Bio151 WI22-23 Topic 7 Problem Set Answer Key Francis Instructions: ✓ Download this problem set, keep the questions in the document and please type your answers in a color other than black so that your answers are easily discernable. ✓ Complete this entire problem set – give robust, detailed responses – this is practice so use it as such. ✓ If you get stuck or need clarification on any of these questions… just ask! ✓ Upload this document with your answers to the appropriate TurnItIn link in our Moodle page in PDF format ✓ Please be advised that TurnItIn is a plagiarism and similarity checking software o You are always welcome to work with other people and/or get help on the problem set, however… o Make sure that you close and put away all sources of information before writing your answers so that you can be sure that your answers are in your own words and to convince yourself that you understand the concept and can explain it yourself. o If your answers are too similar to either someone else’s responses (past or present) or from the internet, points will be deducted as the assumption will be made that the work you’re doing is not your own. Complete the entire problem set. For grading, a problem or two will be randomly chosen for grading of 10 points and will be graded for completeness and originality worth 5 points; 15 points total. Due date: Sunday, January 22nd by 11:59pm Question 1: Events of the Cell Cycle For cells, cell division is a high-risk high-reward activity. However, this process is required for cells to make more cells, so they don’t really have a choice – thus, when they do undergo the cell division cycle, they do so very carefully. Describe what happens in each stage of the eukaryotic cell cycle and what cells are paying attention to or checking for at each of those stages. Bio151 WI22-23 Topic 7 Problem Set Answer Key Francis Question 2: Regulation of CDK Activity CDK is the “master cell cycle regulator” in eukaryotic cells. Its activity is carefully regulated. Describe and explain three different ways in which CDK activity is regulated in the cell during the cell cycle. Please number or “bullet point” your answers. Suggested resources: https://www.nature.com/scitable/topicpage/cdk-14046166/ https://en.wikipedia.org/wiki/Cyclin-dependent_kinase Question 3: G1-phase CDK Regulation Use the diagram and information below to answer the following questions: Growth factors Bio151 WI22-23 Topic 7 Problem Set Answer Key Francis During G1-phase, CDK is phosphorylated at two different amino acids by two different kinases, called Wee1 Kinase and CAK (CDK Activating Kinase). As you can imagine by its name, CAK phosphorylation of CDK activates CDK activity. Wee1 phosphorylation of CDK causes CDK to be inactive (even when CDK is bound to cyclin and phosphorylated by CAK). As cells are in G1-phase, preparing for S-phase, the proper cyclins are made due to growth factor signaling, and CDK is phosphorylated at both positions and is thus inactive. At the same time, a transcription factor called E2F is made and is kept inhibited by a protein called Rb. Once the cells are ready to commit to going through the cell cycle, a phosphatase is activated, which removes the inactivating phosphate from CDK (the phosphate that Wee1 kinase put on), thus activating CDK. CDK phosphorylates Rb, which causes it to have poor affinity for E2F. This causes E2F to be active as a transcription factor, which activates transcription of proteins needed for further movement through the cell cycle. E2F activation is the “commitment point” of the cell cycle. This is an important decision point because cells are committing themselves to completing the cell cycle (or undergo programmed cell death if they can’t or if things go badly wrong). When there are mutations in these regulatory mechanisms, this can affect the amount of time cells spend in G1-phase. Since cells grow during G1-phase, researchers found that mutations in particular proteins that cause CDK to become active too early caused the cells to be smaller than normal, and mutations that caused CDK activity to be delayed caused cells to be larger than normal. For each of the following mutations, which mutations do you expect would lead to cells that are smaller than normal or which would lead larger than normal cells? Explain your reasoning. A. A gain of function in Wee1 kinase (more active than normal). Bio151 WI22-23 Topic 7 Problem Set Answer Key Francis B. A loss of function in the phosphatase that takes the Wee1 phosphate off. C. A mutation in CDK at the amino acid that normally gets phosphorylated by Wee1 such that CDK cannot be phosphorylated by Wee1 kinase. Question 4: CAK CAK (CDK Activating Kinase) is a serine/threonine kinase that phosphorylates CDK at a specific threonine amino acid in the CDK polypeptide. What would happen if we changed that threonine to an amino acid that can’t be phosphorylated, like alanine? Based on your knowledge of cell cycle regulation, be as specific in your answer as possible. Question 5: Chronology of Cell Cycle Events and Regulation Re-write the following cell cycle events in chronological order: Cohesin cleavage Chromosome segregation Bio151 WI22-23 Topic 7 Problem Set Answer Key Francis Dephosphorylation of G1-cyclin/CDK (of phosphate that Wee1 kinase put on) DNA replication Growth factor receptor activation Spindle Assembly E2F activation Cytokinesis G1 cyclin proteins are made G2 checkpoint Questions 6: Getting Stuck? In which phase of the cell cycle would cells get stuck in the following mutated protein scenarios? Briefly explain your reasoning. For each question below, choose from the following: G1-phase S-phase G2-phase M-phase The cells would not get stuck but might have an over-proliferative phenotype A. A loss of function mutation in the phosphatase that dephosphorylates CDK B. A gain of function mutation in E2F Bio151 WI22-23 Topic 7 Problem Set Answer Key Francis C. A gain of function mutation in Rb D. A loss of function mutation in a CDK inhibitor Questions 7: Checkpoints Our cells have robust checkpoint and DNA damage responses because they do not want to divide if their DNA is too damaged. Based on what we discuss in this topic, would you expect the following events to occur if some DNA damage occurs during the cell cycle? Bio151 WI22-23 Topic 7 Problem Set Answer Key A. CDKI binds to CDK B. Rb binds to E2F C. p53 bind to DNA D. Rb is phosphorylated E. Apoptosis might be activated if needed Francis Bio151 WI22-23 Topic 7 Problem Set Answer Key Francis F. E2F binds to DNA Questions 8: Chromosome Segregation and the Spindle Assembly Checkpoint in M-phase Your graduate student advisor has a population of cancer cells that seem to have a defect in chromosome segregation. She hypothesizes that the cells are prematurely cleaving their cohesin before chromosomes can be aligned at the metaphase plate. She devises a number of scenarios that she thinks could cause premature cleavage of cohesin or that she thinks would be a possible outcome of premature cleavage of cohesin. Do you think her ideas are valid? Here’s some helpful info for this question: Overview of Spindle Assembly Checkpoint: This is a key event in M-phase and there is a cascade of events that must take place to trigger the onset of anaphase. When cells “sense” that all sister chromatids have their proper microtubule attachments in the spindle, they activate this cascade of events. A. The graduate student thinks that she should see an abnormal number of chromosomes in the resulting daughter cells after cytokinesis in these cancer Bio151 WI22-23 Topic 7 Problem Set Answer Key Francis cells. B. The graduate student thinks that a gain of function mutation in Cdc20 could lead to premature cleavage of cohesin. C. The graduate student thinks that a loss of function mutation in securin could lead to premature cleavage of cohesin. D. The graduate student thinks that a loss of function mutation in APC/C could lead to premature cleavage of cohesin. Question 9: Cancer Genetics A. Define a proto-oncogene. What type of mutation in a proto-oncogene tends to lead to a cancerous cell phenotype? What is the proto-oncogene called once it has been mutated in this way? Suggested resource: https://www.nature.com/scitable/topicpage/cell-cycle-control-by-oncogenesand-tumor-14191459/ Bio151 WI22-23 Topic 7 Problem Set Answer Key Francis B. Define a tumor suppressor. What type of mutation in a tumor suppressor tends to lead to a cancerous cell phenotype? What is the tumor suppressor called once it has been mutated in this way? C. Which combination of these types of mutations is thought to lead to an overproliferative phenotype and why? Which of the following are examples of situations that would likely lead to an over-proliferative cell phenotype? Yes or no and explain your reasoning. When you explain, be sure to discuss whether the affected protein is a tumor suppressor or a proto-oncogene/oncogene. D. A mutation in CDK that causes it to be active even when not bound to cyclin E. A mutation in p53 such that it cannot bind to the DNA F. A mutation in p53 such that it is always active as a transcription factor Bio151 WI22-23 Topic 7 Problem Set Answer Key G. An E2F transcription factor that cannot bind Rb and is always active Francis