12. Consider a protein that can exist in two forms: folded (F) and unfolded (UF). Calculate the free energy of protein unfolding at 25 C (i) a state in which 70% of the protein is folded (ii) a state in which 90% of the protein is unfolded
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- 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.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!)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?
- 15. The free energy of folding of a protein is -17kJ/mol. What tenoerature (C) do you have to heat the protein to unfold 10% of the proteins in solution?1. Hen Egg Lysozyme (HEL) is a commonly studied protein. One study reported that HEL unfolded at a "melting" temperature (TM) of 77.8 °C and calorimetric measurements determined the enthalpy for melting to be 500 kJ/mole. At the melting temperature, what are AG and AS°?→x D. Two physical 5. A protein unfolds according to the scheme N properties (property 1 and 2) are measured at three points in the unfolding reaction where the true values of fp are 0.2, 0.5 and 0.8. The corresponding values of K = fx/ fp are 1.0, 0.4 and 0.125. For property 1, d₁ = 0.1; for property 2, d₁ = 0.2. (a) Write an equation that can be used to calculate fapp. (b) Calculate fapp using d₁ = 0.1 (property 1) and fapp using d₁ = 0.2 (property 2). (c) The error in measurement of each physical property is 5 %. Can you detect the presence of the intermediate by measuring the physical properties? Explain your answer
- 5. Indicate whether the following amino acid residues would be more likely to be found on the surface or in the interior of a folded protein: Leu, Arg, Phe, Asn, and Glu. Give your reasoning for each case (diagrams not required).. 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?Which statement is true about protein folding? ○ The equilibrium between folded and unfolded states is best determined by measuring the time course of unfolding ○ Refolding of a protein typically exhibits a linear dependence on the concentration of denaturant ○ The sigmoidal shape of the unfolding transition reflects the complex architecture of proteins ○ Proteins with stable folding intermediates usually exhibit smooth free-energy funnels ○ The rate of unfolding increases as the temperature increases towards the Tm value
- The process of a protein folding from an inactive unfolded structure to theactive folded structure can be represented by the following equation: unfolded protein ⇌ folded proteinThe values of ΔH° and ΔS° for the folding of the protein lysozyme are: ΔH ° = -280 kJ/ mol ΔS ° = -790 J/mol • K(a) Calculate the value of ΔG° for the folding of lysozyme at 25 °C.(b) At what temperature would you expect the unfolding of lysozyme tobecome favorable? (c) At what temperature would the ratio of unfolded protein to foldedprotein be 1:5?7. Consider the role of energetic and entropic factors for protein folding. a. Draw a PEC diagram that represents the relative potential energy and number of configurations for the unfolded and folded protein.4) Explain the physical implications of the following diagram: ENERGY vum им Intermediate folding states m W Folded protein W CONFIGURATION Figure 1: The Thermodynamics of Protein Unfolding²