Week 4 cell bio activities

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Apr 3, 2024

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Week 4-Membrane trafficking, Protein Folding and Degradation, Chromatin Lecture 6 Learning Outcomes (Membrane trafficking, protein folding and degradation) Membrane Trafficking What is a GTPase, and how are Rab proteins an example of that? How are GEF and GAP proteins involved? In a folded protein, where are most of the nonpolar vs. polar residues located? Why? What is cotranslational folding? What are possible issues that can arise during cotranslational folding? How does Hsp70-mediate correct protein folding? Describe each step. What is an example of how Hsp70-like proteins affect existing interactions between proteins? How does Hsp60 enable protein re-folding? Describe each step. What is the structural difference between normal and misfolded prion proteins? Describe why misfolded prion proteins are toxic. Related: Why are disease-related amyloid fibrils so structurally stable? Practice: Identify controls in cell biology experiments. Plan experimental design based on current research “knowns”. Protein folding and degradation What are the main players in the ubiquitin-proteasome system (UPS)? What is the function of each component, and how do they work together? How are misfolded proteins recognized and tagged by the E2-E3 ligase complex? How/why does a proteasome degrade just ubiquitin-tagged proteins? (not all proteins) Is the ubiquitin pathway only used for protein degradation? Lecture 6 Playposit Questions: 1. Warm up from last time: People often talk about “blowing soap bubbles” as an analogy for endocytosis. This is misleading, however. How is blowing a bubble completely different from endocytosis? Soap bubbles are blown in, whereas endocytic vesicles are pulled in. 2. GEFs are responsible for stimulating Rab to hydrolyze its GTP. False 3. The effector protein for a Rab is located on: the target membrane 4. Apply your reasoning: What determines the site where a Rab will be active? Where the Rab-GEF is 5. Observe and reason: What causes Hsp70 chaperonins to bind to a target protein? D. Hsp70 binds radom sites within a target. 6. Review your knowledge: You saw last week that an Hsp70 homolog (Hsc70) helps Clathrin baskets fall apart. How/why does that happen? Hsp70 loosens hydrophic interactions b/w clathrins. 7. Create a hypothesis: Which fly is carrying a mutation in the Hsp60 gene? B. the fly shown in the right side panel is an Hsp60. 8. Based upon what you know: Create a hypothesis: You read in an article that the center of an amyloid fibril “excludes water.” What does that mean? D. hydrophobic amino acids side chains are facing the center of the fibril. 9. You are a researcher hoping to develop a treatment or cure for Alzheimer's disease. Based on what we know about protein aggregation and disease, what courses of action to develop a drug soon make sense to take? A. design a drug that stops proteins from misfolding. B. design a drug that stops misfolded proteins from aggregrating 10. Of the two images pictured in this slide in the video, which one is the biological "control"? the top one “without therapeutic antibody” 11. Analyze and evaluate: The video we just watched was pretty good... however THIS movie (go to this link: https://www.youtube.com/watch?v=hvNJ3yWZQbE ) animates something inaccurately. What is wrong with the mechanism shown in this movie? C. the proteasome does not open and close like a recycle bin. 12. Pick the correct statement: E3 attaches to the target protein that needs to be degraded so that the Ubiquitin can attach to the target protein
13. Based on what we have learned previously in this course, how do you think E3 ligase recognizes mis-folded proteins? E3 has hydrophobic areas that recognize the misfolded protein. 14. Why is it important that cellular proteins are unstable? So that cells can respond to changing conditions rapidly, if needed. 15. True or False: The ubiquitin pathway is only used for protein degradation. False 16. True or False: Monoubiquitinated proteins are tagged for degradation.False 17. Lecture 7 Playposit- Chromatin and Nuclear Export/Import Lecture 7 Learning Outcomes (Chromatin, Nuclear import/export)   Chromatin What are the basic structural, organizational, functional features of the nucleus? What is a histone octomer comprised of? What is a nucleosome comprised of? How does modifying histone charge affect 1) DNA affinity for the octomer, 2) chromatin compaction, and 3) gene expression? What is the relationship between chromatin compaction and gene expression? How can histone tails be modified? What enzymes do those modifications? What are the consequences on chromatin state and gene expression with each type of modification? (i.e. acetylation, phosphorylation, methylation) Why/how is the “histone code” relevant to human health? What is peripheral heterochromatin, and what is its relevance to the human genetic disorder progeria? Explain 3 different ways that the nuclear lamina (or proteins associated with the nuclear lamina) can suppress gene expression. Nuclear import/export What are some basic properties of the nuclear pore? Can you describe structure/function? What is a nucleoporin? Why can’t all content simply float right through the nuclear pore? (what is the size limit?) What is a nuclear localization signal (NLS)? How does that become attached to a protein? How does an NLS help proteins interact with Karyopherin proteins? What is the function of a karyopherin? How do they aid protein transit thru a nuclear pore? How does GTP-Ran control the directionality of import by Importin proteins? What is a GTPase, and how is the activity of a GTPase generally controlled? Why is Ran GTP-associated inside the nucleus vs. GDP-associated when outside the nucleus? How are proteins removed from the nucleus by Exportin? Can you compare/contrast Importin and Exportin? (and how does Ran affect each of those? Week 4 Smartwork 5 Assignment: 1. Chaperone proteins can aid in protein folding by doing which of the following? B . Isolating a polypeptide chain within the crowded cytoplasm to prevent aggregation of proteins. C.steering partially folded polypeptide chains along the most energetically favorable folding pathway 2. A protein can be unfolded by a process called denaturation 3. How does the GTPbound form of a GTPbinding protein switch to a GDP- bound form? E. it hydrolyzed GTP, releasing a phosphate. 4. Many proteins are regulated by the binding of GTp or GDP. Which form is the activate state of the protein? C. the GTP-bound form.
5. What kind of enzyme removes a phosphate group from a protein? C. phosphatase 6. What kind of enzyme adds a phosphate group to another protein? B.kinase 7. Which of the following correctly describes phosphorylation of a protein? D. it can increase or decrease the protein’s activity. 8. Proteasomes act primarily on proteins that have been marked for destruction by the attachment of which small protein? A. ubiquitin 9. Where in a cell are most damaged proteins broken down? A. cytosol 10. In the living cell, histone proteins pack DNA into a repeating array of DNA–protein particles called what? Nucleosomes 11. The DNA in eukaryotic chromosomes is folded into a compact form by interactions with which of the following? Histones 12. The tails of the core histone proteins can be chemically modified by the covalent addition of what type of chemical group? D. all of these 13. Determine whether the following statement is true or false: In the chromatin of interphase chromosomes, regions of the chromosome that contain genes being expressed are generally more compact, while those that contain non-expressed genes are generally more extended. False 14. What is the general name given to the most highly condensed form of chromatin? C. heterochromatin 15. Based on these results, which part of the nucleoplasmin protein bears a nuclear localization signal? the tail only 16. Nuclear import is driven by the hydrolysis of GTP, which is triggered by an accessory protein called Ran-GAP ( G TPase- a ctivating p rotein). Which is true of this process? Nuclear receptors carry Ran-GTP from the nucleus to the cytosol. 17. Determine whether the following statement is true or false: The nuclear lamina disassembles and re-forms at each cell division. True Lecture 7 Playposit Questions: 1. Which of these histones are you more likely to find associated with an expressed gene? The histone on the right 2. Practice your knowledge: How much gene expression do you expect from the centromere and telomeres? Not much expression 3. Test your knowledge: What would you expect to happen in a cell treated with an HDAC-inhibitor drug? B. the cell will have more euchromatin than normal. 4. Apply your reasoning: Consider: As the gut microbiome digests dark leafy green foods, it makes an HDAC inhibitor (NaBu). Since veggies are generally “good for you”, how do you explain this? Loosening of DNA structure will prevent/suppress gut cancer. 5. Create a hypothesis: Why does methylating a histone sometimes drive heterochromatin formation? A. the methylating a histone sometime drive heterochromatin formation 6. Apply your reasoning: What would you expect to happen to the chromatin state of a cell if nuclear lamin proteins are mutated? A. There will be more euchromatin than normal. 7.
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8. Confirm your knowledge: S ince Karyopherins can travel in OR out of the nucleus, why do NLS-proteins stay in the nucleus? B. Importin binds Ran-GTP in the nucleus, preventing Importin from re-bind Importin. 9. Confirm your knowledge: What makes transport of NES-tagged proteins directional (out of the nucleus only) Ran-GTp is created in the nucleus, and NES can’t bind Exportin without it 11. Click "yes" below (this confirms to me that you have completed all the interactions) yes

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