Department of Chemistry, Indiana University, 800 E. Kirkwood Ave. Bloomington, IN 47405. afeig@indiana.edu
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On the whole, I was pleased with the level of student achievement I observed during Fall 2001. The attitude of the students toward learning this year was dramatically better than that I experienced during the first rendition of this course. The difference in student perceptions led them to be more receptive to the teaching methods I employ. Having applied themselves harder over the course of the term, it is no wonder that they achieved a higher level of proficiency and moved beyond the level of factual recall often expected of these students. Their ability to independently find and analyze information through on-line databases has been commented on by the professor teaching C485, second semester of the biochemistry sequence.
This term was the first time I taught the full C484 curriculum and I am using a new textbook relative to last year when I team-taught the course. Furthermore, it is dramatically different from previous versions of the course in that catabolism has been removed from the first semester and transferred to C485, the companion course. On the whole, the syllabus worked pretty well. The removal of catabolism allowed a much more relaxed and detailed treatment of several key topics like protein structure and enzyme mechanisms.
The shift to Garrett and Grisham was very well received by the students. The level of the textbook is excellent for the way I wish to teach this course. In addition, the textbooks web site complements the site I have developed for C483. For instance, the publisher's site for Garrett and Grisham has Chime based web pages for every protein mentioned in the book providing an easy way for the students to access the exact material from the text in a format amenable to more independent student exploration of these structures. Overall students preferred this text to Voet and Voet although there were a few students who commented on the evaluations that they thought Garrett and Grisham was too superficial. Voet & Voet as well as 3 or 4 other biochemistry texts are kept on reserve for use by any students who want different perspectives on these topics.
Student satisfaction with the bioinformatics exercises has improved dramatically since the first implementation of these assignments. The incorporation of questions at the end of the assignments to force the students to think about and interpret their data has been very beneficial. Having used the exercises before, I also now know exactly where specific problems might crop up and can try to forewarn students and avoid frustration with some of the idiosyncrasies that accompany specific unknowns.
Plans for future improvements
Hindsight is extremely useful. Below are several observations regarding improvements that I will incorporate when I teach this course Fall 2002.
Whereas the syllabus was dramatically better than previously, there were still some minor problems. The main issue was that, in spite of having expanded the time allotted to several of the topics, I still fell behind. I dropped several topics from the curriculum on the fly, some of which I will not even schedule in next year (such as G-proteins and trans-membrane signaling). One topic, Ribozymes and Abzymes (discussion 36) was also misplaced on the syllabus. This mistake became clear as the discussion approached and I recognized that the students had not seen some of the concepts I generally discuss together with this topic and they must first be introduced with proteins. I therefore moved it to Discussion 42 on the fly. It will be after enzyme mechanisms in future syllabi.
Many students still have trouble thinking about protein architecture at the end of the protein structure unit. Currently, we talk about protein topology by doing a few simple examples as part of a class discussion. I will convert this discussion to a small group exercise to make sure that everyone in the class participates more fully as it is a very important concept. I will also add to the problem set an assignment in which the students have to draw a topology sketch of their unknown protein.
The instructions on how to use Protein Explorer were first written in fall 2000 and have only undergone relatively minor updating since then. Last summer, Protein Explorer was upgraded to version 2b which has many new features. Before the instructions are used again, they need to be updated to incorporate the relevant changes in the program.
The overlay of the multiple sequence alignment onto the 3-D structure is a really powerful visualization tool. In version 1 of Protein Explorer, the students had to do this exercise manually and the students this fall continued to do it by hand. A new feature of PE version 2b is a script called MSA3D which allows one-step superposition of the alignment on the structure. This script will shorten the length of time it takes the students to perform the manipulations necessary to get the output and hence allow them to spend more time analyzing their data. The instructions have to be modified to show the students how to use this excellent feature of Protein Explorer 2b.
Right now, the bioinformatics exercises work well here at IU in part because I have spent time figuring out how to help the students work through their computer problems and hence keep their frustration level at a minimum. Implementation of these exercises at other universities might face some hurdles and require a significant investment of time by the local instructor. The broad dissemination of these exercises for use in other classroom settings would be facilitated by conversion of these projects into a tidy web-page format where students can log in to work on the assignments. In this way, other instructors can select which parts of the projects their students perform and have all of the necessary pieces (instructions, web links, assessment questions, etc.) in one place. In addition, better assessment tools can be placed in the background to monitor how students use the pages.
Several students complained that problem set 5 took substantially longer than previous assignments. After more detailed probing, it turns out the main difficulty was in the use of graphics programs to plot experimental data with which they were provided. The students were given a head start with Excel in the form of a downloadable Excel spreadsheet and instructions to help with non-linear least-squares curve fitting in excel. In spite of having instructions to contact the AI or me regarding specific questions of the type, “How do I do _______ in Excel?”, very few students approached us. Next year, I will institute an out of class recitation section lead by the AI to teach Excel 101 to alleviate some of these frustrations. The students all use Excel in the General Chemistry Lab freshman year, but there is a clear problem of knowledge retention here.