4: Exploring the Effect of Amino Acids on Protein Structure.
1. Designate each student as a type
of amino acid. Indicate who represents one
of the amino acids that cannot form alpha helix coils (make it
about 10% of the class). Make
most of the students represent coil-capable amino acids.
2. Have the students form a
long chain by holding hands. Put the students who cannot form
coils together at one end of the line. Students that represent non-coiling
amino acids should turn and face the opposite direction of the
3. It is not possible to duplicate
alpha helix coils, but you could have the students representing
coil-capable amino acids to form little recurrent loops in their
4. Now represent tertiary folding by having the line
fold back on itself (you could do this with the first third
and last third of the line). Have them make note of their "structure."
Note where the non-coiling segment is.
You might even want to sketch it out on the blackboard.
5. Now represent the effect of changing
the amino acid sequence on the coiling and folding. Shuffle
the position of students so they can get a feel for how many
different ways they can combine to make a chain and how that
affects the overall conformation of the protein.