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Question 1 Fill in the blanks a) Antibody diversity is derived by recombination of the __, ___, ___, regions. True or False. If false, change the statement so that it is true. b) Secondary exposure to an antigen results in a longer delay before there’s an immune response. c) T cells are part of the innate immune system. d) Macrophages kill bacterial microbes by secreting a chemical that punches holes in the bacterial membrane. e) A single B cell can produce many different kinds of surface antibody molecules. f) Antibodies that recognize self proteins may result in disease. g) Pathogens cause disease by entering a host, colonizing, multiplying, evading the immune system, and disseminating. h) B cells are activated by killer T cells to secrete antibodies into the blood. i) MHC class II molecules are receptors found on all nucleated cells. j) By changing their surface proteins, bacteria are able to avoid cell-mediated immunity. 7.012 Exam III Handout 3 Question 2 a) A viral infected insulin-producing pancreatic cell presents viral peptides (antigens) as well as self peptides on its surface. i) What will recognize the foreign peptide displayed on the MHC Class I molecule? ii) This recognition results in what two responses? iii) Briefly explain what would happen if the immune system inappropriately recognized a pancreatic self peptide on non-infected pancreatic cells? What disease could this lead to? Question 3 You are studying the cell cycle in haploid yeast cells. You isolate a cell that is a temperaturesensitive cell division cycle (cdc) mutant, cdcX-. cdcX- grows normally at 25C, but arrests at 36C at the point in the cell cycle where the expression of the normal cdcX gene is required. To determine where in the cell cycle expression of cdkX is required, you design experiments based on the following facts: 1) The drug nocodazole arrests, but does not kill yeast in mitosis (M phase). 2) Cell density can be measured to determine if the yeast cells have completed a cell division. 7.012 Exam III Handout 4 Question 3, continued For your experiments: You incubate cdkX- cells at 25C with nocodazole until all the cells are synchronized. You then shift the cells to 36C and remove the nocodazole. The cells divide once and then arrest. You incubate cdkX- cells at 36C until all arrest. You then add nocodazole and shift the cells to 25C. The cells arrest without dividing. a) Given these experiments you can assume that the protein encoded by the cdkX gene is not required at what phase(s) of the cell? Another mutant cdkY- is a cold-sensitive mutant that arrests at 18 C, but grows normally at 25C. cdkY- cells arrest between the S and G2 phases of the cell cycle. You make cdkX- cdkYdouble mutants and perform the following experiments. You incubate cdkX- cdkY- double mutants at 36C until all the cells are synchronized and then shift the cells to 18C. The cells arrest without dividing. You incubate cdkX- cdkY- double mutants at 18C until all until all the cells are synchronized and then shift the cells to 36C. The cells divide once and then arrest. b) Given these experiments you can assume that the protein encoded by the cdkX gene is not required at what phase(s) of the cell? c) You perform another experiment where you incubate cdkX- cells at 36C until all the cells are synchronized and then shift the cells to 18C in the presence of hydroxyurea. The cells remain arrested without dividing. i) In what stage of the cell cycle do you expect the protein encoded by the cdkX gene to act? ii) At this block point, in what state would you find the pRb protein? d) A cell in the process of DNA replication (cell A) is fused with a cell in early G1 (cell B). i) How does the timing of the cell cycle for the cell B nucleus in the fused cell compare to that expected for the cell B nucleus if the cells remained independent? 7.012 Exam III Handout Question 3, continued 5 ii) What soluble factor(s) are found in cell A but not in cell B (check all that apply)? ___ ___ ___ ___ ___ pRB protein ___ TGF___ Human papilloma virus ___ a cyclin dependent kinase ___ a G1 cyclin a cAMP dependent kinase a G2 cyclin an S-phase cyclin an oncogene Question 4 Familial cancer syndromes such as Retinoblastoma and Neurofibromatosis are inherited as genetic diseases. Individuals that have an inactivating mutation in one allele of the above mentioned genes are likely to develop cancer. (These individuals are heterozygous for the mutant Rb or NF-1 gene, respectively) The majority of cells in these individuals are normal, but tumors arise from individual cells in specific tissues. In the case of Rb heterozygotes, tumors develop in the retina. Nf-1 heterozygotes develop peripheral nerve sheath tumors and neurofibromas. a) What class of cancer causing genes are Rb and Nf-1? b) In most cases, the heterozygous individuals are not born with tumors but develop tumors several years after birth or even later in life. What specific event triggers tumor formation? c) Why are familial cancer syndromes involving activating (dominant) mutations not seen? d) Many tumor viruses exert their tumorigenicity by producing viral proteins that functionally inactivate normal cellular proteins. What class of cancer-related proteins would likely be affected? 7.012 Exam III Handout Question 5 6 When a cell is transformed from a normal, growth-regulated cell into an unregulated, tumorlike cell, several changes take place in the cell. Some of these changes can be seen directly when cells are grown in culture while other cellular changes are inferred from experiments. One of these changes, a change in cell shape, is shown below. a) You find two culture plates each containing transformed cells that arose by different mutations. For each plate, you want to know whether the transformed phenotype is due to an oncogene or a mutated tumor suppressor gene. You can determine this by fusing one of your transformed (tumor) cells with a wild-type cell and observing whether the fusion cell behaves like a wild-type or a tumor cell. You perform the cell fusion experiments with a transformed (tumor) cell isolated from each of your two plates. Case I: Case II: For each fusion experiment (Case I and Case II), explain whether or not the tumor cell used in the fusion had a mutation in an oncogene or a tumor suppressor gene, and also indicate the type of mutation (gain-of-function or loss-of-function) which produced the mutant allele in the tumor cell. i) Case I: ii) Case II: b) You then clone the mutated gene from the tumor cell in Plate 1 (part b) and determine that the mutation is in a gene that encodes a growth factor receptor. Explain what kind of mutation in a growth factor receptor gene might cause the tumor cell phenotype observed in Plate 1. c) You also clone the mutated gene from the tumor cell in Plate 2 (part b) and determine that the mutation is in a gene that normally encodes protein X, which binds and inactivates a transcription factor involved in a growth-promoting signal transduction pathway. Explain what kind of mutation in the protein X gene might cause the tumor cell phenotype observed in Plate 2. 7.012 Exam III Handout 7 Solutions: Question 1 a) Antibody diversity is derived by recombination of the __, ___, ___, regions. V, D, J Note that there are many ways to correct the false statements below. We have given only a few examples. b) Secondary exposure to an antigen results in a longer delay before there’s an immune response. Shorter than primary. c) T cells are part of the innate immune system. T cells are part of the Acquired immune system. or T cells are part of the cell-mediated and humoral immune system. d) Macrophages kill bacterial microbes by secreting a chemical that punches holes in the bacterial membrane. Macrophages kill bacterial microbes by ingesting and lysing. or Complement kills bacterial microbes by punching holes in the bacterial membrane. e) A single B cell can produce many different kinds of surface antibody molecules. A single B cell can produce only one kind of surface antibody. f) Antibodies that recognize self proteins may cause disease. True g) Pathogens cause disease by entering a host, colonizing, multiplying, evading the immune system, and disseminating. True h) B cells are activated by killer T cells to secrete antibodies into the blood. B cells are activated by helper T cells… i) MHC class II molecules are receptors found on all nucleated cells. MHC class I molecules are receptors found on all nucleated cells or MHC class II molecules are receptors found on B cells and/or macrophages j) By changing their surface proteins, bacteria are able to avoid cell-mediated immunity. By changing their surface proteins, bacteria are able to avoid humoral immunity. 7.012 Exam III Handout 8 Question 2 a) A viral infected insulin-producing pancreatic cell presents viral peptides (antigens) as well as self peptides on its surface. i) What will recognize the foreign peptide displayed on the MHC Class I molecule? This will be recognized by a killer T cell which is specific for this foreign antigen in conjunction with the MHC Class I molecule. ii) This recognition results in what two responses? The killer T cell will kill the infected pancreatic cell. The killer T cell will stimulate its own amplification so that there will be more of the same specific killer T cells for this particular infection. iii) Briefly explain what would happen if the immune system inappropriately recognized a pancreatic self peptide on non-infected pancreatic cells? What disease could this lead to? Recognition of a self peptide by a killer T cell would lead to lysis of all cells displaying that peptide. If this were a peptide that was found exclusively in pancreatic cells, then the pancreas would be destroyed by autoimmune disease leading to diabetes. Question 3 a) Given these experiments you can assume that the protein encoded by the cdkX gene is not required at what phase(s) of the cell? M phase b) Given these experiments you can assume that the protein encoded by the cdkX gene is not required at what phase(s) of the cell? G2 phase or M phase c) i) In what stage of the cell cycle do you expect the protein encoded by the cdkX gene to act? S phase ii) At this block point, in what state would you find the pRb protein? pRb would be hyperphosphorylated d) i) How does the timing of the cell cycle for the cell B nucleus in the fusion cell compare to that expected if the cells remained independent? In the fusion cell, the DNA of cell B immediately begins replication (S-phase). If cell B had remained independent, S-phase would have occurred later. ii) What soluble factor(s) are found in cell A but not in cell B (check all that apply)? ___ RB protein ___ a cAMP dependent kinase ___ TGF___ a G2 cyclin ___ Human papilloma virus _X_ an S-phase cyclin ___ a cyclin dependent kinase ___ an oncogene _X_ a G1 cyclin 7.012 Exam III Handout 9 Question 4 a) What class of cancer causing genes are Rb and Nf-1? Tumor suppressor genes b) In most cases, the heterozygous individuals are not born with tumors but develop tumors several years after birth or even later in life. What specific event triggers tumor formation? The second working allele of the tumor suppressor gene must be mutated or lost before the cell is transformed. c) Why are familial cancer syndromes involving activating (dominant) mutations not seen? An inherited mutation in an oncogene would mean that every cell in the body would have abnormal growth properties. This would probably not allow for survival of the embryo. d) Many tumor viruses exert their tumorigenicity by producing viral proteins that functionally inactivate normal cellular proteins. What class of cancer-related proteins would likely be affected? Tumor suppressor proteins Question 5 a) Explain whether or not the tumor cell used in the fusion had a mutation in an oncogene or a tumor suppressor gene, and also indicate the type of mutation (gain-of-function or loss-offunction) that produced the mutant allele in the tumor cell. i) Case I: Since the tumor cell phenotype is dominant to wild-type, the mutated gene is an oncogene and was created by a gain-of-function mutation in a proto-oncogene. ii) Case II: Since the tumor cell phenotype is recessive to wild-type, the mutated gene is a tumorsuppressor gene and was inactivated by a loss-of-function mutation. b) Explain what kind of mutation in the growth factor receptor gene might cause the tumor cell phenotype observed in Plate 1. A mutation that would make the growth factor receptor constitutively active even without growth factor. The active receptor would always be signaling the cell to grow even in the absence of growth factors. c) Explain what kind of mutation in the protein X gene might cause the tumor cell phenotype observed in Plate 2. A mutation in protein X that would prevent protein X from binding the transcription factor. The transcription factor would always be stimulating the expression of growth genes. 7.012 Exam III Handout 10
