiently advanced now to handle animations of the actual molecules involved in the biochemical pathways.  This type of multimedia presentation can provide students with three-dimensional representations of the biomolecules and three-dimensional animations of binding and enzyme catalyzed reactions. 

 

Our goal is to bring the molecular aspects of biochemistry to the forefront.  The chemistry for the bio-organic processes is documented and the 3D visualization software is now accessible.  There is a need for more accurate molecular representation and we are eager to provide it.  We expect that students, regardless of their major, will benefit from this teaching tool.  We hope that it will improve student appreciation of the organic chemistry that occurs in biological systems. 

Evaluation
Evaluation Methods: 

Through interviews with faculty, focus group interviews, and student surveys, we have explored the following research questions: What are faculty perceptions of BioORA’s impact on student learning? What are student perceptions of BioORA’s impact on their own learning and understanding?

An inductive mode of analysis of qualitative data in which patterns and themes emerge let us discover the specific technical features of BioORA that the instructors and students found useful, as well as the ways in which BioORA increased student engagement and helped students with visualization skills, which both the instructors and students recognized as fundamentally difficult for novices in the fields of biology and chemistry. Additionally, analysis revealed similarities and differences between the perceptions of instructors and students. For example, the instructors emphasized BioORA’s function as a link between specific concepts or principles and the larger context of the class, as well as its function as a link between lectures and lab sections, organic chemistry and biochemistry, what students learn in class and their future work in science, and the individual steps within the reaction.

See: 

“Faculty and Student Perceptions of Student Learning and Experiences with a 3D Simulation Program” Gunersel, A. B.; Fleming, S. A.; J. Chem. Ed., 2013, 90, 988-994.

“Bio-Organic Reaction Animations (BioORA): Student Performance, Student Perceptions, and Instructor Feedback” Gunersel, A. B.; Fleming, S. A.; Biochem. Mol. Biol. Ed., 2014, 42, 190-202.

Evaluation Results: 

 

See:

“Faculty and Student Perceptions of Student Learning and Experiences with a 3D Simulation Program” Gunersel, A. B.; Fleming, S. A.; J. Chem. Ed.201390, 988-994.

“Bio-Organic Reaction Animations (BioORA): Student Performance, Student Perceptions, and Instructor Feedback” Gunersel, A. B.; Fleming, S. A.; Biochem. Mol. Biol. Ed.201442, 190-202.

Creative Commons License: 
Creative Commons Licence

Comments

This tool is really fun to use and very helpful. It shows the size of macromolecules versus the one of active sites, how the molecules move around and interact with each other. I can see now how all those arrows in orgo actually look like on actual molecules. Also, the recorded voice helps reading the dry information more engageable somehow. Overall, *five star* 

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