Protein Folding Virtual Activity 1
Protein Folding Virtual Activity 1
Protein Folding Virtual Activity 1
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.
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
Change in settings:
● Change water to oil
Change in settings:
● Click Generate Random Protein.
● Click All Hydrophilic
● Click Water
● Push Play
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