Study guide BIO 344 Exam II

Chapter 12

1. How do proteins get moved between the nucleus and the cytosol? All protein synthesis begins on ribosomes in cytosol except those synthesized by ribosomes of mitochondria and plastids. Amino acids on proteins contain sorting signals which direct to nucleus and elsewhere. Proteins move from cytosol to nucleus via gated transport.

2. What are nuclear pore complexes? Selective gates that actively transport specific macromolecules and marcromolecular assemblies as well as free diffusion of smaller particles.

3. What is a nuclear import receptor? A gene encoded for the recognition of nuclear localization signals which initiate nuclear import. Each family of such genes encodes for a specific receptor protein for the specialized transport of cargo protein subsets that contain nuclear localization signals to which the receptor can bind.

4. What molecule delivers energy to facilitate transport of large proteins into the nucleus? 5. Describe the subcompartments of mitochondria and chloroplasts. 6. What are protein translocators? 7. Why does it matter that the mitochondrial signal sequence for protein import forms an alpha helix? Describe the properties of this alpha helix. 8. Describe how proteins are imported into mitochondrial matrix. 9. What molecule provides energy for transport of proteins into the mitochondria? 10. How do proteins get directed to the intermembrane space? 11. What is the difference between smooth ER and rough ER?

12. Where does protein synthesis start? 13. How does a protein get directed to the ER? 14. What happens to the signal sequence after a protein has passed into the ER? 15. How do transmembrane proteins end up in the ER membrane? 16. What are start transfer and stop transfer signals? 17. How are proteins that pass the membrane multiple times inserted into the ER membrane? 18. How are proteins glycosylated in the ER? 19. What is the link between protein glycosylation and protein folding? 20. What happens when a protein does not fold correctly? 21. Where are membrane lipids assembled? 22. How do they end up in different organelles? 23. How come phospholipid exchange proteins are needed to transfer phospholipids from the ER to the mitochondria but these proteins are not needed to move phospholipids from the ER to the Golgi apparatus?

Chapter 13 1. Describe the endocytic and biosynthetic-secretory pathways in the cell. 2. How is vesicular transport different from transmembrane transport? 3. Describe the different intracellular compartments involved in the secretory and endocytic pathways 4. What is a coated vesicle? Name three types. Describe the compartments each of the three types move between. 5. Describe the steps involved in the formation of a clathrin coated vesicle. 6. What is a dynamin and what does it do? 7. How come a fruit fly with a dynamin mutation ends up paralyzed?

8. What is a SNARE protein? How does it lead a vesicle to the correct cellular address? How does it help the membrane of the vesicle and target compartment to fuse? 9. How is the HIV fusion protein similar to a SNARE protein? 10. How are proteins transported from the ER to the Golgi? 11. How are the correct proteins recruited into cargo vesicles? 12. What is a vesicular tubular cluster? 13. What type of proteins do you suspect to be retrieved from the Golgi back to the ER? 14. What is the cis and trans face of the Golgi? Which side is closest to the ER? Where do proteins enter? Where do they exit? 15. Describe some of the functions of the Golgi apparatus. 16. Where in the cell are the first polysaccharides added to proteins? Describe this polysaccharide. 17. What two main types of polysaccharide are formed after modification in the Golgi? How are these two types different? 18. Why does a goblet cell in the small intestine have most of is Golgi on one side of the nucleus (i.e. polar distribution)? 19. Are the enzymes in the cis face of the Golgi identical to enzymes in the trans face? 20. What do lysosomes do? 21. How is the interior of the lysosome different from the cytosol? 22. What kind of enzymes are present in the lysosome? 23. What label directs proteins from the Golgi to the lysosome? 24. Describe three different pathways that lead to degradation in the lysosome. 25. What is endocytosis? 26. What is phagocytosis? 27. What is autophagy?

28. What is exocytosis? 29. What kind of protein coat is present on endocytic vesicles? 30. Describe in detail how low density lipoprotein particles are taken up by the cell and how they provide cholesterol to the cell. 31. How can a defect in the low density lipoprotein receptor lead to heart disease? 32. Where do endocytosed materials go first? 33. What happens to the low density lipoprotein receptor after it is present in an endocytic vesicle? 34. Can you predict what types of proteins would be recycled and what types would be degraded? 35. What is a multivesicular body? 36. What is transcytosis and what do endosomes have to do with it? 37. What are differences between and early and late endosome? 38. What is the difference between a late endosome and a lysososme? 39. Why do recycling endosomes store important proteins? Describe the example of glucose transporters. 40. How come an intestinal epithelial cell has two distinct early endosomes? 41. Describe the two different pathways that deliver cell components to the cell exterior. 42. Why are neurotransmitters delivered to the cell exterior via a regulated pathway? 43. What signal is required on the protein to deliver it to the cell surface via the constitutive pathway? What about diversion to the lysosome? 44. What are mast cells? 45. What determines if histamines are released from cells? 46. What do histamines do?

Chapter 15

1. What is a signaling pathway? 2. Why do cells have signaling pathways? 3. What is the difference between a cell surface and an intracellular receptor? How do the signals for these two types of receptors differ? 4. Describe 4 forms of intercellular signaling. 5. What is autocrine signaling? Why do cells use it when deciding to differentiate (i.e. change cell type)? 6. What is a hormone? 7. What are gap junctions? 8. What determines if a cell survives, divides, differentiates or dies? 9. Does acetylcholine always cause the same changes in different cells? Describe some of the effects acetylcholine can cause in different cells. 10. Why must the lifetimes of signaling molecules be short? 11. What is nitric oxide? What role does it play in signaling pathways? 12. What are nuclear receptors? 13. What types of ligands do they bind? 14. Describe three domains of a nuclear receptor. 15. Describe the three largest classes of cell-surface receptors. Give an example of each. 16. What are second messengers? Describe three types. 17. What is a G-protein-linked receptor? 18. Describe the structure of the G-protein-linked receptor. 19. What is a G-protein? 20. Describe the structure of a G-protein. 21. What happens to a G-protein when it is activated? 22. Give an example of a signal that binds a G-protein-linked receptor. 23. How is a G-protein deactivated?

24. How can the G-protein-linked receptor be deactivated even when the signal remains present? 25. Describe in detail how G-proteins can change transcription patterns via cyclic AMP. 26. What is a kinase? 27. How is cAMP made? 28. Describe in detail how G-proteins activate kinase C. 29. What is a function of Ca2+ in the cell? 30. How do cells keep Ca2+ concentrations in the cytosol low? 31. What are 2 differences between enzyme linked cell surface receptors and Gprotein-linked cell surface receptors? 32. Give an example of a signal that binds an enzyme linked receptor. 33. What happens to an enzyme-linked cell surface receptor when the correct signal docks? 34. What is the Jak-STAT signaling pathway? What does Jak and what does STAT do? 35. Give an example of a signal that activates the Jak-STAT pathway.