January 2011

JBC in the Classroom: Selecting appropriate research articles to introduce undergraduate students to primary literature

In this special online-only article, Ben Caldwell explains how he uses a Journal of Biological Chemistry paper for a more in depth examination of trimeric G-proteins in a biochemistry II course.


Figure 1 clearly demonstrates the different elution profiles of the two proteins.

Reading primary literature is one of the essential skills undergraduate students need to learn and master. This takes a great deal of practice and certainly does not happen overnight. Unfamiliar jargon and methodologies can be frustrating for students, making finding journal articles at an undergraduate reading level challenging for many instructors. The unfortunate truth is that most scientific research articles simply are not written for novice readers. Identifying an appropriate article that is well written, readable AND content-rich for undergraduates is challenging.

For novice readers, articles need to be written clearly. (On the other hand, reading poorly written paper can also serve as a good example of how not to write). A reader needs to consider a number of questions while reading any research paper, and students need to build an awareness of these issues in addition to being knowledgeable about vocabulary, jargon and applicable methodologies. Students should be given this list of questions to consider:

1) What is the purpose of the study or the questions being examined?
2) What are the conclusions?
3) What are the bases for the conclusions, and are they supported by the experimental evidence?
4) Are the experiments presented in the article applicable to the question(s) being examined?
5) Are the conclusions reasonable based on the evidence or data?

One of the papers I particularly like to use is “Fluoride Activation of the Rho Family GTP-binding Protein Cdc-42Hs” by G. Hoffman et al. We use this article for a more in depth examination of trimeric G-proteins in our biochemistry II course. Although the work described in the paper is not  current by today’s publishing standards, G-proteins are an important area of ongoing research, and this paper provides a good example of a well done study of the factors required for association of the alpha-subunit of Rho family GTPases with their corresponding GTPase-activating proteins. More importantly, it is well written and relatively easy for students to read and comprehend. The article effectively demonstrates to students how a variety of seemingly unrelated experimental methods can be used in a complementary manner to provide supporting evidence. I like this particular paper because it presents the research questions methodically, and progressively moves through the data in a manner students can follow.

It should be noted that I provide the article to students initially without the abstract or the discussion sections so as not to provide the students with the authors' final conclusions. When BeF3-1 enters the paper there is usually a great deal of conversation about why the authors included this variation. Examination of the crystal structures of myosin and comparison of the binding data generated by the fluorescence anisotropy experiments usually leads to lively discussions about whether the BeF3-1 or AlF4-1 is a more true analogy of GTP in the active site. We often take three to four class periods to dissect the experiments, discuss the data and examine the crystal structures. By the time we are done, students generally have a good understanding of G-proteins and their co-factors and targets, as well as having reviewed some known methods and learned a few new techniques.

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COMMENTS:

It would be great if every issue of ASBMB Today had suggestions for papers for the classroom, as well as suggestions on best practices (discussion, clicker questions, etc.) for using research papers in the classes.

 

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