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Protein Modeling Lab

Protein Modeling Lab. Things 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

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Protein Modeling Lab

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  1. Protein Modeling Lab • Things 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.

  2. Protein Modeling Lab: Primary • Purpose: 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)

  3. Protein Modeling Lab: Secondary • Purpose: 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

  4. Protein Modeling Lab: Tertiary • Purpose: 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)

  5. Protein Modeling Lab: Tertiary • Purpose: 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.

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