Using JBC Articles in an Upper Level Biophysics Course
Box 1. Steps for Evaluating a Journal Article
1. What is the context of the paper?
2. What work by others is critical to the paper?
3. Identify three critical background references.
4. Summarize the big picture aspect of the work.
5. What is the central hypothesis being tested?
6. Identify preparative experiments.
7. What are the critical experiments that test the hypothesis?
8. Which is the most important figure in the paper?
9. What are the major conclusions reached?
10. What evidence are the major conclusions based on?
11. What is the reproducibility of the experimental data and how might this affect the conclusions that will be reached for each experiment?
12. What controls are used?
13. What are the potential pitfalls of the techniques used?
14. What is the next logical step suggested by the authors?
15. What additional experiments do these results suggest to you?
The challenges facing education in the molecular life sciences have been well documented (1–3). For a number of years, the biology community has advocated using primary literature (4–6), and much has been written about the effectiveness of journal clubs (7) or literature-based courses (8, 9). These courses are ideal for teaching both fundamentals and skills necessary for a major in biochemistry, molecular biology or biophysics.
For the past twenty years, I have taught a course with a significant component of primary literature to biochemistry and molecular biology majors. The course is called “Protein Structure, Function and Biophysics.” Usually, about half the students in the class have had physical chemistry, and the other half is planning to take it the following semester.
The course is divided into the following seven blocks, each two-weeks-long, with a focus on some aspect of structure, function and biophysics:
1. Protein structure: primary, secondary, tertiary and quaternary structure
2. Enzyme kinetics
3. Ligand binding
4. Fluorescence spectroscopy and its uses in biochemistry and biophysics
5. Protein folding, stability and flexibility
6. Structure determination (NMR or x-ray crystallography)
7. Computational approaches (either molecular dynamics or QM-MM approaches)
Each block consists of a two-week lab and the following four lecture sessions:
1. Introductory material: lecture and discussion
2. Discussion of primary literature: small group work and report
3. Quantitative aspects: problem sets, small group work and report
4. Laboratory wrap-up and discussion
Using Primary Literature
I usually assign a Journal of Biological Chemistry paper by Sayer et al., titled “Effect of the Active Site D25N Mutation on the Structure, Stability, and Ligand Binding of the Mature HIV-1 Protease” (10) as a follow-up to an HIV protease problem set that we developed (2). The students have to turn in a written report on the paper before Session 2 of each block using the steps in Box 1 (adapted from reference 11) as guidance.