Study Question Sets for Exam 2
Study Question Set 13 -- Cytoplasmic Protein Targeting

1. Describe the general features of the process by which nuclear-encoded mitochondrial proteins reach the mitochondrial matrix as mature proteins.
2. Site-directed mutation of the gene for a plant nuclear-encoded mitochondrial matrix protein such that the cationic amino acids in the signal sequence are changed to neutral amino acids prevents import into mitochondria and often redirects the protein to chloroplasts.   Explain why.
3. Compare and contrast the matrix targeting signal equences of mitochondria to the stroma targeting signal sequences of chloroplasts.
4. Explain briefly how mitochondria and chloroplasts differ in the energetic factors directing the signal sequence of a nuclear-encoded protein into the matrix/stroma.
5. What do the acronyms TOM, TIM, TOC, and TIC stand for?   Explain briefly.
6. Describe the role(s) of TIM23.
7. Describe the roles of the following in targeting proteins into the mitochondrial inner membrane :
1. TIM23
2. TIM22
3. OXA
8. What does "PAM" stand for in the context of mitochondrial protein import?   What is the role of the PAM involved in mitochondrial protein import?
9. Describe two ways by which a nuclear-encoded protein might reach the mitochondrial intermembrane space.
10. Indicate the different mechanisms for import of nuclear-encoded proteins into the chloroplast thylakoid space.
11. Distinguish between mitochondrial matrix enzymes and lysosomal enzymes in terms of their sites of synthesis and the mechanism(s) by which they reach mitochondria and lysosomes, respectively.   Provide an evolutionary explanation for these differences.
12. Indicate the minimal requirements, as we understand them, for "tagging" nuclear proteins for correct compartmentation.
13. Describe the role(s) of nuclear import receptor proteins in the targeting of proteins into the nucleus.
14. Indicate the role of the Ran-GTP in delivery of a protein with an NLS into the nucleus.
15. Indicate the role of the Ran GTPase in delivering nuclear import receptor proteins to the cytosol.   Be complete.
16. Describe the role(s) of nuclear export receptor proteins in the targeting of proteins or protein complexes from the nucleus to the cytosol.
17. Explain how the Ran GTPase cycle can promote both nuclear import and nuclear export of appropriately "marked" proteinss.
18. Indicate the folding state of proteins during targeting of nuclear-encoded proteins into (a) the chloroplast stroma, (b) the mitochondrial inner membrane, (c) the nucleus, and (d) the peroxisome matrix .
19. What is an "SKL" signal?
20. Distinguish between PTS1 and PTS2.
21. Identify Pex 5 and Pex 7.
22. Describe the mechanism for inserting peroxisome matrix proteins with a C-terminal SKL targeting sequence into the peroxisome matrix.   Be complete.
23. Contrast the general mechanism for getting nuclear-encoded proteins to the mitochondrial matrix to that for getting enzymes into the peroxisome matrix.   Be complete.
24. Describe experimental evidence using mutants of Pex 1 and Pex 3 thatshowed that insertion of membrane proteins into the peroxisome membrane is independent of insertion of peroxisome protiens into the peroxisome matrix.   A well-constructed answer will include an indication of the functions expected of normal Pex 1 and Pex 3.
25. What feature of Pex 2 and Pex 16 provided circumstantial evidence that peroxisome membranes may arise from the membrane of the ER?   Explain briefly.
26. A paper published in 2003 (Molecular Biology of the Cell, 14: 2900-2907. 2003), which we discussed breifly in class, presented evidence suggesting that at least some peroxisome membrane proteins are of ER origin.   Describe the type of observations in this study that lead the authors to draw this conclusion.

Last Study Question Set for Examination 2

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