5. You are imprisoned in a biochemistry lab by an ogre (one of Shrek's kids) who wants you to purify a specific protein from E. coli. You know the protein has a pl of 6.0, and besides lots of buffers, you also have access to DEAE ion exchange resin. What will you do and at what pH will you do it? 6. If the only ion exchange resin available was carboxymethyl (CM) how would you modify the protocol you described in question 5?
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- 9. Metabolically active tissues require lots of ATP, and making lots of ATP requires lots of oxygen. Luckily, metabolically active tissues have some tricks for encouraging hemoglobin to give up oxygen. Name and explain the "trick" depicted by images below. In your answer, be certain to explain the effect on hemoglobin structure. 1.0 a2 Lys 40 pH 7.6 Y 0.5- `pH 7.4 C terminus pH 7.2 Added + proton B, His 146 B, Asp 94 6. 10 po2 (kPa) Figure 7-19 Biochemistry, Sinth Edition 2ea/ H freenard Camny Figures16 Lhninge Principies of iecheminy Seventh dton 2017W.H Feenan and Company1. You want to purify a protein using anion exchange column chromatography. In this technique, the solid state beads are positively charged. What charge would you want your protein to have in order for it to "stick" to the beads? Neutral Positive Negative 2. In your anion exchange experiment, your protein of interest has a pI of 6.0. Which of the following buffer solutions would you want to use when loading your protein extract onto the column so that your protein "sticks" to the beads? pH 4.5 pH 7.3 pH 6.0 3. You want to analyze your chromatography results using gel electrophoresis. If your protein is a pentamer consisting of 2 alpha subunits, 1 beta subunit, and 2 gamma subunits, how many bands would you expect to see on your gel? The alpha subunits are 32kDa. The beta subunit is 32kDa. The gamma subunits are 15kDa. 1 5 2 3 4. You want to analyze your chromatography results using gel electrophoresis. If your protein is a pentamer…6. Treatment of cholesterol with mCPBA results in formation of a single epoxide A, with the stereochemistry drawn. Why isn't the isomeric epoxide B formed to any extent? H. H H HO HO A B
- 1. Complete the table below with information about the amino acids utilized in this pro- cedure. Remember that smaller amino acids will travel further and so will amino acids that are soluble in the solvent. Table 9-1. Amino Acids Procedure AMINO ACIDS Phenylalanine Aspartic Acid Leucine Proline matemps DRAW THE MOLECULAR STRUCTURE in POLARITY (IS IT POLAR OR NONPOLAR?) odme her basalu la MOLECULAR WEIGHT SIZE (RANK LARGEST = 4 AND SMALLEST = 1) SHOULD IT REACT WITH NINHYDRIN?6. A control phospholipid membrane is isolated in which the phospholipid tails all have an 18-C chain length and are comprised of a 50:50 mixture of saturated and unsaturated tails. In addition, about 25% of the lipids are fluorescently labeled on the head groups. a) Draw a single plot of Fluidity vs. Temperature that contains the expected curves for: Control phospholipid (line- -) Control supplemented with 18-C saturated phospholipids (dashed line - Control supplemented with 16-C chain length (dotted line • • • • • • ) b) Draw a single plot of the Fluorescence Intensity vs. Time that contains the expected curves of a Fluorescence Recovery After Photobleaching (FRAP) using the same samples as in (a) above. The FRAP experiment is conducted at the same temperature for each sample (which is the Tm of the of the control phospholipid).4. Amphiphilic Lipids. Detergents are small amphiphilic molecules that tend to form micelles in water. (a) Draw the structures of sodium dodecyl sulfate (SDS) and Triton X-100 (b) For each drawn detergent, indicate which portions (ends) of the molecules are hydrophilic and hydrophobic. Justify your answer (explain why hydrophilic vs hydrophobic). (c) Draw the micelle structure for one of the detergents. (d) Why does the detergent form a micelle and not a bilayer? Why do detergents denature proteins and remove grease from your clothing?
- 3. In a solution of alanine molecules, approximately what fraction of the alanine will exist as the zwitterion at pH of 2.34? What would be the average net charge of a solution of alanine molecules at pH 2.34? 50% will exist as the zwitterion and 50% will exist as the fully protonated (COOH/ NH3+) form. The average net charge of this solution would be +0.5.4. A protein solution is prepared by dissolving 350 µg of protein in 200 µL of water. A 150 μL sample of this solution is diluted to a total volume of 4.5 mL. How many mg of protein will be in a 2 mL sample of the diluted protein solution? Space to show your workings:6. Consider the following proteins to answer the questions below: Protein Size (kDa) ε at 280 nm 10 7000 14000 3000 50000 A B C D 50 10 50 pl 4 4 8 8 Red Colored? Yes No No No a. Sketch the UV-Vis spectrum of each pure protein (A, B, C, and D) from 240- 480 nm if they were all present at 20 µM. Note: I want four clearly labeled spectra on one plot.
- 2. A functional protein that is approximately 110 kDa in size has all its cysteine residues joined with disulfide bonds. It has one cysteine residue per 100 amino acids. When heated at 85°C it lost activity, but when it was allowed to cool, the activity was restored? Please answer the following questions: a) How many disulfide bonds the protein has? Show how you came up with the answer. b) What is the molecular basis for the protein behavior in restoring activity?13. Draw the structure of the amino acid lysine showing the correct protonation states of its acid and base functional groups in a solution of lysine at pH 10.5. What is the net overall charge on lys at this pH? 14. Draw the structure of the amino acid lysine showing the correct protonation states of its acid and base functional groups in a solution of lysine at pH 8.5. What is the net overall charge on lys at this → Practice other questions like sample questions 12-14 using the 20 amino acids at varying pHs!!! (eg. pH? "Draw the structure of the amino acid Histidine showing the correct protonation states of its acid and base functional groups in a solution of his at pH 5. What is the net overall charge on his at this pH?" etc...)2. Mixtures of amino acids can be analyzed by first separating the mixture into its components through ion-exchange chromatography. Amino acids placed on a cation-exchange resin containing sulfonate (-SO₁) groups flow down the column at different rates because of two factors that influence their movement: (1) ionic attraction between the sulfonate residues on the column and positively charged functional groups on the amino acids, and (2) hydrophobic interactions between amino acid side chains and the strongly hydrophobic backbone of the polystyrene resin. For each pair of amino acids listed, determine which will be eluted first from the cation-exchange column by a pH 7.0 buffer. (a) Asp and Ly, (b) Arg and Met, (c) Glu and Val, (d) Gly and Leu, (e) Ser and Ala