BIO353: Exam 2 Short Answers Module 11: Actin Filaments 1. Draw an actin monomer and an actin filament and label all the parts, molecular weights, etc..
... [Show More] 2. Explain the geography of actin filaments. Explain the geography of stress cable, filapodia and lamelliapodia in a cell, and locomoting in a culture plate. 3. Focusing on actin monomers and actin filaments: explain what occurs when a cell reverses its direction by 180 degrees. 4. Explain how the binding of ATP affects cytoskeletal monomers. Explain how the function of cytoskeletal networks can change depending on reversible binding of cytoskeleton associated proteins 5. Describe how myosin II can be made into a tool to analyze the different polarities of actin filaments in the cell. 6. Draw the structure of a myosin II molecule when its light chains are not phosphorylated. 7. Explain the geography of actin filaments as it relates to a living cell. 8. Explain how myosin II can be made into a tool by scientists using biotechnology. And explain how this can be used to determine the orientation of an actin filament in: 9. Explain what cell permeabilization is. Module 13: Microtubules 1. Describe the physical and chemical properties of the monomer and polymer of microtubules. 2. Explain how microtubules assemble and disassemble. 3. Explain what molecules in a living cell are necessary to nucleate microtubules. 4. Explain the geography of microtubules. 5. Explain how the geography of the cytoskeleton integrates with the transport of membrane vesicles that are part of the endomembrane system. 6. Explain how the structure of the microtubule singlet is altered when associated with a cilium or flagellum, or in an animal cell, the centrosome. Can you draw the cross section of the 9+2 configuration of microtubules? 7. Describe how to determine the (+) and (-) ends of a microtubule under laboratory conditions. 8. What “job” do molecular motors have? What is their energy source? 9. Describe the eight (8) representative microtubule network-associated proteins that regulate and act on the microtubule network. Module 14: Intermediate Filaments & Intercellular Junctions 1. Classify a) actin filaments, b) microtubules, c) intermediate filaments based on their ability to treadmill 2. Describe the physical and chemical properties of the monomer and polymer of intermediate filaments. 3. Illustrate the types of junctions that can exist in an epithelium and include the cytoskeletal components as well as essential transmembrane proteins. 4. Contrast the function of the Gap Junction with the other types of junctions in epithelial tissues. 5. Discuss why it is likely that epithelial cells evolve backup mechanisms to prevent leakiness of epithelia, and why this likely increased the fitness of the organism. 6. Explain how an epithelium can develop a barrier function similar to that of the plasma membrane. Explain the roles of the cytoskeletal networks in establishing an epithelium. 7. Describe the function of an anastomosing layer of a tight junction. In answering this question also explain the role of an anastomosing layer of adhering junctions in the same area. 8. Within the three-dimensional shape of the cell, explain the organization of tight junctions and adhering junction so that they do their job properly. 9. Write a paragraph to provide an overview about the molecular motors that function using intermediate filaments. 10. Fill in the blanks on this chart: polarity assembly/disassembly nucleation site nucleotide triphosphate molecular weight of the monomer Actin filaments Microtubules Intermediate filaments 11. Explain the geography of intermediate filaments. 12. Explain how the unique geography of nuclear lamins could serve to protect the DNA. 13. Explain what molecules in a living cell are necessary to nucleate intermediate filaments. 14. Explain the component needed to link nuclear lamins to the surrounding cytoskeletal network in the cytoplasm 15. Illustrate and explain how the strongest of the cytoskeletal filaments systems is organized. 16. Explain how intermediate filaments assemble and disassemble. 17. Compare and contrast how actin filaments, microtubules, and intermediate filaments react when placed in distilled water. Module 15: Cell Fractionation 1. What is the difference in results between a) conducting a cell permeabilization and b) detergent extraction of a living cell to prepare the cytoskeleton? 2. List the components of the homogenization buffer, and what each component does. 3. Why is the nucleus removed by a low speed centrifugation? 4. Why does detergent have to be applied well above the critical micelle concentration when detergent extracting a living cell? 5. Would Tris (also called Trizma) buffer be a good buffer to be placed in an "intracellular buffer"? Explain your answer. 6. After detergent extraction, how do you concentrate the soluble fraction? Explain this in detail. Module 16: Endomembrane System 1. Explain the signal sequences that have a role in getting a newly synthesized mRNA, that has just exited the nuclear pore, to the rough endoplasmic reticulum (RER) with the nascent peptide extending into the ER (i.e., co-translational insertion). Your answer should include all the receptors and where they recycle to. 2. Explain how to make a luminal protein. Explain how to make a transmembrane protein. Explain how to make multi-pass transmembrane protein. Define the function of 3 Resident Proteins of the ER. 3. Explain how a membrane vesicle is separated from the ER for transport to the Golgi? 4. Explain how evolution of the endomembrane system gave rise to a new type of protein synthesis in cells 5. Based on the physical and chemical characteristics of a biological membrane estimate what you think will happen to the extensive biological membrane of the RER and smooth endoplasmic reticulum (SER) as a result of the homogenization technology 6. Explain the relationship between the endomembrane system and membrane-bound polyribosomes Module 17: Membrane/Protein Flow 1. Assess the endomembrane system and decide whether its evolution decreased or had no effect on the fitness of cells. 2. Illustrate the geography (subcellular localization) of the components of the endomembrane system and label all the parts. 3. Explain how all parts of the endomembrane system acquire new membrane and new lipids. 4. Explain how the pre assembled carbohydrate tree is assembled and then covalently linked to a protein in the endomembrane system. 5. Explain how a membrane vesicle is separated from the ER for transport to the golgi apparatus. 6. Describe how these vesicles are first targeted to the correct location in the endomembrane system and subsequently how they fuse into that endomembrane compartment. 7. There are six functions of the smooth endoplasmic reticulum (SER). Name five of them. Module 18: Golgi Apparatus and Exocytosis 1. Explain how membrane flow participates with membranes that are part of the endomembrane system, but also part of the plasma membrane. 2. Contrast constitutive exocytosis with regulative exocytosis with attention to the number of signal sequences needed for each. 3. Explain the "inside-outside rule.” 4. Explain how evolution of the endomembrane system gave rise to a new type of protein synthesis in cells 5. Explain how the inside rule is involved in preventing pathological polyspermy. Module 19: Making a Lysosome 1. Explain how unique proteins and lipids are targeted to the primary lysosome and what prevents these proteins from destroying the cell. 2. Explain how the pre assembled carbohydrate tree is assembled and then covalently linked to a protein in the endomembrane system, and later modified in the endomembrane system. 3. Explain what cytoskeletal system is involved in the movement of proteins and lipids to make the primary lysosome. 4. What is the name of the enzyme that digests: a) lipids, b) proteins, c) nucleic acids? Module 20: Protected Compartment of the Nucleus 1. Describe how new lipids enter the nuclear envelope. 2. Explain how histones enter the nucleus. 3. Draw the structure of nuclear pore and label all the parts. 4. Do all proteins with nuclear localization signals enter the nucleus? 5. Explain how the unique geography of nuclear lamins could serve to protect the DNA. [Show Less]