BIOC 511 Signaling Mechanisms and Proteolytic Process Questions

Read me First for Zandi lectures (BIOC511): Dear students, Here are some instructions for the BIOC511, Principles of Intracellular Signaling for October 27 and November 10. There will be two sessions. The first is a lecture on October 27. In this lecture will be an introduction to principles of signal transduction in cells. You will find a power point file for this lecture on the Blackboard. Please follow these instructions for the first lecture: (i) before class: Please go over the lecture Power Point and think about the questions that I have in some of the slides. I would like you to be ready to discuss your answers during the class. It is important to watch the attached video clips as well. (ii) After the class: Study the lecture material and answer the homework questions (see below) and email them to me. Answering the “after class” questions (see below) and emailing them to me will earn you 30% credit towards your total point for my exam question. Homework questions for BIOC511: What signaling mechanisms and biological regulatory advantages can you think of for receptors to be at various locations on and inside a cell? What is your understanding of “cell context” in regard to specific responses of different cell types to the same ligand? Describe advantages and disadvantages of having many sequential signal transmission steps in a signaling pathway? If you would design a new second messenger for a signaling pathway (pick a pathway of your choice) , what properties do you think the molecule should have? Compare it to known second messengers and explain why your second messenger is better. How many different post-translational modifications (PTMs) of proteins and non-protein molecules have been identified as a mechanism of transferring signal from one molecule to the next? Try to find out PTMs that are not mentioned in the lecture material. Discuss the mechanisms by which PTMs of proteins result in signal transmission. Compare and contrast phosphorylation/dephosphorylation to ubiquitination/de-ubiquitination of signaling proteins (enzymes and non-enzymes). Consider these questions: Which one is faster? Which one is reversible? Which one can be used in more than one way to relay specific signals (using the same molecule ubiquitin) for a different biological process? Which one is more economical for cells? What are the advantages and disadvantages of a proteolytic process (cleaving a protein by a protease) as a mechanism for signal transmission from one protein to another in a signaling pathway? Explain your understanding of properties of signaling in terms of specificity, amplification, desensitization/adaptation, and integration. Find one or more signaling pathways to help you with your explanation and highlight each properties of signaling in the pathway. What is your understanding of “speed” and “duration” of signaling pathways? Are these related? How do you think duration of signaling can determine the outcome? Provide biological examples. Think of mechanisms that would change signaling from “oscillation” to “sustained.” Discuss advantages of optogenetic methodology for investigating mechanisms of signaling pathways. Compare it to other methods used for signal transduction analyses methods. What is the most important advantage? You are working in your lab on a signaling project. List the questions (from high to lower priority) that you will consider to determine mechanisms and biology of the signaling pathway you are investigating. What methodologies you would use to investigate each question? Provide rational for as to why each method you plan to use will provide sufficient data to answer the question you are asking. Instructions for session 2: The session 2 will be on November 10. For this session, students are divided to 6 groups of 5. Each group is assigned a signal transduction topic to study and present to the class. The study and presentation preparation should be done before the class. The presentation time for each group is 9 minutes and 4 minutes for questions and discussions. The groups and their assigned signal transduction topics are shown below. This presentation will earn each group member 20% credit towards their exam question for my two lectures. Each presentation should include: • • • • • Brief discussion of biology of ligand(s) and receptor(s) and involvement in human diseases Description of Mechanisms of intracellular signaling pathway(s). Discuss and differentiate common (with other pathways) and unique signaling steps of the pathway(s). Description of the methodologies to study the mechanism(s) of that specific pathway Role in human diseases Application of signaling mechanisms in preventing, diagnosing, and treating human diseases I recommend to use this link: (https://www.cellsignal.com/pathways/pathways) for signaling pathways. However, you are encouraged to use other resources as well. These are the groups and their assigned signaling pathways. It is important that each group emails the power point presentation to our TA Benjamin H. Weekley ([email protected]) on or before November 9. Ben will upload the power points on the lecture hall computer before the class starts. Group 1: Topic: Alzheimer Disease Signaling Group members: Malia Stephanie Tammy Sanika Olivia Byun Dihardjo Doan Gulavani Henshaw [email protected] [email protected] [email protected] [email protected] [email protected] Group 2: Topic: NF-kB Signaling Group members: Yuzhou WenChien Paofen Gulbahar Yifan Hu [email protected] Jea Ko Kutluturk Liu_PreviewUser [email protected] [email protected] [email protected] [email protected] Group 3: Topic: Chimeric antigen receptor (CAR) Signaling Group members: Shruthi Angie Ethan Jemima Lingxi Melinamani Moreno Pan Pangemanan Qiu [email protected] [email protected] [email protected] [email protected] [email protected] Group 4: Topic: Inflammasome Signaling Group members: Matthew Zihe Tu Albert Ruichen Rohrig Shi Tang Wang Wang [email protected] [email protected] [email protected] [email protected] [email protected] Group 5: Topic: Signaling Regulating Apoptosis Group members: Xueqing Kathleen Abby Juanxia Shi Wang Watson Wiley Wu Yan [email protected] [email protected] [email protected] [email protected] [email protected] Group 6: Topic: Insulin Receptor Signaling Group members: Yuxin Doris Chentzu Julie Qingya Yang Yi Yu Yu Zhang [email protected] [email protected] [email protected] [email protected] [email protected]

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