My report on "Protein Folding"
Student name: ************
Teacher name: ************
Date: Wed Nov 02 14:02:11 CST 2005
Page 1 : http://mw.concord.org/modeler1.3/part1/eric/proteinfolding2.cml
Snapshot caption : The positive and negative molecules wrapped around one another to create a large coiled amino acid.
Snapshot caption : The majority of the neutral molecules are on the outside of the large cluster. THe amino acid came together in a large circular cluster as before, but took a longer time to do so.
1. What shape did the protein fold into when the amino acids were half positive and half negative? Explain why it folded that way, describing the interactions of amino acids with each other.
The shape created was a circular cluster. The positive and negative molecules coiled around each other due to their charge.
Page 2 : http://mw.concord.org/modeler1.3/part1/eric/proteinfolding3.cml
1. Set the slider so that the blue molecules act like water molecules, then run the model. What happens to the purple hydrophobic molecules? Why?
When the blue molecules were polar they made the purple molecules move around more.
2. Once you have gotten the purple hydrophobic molecules to form clumps, set the slider to make the blue molecules non-polar. What happens? Why?
THe blue molecules whent they were nonpolar moved around more, causing the purple molecules to not clump together easily.
Page 3 : http://mw.concord.org/modeler1.3/part1/eric/proteinfolding4.cml
1. Run the model, and imagine you are one of the hydrophobic amino acids. What do you experience as the chain folds in water? Describe your interactions with other amino acids and with water molecules.
As an hydrophobic amino acid I gathered together with the fellow hydrophobic amino acids in a large cluster.
2. Click on "Hydrophilic amino acids" above, and run the model. Imagine you are one of the hydrophilic amino acids. Describe your interactions with other amino acids and with water molecules.
As a hydrophilic amino acid I, along with my fellow buddies, spread out so that we didn't cluster. We created a straight line.
3. Imagine you are one of the amino acids in the hydrophilic chain, first in oil and then in water. Describe your interactions with the solvent molecules in oil and then in water.
My reactions would be opposite. At first in the oil I clustered, then in the water I spread out creating a straight chain.
Page 4 : http://mw.concord.org/modeler1.3/part1/eric/proteinfolding5.cml
Snapshot caption : The molecules clumped together in a cluster.
Snapshot caption : The hydrophilic molecule was pushed to the outside of the clump while the other molecules continued to cluster.
Snapshot caption : The negative molecule changed the shape by having it lean towards the left instead of the upper right like model A.
1. How did your single substitution cause a change in the shape of the protein? Describe the substitution you made, including the properties of the amino acid you started with and the one you changed it into.
THe cluster did not clump nicely, infact it was more oval and spread out. I made one of the molecules negative.
2. How did you choose a substitution that caused only a small change in the protein's shape?
I made one of the molecules negative, which caused it to lean towards the left instead of the right.
3. Describe a rule for making a substitution that causes a change in the shape of a protein.
Make many molecular changes with charge to create the shape to change.
Page 5 : http://mw.concord.org/modeler1.3/part1/eric/proteinfolding6.cml
1. How many amino acids total make up one hemoglobin molecule?
My answer is (d)
2. How many amino acids in a sickle cell hemoglobin molecule are affected by the mutation?
My answer is (b)
Page 6 : http://mw.concord.org/modeler1.3/part1/eric/proteinfolding7.cml
1. You've seen two Hbs molecules stuck to each other. Imagine a third one randomly bouncing up to them. how could it get stuck on?
Hydrophobic pocket and beta 6 valines.A
2. Describe how a single amino acid substitution causes hemoglobin molecules to stick together. Use what you know about the structure of Hb and HbS, the properties of glutamic acid and valine, and how hydrophobicity causes molecules to behave in water.
A Single amnio acid must be polar to attract, just like water.
Page 7 : http://mw.concord.org/modeler1.3/part1/eric/proteinfolding8.cml
1. In the picture above, where would you expect to find a water-fearing, hydrophobic amino acid: at location A, B, C, D, E or F? Why?
F because it is the furthest away from all of the other molecules.
2. Which pair of amino acids in the picture above is more likely to have opposite charges: A and B, or C and D? Why?
C and D because opposites attract and the two are closer together than A and B.
3. All charged amino acids are hydrophilic. Why is this?
They are hydrophillic because they are positive and when something is positively charged, then they attract to water.
4. The single amino acid substitution in sickle cell anemia replaces glutamic acid with valine. What properties differ between these amino acids? Use the amino acid menu and color key, shown on the right.
Glutamic acid is negative and valine is hydrophobic.
5. Select two amino acids that could substitute for glutamic acid and, like valine, cause hemoglobin to form fibers.
My answer is (b) (d)
6. Select three amino acids that could substitute for glutamic acid and would not cause hemoglobin to form fibers.
(c) Aspartic acid
My answer is (a) (c) (e)
7. Choose one of the three amino acids you selected that would not cause hemoglobin to form fibers if substituted for glutamic acid. Suppose you are riding on this amino acid as it moves randomly toward another hemoglobin molecule. You are surrounded by water molecules. The hydrophobic pocket of the other hemoglobin comes near you. Do you stick to it? Describe why or why not, in terms of the interactions between your amino acid, the water molecules, and the hydrophobic pocket.
No I wouldn't stick to it because amino acids and water molecules attract, however not with hydrophobic pocket, since they "fear" water.
Page 8 : http://mw.concord.org/modeler1.3/part1/eric/proteinfoldingTOC.cml