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- 1. What are the effects of a) amino acid composition and sequence and b) intramolecular and intermolecular forces of attraction to protein folding? 2. What molecular property of amino acids can be used to justity the concept that the "molecular part of the protein can exhibit the same property as the molecular 'whole' (protein molecule?). Provide a comprehensive discussion using one molecular property. 3. Discuss two metabolic disorders which are caused by protein misfolding. Explain the metabolic consequence of the disorder. 4. If a non-science person asks you what protein folding is and how the concept is related to metabolic disorders, how are you going to explain the concept? (please summarize the concepts used, thank you!)11. Below is a folding energy funnel describing folding energy landscape of a protein. The width of the funnel indicates the entropy of the protein, and the height corresponds to the free energy. A) If A is the native fold structure, which state is a molten globule? How does this state differ from A in term of structures. B) Does this protein have multiple folding pathways or just one? C) which state has the lowest free energy? D) According to the width of the funnel, the native state B of the protein has the lowest entropy. If the protein fold A spontaneously to this state, does it violate the 2nd law of thermodynamics? Why or why not? (Hint: in the folding funnel, only the entropy of the protein alone is considered). E) Does the native state also have the lowest enthalpy. What makes the enthalpy decrease as the protein folds? 12. List four methods by which a protein can be denatured and briefly describe how these methods act to disrupt protein structure.17. Protein folding results in a large decrease in entropy since a polypeptide is now constrained and more ordered. However, what counterbalances the loss of entropy associated with protein folding?
- 9. A) Please write down the names of the following protein folds. A B C B) Which one(s) is made of more than one polypeptide? D E 000 C) Give an example of a protein containing the motif in C and explain how the structure of this motif facilitates function. 10. What is Levinthal's paradox? Describe the paradox and explain the conclusion to which it led.4) For various amino acid pairs (for example: F to A, E to R, D to N, V to L, S to W), ask yourself: a) Based on what you know about the chemical properties of the side chains, what effect would you expect on the stability of the protein if you mutated one residue of the pair into the other in the interior of the protein? What forces might have an impact on this change (ie: what types of interactions would you expect that amino acid to be involved in?) How would your answer change if the amino acid were located on the surface of the protein? b) c)29. In sickle cell anemia, a hereditary disease, there is substitution of one amino acid by another in one of the four polypeptide chains of hemoglobin. In this case are all of the structural levels of the protein modified?
- 36. Which of the following is true? A. All proteins possess primary, secondary, tertiary and quaternary structure B. Proline is the least common amino acid in alpha-helices due to its inability to fully participate in intrahelical hydrogen bonding C. Once denatured, proteins cannot be renatured or restored to the native state D. The subunits of oligomeric proteins are always identical 37.The pka's of the side chain group and the alpha-carboxyl group of glutamate are 4.1 and 2.1, respectively. Which statement accounts for this difference? A. The side chain has more resonance structures B. The alpha-carboxyl group has less steric hindrance and it is therefore ionized more easily C. The side chain is a different functional group than alpha-carboxyl group D. The alpha-carboxyl group is closer to the alpha-amino group than the side chain is E. None of the above2. 3. Where in your cell can you find the instructions for how to make all of the proteins?*1. What is the isoelectric point (pI) of lysine which has pKa values of 2.1 for the α carboxyl group, 9.7 for the α amino group and 10.5 for the side chain amino group? 2. Which of the following is most likely to be found on the exterior of a protein? A) Pro B) Trp C) Ser D) Glu 3. The type of reaction that forms a peptide bond is A) Elimination B) Hydrolysis C) Nucleophilic substitution D) Condensation
- 1. Draw three-dimensional representations of the following amino acids. Explain theirstructures.(a) L-phenylalanine(b) L-histidine(c) D-serine(d) L-tryptophan3. A. Briefly discuss the four levels of structure in proteins. Knowing that the 3-dimensional shape of a protein is important to its function, discuss on a qualitative basis whether the changes below will likely alter the function of a protein, justifying your answer with why or why not. B. What would happen to a protein's functionality if a serine residue were replaced with threonine? C. What would happen if serine were replaced with leucine? D. What would happen if serine were replaced with cysteine? E. What would happen if aspartic acid were replaced with tryptophan in the part of the protein (an enzyme) that serves as an active site to catalyze a reaction? F. What would happen if aspartic acid were replaced with tryptophan in a non-active site?. Assume that some protein molecule, in its folded native state, has one favored conformation. But, when it is denatured, it becomes a "random coil," with many possible conformations. (a) What must be the sign of AS for the change: native → denatured? (b) How will the contribution of AS for native → denatured affect the favorability of the process? What apparent requirement does this impose on AH if proteins are to be stable structures?