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 (Rgroups):
 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: 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)
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
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)
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.