Ideas for Lessons Employing 3D Molecular Visualization
- Illustrating Lectures
- Existing tutorials, or any molecule loaded into the
can serve to illustrate lectures. Students can review the illustrations
at home, or in computer labs.
If you show arbitrary molecules loaded into the
web page of links for your class
which brings up these
When illustrating lectures, Don't forget to
move your molecules
early and often!
You may be familiar with the
3D structure of the molecule you are showing, but it is all new to your students.
Forgetting to move the structure often enough is a common
pedagogic mistake -- it makes the molecule go "flat". The students can't
see its 3D structure without rotation.
Each segment of your molecular visualization presentation should
answer a question. The question and the answer should be explicitly
- Questions on Paper
- Hand out questions on paper, and assign your students
to answer them while viewing a particular tutorial. This can be done
during a scheduled computer lab, or as homework. The questions give
the students focus and a defined and limited set of goals while going
through the tutorial images. Sets of questions, ready to print and
hand out, are provided with the tutorials on
Major Histocompatibility Complex. If you
write such questions for another tutorial, please email them to
me so they can be posted
- Amino Acid Quizzer
- Assign each student or group a sequence number, or range of numbers,
and ask them to identify the corresponding amino acids using the
Amino Acid Quizzer. Ask them to
tell whether the amino acid(s) are hydrophobic, polar, or charged, and which
are at the amino and carboxy termini.
- Structure Analysis
- Assign your students to explore a molecule in the
Protein Explorer. Ask them to write a description of the secondary
structure, distribution of hydrophobic sidechains, active site, or other
features you have covered in class. Optionally, have each student or
group show their molecule to the class.
- Sequence to Structure
- Assign each student or group a short nucleotide sequence. Ask them
to translate it to the amino acid sequence, then use
to find the protein containing this sequence. Then ask them to view the
3D structure of this protein, describe where in the 3D structure
the sequence segment fits, and the function of that segment.
Gary Harris, Wellesley College, Wellesley MA.)
ready-to-assign exercise is offered by Charles Sackerson, Iona
College, New Rochelle NY. A sequence is given, with instructions for
finding the molecule with BLAST. Next, using BLASTX, the six possible
translated amino acid sequences are obtained and matching proteins
are listed. Disease associations are noted. The molecule is then searched
for at the PDB, and the 3D structure viewed in Chime.
Feedback to Eric Martz.