Part 1: Amino acid properties.
Run the 2D protein simulation found at: https://learn.concord.org/resources/787/protein-folding, then answer the following questions.
Q1: Assuming the solvent is water, what rough shape will a protein entirely composed of hydrophobic residues be? How about a protein entirely of hydrophilic residues?
Q2: Given that proteins have to adopt a very specific 3D shape to be functional, would you expect the amino acid composition of a functioning protein to be mostly hydrophobic, mostly hydrophilic, or a mix? Why?
Part 2: This assumes you have already read chapter 4
Download and install the 3D protein folding game foldit, create an account, and play through at least the first 10 levels of the introductory puzzles. If you get frustrated, don't worry, you don't actually have to beat all the levels to complete the assignment.
https://fold.it/portal/
Q3: An important part of this "game" is packing amino acids to fill the flashing purple voids on the inside of the protein. Why is having voids bad? Think about what important class of molecules is notably missing from this simulation when you formulate your answer (hint, think about chapter 2).
Q4: In this game, the more realistic the protein shape, the better the "energy score" the player gets. In real life, proteins shuffle around different possible conformations without outside guidance until they find their native state, and this happens spontaneously. If you had X-ray vision and could see this happen, would you expect to see some trend between each conformation's "energy score" and the likelihood that the protein actually tries this conformation?
Part 1: Amino acid properties.
Run the 2D protein simulation found at: https://learn.concord.org/resources/787/protein-folding, then answer the following questions.
Q1: Assuming the solvent is water, what rough shape will a protein entirely composed of hydrophobic residues be? How about a protein entirely of hydrophilic residues?
Q2: Given that proteins have to adopt a very specific 3D shape to be functional, would you expect the amino acid composition of a functioning protein to be mostly hydrophobic, mostly hydrophilic, or a mix? Why?
Part 2: This assumes you have already read chapter 4
Download and install the 3D protein folding game foldit, create an account, and play through at least the first 10 levels of the introductory puzzles. If you get frustrated, don't worry, you don't actually have to beat all the levels to complete the assignment.
https://fold.it/portal/
Q3: An important part of this "game" is packing amino acids to fill the flashing purple voids on the inside of the protein. Why is having voids bad? Think about what important class of molecules is notably missing from this simulation when you formulate your answer (hint, think about chapter 2).
Q4: In this game, the more realistic the protein shape, the better the "energy score" the player gets. In real life, proteins shuffle around different possible conformations without outside guidance until they find their native state, and this happens spontaneously. If you had X-ray vision and could see this happen, would you expect to see some trend between each conformation's "energy score" and the likelihood that the protein actually tries this conformation?
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