BIO 151 NYU Biological Data Signals And Communication Discussion

BIO 151 NYU Biological Data Signals And Communication Discussion

Sample Answer for BIO 151 NYU Biological Data Signals And Communication Discussion Included After Question

Bio151 WI22-23 Topic 6 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, Thursday, January 19th by 11:59pm —————————————–Some general helpful resources – places to start: https://www.khanacademy.org/science/biology/cell-signaling/mechanisms-ofcell-signaling/a/intracellular-signal-transduction https://www.nature.com/scitable/topic/cell-communication-14122659/ https://courses.lumenlearning.com/boundless-biology/chapter/signalingmolecules-and-cellular-receptors/ Bio151 WI22-23 Topic 6 Problem Set Answer Key Francis Question 1: The Concept of Signal Transduction In our everyday lives, we communicate in a variety of ways. Take a second and think about how you communicate every day and the variety of ways that those signals are sent or how communication happens. Cells need to signal and communicate as well – signaling and communication changes how cells behave, which means it changes which genes are being transcribed and which proteins are active and when, and thus changes the behavior of the cell. Write about how cells communicate and transduce signals, both inside the cell and from the outside into the cell, as well as from the inside of the cell to the outside (and presumably to other cells). What is happening during “signal transduction”? When an extracellular physical molecule is being used as a signal from outside the cell, must it physically enter the cell? If not, then how does the signal get “transduced” across the cell membrane? Question 2: The Shape, Chemistry, and Size of Signals Physical signaling molecules that signal to cells from outside the cell can come in a variety of different shapes, sizes and chemistry. Some can diffuse across the cell membrane and some cannot. What chemical characteristics would you expect signals to have that CAN diffuse across the cell membrane and what chemical characteristics would you expect signals to have that cannot diffuse across the cell membrane? https://www.khanacademy.org/science/biology/cell-signaling/mechanisms-ofcell-signaling/a/signal-perception Bio151 WI22-23 Topic 6 Problem Set Answer Key Francis Question 3: Signal Amplification The cell is a relatively big place with a lot going on. In this question, I want you to think about how cells might take a single extracellular signaling molecule binding to a single receptor, and end up activating a higher concentration of downstream signaling molecules inside the cell so as to “amplify” the original one single signal. The process of signal amplification can be important for increasing the speed of transduction from a single signal because it increases the concentration of active downstream molecules in the pathway, which means they will be more likely to find and bind to the next effector molecule in the pathway. **Remember that most things happen inside the cell by physical interaction and most molecules are moving around by random diffusion. Concentration really matters then because the more of two particular molecules you have in the cell, the more likely they are to interact with one another. Here, your job is to describe the concept of signal amplification, then create some sort of drawing or diagram to go with your description. Question 4: Comparing and Contrasting Signal Transduction Pathways To continue in the theme of thinking big picture about signal transduction pathways, I want you to realize that there are many, many different signal transduction pathways out there and that each pathway has evolved to function in the way that makes the most sense for that pathway and its function or outcome. Here I want you to think about, and practice applying, the concepts of crosstalk, signal amplification and speed of signal transduction in shorter pathways (less component steps) and longer pathways (more component steps). A. Do you think there would be more opportunities for crosstalk in a shorter pathway or a longer pathway? Explain your reasoning. Bio151 WI22-23 Topic 6 Problem Set Answer Key Francis B. Do you think there would be more opportunities for signal amplification in a shorter pathway or a longer pathway? Explain your reasoning. C. Do you think there would be a quicker speed of transmission in a shorter pathway or a longer pathway? Explain your reasoning. Question 5: Kinases and Phosphorylation Kinases are very common signal transducing/regulatory enzymes in the cell. In reference to when a kinase phosphorylates a protein in a eukaryotic cell, answer the following questions: A. Draw a phosphate group and describe its chemistry. B. In eukaryotes, which amino acids are phosphorylated and to what in those amino acids does the phosphate get attached? Bio151 WI22-23 Topic 6 Problem Set Answer Key Francis C. Is this reaction reversible? Can the phosphate be taken off after it gets put on, and if so, is there an enzyme that performs this action? D. What type of bond occurs between the phosphate and the protein – is it covalent or non-covalent and why does this matter? E. What is the source of the phosphate in eukaryotes? Draw the structure of that molecule. Draw a circle around the phosphate that is transferred from this molecule. F. How does phosphorylation change the activity of a protein? Does it cause the protein to be active? Inactive? Are there other outcomes of phosphorylation? Question 6: General Principle of Cell Signaling and Signal Transduction Is each of the following statements true or false? Explain your reasoning. A. There is never a time in which more than one signaling pathway is functioning at the same time. Bio151 WI22-23 Topic 6 Problem Set Answer Key Francis B. Cells in the human body that aren’t receiving any signals remain quiescent (meaning inactive but alive) C. The same signal can lead to different outcomes in different cell types in the body D. Receptor-mediated endocytosis always results in degradation of cell surface receptors. E. Phosphorylation of a protein changes its amino acid sequence. Question 7: Self-Renewal Signaling Diagram Use the basic signaling diagram (Diagram 1) to answer the following questions: Do you agree with each of these statements? For each answer yes or no and explain your reasoning. Diagram 1: Bio151 WI22-23 Topic 6 Problem Set Answer Key Francis A. TK2 inactivates the transcription factor TF by transferring a phosphate from ATP to the TF. B. Before the cell is exposed to signal, TK1 must have been transcribed and translated. C. TFa is a kinase. Bio151 WI22-23 Topic 6 Problem Set Answer Key Francis D. This signal can diffuse across the cell membrane. E. Even when not phosphorylated, receptor (RTK) can activate TK1. Question 8: The Mechanism of RTK Activation This question refers to the mechanism of RTK activation. Here is a good resource for this: https://www.nature.com/scitable/topicpage/rtk-14050230/ A. If a mutation occurs such that the signal molecule cannot dimerize, will RTK be phosphorylated? B. If a mutation occurs such that several of the tyrosines on RTK cannot be phosphorylated, will RTK dimerize? Bio151 WI22-23 Topic 6 Problem Set Answer Key Francis Questions 9: Broken Self-Renewal Signaling Pathway When mutations occur in the genes that code for signal transduction pathway protein components, then signal transduction pathways can become dysregulated. In this question, imagine that you have a cell that expresses and uses the signal transduction pathway outlined in Diagram 1. You observe that the cell is failing to respond to the extracellular signal for this pathway. The cell appears to be permanently insensitive to the signal molecule (no signal transduction outcome in response to the signal). Which of the following could explain the behavior of this cell? Answer yes or no and explain your reasoning. A. The receptor (RTK) has a mutation in the kinase portion of the receptor. B. There is a mutation in the transcription factor such that it is active even when not phosphorylated by TK2. C. There is a mutation in TK2 such that it is always active as a kinase. D. The cell surface receptor that binds this signal is not being expressed due to a mutation in its promoter and so is not present on the surface of the cell. Bio151 WI22-23 Topic 6 Problem Set Answer Key Francis Question 10: Signal Transduction and Feedback Loops A. What is a feedback loop (give an explanatory definition)? How is a positive feedback loop different from a negative feedback loop? B. Using our hypothetical signal transduction pathway from class, draw and describe an example of a positive feedback loop and a negative feedback loop. You’ll probably need to add in additional proteins and cellular processes in your loops and explanations. C. More feedback loops questions…. (i) What would happen if activation of the transcription factor in the Diagram 1 signal transduction pathway led to transcription (and then translation) of a protein involved in ubiquitin-mediated proteolysis targeting TK2? Would this be an example of a positive feedback, a negative feedback or not a feedback loop? Explain your reasoning. (ii) What if activation of the transcription factor led to receptor-mediated endocytosis of the receptor for this pathway? Would this be an example of a Bio151 WI22-23 Topic 6 Problem Set Answer Key Francis positive feedback, a negative feedback or not a feedback loop? Explain your reasoning. Question 11: Problem Solving in a Signal Transduction Pathway You are working in a lab and working on cells with the Diagram 1 signal transduction pathway. You analyze the proteins in the pathway and get the following the results (note that you are also going on the assumption that there are other components and pathways around in the cell.) The following table shows the status of several important factors in signal transduction in the cells: Receptor Present? Yes (in environment surrounding cell) No TK1 TK2 TFa Response occurring Yes Yes Yes Yes Signal Phosphorylation state Not applicable Not applicable (because receptor isn’t present) Yes No Yes Not applicable Which of the following scenarios could explain some or all of these results? Treat each question independently of the others and please be sure to thoroughly explain your reasoning. A. If signal is present, why aren’t all components of the pathway activated? Bio151 WI22-23 Topic 6 Problem Set Answer Key Francis B. Is it possible that ubiquitin-mediated proteolysis has removed the receptor from the cell surface? C. Imagine that there is a phosphatase targeting TK2. (i) What enzymatic activity does a phosphatase perform and what happens to TK2 activity as a result? (ii) If this phosphatase were being made or activated in response to TFa activation, would this be a feedback loop and if so, negative or positive? (iii) If this phosphatase were being made or activated through activation of a different pathway, what would this be called? Bio151 WI22-23 Topic 6 Problem Set Answer Key Francis (iv) If TK2 is dephosphorylated, hypothesize how TFa could still be phosphorylated and that response to the signal is still occurring. Feel free to include methods of modulation that we’ve discussed, such as feedback loops, proteolysis, endocytosis or pathway crosstalk. Explain your hypothesis.

A Sample Answer For the Assignment: BIO 151 NYU Biological Data Signals And Communication Discussion

Title: BIO 151 NYU Biological Data Signals And Communication Discussion

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