Hao Nguyen

1. You want to synthesize an integral membrane glycoprotein to be embedded into the exoplasmic leaflet of the plasma

membrane. Describe, in detail, all the steps that are involved in the synthesis, post-translational modification, and transport of

this protein. Pay close attention to the location of the protein (with regards to which leaflet of each membrane encountered and

whether the hydrophilic region of the protein contact the cytosol or the lumen) in the organelle in each step of the process.

2. You have discovered a new organelle in eukaryotic cells. This organelle has a triple membrane (that is, there are three phospholipid bilayers that surround this organelle). It contains a small DNA molecule in the lumen; however, there is no sign of translation. Glycolysis occurs in the lumen of this organelle, but there are no enzymes necessary for the Krebs cycle or the Electron Transport System. What can you say about the evolution of this organelle, both structurally and functionally?

3. The transmembrane transport of polypeptides from the cytosol into the matrix of the mitochondrion (or the stroma of the plastid) requires the function of three types of membrane transports: TOM, TIM, and OXA. Why are all three required? Can one or two out of the three types be sufficient for this function? Why doesn’t the cell synthesize a transmembrane transport that crosses both mitochondrial membranes to allow a direct transport of molecules from the cytosol into the matrix of the mitochondrion?

4. The vesicular transport of cargo molecules like proteins requires the function of three types of coat proteins: clathrin, COP I, and COP II. Why are all three required? Can one or two out of the three types be sufficient for this function? Why are there so many other types of proteins that are involved in regulating vesicular transport? What happens to the pathway if one of these proteins is missing or present in a mutated, non-functional form?

5. Discuss the relationship among the following processes: flip-flop, membrane recycling via both vesicular transport and phospholipid exchange protein, and the function of flippase.

6. Why does each post-translational modification occur within a very specific organelle? For example, why can’t glycosylation occur in the medial-cisterna of the Golgi apparatus?

7. Also from lecture so far, we learned that many proteins and enzymes belong to specific families. Why should there be more than one protein for each cellular activity? Seems like a waste, don’t you think? Isn’t one protein/enzyme per activity enough?

8. Why are there are so many post-translational modifications? What happens if one or a few of these modifications were missing, would cellular function remain the same?

9. From lecture so far, we discovered that many different types of proteins with a variety of sizes and shapes could be embedded into the different cell membranes. What do you think is the property of the cell membrane that allows this type of insults by the proteins? That is, is it really that easy to embed a protein into the cell membrane? Why or why not?

10. Compare the endocytic pathway with vesicular transport. Describe similarities and differences between the two processes. Discuss about the significance of the similarities as well as the differences. (That is, why should there be steps that are used by both processes? On the other hand, why should there be steps that are used by one process, but not the other?)

11. Think about why the evolution of the various organelles in a eukaryotic cell was necessary. They evolved separately, differently, and for different reasons; so why and how?

12. Think about the importance of endosomes, what is/are the function(s) of these transient organelles? What would happen to the endocytic and/or exocytic pathways if these organelles were absent?