First time at Proteopedia? Click on the green links: they change the 3D image. Click and drag the molecules. Proteopedia is a 3D, interactive encyclopedia of proteins, RNA, DNA and other molecules. With a free user account, you can edit pages in Proteopedia. Visit the Main Page to learn more.
Teaching Strategies Using Proteopedia
This page presents some ideas for how educators/teachers/professors might use Proteopedia in their teaching.
Use Existing Pages
Of course, you can use existing pages in Proteopedia. Be sure to consider those specifically designed for and by educators, which are listed at Teaching Scenes, Tutorials, and Educators' Pages.
Proteopedia pages can be projected during lectures (if you have an Internet connection in the classroom), and/or assigned to students as homework.
Author Your Own Pages
If you create your own pages, you will have scenes of the molecules that you are emphasizing in your teaching -- scenes that show exactly the structural features you wish to emphasize. See the Main Page for links to videos that show you how to author pages in Proteopedia. Customizing molecular scenes is amazingly easy with Proteopedia's Scene Authoring Tool.
Again, see some examples at Teaching Scenes, Tutorials, and Educators' Pages.
A low tech, but quick-to-prepare lesson plan involves distributing worksheets of questions regarding the molecular scenes on a particular Proteopedia page. These worksheets can be on paper, a web page (which could be on a page in Proteopedia), or within your local courseware system. Students in a computer lab can do such worksheets in class, concurrently, perhaps in pairs, which fosters discussion. The questions can be purposefully vague, to encourage discussion -- in which case completion could be simply "checked off" rather than graded in detail. Such worksheets give focus and a finite completion goal to each student. In contrast, simply assigning students to read a Proteopedia page may leave them less focused and perhaps uncertain about whether they have absorbed what you intend from the page.
Proteopedia has a mechanism to include quizzes on pages you prepare for your students. See Help:Quiz.
Molecular Structure: FirstGlance in Jmol
Every page in Proteopedia that is titled with a 4-character PDB code has a link to FirstGlance in Jmol. FirstGlance makes it easy to explore the molecular structure in more detail (and, like Proteopedia, it can use Java but also works without Java). FirstGlance reports the number of chains of protein, DNA, RNA, and lists all ligands and non-standard residues with their full names. You can click on any of these to find them. Sequences can be displayed and short sequences can be found. With one click each you can see secondary structure, amino and carboxyl termini, hydrophobic cores (two clicks, one to slice through the center with "Slab"), positive and negative charges, and much more. Tools locate disulfide bonds, salt bridges, cation-pi interactions, and non covalent bonds to any moiety you specify. Help and color keys appear automatically.
When students are given a worksheet or a list of suitable questions, FirstGlance provides an easy way to see answers. Here are 20 questions assigned to students in a workshop. These questions apply to any protein; each student chose a different protein to investigate.
Jaswal, O'Hara, Williamson and Springer (2013) describe in detail how they use Proteopedia, FirstGlance in Jmol and student-authored presentations about their structure-function analysis projects in a one-semester biochemistry course at Amherst College (Amherst, Massachusetts, USA).
Capturing Molecular Scenes in Powerpoint
Powerpoint (® Microsoft) or the free presentation software in OpenOffice make it easy to capture snapshots from Proteopedia or FirstGlance, and to record answers to questions. The resulting file can be presented in class and/or emailed to the teacher/professor for grading.
Instructions for making snapshots from FirstGlance (or Proteopedia) are linked to the bottom of the help panel in FirstGlance. In addition to static snapshots, rotating or rocking molecular scenes in Powerpoint slides can be generated with the free server Polyview-3D.
Student Authoring of Temporary Proteopedia Pages: Sandboxes
Some educators have assigned their students to try out authoring a Proteopedia molecular scene or two, just to learn the process, without making permanent pages in Proteopedia. Proteopedia has Sandbox pages where you or your students are invited to try authoring. The contents of these pages is not permanent, and will be erased or replaced at a later time.
One strategy is to assign a number to each student. For example, if a student is assigned number 17, that student uses the page titled Sandbox 17. A student assigned number N should enter Sandbox N in the search slot at the upper left of any Proteopedia page, and click on Go. If the page does not exist, there will be a red link on the resulting page. Clicking on the red link will create the page, which can then be edited.
If you want to protect a range of Sandbox page numbers for a specified number of weeks, so that your students need not worry about other Proteopedia users changing their pages, please contact in advance. See Help:Sandboxes for more information. There is always a safety net: the History tab on each page allows you to revert to an earlier version, even if the entire content was deleted and replaced.
How to assess completion of this assignment? One method is to require students to take a screenshot of their Sandbox N page, and convey it electronically to their professor (via email, in a Powerpoint presentation .ppt file, via courseware, etc.). If the block of Sandbox page numbers is still reserved, the professor can simply view each page directly. Putting the screenshot in e.g. a Powerpoint presentation has the advantage of making something tangible that the student can keep.
Student Authoring of Projects as Permanent Proteopedia Pages
Upper level undergraduates, e.g. biochemistry majors, or graduate students may be assigned to complete a project in the form of a permanent Proteopedia page. A particularly outstanding example, Photosystem II, was authored by Emily Forschler while she was a senior biochemistry major at Messiah College (Grantham PA US) in a class taught by Karl Oberholser.
Professor Oberholser reported "I think that Emily's work on Photosystem II shows that Proteopedia is a system that a Jmol novice can use with good effect. Emily had no experience with using Jmol. The other students in the class ... [made] PowerPoint presentations of their chosen proteins, and after seeing Emily's Proteopedia presentation one student's response was all of us should have used Proteopedia. Thank you for a great product!"
Another strategy for a small, upper level class is to have individuals or small groups author pages that address a particular topic. Ann Taylor has used this at Wabash College to create pages on Glycolysis Enzymes, Citric Acid Cycle and Proteins involved in cancer.
Any student planning to author a permanent page should request a personal user account in their own real name, identifying themselves as a student, and their college. See, for example, Emily Forschler. The pages for the project can then be created as subpages of an individuals user p|age (find out how to do that at Help:Protected_Pages). The use of the protected pages insures that the page will be editable only by the student and not subject to alterations possible for typical sandbox pages. The project could then later always be copied to standard Proteopedia page so others can improve it.
Ready To Use Resources
- Teaching Scenes, Tutorials, and Educators' Pages
- High school teachers' resources
- Understanding Science
How To Use Proteopedia
- Proteopedia:Primer for teachers.
- Proteopedia:Practical Guide to Advanced Proteopedia Authoring and Its Use in Teaching
- Help:Quiz: how to create quizzes in Proteopedia.
- How to Author Proteopedia Pages
- Molecular Scene Authoring Tools
- Movies Showing How to Author Proteopedia Pages
Use in Education
- ↑ Jaswal SS, O'Hara PB, Williamson PL, Springer AL. Teaching structure: student use of software tools for understanding macromolecular structure in an undergraduate biochemistry course. Biochem Mol Biol Educ. 2013 Sep-Oct;41(5):351-9. doi: 10.1002/bmb.20718. Epub, 2013 Sep 10. PMID:24019219 doi:http://dx.doi.org/10.1002/bmb.20718