Part 2 This assumes you have already read chapter 4 Download and install the 3D
ID: 142941 • Letter: P
Question
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 tirst 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 lashing 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?Explanation / Answer
ANSWER-(3)
It is bad to have voids in a protein structure.
A good protein structure is compact protein structure with almost less internal voids. This gives a good score to the protein. It means the protein has adopted a confirmation with highest score. A well folded protein hides its hydrophobic residues inside the interior. This is lowest energy confirmation and given the highest score.
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ANSWER-(4)
If we had an X-ray vision we would see a relation between energy score and whether the protein tried this confirmation.
If the Energy score was higher it was more likely that the protein would try this confirmation.
If the Energy score was lower it was more likely that protein will not try the confirmation.
Since the Score is related to the folding of protein. A properly folded protein is given a high score and vice versa. Amino acid residues and their side chains have charges on them which interact with each other. These interactions help guide the folding process.
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