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This activity is designed to help students visualize how amino acids are strung together to create a protein and how the sequence affects the protein conformation.

None are essential, but it might help to have little tags that students can wear to indicate what kind of amino acid they represent.

Activity 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 other students.

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 line up.

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.


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