Study Question Sets for Exam 2
Study Question Set 10
Protein Synthesis and the Secretory Pathway: RER

1. What sorts of proteins are synthesized entirely on free cytosolic polysomes?
2. What sorts of proteins are synthesized by polysomes bound to the endoplasmic reticulum?
3. Describe the essential feature of the signal sequence of proteins inserted co-translationally into the ER lumen.
4. Describe the process by which a ribosome destined to synthesize a protein inserted into the ER lumen cotranslationally reaches the ER.
5. Describe an experiment that would distinguish between co-translational and post-translational insertion of a secretory protein into the RER (or microsomes!).
6. Describe the role(s) of the SRP in positioning the ribosome-nascent protein complex at the translocon.
7. Explain briefly why it is important that SRP binding to the signal sequence causes translation to pause.
8. How does binding of SRP to the signal sequence of a nascent protein cause a pause of translation?
9. Describe briefly the current view of how SRP binding to its ER receptor positions the signal sequence for insertion into the translocon.
10. Expalin briefly why hydrolysis of GTP on the SRP and the SRP receptor might cause SRP to release from the signal sequence and from its receptor.
11. What is the role of the "signal peptidase"?
12. See if you can design an experiment that would demonstrate the importance of the fact that SRP pauses translation when it binds to a signal peptide emerging from the ribosome exit site.
13. What is the Sec61 complex of eukaryotes?
14. Which subunit of the Sec61 complex forms the protein translocation channel of the translocon?   How would we know this simply by looking at the structurs of the Sec61 subunits?
15. What is the nature of the "plug" that insures that a translocon not engaged in protien translocation does not form an open channel from the ER lumen to the cytosol?
16. What factors are believed to displace the "plug" in the protein translocating channel and allow transfer of proteins to the ER lumen?
17. Describe briefly the most recent model (based on X-ray data) for how the signal sequence is released form the translocon.   Is this model relevant to the insertion of membrane-spanning sequences of integral membrane proteins into membrane?
18. Explain the role of disulfide bonds in the folding of many proteins entering the ER lumen.
19. Indicate the role of protein disulfide isomerase (PDI) in the correct folding of many proteins translated by ribosomes of the RER.
20. Describe the general role of dolichol in the formation of an oligosaccharide chain that will be attached to the side chain of an asparagine.
21. Describe the roles of calnexin and calreticulin in preventing premature aggregation of segments of nascent glycoproteins during their translational insertion into ER.
22. Describe the roles of each of the following in "quality control" of glycoproteins in the ER lumen:(a) calnexin, (b) protein disulfide isomerase, and (c) glycosyl transferase.
23. Given that the Sec61 complex participates in cotranslational insertion of proteins into the ER lumen, posttranslational insertion of proteins into the ER lumen, and elimination of improperly folded proteins from the ER, what types of factors determine which role will be played by a translocon at any given time?   Explain briefly.
24. Compare general modes of action of the "motors" used by eukaryotic systems and bacterial systems for posttranslational translocation of proteins across the ER membrane (eukaryotes) and the cytoplasmic membrane(bacteria).   (Indicate the names of the "motor" proteins or protein complexes for each case.)
25. What is "BiP"?   Describe the role of BiP in posttranslational insertion of proteins into the ER lumen in yeast.
26. If a single-pass membrane protein has an internal signal sequence, what determines whether the N-terminus of the mature protein will be cytosolic or exoplasmic? Explain.
27. Describe a model that would account for the cotranslational insertion of a single-pass protein into membrane so that the N-terminus of the protein is cytosolic.
28. Describe two mechanisms for cotranslational insertion of a single-pass protein into membrane so that the N-terminus of the protein is exoplasmic.
29. Describe a model that would account for the insertion into membrane of a multi-pass protein having a cytosolic N-terminal tail.   Explain the essential features of the model.   What changes would be needed in order to make the protein have an exoplasmic N-terminus?   Explain briefly.
30. See if you can design an experiment that would demonstrate the importance charges at one or both ends of the start-transfer sequence in determining the orientation of a single-pass transmembrane protein inserted into the RER.   (Assume you have access to techniques that allow you to modify gene sequences to change the amino acid sequence of a protein.)

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