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?

The brown amino acids are all exhibiting nonpolar hydrophobic properties.
2. What properties do the purple amino acids exhibit?
The purple amino acids are exhibiting positive charges.
3. What properties do the green amino acids exhibit?
The green amino acids are exhibiting polar hydrophilic properties
4. What properties do the pink amino acids exhibit?
The pink amino acids are exhibiting negative charges

Use the simulation to answer the following questions.

5. Where do most of the brown amino acids congregate? Why?

Most of the brown amino acids congregate in the center away from the water because
they are nonpolar and do not like water.
6. Where do the green amino acids tend to be exhibited? Why?
The green amino acids are generally on the outside of the protein because they are
hydrophilic and polar and are attracted to water.
7. Why do purple and pink amino acids attract each other?
The pink and purple amino acids are attracted somewhat to the water but also to
themselves because the pink are negative and the purple are positive and opposites
attract. Also, since the water has partial charges, they are attracted to the water.
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?

The amino acids are crowded together to the center. That is because the amino acids
are hydrophobic and afraid of water, so they immediately moved to the center to get
away from the water.

Change in settings:
● Change water to oil
9. What happened? Why do you think this occurred?
The amino acids spread out and stopped being attracted to each other. This happened
because the oil is nonpolar like the amino acids and the amino acids are no longer
afraid of the water solvent, causing the amino acids to spread out in the oil.

TAKE A SCREEN SHOT

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 amino acids spread out again, although some are still attracted to each other. That
is because the amino acids are polar and attracted to water, so they want to get close to
the water, thus spreading out.
11. Why do some still cluster?
Some still cluster because there are also charged amino acids in the hydrophilic amino
acid, since charged amino acids are attracted to the partially charged water. Some
cluster because the charged amino acids are attracted to each other due to their full
charges.

Further Thinking:
12. What causes amino acids to fold in different patterns to form different looking
structures?
The bonds and properties of the amino acids cause the different patterns that form
different structures.

Research:
12. What would happen if you changed ONE amino acid in the primary chain?
Depending on what the amino acid was changed to, there might have a serious effect,
little effect, or no effect.
13. How would this affect its shape?
If there is no effect, nothing will change. If there is little effect, something minor changed
in the shape(that might go on later to do serious damage). If there is a serious effect,
the shape would be completely different and create a different function for the different
structure.
14. What type of bond occurs between two cysteines? What is its purpose?
Disulfide bonds occur between two cysteines. It’s purpose is to stabilize the 3-D
Structure
15. What type of bonds occurs between the amino acids?
Amino acids form peptide bonds, which are covalent bonds between the amine group
and carboxyl groups of different amino acids.
16. What type of bonds occurs between neighboring amino acids in a secondary
structure in creating alpha helices and beta pleats?
Hydrogen bonds occur between amino acids in a secondary structure in creating alpha
helices and beta pleats.
17. What type of bonds occurs in tertiary and quaternary structures to cause a
“globular” look?
Some bonds that can occur in tertiary and quaternary structures are Van der waals
bonds, ionic bonds, and covalent bonds depending on the R side group.