Protein Folding Virtual Activity

Learning Objective:
Explain how a change in the subunits of a polymer may lead to changes in structure or
function of the macromolecule. (protein)

Website: https://learn.concord.org/resources/787/protein-folding
(You will have to create a free account.)

Setup:
● Make sure 3-letter codes are checked.
● Click on the hydrophobicity section and click on Charge and Hydrophobicity.
● Click on solvent type as Water.
● Generate a random protein
● Push play (at bottom)

Directions:
Use Amino Acid Chart at the end of the handout to answer questions 1-4.

1. What properties do the brown amino acids exhibit? Non-polar charge

2. What properties do the purple amino acids exhibit? Positive charge
3. What properties do the green amino acids exhibit? Polar charge
4. What properties do the pink amino acids exhibit? Negative charge

Use the simulation to answer the following questions.

5. Where do most of the brown amino acids congregate? Why? In the middle
because since they are non-polar, they don’t like to interact with water
6. Where do the green amino acids tend to be exhibited? Why? On the outer edge
because water attracts polar molecules
7. Why do purple and pink amino acids attract each other: Because a negative and
positive charges attract

Change in settings:
● Click on Generate random protein
● Click on All hydrophobic
● Push Play

TAKE A SCREEN SHOT

 8. What happened? Why do you think this occurred? All of the non-polar
molecules formed a ball in the middle. This is probably because these molecules
are mostly hydrophobic

Change in settings:
● Change water to oil

TAKE A SCREEN SHOT

 9. What happened? Why do you think this occurred? The previously ball that was
in water, spread a part in oil. This is because since the molecule is hydrophobic
(meaning it hates water), it spreads out and absorbs the oil.

Change in settings:
● Click Generate Random Protein.
● Click All Hydrophilic
● Click Water
● Push Play

TAKE A SCREEN SHOT

10. What happens? Why do you think this occurred? The molecule is trying to
dissolve into water and spread out
11. Why do some still cluster? They formed hydrogen bonds with water

Further Thinking:
12. What causes amino acids to fold in different patterns to form different looking
structures? Due to the change in pH

Research:
12. What would happen if you changed ONE amino acid in the primary chain?
- A different amino acid would be added into the chain instead of a normal one, so the
protein structure and function would change.
13. How would this affect its shape?
a. The protein’s shape will become dysfunctional
14. What type of bond occurs between two cysteines? What is its purpose?
a. Covalent bond, the hydrogen is removed and a bond is formed by the 2
sulfurs
15. What type of bonds occurs between the amino acids?
a. Peptide bonds
16. What type of bonds occurs between neighboring amino acids in a secondary
structure in creating alpha helices and beta pleats?
a. Hydrogen bonds
17. What type of bonds occurs in tertiary and quaternary structures to cause a
“globular” look?
a. Hydrogen bonds, disulphide bridges, and hydrophobic/hydrophilic
interactions