BIO360 Fall 2013 Quiz 1 Name: Key 1. Examine the diagram below. There are two homologous copies of chromosome one and the allele of YFG carried on the light gray chromosome has undergone a loss-of-function mutation. If a mitotic recombination event occurs (as shown below), two different sets of daughter cells are possible. Diagram chromosome 1 in the four possible cells and put a star next to those which show a loss-of-heterozygosity. (4 points) * * 2. The Warburg Effect refers to the phenotype that cancer cells (2 points) A. have been transformed by a retrovirus. B. effectively resist being killed by the immune system. C. are resistant to death by apoptosis. D. primarily use anaerobic cell respiration. E. are capable of anchorage-independent growth. 3. Which of the following is not and example of an epigenetic modification? (2 points) A. Histone methylation B. Histone acetylation C. Substitution mutation of a G to an A D. Methylation of a GC dinucleotide 4. All stem cells share what two characteristics? (2 points) Self-Renewal Progeny differentiate
BIO360 Quiz 2 September 30 1. Imagine that the p21 gene (which encodes a CDK inhibitor) has been transcriptionally silenced due to extensive methylation upstream of the gene and that this modification is contributing to the transformation of the cell. Which of the follow terms would apply to p21? Circle all that apply. (2 points) Aneuploid Caretaker Epi-Driver Indel Mut-Driver Oncogene Passenger Protooncogene Tumor Suppressor Gene 2. Name that term. (2 points each) Orthologs Exome Restriction Point Two genes from different organisms that share an evolutionary history and carry out the same function. All of the DNA which is transcribed and retained after splicing. The point in the cell cycle after which growth factors are no longer needed for cycling to occur. 3. In one sentence or less, what is the appropriate conclusion for Figure 4C from the Zhang et al paper? Patients whose NSCLCs lack cytoplasmic CDK1 tend to die earlier than those who retain cytoplasmic CDK1. (2 points)
BIO360 Quiz 3 October 7 1. What protein deactivates Ras protein? GAP (2 points; standard abbreviation is fine) 2. In class, we said that Elk-1 is a transcription factor that moves to the nucleus when it gets phosphorylated by ERK. When it is in the nucleus, it activates the transcription of the DHFR gene. Imagine the following experiment: We create a mutant Elk-1 which adds a Nuclear Export Signal to the protein so that it is never located in the nucleus. We find that DHFR is never transcribed under these conditions, regardless of ERK activity. This experiment demonstrates that Nuclear localization is necessary for Elk-1 to activate transcription of DHFR. Nuclear localization is sufficient for Elk-1 to activate transcription of DHFR. Nuclear localization is both necessary and sufficient for Elk-1 to activate transcription of DHFR. Nuclear localization is neither necessary nor sufficient for Elk-1 to activate transcription of DHFR. Please circle your answer and then briefly explain your logic below. (2 points) It s a negative experiment, in which we have removed an ability. By blocking the ability of Elk-1 to move to the nucleus, it blocks the resulting phenotype of DHFR activation. 3. Which one statement correctly describes the Myc protein? (2 points) A. Only Myc-Max heterodimers can bind to the enhancer. B. The G12V mutation of Myc is commonly found in human tumors. C. Phosphorylated Myc has a shorter half-life than dephosphorylated Myc. D. Max-Max homodimers bind to the enhancer and repress transcription. E. Dimerization happens through the Helix-Loop-Helix domain. 4. Reporter genes are designed to report upon whether or not what event has happened? (2 points) Transcription from the promoter being studied. 5. For each underlined pair of terms, circle the one that is correct. (½ point each) In the paper by Hoare et al., Tnk1/Kos1 is a putative oncogene/tumor suppressor gene which affects the activity of Raf/Ras. To study this gene, Hoare et al. deleted/overexpressed Tnk1 in mice. The Tnk1 protein is a kinase/phosphatase.
BIO360 Quiz 4 October 14 1. In the diagram below from the paper by Hoare et al., why is it necessary to have TK in the targeting construct? The Thymidine Kinase gene allows for the scientists to select for it s loss in the ES cells. TK is lost when the targeting construct is inserted by homologous recombination but retained if it was inserted into the genome by nonhomologous recombination. 2. In the diagram below, what is represented by the black box that I circled with a dashed line? An exon 3. What is the principle way that the Rb protein is regulated through the cell cycle? A. protein degradation B. acetylation C. phosphorylation D. transcriptional activation E. transcriptional repression 4. To determine if the E2F-1 protein and the DP-1 protein are bound to each other in a living cell, which technique should I use? A. microarray B. methylation-specific PCR C. coip D. sirna E. northern blot 5. A portion of a figure from the Hoare et al. paper is shown on the right. The lane labels refer to Tnk1 genetic status of the cells used in the western blot. In one sentence or less, what is the conclusion of this experiment? The loss of Tnk1 leads to more phosphorylation of the Erk2 protein
BIO360 Quiz 5 October 21 Name: Key 1. When the E2F-1/DP-1 heterodimer is bound to an enhancer and prb is highly phosphorylated, the transcription of nearby genes is A. Repressed B. Derepressed C. Activated D. Deactivated (1 point) 2. p53 is a tumor suppressor gene that is frequently mutated in human cancers. As discussed in the review by Vogelstein et al. ( Cancer Genome Landscapes ), most mutations in tumor suppressor genes are deletions. Unlike most tumor suppressor genes, why are 95% of the cancer-associated mutations in p53 substitution mutations in the DNA binding domain? (3 points) Many substitution mutations in the DNA binding domain of p53 act in a dominant negative fashion. In this way, only a single mutation is able to disable all of the functional p53 in the cell. 3. Classify each of the following proteins as anti-apoptotic, pro-apoptotic, both or neither. (½ point each) Apaf-1 Anti-apoptotic Pro-apoptotic Both Neither ATM Anti-apoptotic Pro-apoptotic Both Neither Bcl-2 Anti-apoptotic Pro-apoptotic Both Neither p53 Anti-apoptotic Pro-apoptotic Both Neither 4. You identify a protein in lab and find that it contains four BH domains (BH1, BH2, BH3 and BH4). Based on this fact, what do you hypothesize the function of this protein will be? (2 points) It is likely to act in an anti-apoptotic fashion, like Bcl-2. 5. The paper by Zhang et al. places three molecules into a sequential pathway. Which is the correct order of how these three molecules affect each other? (2 points) A. p53 DYRK1A mir-1246 B. p53 mir-1246 DYRK1A C. DYRK1A mir-1246 p53 D. DYRK1A p53 mir-1246 E. mir-1246 p53 DYRK1A
BIO360 Quiz 6 October 28 1. Name one technique that could be used to answer each of the following questions: (1 point each) Upon the overexpression of the DYRK1A kinase, which human genes become transcriptionally activated? Does the Ets1 transcription factor bind to the DNA near the RB promoter in vivo? Does the deletion of the E2F-2 gene affect the amount of Apaf-1 mrna in a living cell? Do the E2F-4 and DP-2 proteins bind to each other in vivo? What proportion of my cultured cells are in G 0? Microarray ChIP qrt-pcr (or Northern Blot) coip FACS 2. A portion of Figure 4A from the Zhang et al. paper is shown on the right in which an inhibitor of mir-1246 (or control oligonucleotide) was added to these cells, which were subsequently treated with etoposide or left untreated. Assuming that the model of Zhang et al. is correct, what will these two lanes in these western blots show for the levels of DYRK1A, p53 and Actin? Please briefly explain your answer. (3 points) DYRK1A levels should be high but unaffected by etoposide. This is because the inhibition of mir-1246 should releive the repression of DYRK1A and block the ability of p53 to decrease DYRK1A levels.? p53 levels in lanes one and two should look very similar to lanes three and four. Etoposide causes DNA damage which should lead to the stabilization of p53 -actin should be unaffected, since it s just our beloved loading control. 3. Telomere shortening leads to (2 points) A. Cell senescence B. Apoptosis C. Transformation D. Metastasis E. Immortalization
BIO360 Quiz 7 November 4 1. Name the two proteins encoded by the INK-ARF locus and briefly describe the function of each. (3 points) p16 Ink4A is a protein that inhibits CyclinD/Cdk4/6 complexes and thus inhibits passing through the restriction point. ARF is a protein that antagonizes Mdm2 and thus stimulates p53. 2. The diagram on the right helps to explain cellular senescence. Label both axes and circle the one point on the diagram where most cells enter senescence. (3 points) Telomere Length Cell Divisions 3. Imagine that instead of LIN52-Ser28 phosphorylation controlling assembly of the DREAM complex, what actually happens is that phosphorylation of LIN37-SER182 allows the MMB complex to form. In that case, what would Livtochick et al. s coip experiment have looked like? Draw in bands for the missing four lanes on the figure below. (4 points).
BIO360 Quiz 8 November 11 2 points each 1. pvhl directly transfers a ubiquitin molecule to HIF1- and thus would be classified as a(n) A. Ubiquitin Ligase. B. Ubiquitin Esterase. C. Ubiquitin Activating Enzyme. D. Ubiquitin Conjugating Enzyme. E. Ubiquitin Lyase. 2. What cell type makes up the wall of capillaries and other blood vessels? Endothelial 3. Interruption of Integrin binding commonly leads to which phenotype? A. Apoptosis B. Proliferation C. Quiescence D. Senescence E. Genomic instability 4. Tumors frequently become resistant to chemotherapuetic drugs over time. Why are angiogenesis inhibitors expected to avoid this problem? Angiogenesis inhibitors target normal (untransformed) cells which are genetically stable and thus much less likely to evolve resistance. 5. According to Chaffer and Weinberg, what are the two phases of cancer cell metastasis? The ability to move from the primary tumor to a distal site and then the ability to colonize the distal site.
Fold Enrichment BIO360 Quiz 9 November 18 1. Alphabet Soup: What does each of the following acronyms stand for? Answer any five of the six. (1 point each) DSB EMT HR MMP NER NHEJ Double strand break Epithelial to mesenchymal transition homologous recombination matrix metalloproteinase nucleotide excision repair Non-homologous end joining 2. In one sentence or less, what is the question that Fang et al. were asking in the figure shown on the right? (2 points) Does the ability of ionizing radiation to lead to the stabilization of MEN1 depend upon the ability of the protein to be phosphorylated on Ser394 and Ser399? 3. BRG1, p300 and Sp1 are all proteins that are believed to form a complex on the SPD promoter. Each gene was knocked down using the indicated shrna, followed by IP of one of the three proteins and PCR for the SPD promoter. Based on the data below, draw which protein binds to which other proteins on this promoter. (3 points) 20 18 p300 16 14 12 10 shrna NS Sp1 Sp1 BRG1 8 6 4 BRG1 p300 2 0 Sp1 ChIP p300 ChIP BRG1 ChIP