Start the Protein Investigator.

Consider the protein arg-arg-arg-arg.

Based on the simplifications described previously, predict how this protein would fold. Sketch your predicted folded protein below.

Build the protein using the simulator in the Lab 6 Page in your course.

Does the actual folded shape match your prediction? If not, make sure you understand why it didnt and draw it correctly.

Consider the protein phe-phe-phe-phe.

Based on the simplifications described previously, predict how this protein would fold. Sketch your predicted folded protein below.

Build the protein using the simulator in the Lab 6 Page in your course.

Does the actual folded shape match your prediction? If not, make sure you understand why it didnt and draw it correctly.

Consider the protein phe-arg-arg-arg-arg-phe.

Based on the simplifications described previously, predict how this protein would fold. Sketch your predicted folded protein below.

Build the protein using the simulator in the Lab 6 Page in your course.

Does the actual folded shape match your prediction? If not, make sure you understand why it didnt and draw it correctly.

Consider the protein ile-phe-met-gln-ser-arg-thr-asp-ala-ala. (IFMQSRTDAA).

Based on the simplifications described previously, predict how this protein would fold. Sketch your predicted folded protein below.

Build the protein using the simulator in the Lab 6 Page in your course.

Does the actual folded shape match your prediction? If not, make sure you understand why it didnt and draw it correctly.

Suppose a mutation in the gene for this protein caused the Arg in the middle (amino acid #6) to be replaced by a Glu. How might this effect the shape of the protein? Sketch your prediction below.

Make the mutant protein. The mutant protein is: ile-phe-met-gln-ser-glu-thr-asp-ala-ala (IFMQSETDAA). Does the actual folded shape match your prediction? If not, make sure that you understand why it didnt.

Consider a different mutation, one that causes the same Arg (#6) to be replaced by an Ile. The mutant protein is: ile-phe-met-gln-ser-ile-thr-asp-ala-ala (IFMQSITDAA). What happens to the shape now?

Make a mutant protein that has Asn instead of Gln. (IFMNSRTDAA) What is the effect on the shape? Why do you think this is?

Make a mutant protein that has Val instead of Arg. (IFMQSVTDAA) What is the effect on the shape? Why do you think this is?

What type of bond is critical in the protein formed from the amino acid sequence ala-arg-asn-asp-his (ARNDH)?

The importance of this bond can be demonstrated by mutating one of the amino acids so that the new sequence is ala-arg-asn-lys-his (ARNKH). What happens? Why?

What type of bond is critical in the protein formed from the amino acid sequence arg-arg-asn-arg-tyr (RRNRY)?

The importance of this bond can be demonstrated by mutating one of the amino acids so that the new sequence is arg-arg-gly-arg-tyr (RRGRY). What happens? Why?