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- You have an initial solution in which you added quantities of “A” and “B” such that there is 4.5 M “A” and 2.5 M “B” and no complex (“AB”) at time 0. After equilibrium, you are able to isolate and quantitate the “AB” complex, and find its concentration is 1.5 M. Given that RT is 0.59 kcal/mol, what is the delta Go’ for the association reaction?Consider the binding reaction L + R → LR, where L is a ligand and R is its receptor. When 1 × 10−3 M of L is added to a solution containing 5 × 10−2 M of R, 90 percent of the L binds to form LR. What is the Keq of this reaction? How will the Keq be affected by the addition of a protein that facilitates (catalyzes) this binding reaction? What is the dissociation equilibrium constant Kd?Calculate the net charge on the following tripeptides at pH 5.0: (a) Leu-His-Asp [0] (b) Ala-Ile-Val [0] (c) Met-Lys-Arg [+2] (d) Which tripeptide will be retained the shortest on a cation-exchange chromatographic column in a pH 5.0 buffer? Why?
- 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?A binding protein binds to a ligand L with a Kd of 400 nM. How much ligand is present when Y is (a) 0.25, (b) 0.6, (c) 0.95?1)Ubiquitin is a small protein with a monoisotopic mass of 8560 Da. a) Electrospray ionization of this small protein typically results in major charge states of +8, +9, +10, +11, +12, and +13. Using this information, complete the table below, assuming the charges on each come from protonation. Report mass and m/z values to the ones place. b) Using the data you entered in the table, sketch an expected ESI-MS spectrum for ubiquitin. Label each peak with its charge state. What do you notice about the spacing of peaks along the x-axis. c)The figure shows an experimentally obtained electrospray mass spectrum for ubiquitin. Compare this spectrum to the spectrum you predicted. Are there any differences? If so, what might cause these differences?
- Given a tripeptide Cys-His-Lys, Cys: Pk1 = 1.71; Pk2 = 10.78; PkR = 8.33 His: Pk1 = 1.82; Pk2 = 9.17; PkR = 6.0 Lys: Pk1 = 2.18; Pk2 = 8.95; PkR = 10.53 draw the protonic equilibria for the tripeptide what is the IpH? What is the dominant structure at pH 2.0? What is the first buffering region of the tripeptide?Which nuclear isotope used in protein NMR spectroscopy is the most sensitive to detect? Briefly explain why.A mixture of proteins contains four different polypeptides, all in ~equal concentration, in solution with the following properties: Protein Molecular Mass (kDa) Isoelectric point A 45 4.5 B 77 6.0 C 28 4.1 D 14 10.7 A fraction of the protein solution is applied to a strong cation exchange column using a buffer at pH 8.0 with increasing [NaCl] from 0.05 M – 1.0 M. The chromatogram is shown below: 1. Based on the data presented, which of the following statements is true: Peak #1 is protein D Peak #4 is protein C Peak #3 is protein A Peak #4 is protein D Peak #2 is protein B 2. Since you know that the proteins are all present in approximately equal concentrations, the different relative peak areas tell you that: There are more neutral amino acids in protein #4…
- The twisted proteins store elastic potential energy as it twists or untwists from its equilibrium state. The energy function for this system is shown in the figure where the energy is given in multiples of kBT which is a unit of energy used by biochemists when working at the molecular level. (1.0 kBT = 4.11×10−21 J). Figure 6 shows a horizontal line at an energy level of 136 kBT , which gives a total angular range of 2.095 radians. If the energy level of the ATP-synthase stalk is 100 kBT instead, between what angles is the stalk confined? Explain your reasoning.Given a tripeptide Cys-His-Lys, Cys: Pk1 = 1.5; Pk2 = 10.8; PkR = 8.5 His: Pk1 = 1.6; Pk2 = 9.0; PkR = 7.0 Lys: Pk1 = 2.2; Pk2 = 8.5; PkR = 9.8 a.draw the protonic equilibria for the tripeptide. b.what is the IpH? c.What is the dominant structure at pH 3.0? d.What is the first buffering region of the tripeptide?Consider the following chemical equation whose delta(G) = 9kcal/mol: AC + BD ---> AB + CD what are the reactants and what are the products is this reaction spontaneous? How do you know? Is energy released or consumed by this reaction? If an enzyme, which catalyzes this reaction is added, what will happen to delta (G) If this reaction is coupled to another reaction, whose delta(G) is -12 kcal/mol, what will be the net delta(G) value? will the overall reaction be spontaneous