Problem Set 2 for BIBC 100 Winter 2008 1a) What do the pK values in the chart below tell you? Compound pK1 pK2 pKR pI Glycine 2.34 9.60 5.97 Glutamate 2.19 9.67 4.25 3.22 Arginine 2.17 9.04 12.48 10.76 b) Will the following amino acids have an overall positive, negative or zero charge at pH 3.22, pH 5.97, pH 10.76? Fill in the chart. pH 3.22 pH 5.97 pH 10.76 Gycine Glutamate Arginine 2. Calculate the net charge on the following tripeptides at pH7. a) Asp-Glu-Ser b) Ser- Gly-Thr c) Gly–Lys-Arg 3. Refer to Table 3-2 in the textbook for this question: a) How many proteins in the table exhibit quarternary structure? How can you tell? b) How many proteins exhibit supersecondary structures? How can you tell? 4. How would the following agents/procedures interfere with/disrupt the different levels of protein architecture? Why? a) addition of SDS b) addition of protease 5. Histones are proteins found in eukaryotic cell nuclei, tightly bound to DNA. Remember that DNA has many phosphate groups. The pI of histones is about 10.8. a) What amino acid residues must be present in relatively large numbers in histones?b) In what way do these amino acid residues contribute to the strong binding of histones to DNA? 6. Following are 3 different protein sequences. A) IVMMIALFMIILVP B) IRWHMYGPQNKLQ C) REDQYTWWKRRS i) Which one would most likely be found traversing the hydrophobic interior or a lipid bilayer? ii) Which would most likely be found on a loop region of a protein? iii) Which one would most likely be found lying on a protein surface? 7. The side chains of which of the following amino acid are able to form H-bonds in water? Y R V Q G 8. Two amino acids of the standard 20 contain sulfur atoms. They are: 9. For amino acids with neutral R groups, at any pH below the pI of the amino acid, the population of amino acids in solution will have: A) a net negative charge B) a net positive charge C) no charged groups D) no net charge E) positive and negative changes in equal concentration 10. By adding SDS (sodium dodecyl sulfate) during the electrophoresis of proteins, it is possible to: A) determine a protein’s isoelectric point B) determine an enzyme’s specific activity C) determine the amino acid composition of the protein D) preserve a protein’s native structure and biological activity E) separate proteins on the basis of molecular weight11. About how many different kinds of proteins are found in a typical human cell? A) hundreds B) thousands C) more than a hundred thousand, less than a million D) millions E) billions 12. In an α helix, the R groups on the amino acid residues: A) alternate between the outside and the inside of the helix. B) are found on the outside of the helix spiral. C) are each 5.4 Angstroms apart. D) generate the hydrogen bonds that form the helix. E) stack within the interior of the helix. 13. The interactions of ligands with proteins: A) are relatively nonspecific. B) are relatively rare in biological systems. C) are usually irreversible. D) are usually transient. E) usually result in the inactivation of the proteins. 14. Before running protein samples on an SDS-PAGE gel, they must first be treated with two substances. What are these substances and why are they important? You have a semi-purified protein sample that contains just three proteins: Protein A (100 kD), Protein B (45 kD), and Protein C (60 kD). You run this sample on a SDS-PAGE gel and stain it with coomassie blue (a protein dye). Draw your gel below. Be sure to label each protein, the top and bottom of the gel, placement of electrodes, and the direction of travel. How do you know the identity of each protein on the gel?You have a semi-purified protein mixture containing two proteins that have nearly identical molecular weights. Will SDS-PAGE be sufficient to visualize both proteins? Why or why not? If not, what other technique would you use? 15. You are analyzing the following immunoglobulin. You want to separate the Fab regions from the rest of the antibody. What enzyme can you use to isolate the Fab fragments? Circle the location which this enzyme acts. If this antibody was an IgG, how many domains would be present on the protein in its native conformation?16. You are working with a Class I MHC molecule that has 3 variable specificity pockets at positions 3, 5, and 7. The residues at these pockets on the MHC are Val at position 3, Lys at position 5, and Asp at position 7. Name any peptide that would be most likely to bind to the MHC I molecule you are working with. Explain your answer. 17. Where can you find CD4 and CD8 proteins and what roles do they
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