PDB EDUCATION CORNER: Margaret A. Franzen, Pellissippi State Technical Community College

Margaret Franzen earned her Ph.D. in Biological Sciences from Northern Illinois University. Since 1997, she has been at Pellissippi State Technical Community College, where she teaches general biology, genetics and microbiology. In addition to covering course content, her teaching focuses on developing analytical thinking skills and exposing her students to the process of science. A number of her students have presented papers at collegiate meetings of the Tennessee Academy of Science. She recently won the Innovations in Teaching award at Pellissippi State and was a finalist in the Wiley Life of the Classroom innovative teaching competition in 2005. She has presented papers in state and national science education forums relating to the use of physical models and hands-on learning in the college classroom. Currently she is developing teaching materials for use with visually impaired, learning disabled and kinesthetic learners.

Located in the beautiful Tennessee Valley between the Cumberland and Smoky Mountains in Knoxville, Tennessee, Pellissippi State serves over 7000 students on four campuses in both rural and urban settings. In addition to providing continuing education courses, the college offers two-year career and technical degrees as well as coursework for transfer to four-year institutions. Pellissippi State offers inexpensive educational opportunities to a diverse student body in small classrooms that permit excellent student-student and faculty-student interactions.

Background

I teach a sophomore-level college genetics course for biology majors as well as pre-vet and pre-med students. In the past few years, I have modified my syllabus to focus more on the relationship between the structure and function of proteins, as well as bioinformatics tools available on the Internet. This article will briefly outline the activities I use in the classroom as well as the independent research projects that have developed as an offshoot of the course. The article will conclude with an overview of a bioinformatics activity that incorporates RasMol analysis of protein structure and physical models to study insecticide resistance that was developed as part of a National Science Foundation (NSF)-funded project.

A few years ago, the bulk of my genetics course was on Mendelian, transmission and population genetics; I emphasized regulation of gene expression, and only briefly addressed the nature of mutations. Students could define mutations but they never understood the relationship between the structure and function of a mutant protein.

In 2003 I participated in a summer workshop conducted at the Center for Biomolecular Modeling of the Milwaukee School of Engineering (CBM MSOE), where I discovered the value of a handheld physical model as a teaching tool. I also was exposed to RasMol, an elegant but compact computer program developed by Roger Sayle for manipulating protein coordinates.[1] Although RasMol doesn't have the 'point and click' features of some newer protein visualization programs, this program has the advantage of forcing students to think about what they are trying to do instead of simply pushing buttons to discover the effects on the visual appearance. Early exposure to RasMol also better equips our students for organic chemistry, which utilizes RasMol as a study tool.

Genetics Course

Early in the semester, I introduce my students to the Online Mendelian Inheritance in Man (OMIM) website.[2] As we discuss various genetic diseases or as they ask questions, I refer them to the website to discover the details of the diseases or the mutations that cause disease. By exploring, they learn that a mutant phenotype can often be caused by more than one mutation, sometimes involving completely different proteins. They also discover that mutations at different locations within the same gene can result in different diseases (e.g., thalasemia and sickle cell anemia).

After students have learned the basic commands of RasMol, I have them pick a protein that is related to an altered human phenotype. Many of the students start at David S. Goodsell's Molecule of the Month features at the RCSB PDB site, where they learn about the normal functioning of the protein. They also utilize OMIM to learn more about genetic diseases related to their selected protein. Next, they are asked to design a model in RasMol that depicts the important features of the protein. This process forces the students to think about how the structure relates to the function of the protein. Students then post the PDB file, the RasMol script file they authored, and a paragraph describing the protein on a course discussion board within WebCT. The entire class is then able to visit the class 'protein gallery' to learn of multiple structure/function relationships.

Independent Study Projects

A number of students have taken a real interest in exploring protein structure in greater detail. These students have enrolled in an independent research course that is modeled after the SMART teams, described in an earlier Education Corner article (Spring 2003). The significant differences in the program are that the college students work individually rather than in teams to study a protein, and physical models are not always constructed at the completion of the project. Each student begins by locating the protein (often in various forms) in the PDB. After searching through the structure summary and sequence details of the various forms of the protein, students obtain copies of the original research papers as well as more recent articles by the primary investigators. Typically the depth of these articles is well beyond the background of the students, but they are able to make sense of the papers by using RasMol to highlight the features discussed. I encourage students to read the articles as though they were mastering a new language – by grasping the meaning of the unknown words from their context and immersing themselves in the papers. After a couple of readings of the papers in this fashion, students have grasped enough information to do a literature search on their protein, quickly ascertaining whether the articles are applicable to the features they want to study. I find that Google Scholar is a very useful tool for obtaining original articles. After digesting these articles, students are ready to interact, either directly or through email, with the original researchers. Although this step is not always possible (depending on the availability and interest of the researcher), it is incredibly beneficial for the students to discover 'how far they have come' in digging into a research topic. Next the students decide which features of the protein they want to demonstrate in their visual and, if possible, physical models. This requires a lot of playing around with RasMol and going back to the papers to verify details. At the conclusion of their work, students demonstrate their accumulated knowledge of the protein in a presentation at the collegiate meeting of the state science association. Students participating in the independent research project gain confidence in their ability to tackle 'real' science papers and communicate with others. Most are interested in science as a career before enrolling in the course, but are turned on to the possibility of doing research as a result of the program.

Insecticide Resistance Activity

This exercise was developed in conjunction with Dr. Tim Herman (CBM MSOE) and Dr. David S. Goodsell (The Scripps Research Institute) as part of an NSF Undergraduate Education (DUE) grant (#0442409). The activity incorporates both bioinformatics and analysis of protein structure (using PDB files) to determine the nature of insecticide resistance in mosquitoes. Many insecticides target the enzyme acetylcholinesterase, which breaks down the neurotransmitter acetylcholine in cholinergic junctions. Students repeat the work of Weill et al. [3] in determining the differences in acetylcholinesterase isolated from insecticide sensitive (S) and resistant (R) strains of the mosquito Culex pipiens. First they compare the DNA sequences of S and R strains, and then translate the sequences and align the protein sequences. Students discover a number of silent mutations, typically due to changes in the third position of the codons. There is only one amino acid difference (a Gly to Ser mutation) between the two strains! Optionally, students can also align a series of twenty-nine S and R strains (all posted at NCBI) to show that there is only one mutation that is consistently found in all resistant strains and none of the sensitive strains. Students then access acetylcholinesterase structures from the PDB to determine the location of the amino acid change. Working with RasMol, Jmol images, and physical models, students determine how the mutant enzyme can break down the substrate yet does not respond to inhibitor. One student's response to the exercise was, "I never realized that one carbon could make such a big difference." This activity is currently being developed as a Waksman Challenge for high school students, and physical models will be available from the MSOE Model Lending Library in the near future. This exercise allows students to relate much of what they have learned in the course of the semester to a practical application, thus reinforcing their understanding while also exposing them to useful research tools available on the Internet.

Links


A physical model of the acetylcholinesterase active site from CBM, with removable substrate and inhibitor molecules, as well as interchangeable glycine and serine residues for insecticide sensitive and resistant enzymes, respectively.

References

  1. Sayle, R. and E.J. Milner-White, RasMol: biomolecular graphics for all. Trends Biochem. Sci., 1995. 20: p. 374.
  2. Wheeler, D.L., et al., Database resources of the National Center for Biotechnology Information. Nucleic Acids Res, 2005. 33(Database issue): p. D39-45.
  3. Weill, M., et al., Comparative genomics: Insecticide resistance in mosquito vectors. Nature, 2003. 423: p. 136-137.