Protein Modeling LabThings to check before the modeling lab:

Attach the amino end and the carboxyl end into your tubing.

Add the circle adhesives to your placemat. Attach placemat holders to the amino acid residual groups (R-

groups): Hydrophilic- yellow Hydrophobic-white Basic (+charged)-blue Acid(-charged)- red

Place the R-groups in the appropriate spot on placemat.

Take a picture of your placemat! Make sure you can clearly see which amino acid’s R-group is hydrophilic, hydrophobic, basic/acidic.

Protein Modeling Lab: PrimaryPurpose: Model the four levels of protein structure.

• Primary: create a sequence of 10 amino acids…- Two must be cysteines, - Two must be acidic- Two must be basic- Other four amino acids are up to your group… - Space them out evenly on your foam chain. Take a picture!Write a description of what occurs in this level and how it contributes to protein shape/folding.

Cannot remember your amino acid sequence based on your pic? Too small to see? Record the sequence on a piece of paper.

Due: Tuesday, Oct 14th! (mckay)

Protein Modeling Lab: SecondaryPurpose: Model the four levels of protein structure.

• Secondary: Create alpha helix coils and/or beta pleated sheets. Take a picture!Write a description of what occurs in this level and how it contributes to protein shape/folding. Compare/Contrast the formation of hydrogen bonds between the two. How do having coils and/or sheets suggest about your model protein’s function?

Remember, hydrogen bonds from these coils or sheets. And some proteins have both.

Due: Monday, Oct 13th!

Pleated Sheets

Protein Modeling Lab: TertiaryPurpose: Model the four levels of protein structure.

• Tertiary: Create disulfide bridge, salt bridge, and hydrophobic interactions.- Find your two cysteines, connect them together using the clear

connectors. This is a disulfide bridge.- Find your basic and acidic amino acids, connect them too. This is a

salt bridge. (Should be a total of two salt bridges)- All hydrophobic amino acids must now turn inward away from

water. Take a picture!Write a summary of what occurs in this level and how it contributes to protein shape/folding. How did these three interactions affect your protein shape/folding?

Is your protein looking weird yet?

Due: Tuesday, Oct 14th!(mckay)

Protein Modeling Lab: TertiaryPurpose: Model the four levels of protein structure.

• Quaternary: Time to pair up!- Find other group(s)! And link your polypeptide chains together. How many

subunits do you have for your protein? Take a picture! Write a summary of what occurs in this level and how it contributes to protein shape/folding. Based on your final protein structure, hypothesize what your protein’s function might be. Look at the general shape of your protein, what do you think it might do?

Multiple subunits are formed when they form hydrogen bonds among each other. Remember, not all proteins show a quaternary structure!

Please help welcome “Bucky” to the world of proteins.