Lesson Plans for Molecular Visualization

All of these lesson plans require that your students have access to computers where they can use Protein Explorer or other Chime-based tutorials. If not, in some of the plans below, you could project the molecular images while having students complete worksheets. Of course, that requires that you have a projector and at least one computer.

Contents

  I. One-Molecule Tutorial + Worksheet (without Protein Explorer)

If you have emphasized a single particular molecule in your class, and you don't have the time for Protein Explorer, here is a good lesson plan.

  1. Choose an appropriate on-line Chime-based tutorial dedicated to your single molecule by visiting the World Index of Molecular Visualization Resources, www.molvisindex.org. Downloadable tutorials on DNA structure, hemoglobin, lipid bilayers and channels, antibody, major histocompatibility are available from MolviZ.Org.
  2. Hand out a worksheet of questions on paper, and direct your class to answer the questions by exploring the on-line tutorial you specify.
  3. Optional: Have groups/students exchange their answers and check each others' work. Or have students form groups and compare their answers in group discussions. (Disputes or issues they aren't sure about should be referred to the teacher.)
  4. Optional adaptation: A modified form of this plan is to assign different molecules (hence different on-line tutorials) to different groups in the class. Then you can have each group report their results to the class orally (optionally, with projected computer graphics as illustration).
  Here are some things to consider about this lesson plan:
  1. The number and difficulty of questions can be tailored to your class and the time available.
  2. The questions can be answered by small groups, or individual students.
  3. The questions give each group/student concrete goals, benchmarks for their progress, and a clear gage for completion. Without the questions, regardless of how excellent the on-line tutorial, these features are usually missing (since few on-line Chime-based tutorials provide questions).
  4. The questions can be generic (suitable for all molecules, see example below), or specific to the particular molecule. Obviously, the latter case requires at least partially different sets of questions for each molecule.
  5. If you do not have fast and reliable Internet access, some tutorials can be downloaded for off-line use. If downloading is not offered by the tutorial in question, email the authors and ask them to send you a copy for off-line use along with instructions for installation.
  6. A few tutorials are available in both English and Spanish (or other languages), and the number is growing. Check the Non-English section of the World Index of Molecular Visualization Resources.
Here are some tutorials that provide lists of molecule-specific questions ready to print or adapt to your class. If you write questions for your class, to accompany an on-line Chime tutorial, we would very much like to put your questions on the web and link the questions to the tutorial (at molvisindex.org). If you are willing to have your questions "published" on-line in this way (crediting your authorship of course!), please send the questions by email to Eric Martz (emartz@microbio.umass.edu), mentioning the URL of the tutorial for which they were written. We are particularly interested in having sets of questions for popular molecules such as hemoglobin and DNA.

  II. Protein Explorer + Molecule + Worksheet.

Each lesson plan for Protein Explorer (www.proteinexplorer.org) has two parts.

  1. Have your students do the 1-Hour Tour to learn how to use Protein Explorer. This Tour takes at least one hour; two hours is better. It is best if you can lead them through the Tour in a computer lab, but if a lab is not available, you can assign them to do it individually. (There is a prominent link to the 1-Hour Tour at the FrontDoor page of Protein Explorer at proteinexplorer.org. A printed copy of the Tour is very helpful.)
  2. Have each group/student pick a molecule from a pre-selected list (or assign one). A starter list is below.
  3. Apply Protein Explorer to a problem. The problem can be handed out on paper. Below are suggested problems.
Most of the things to consider listed above apply here as well. Protein Explorer is downloadable for off-line use, and has been translated into Spanish (see link at the top of the FrontDoor).

  Pre-selected molecules.

  Questions & Worksheets for Applications to Problems.

Discovery in Protein Explorer is a generic list of questions suitable for any molecule. Answers are not provided here, but can be worked out by the teacher, if desired, for the subset of molecules assigned to the students. There is a separate page of hints on how to use Protein Explorer to answer each question. Whether you provide the hints to your students is optional.

Finally, there is the Tutorial linked at the FrontDoor (under About Protein Explorer). It has fallen considerably behind the capabilities of PE, but may be useful as far as it goes. This is an extensive tutorial designed for college students. Completion of the entire tutorial, including the study questions, requires over twelve hours of work.

Bioinformatics Laboratory for Biology 100 (at the University of Massachusetts, Amherst) is a lesson plan that invites students to compare sequences of two proteins (from a short, pre-selected list), explore and compare their 3D structures, and visualize their evolution using the ConSurf server. This lesson plan was developed by Steve Brewer.

 
III. Student Assessment of Learning Gains from Protein Explorer

If you use Protein Explorer in your course, at the very least, please tell me by email! emartz@microbio.umass.edu I and the NSF would like to know!

Also please consider using the free, customizable Student Assessment of Learning Gains (SALGains) website for on-line feedback from your students. Alternatively, you can hand out a set of questions on paper. For details, see Student Assessment of Learning Gains from Protein Explorer. Assessment results from you and your students will help determine development priorities and future funding for Protein Explorer!

  IV.A. "Incorporation of Bioinformatics Exercises into the Undergraduate Biochemistry Curriculum"

Feig, Andrew L., and Evelyn Jabri (July 2002) Incorporation of Bioinformatics Exercises into the Undergraduate Biochemistry Curriculum. Biochem. Mol Biol. Ed. 30:224-231.

The project course websites are chemlearn.chem.indiana.edu/c483 and chemlearn.chem.indiana.edu/c484.
For a reprint, contact afeig@indiana.edu.
Since the paper was published, the student exercises have been made available in HTML as well as PDF, www.indiana.edu/~c484/afeig/bioinformatics.htm.

In this highly recommended article, Feig and Jabri describe "an open-ended, inquiry-based ... integrated set of exercises based on pet proteins ... applicable to either a lecture or laboratory format ....". Their goal is "to introduce junior/senior level undergraduates to some of the common computational tools used by biochemists." The pet enzymes (provided on-line) have been selected as commonly encountered in biochem courses and textbooks, have published 3D crystal structures, and are present in the KEGG and OMIM databases. A sequence of five projects is described, in which each student pursues their assigned protein:

  1. Two fragmentary peptide sequences are given to each student (different for each student), and BLAST searches at NCBI are used to identify each unknown protein.

  2. Finding additional information about each enzyme with ExPASY, NiceZyme and NiceProt, with KEGG for a friendly source of metabolic maps, and with OMIM for human heritable diseases involving each protein.

  3. Finding, manipulating, and understanding the 3D structure from the Protein Data Bank. This section exploits Protein Explorer and Chime The authors prefer to teach their students some Chime controls and commands to enable their students to use a diverse range of Chime sites. To this end they have written their own short introductory tutorial (available on-line).

  4. Students align the sequences of their protein from several different organisms using ClustalW. The alignment results are used to identify conserved patches, typically catalytic sites or key regulatory sites, using ConSurf (which is integrated with Protein Explorer).

  5. Enzyme kinetic data available from the BRENDA database are analyzed.
The authors use writing assignments that are marked, returned and then revised by the students to facilitate achieving an in-depth understanding. The article includes practical guidance for educators and pitfalls to avoid at each website employed.

  IV.B. "Lesson Plan for Protein Exploration in a Large Biochemistry Class"

Honey, David W. and James R. Cox (Sept/Oct 2003) Lesson Plan for Protein Exploration in a Large Biochemistry Class, Biochem. Mol. Biol. Ed. 31:356-366.

Prof. Cox teaches macromolecular structure partly by having students search for noncovalent interactions with Protein Explorer. In small classes, students give oral presentations. This paper describes his approach to a class with an enrollment of 50-60 students. Students are given a series of assignments investigating the structure of proteins and protein complexes, along with questions they are required to answer. This paper details lesson plans and question sets for a series of three assignments. The questions are challenging, such as "List and describe four ionic interactions", or "Find a serine residue forming a hydrogen bond with a water molecule" or describing the bonds holding GMP into an enzyme. In some cases, students are asked to decide whether a particular pair of sidechains is significantly bonded, and to defend their decision.

  IV.C. "Exploring Protein Function and Evolution Using Free Online Bioinformatics Tools"

Weaver, Todd. and Scott Cooper (Sept/Oct 2005) Exploring Protein Function and Evolution Using Free Online Bioinformatics Tools Biochem. Mol. Biol. Ed. 33:319-322.

This article describes a protein structure exercise within a bioinformatics course at Univ. Wisconsin-La Crosse, taught to about 40 students twice a year. This exercise is allocated 6-8 h in class (computer laboratory) plus homework. The software employed is Biology Workbench, Protein Explorer, and ConSurf. Students are assigned an amino acid sequence, and asked to make predictions about functional motifs, secondary structure (noting differences obtaine with different programs), hydrophobic and transmembrane regions. Students are then asked to assess the accuracy of the preditions, including secondary structure predictions assessed with an empirical 3D structure in Protein Explorer. Finally, students explore conservation in multiple sequence alignments between orthologs and paralogs, and examine conserved or hypervariable patches in the 3D structure. Seventeen proteins are listed that work well for this exercise. Online materials are provided.

Send lesson plan feedback to Eric Martz.