5. A protein unfolds according to the scheme NX D. Two physical properties (property 1 and 2) are measured at three points in the unfolding reaction where the true values of fo 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. A protein unfolds according to the scheme NX D. Two physical properties (property 1 and 2) are measured at three points in the unfolding reaction where the true values of fo 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

Biochemistry

6th Edition

ISBN:9781305577206

Author:Reginald H. Garrett, Charles M. Grisham

Publisher:Reginald H. Garrett, Charles M. Grisham

Chapter31: Completing The Protein Life Cycle: Folding, Processing, And Degradation

Section: Chapter Questions

Problem 3P: Understanding the Relevance of Chaperones in Protein Folding Protein molecules, like all molecules,...

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2. Subunit Composition of a Protein. A protein has a molecular mass of 400 kDa when measured by size-exclusion chromatography ( F). When subjected to gel electrophoresis in the presence of sodium dodecyl sulfate (SDS), the protein gives three bands with molecular masses of 180, 160, and 60 kDa. When electrophoresis is carried out in the presence of SDS and dithiothreitol (=), three bands are again formed, this time with molecular masses of 160, 90, and 60 kDa. Determine the subunit composition of the protein. Note: dithiothreitol is a reagent to beak down the disulfide bonds.
2 / 9 100% +| 1. Explain why only small areas of the Ramachandran plot (below) are occupied (shaded grey) and what the two dark grey shaded areas represent in terms of a protein structure. +180 120 60 -60 -120 -180 -180 -120 -60 60 120 +180
. 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?
.A protein gives a single band on SDS gel electrophoresis, as shown in lanes 1 and 2 below. There is little if any effect from adding
. The process of a protein folding from an inactive unfolded structure to the active folded structure can be represented by the following equation: unfolded protein = folded protein The values of AH and AS° for the folding of the protein lysozyme are: AH = -280 kJ/mol AS = -790 J/mol · K (a) Calculate the value of AG for the folding of lysozyme at 25 °C. (b) At what temperature would you expect the unfolding of lysozyme to become favorable?
A new protein of unknown structure has been purified. Gel filtration chromatography reveals that the native protein has a molecular weight of 300,000. Chromatography of the protein in the presence of 6 M guanidine hydrochloride (a denaturant) yields a single peak corresponding to a molecular weight of 50,000. Chromatography of the protein in the presence of 6 M guanidine hydrochloride and 10 mM beta-mercaptoethanol (a disulfide bond reductant) yields peaks corresponding to molecular weights of 30,000 and 20,000. What does this data tell you about the structure of this protein? (Be thorough in your answer!)
7 Protein structure.Circle one of the three amino acid sequences that is most likely to form a stable a-helix? RASKTARQ DASKTAEQ KPGKPAGQ In one sentence (that can be accompanied by a small picture) explain why?
The number of distinct protein folds in limited. Why might this be so?
Affinity chromatography You have created a fusion protein tagged with Glutathione-S-Transferase (GST). Your lab mate tells you that the affinity columns for this type of tagged protein are very similar to that of Histadine tagged proteins. Using the following elements set up a purification column and construct a protocol for an affinity purification using this tag. A large amount of glutathione is usually used to elute the tagged protein off the column. How might this work?
Which statements are true? Explain why or why not.1 Each strand in a β sheet is a helix with two aminoacids per turn.2 Intrinsically disordered regions of proteins can beidentified using bioinformatic methods to search genes forencoded amino acid sequences that possess high hydro-phobicity and low net charge.3 Loops of polypeptide that protrude from the sur-face of a protein often form the binding sites for other mol-ecules.4 An enzyme reaches a maximum rate at high sub-strate concentration because it has a fixed number ofactive sites where substrate binds.5 Higher concentrations of enzyme give rise to ahigher turnover number.6 Enzymes that undergo cooperative allosteric tran-sitions invariably consist of symmetric assemblies of mul-tiple subunits.7 Continual addition and removal of phosphatesby protein kinases and protein phosphatases is wastefulof energy—since their combined action consumes ATP—but it is a necessary consequence of effective regulation byphosphorylation.
. Consider a small protein containing 101 amino acid residues. The protein will have 200 bonds about which rotation can occur. Assume that three orientations are possible about each of these bonds. (a) Based on these assumptions, about how many random-coil conforma- tions will be possible for this protein? (b) The estimate obtained in (a) is surely too large. Give one reason why.
t, a The n of 4-19. In a common protein analysis, a dye binds to the protein and the color of the dye changes from brown to blue. The intensity of blue color is proportional to the amount of protein present. Protein (ug): 0.00 9.36 18.72 28.08 37.44 Absorbance: 0.466 0.676 0.883 1.086 1.280 2 (a) After subtracting the blank absorbance (0.466) from the remaining absorbances, use the method of least squares to determine the equation of the best straight line through these five points (n and intercept to express the equation in the form y (±s,) = [m (±sm)]x + [b (±sp)] with a reasonable number of signifi- cant figures. 02 5). Use the standard deviation of the slope and and (b) Make a graph showing the experimental data and the cal- culated straight line. and (c) An unknown gave an observed absorbance of 0.973. Cal- culate the number of micrograms of protein in the unknown, and estimate its uncertainty. nree