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UCSD BICD 110 - Problem Set Week 2

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BICD 110 Summer Session II 2009 Problem Set Week 2 1. What is compartmental diversity? Give an example.. 2. How do cells maintain compartmental diversity? 3. What is the significance of phosphatidylinositol in maintaining compartmental diversity? How are Rab and SNARE proteins involved? 4. T/F All protein sorting signals reside in a stretch of amino acid sequences called signal sequences which are found at N-terminus 5. T/F Most organelles are constructed de novo 6. Matching: a. Cytosol b. Gated Transport c. Organelle d. Transmembrane Transport 1. __________ Movement of proteins across a bilayer from the cytosol to a topologically distinct compartment 2. __________Contents of the main compartment of the cell, excluding the nucleus and membrane-bounded compartments such as endoplasmic reticulum and mitochondria 3. _________ Movement of proteins through nuclear pore complexes between the cytosol and the nucleus 4. __________ Membrane-enclosed compartment in a eukaryotic cell that has a distinct structure, macromolecular composition, and function 7. List three reasons eukaryotic cells require a nucleus as a separate compartment when prokaryotic cells do not? 8. Endocytosis is the process by which cells absorb molecules from outside the cell by engulfing it with their cell membrane. According to your book, what are the two main types, and how are they different? 9. Endocytosis has many different mechanisms, some mediated by receptors, and others not. What is/are the fate(s) of the macromolecules absorbed? The receptors (if they are present)? 10. What is transcytosis? Where does this process frequently occur? 11. Iron is needed by all cells. It is taken into cells via a two-component system. The soluble protein transferrin circulates in the bloodstream,and the transferrin receptor is a membrane protein that is continually endocytosed and recycled to the PM. Iron ions bind to transferrin at neutral pH but not acidic pH. Transferrin binds to the transferrin receptor at neutral pH only when it has bound an iron ion, but it binds to the receptor at acidic pH even in the absence of bound iron. From these properties, describe how iron is taken up, and discuss the advantages of this elaborate scheme. 12.. What is the main structural difference between rough ER (RER) and smooth ER (SER), and what is the functional difference associated with the structure? 13. If the cell has mutated, non-functional SRP (signal recognition particles), is this mutation likely to affect the structure of RER? How about SER? Why or why not? 14. What would you expect to see if you replace a functional Sar1-GEF on the ER with a nonfunctional Sar1-GEF? 15. What would you expect to see if you used nonfunctional tSNARE proteins? 16. Why is it that the acid hydrolases do not digest everything in the Golgi or the ER where they RE synthesized? 17. What is M6P and how do the M6P receptors “know” when to release the hydrolases into the lysosome? 18. What is the mechanism by which this is achieved in the lysosome? 19. Predict what will happen if the contents of a lysosome were to be leaked out into the cytosol. 20. Ran is a small ___ase that is common to all eukaryotes, is found in both the nucleus and cytoplasm, and is involved in nuclear import and export. Ran-___ promotes hydrolysis of GTP to GDP by Ran and is found in the ________. Ran-___ promotes the exchange of GDP for GTP on Ran and is found in the ________. 21. Proteins translated in the cytosol, destined for the Mitochondria, are translocated into the matrix of the mitochondria after the protein has been translated and before it has been folded. What keeps the protein from interacting with itself and folding too soon?22. Mitochondria have both inner and outer membranes, each of which is composed of a phospholipid bilayer. What two protein translocators are used to get a protein through both membranes? 23. If all the ATP was taken out from a mitochondrial matrix, could translocation occur? 24. Could translocation occur if a proton pore was inserted in the mitochondrion’s inner membrane? 25. If all the ATP along with protein chaperones were taken out from the cytosol, could an unfolded protein pass through the mitochondria’s outer membrane? 26. If protons were pumped into the matrix (instead of out) during the electron transport chain, would mitochondrial proteins still be able to be imported? 27. Mitochondria that are defective are sometimes seen with an excess of cristae as a means of compensating for less ATP production. Explain why this would


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UCSD BICD 110 - Problem Set Week 2

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