How to use the Kd to determine the fraction of both bound proteins? The Kd is 0.05uM. protein 1 has [ ] of 0.03 uM and protein 2 has [ ] of 0.05 uM.
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- (a) 1 Normalized fluorescence 0.8 0.6 0.4 0.2 0 50 55 OM 0.100 M 0.200 M 0.300 M 0.500 M 1.00 M 2.00 M 60 113588 65 Temp. (°C) 70 75 80 Where is fully folded protein? • Where is fully unfolded protein? • Where is partially folded protein? • To what does SYPRO orange bind? • Why does fluorescence increase as a function of temperature? ● Define a melting temperature for a protein. • Demonstrate how an estimated melting temperature of the protein in zero molar ligand can be determined. • What is the effect of increasing the molar concentration on melting temperature for this protein? • Why is melting temperature a useful measurement to make for a protein especially if you are interested in protein aggregation?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 +1805 You need to separate the following three proteins, Protein A (MW 76 600 Da; pI 4.5); Protein B (MW 70 000 Da and pI 8.2) and Protein C (MW 42 000; pI 8.6). Describe what column/s you would use, the pH of the buffer/s you would use, which proteins are retained on the column and how you would elute the bound protein/s. How would you monitor where the protein peaks elute and whether the protein in each peak is pure of not?
- 1. A mixture of proteins with the following properties were purified using cation exchange chromatography. Which of the following peaks correspond to the correct protein?Protein M- pI- 11, size- 60 KdaProtein N- pI- 8, size- 112 KdaProtein O- pI- 6, size- 280 KdaProtein P- pI- 4, size- 36 Kda[N.B: I was trying to upload pictures, but it was interrupting, Peak C is the highest peak, Peak D is lowest, Peak B is higher than D; however lower than C and A, Peak A is lower than C only, higher than B and D] a) Peak A is P b) Peak C in N c) Peak D is P d) Peak B is O e) Peak A is M 2. Which transition state analog is the most effective competitor for serine protease such as Chymotrypsin?a) R-C=O-NH-R’b) R-C=O(CH3)-NH-R’c) R-CH(OH)-CH(NH2)-R’d) R-CH(OH)-NH-R’e) R-CH=NR’ 3. If a 14C fatty acid labelled with C14 is fed to a cow, after 30 minutes of Beta oxidation, where will the C14 be found?a) Acetyl coA b) Propionyl coA c) Glutamine d) Glucose 4. How many carbons will…A researcher isolates a new protein and finds that it contains 0.755% serine by weight upon amino acid analysis. The molecular mass of serine is 105 g.mol-¹. What is the minimum molecular mass for the protein assuming only one Ser residue per protein molecule? mmin = The researcher estimates the molecular mass of the protein using gel electrophoresis. From this estimated molecular mass, the researcher concludes the protein contains 3 Ser residues. What is the estimated molecular mass of the protein as shown by gel electrophoresis? g.mol-¹ mest = g.mol-1On an SDS-gel, If the distance traveled by the bromophenol blue dye is 7 cm, and the distance traveled by the protein band is 2.8 cm, the mobility of the protein is 40 4 40% 0.4
- (a) 0.25 Turbidity (AU) 0.20- 0.15- 0.10- 0.05- 0.00+ 0 Wt Mutant 1 Mutant 2 Mutant 3 Mutant 4 2 8 Incubation time (h) 6 10 Define turbidity. • How is turbidity related to protein aggregation? • Where is protein with no aggregation for any condition? • Where is protein with maximal aggregation for any condition? • What area of the plot tells you about the rate of aggregation for any condition? 12 • What area of the plot tells you about total aggregation for any condition? • Slow, medium, and fast rates of aggregation are shown - which samples fall into each category? ● Two amounts of total aggregation are shown - which samples fall into each category? • Name two samples that have the similar rates of aggregation, but different amounts of total aggregation. • Name two samples that have different rates of aggregation, but similar amount of total aggregation. ● Why is protein turbidity a useful experiment to perform for a protein especially if you are interested in protein aggregation?(a) 1 Normalized fluorescence 0.8 0.6 0.4 0.2 0 1.7.0- 50 55 OM 0.100 M 0.200 M 0.300 M 0.500 M 1.00 M 2.00 M Where is fully folded protein? • Where is fully unfolded protein? • Where is partially folded protein? 60 A 65 Temp. (°C) 70 75 80 To what does SYPRO orange bind? • Why does fluorescence increase as a function of temperature? • Define a melting temperature for a protein. • Demonstrate how an estimated melting temperature of the protein in zero molar ligand can be determined. • What is the effect of increasing the molar concentration on melting temperature for this protein? Why is melting temperature a useful measurement to make for a protein especially if you are interested in protein aggregation?a) The pl of a protein is 9.0. What will be the net charge (positive, negative or neutral) on the protein under the following conditions: A buffer with pH 9.0: A buffer with pH 7.0: A buffer with pH 10.0: b) Your protein is present in a sample buffer which has a pH 7.0. The sample is applied to an ANION EXCHANGE column. Will protein 1 bind to the beads on the column? Yes/No
- SDS-PAGE gels separate proteins by charge. Therefore proteins that are 10,000 daltons (g/mol) will move the same distance as proteins that are 80,000 daltons (g/mol). This statement is: True or False (And why)Consider the following protein mixture: Protein A B C D Molecular Weight (kDa) 50 150 200 350 Affinity to Metal ion === Zn²+ === 1. Using hydrophobic interaction chromatography, the protein that will be eluted last is [Select] 2. Using affinity chromatography, the protein that will be eluted last in a Zn²+-containing column is 3. The protein with the fastest migration towards the anode in SDS-PAGE is [Select] IpH value 7 3 9 5 [Select] [Select] 4. Using a buffer solution with a pH of 4, the protein that will bind to an anion exchanger is 5. The protein that will be eluted last in a gel filtration column is [Select] 6. Using isoelectric focusing, the protein that will have a protein band nearest to the cathode (negative electrode) is [Select] % Hydrophobicity 20 45 75 55You perform electrophoresis of 3 proteins, Hemoglobin (pl: 6.8), DNA Polymerase (pl: 5.2) and Porcine pepsin (pl: 1.0) in a Tris-Glycine buffer (pH 5.2). (pl = Isoelectric point). Select which of the following is true. O All proteins will migrate at the same rate O All proteins will migrate at the same direction Porcine pepsin will migrate toward the electrode Porcine pepsin will not migrate and stay in the well
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