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- The extinction coefficient or absorptivity (ɛ) of protein A at 340 nm is 6440 M-1 cm-1, whereas protein B does not absorb at 340 nm. What absorbance will be observed when light at 340 nm passes through a 5 mm cuvette containing 10 µM of protein A and 10 µM of protein B? Beer-Lambert-law; A = ɛ x C x1; A = absorbance, C= concentration, 1= pathlength).Using a detailed scheme, propose a step-wise protocol to purify protein B by ion exchange chromatography (Explain your logic/choices).Explain why it has been very difficult to obtain an X-ray crystal structure for the complete nuclear pore complex. Explain in terms of its size, number of proteins as well as its molecular properties (e.g. charge)
- An engineered ligand binds its target with 5 nM affinity at high pH. However, protonation of a histidine residue in the binding site of the ligand renders it unable to bind. Plot the ligand:target complex concentration versus the initial ligand concentration (in protonated or unprotonated form) at pH 4, 5, 6, 7, or 8 (five lines on one plot). Use a total target concentration of 10 nM.. Suppose you have two genetic variants of a large protein that differ only in that one contains a histidine (side chain pk, = 6.0) when the other has a valine (uncharged side chain). (a) Which would be better for separation: gel electrophoresis or isoelectric focusing? Why? (b) What pH would you choose for the separation?Suppose you have a mixture of the following proteins protein A: pl = 3.5, mw = 35 kDa protein B: pl = 5.5, mw = 22 kDa protein C: pl = 7.5, mw = 77 kDa protein D: pl = 9.0; mw = 52 kDa. Which protein do you expect to elute last if you perform separation using cation exchange chromatography at pH 7.0? A B Oc
- 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 55In a mixture of five proteins listed, draw an elution profile (Absorbance vs. mL eluted, arbitrary) for the purification of the listed proteins on a gel filtration chromatography resin: cytochrome c (pI = 5.4; Mr = 13,000), immunoglobulin G (pI = 7.3; Mr = 145,000), ribonuclease A (pI = 9.6; Mr = 13,700), RNA polymerase (pI = 6.3; Mr = 450,000), human serum albumin (pI = 5.4; Mr = 68,500). Label your elution peaks. Draw a sketch of an SDS-PAGE, reflecting the mobility of the above mixture as they elute from the column. Label you protein bands.Nonspecific elution of affinity bonded macromolecules is used in affinity chromatography explain why?
- Complete the table below by adding (+) or (-) if eahc sample (amino acid or protein) below will test positive or negative, respectively. sample BIURET NINHYDRIN XANTHOPROTEIC MILLON-NASSE SAKAGUCHI LEAD ACETATE PAULY HOSKIN-COLE G W H Y C R HAIR GELATIN CASEIN PEPTONE Identify the amino acid that will give the following data: BIURET NINHYDRIN XANTHOPROTEIC MILLON-NASSE SAKAGUCHI LEAD ACETATE PAULY HOPSKIN-COLE - + + + - - + - Name of amino acid: structurte of the amino acid:(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?You want to treat 10 mL of HL-60 cells with cycloheximide in order to determine the half-life of a newly discovered protein. In order to do this, the final concentration of cycloheximide needs to be 90 µM. How much of a 150 mM stock solution of cycloheximide should you add to your cells?