Protein Degradation Questions: What is protein homeostasis?

Under what circumstances do proteins fold? Unfold? Describe Anfinsens experiment, the results and his conclusions. What determines the 3 dimensional shape, or native conformation, of any protein? Describe protein folding. Describe the source of energy that drives protein folding. Can protein folding be a random process? How was Levinthals paradox resolved? How does the funnel diagram describe the energetics of protein folding? - Describe the parameters depicted on the two axes. - How might these graphs compare and contrast for different proteins. - What might the funnel for RNase A look like? - What might the funnel for a very large, complex protein look like? Chaperones Define Chaperone, Co-Chaperone, Chaperonin and substrate protein. Evolution of chaperones. Which organisms have chaperones? How similar or different are chaperones across phyla? In what contexts and cellular compartments do chaperones function? Describe the Hsp70 cycle. How does the HSP70 chaperone help the cell cope with misfolded or unfolded proteins? How does Hsp70 recognize misfolded proteins? What is chaperonin? Describe its structure.

- Describe the steps of the chaperonin cycle. What events trigger each step? - How does the chaperonin recoginize specifically misfolded or unfolded proteins? - Relate the concepts of multisubunit complexes, protein domains, and allosteric conformational changes to the chaperonin cycle. - Mechanisms: how does the chaperonin help the substrate protein fold properly? - What sources of energy are used in the various steps of the chaperoin cycle? - Compare and contrast the chaperonin to a machine. - Size of chaperonin - Size of the GroEL Chaperonin with the GroES co-chaperonin cap. - Allosteric Conformational Changes of Chaperonin Membrane Transport Questions: Membrane structure and properties Membrane transport of small molecules: describe the processes and the proteins that carry them out. 1) Passive diffusion 2) Coupled transport (secondary active transport) 3) Active transport Describe osmotic pressure and osmosis. Describe the protein complex that facilitates osmosis. Structure, selectivity for water molecules. Describe the experiment that simply demonstrates the ability of this complex to transport water. Voltage-gated ion channels Compare and contrast voltage-gated, ligand-gated, and mechanically gated channels. What kind of transport is carried out by channels? (in terms of the energetics). Compare the rate of channel mediated transport to other types of transport. What are the three states of voltage-gated channels? Describe the structural features and the properties of the channel in each state. What is the basis of ion selectivity? Describe the structure of the channel and how this occurs. How does voltage sensing work? What happens to the structure and properties of

the channel? What is an electrochemical potential? What are its two components? What does it refer to? At one spot/place on a membrane separating two solutions with different solutes, can there be more than one electrochemical potential? How is the electrochemical potential expressed by equations? What is a membrane potential (Em)? Can there be more than one membrane voltage potential at one spot/place on a membrane separating two solutions with different solutes? When a membrane potential is negative or positive, what does this mean? For example, if the Em is -50mV how does this differ from an Em of 50 mV? How is Em measured? Describe the basis of any Em. Estimate how many ions are involved per square micrometer of membrane? Is this a significant number relative to the concentration? Describe two processes that can generate a membrane potential. What are they called? How do we describe in an equation the Em that is be generated by channelmediated transport of ions? What is an equilibrium potential? What does this tell us? How is this calculated? Compare the equilibrium potential for a monovalent cation and a divalent cation for the same concentration gradient (i.e. [10 mM]out vs [100 mM]in). Explain how these ion types have different equilibrium potentials?