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- 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)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.3a) The 3° structure of a protein refers to the protein's overall, 3-dimensional shape in space. This will incorporate any 2° structure the protein has, but is predominantly the result of side-group interactions. Name the type of interaction, if any, that you would expect to see under physiological conditions (an aqueous solution at pH 7.0-7.5) between the following pairs of amino acid side groups. Serine and asparagine: Methionine and lysine: Glutamate and aspartic acid: Alanine and phenylalanine:
- 1. In the Procedure, you were instructed to use your original mixture of phycocyanin and 0.10 M sodium phosphate buffer as your reference solution because the buffer stabilizes the protein in its native (folded) form. Briefly explain how the buffer stabilizes the phycocyanin.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!)3. 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?
- 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.A sample mixture consists of three proteins with the following properties: Protein A MW (kDa) 200 Amino acid composition 40% nonpolar, 60% polar B 45 20% nonpolar, 80% polar C 98 85% nonpolar, 15% polar IpH 9 3 5 1. If the mixture is subjected to ammonium sulfate precipitation, which protein will precipitate out first? [Select] 2. If the mixture is subjected to isoelectric focusing, which protein will stop moving nearest to the positive electrode? [Select] 3. If the mixture is subjected to cation-exchange chromatography using a buffer at pH 7, which protein will bind to the resin? [Select] 4. If the mixture is subjected to SDS-PAGE, which protein will be at the bottommost portion of the gel? [Select] * Previous NexPeptides and small proteins fold spontaneously in aqueous solution at room temperature. Thus, for a small protein in water, we can say ΔG FOLD < 0. Denoting the unfolded protein as Unf and the folded protein as Fld, we can write the following equation:Unf(aq)--DELTA G FOLD----> Fld(aq)Considering the transition from the unfolded state (in which there are many possible conformations) to the folded state (only one conformation), there is clearly a decrease in the entropy of the protein. However, protein folding is (correctly) described as an entropically driven process.a) Resolve this apparent paradox by identifying the enthalpy (ΔH) and entropy (−TΔS)components involved in protein…
- 3b) Both a-helical 2° structure and b-pleated sheet 2° structure result from the same type of interaction; briefly explain in your own words why you might observe an a-helix in one region of a protein and a b-pleated sheet in another region of the same protein.Loop regions play important roles in the secondary structure of protein. Define loop region and give three (3) of the rolesWhich of the following statements best describe(s) the mechanism by which correct protein folding takes place once the misfolded protein binds the open ring of groEL? Select all that apply. The groEL ring closes to isolate the protein and provide enough time for the protein to properly fold on its own. b and d The groEL ring closes to provide a hydrophilic space to isolate the protein and inhibit its aggregation with others until properly folded. The groEL ring closes to isolate the protein and provide steric hindrance that mechanically refolds the protein. The groEL ring closes to isolate the protein and decode the information necessary to achieve the correct three-dimensional structure. None of the above I picked "The groEL ring closes to provide a hydrophilic space..." but it was incorrect..