4410 Final Exam Study Guide

Please note: This list is only meant to serve to remind you of the major points we covered. It has no content nor should it be construed as replacing the content in your notes.

A. Membrane Structure & Transport

  1. Recognize structures of phosphatidyl ethanolamine, phosphatidyl choline, phosphatidyl serine, sphingomyelin, cholesterol
  2. Formation of liposomes & black membranes; isolation of erythrocytes plasma membranes; use of these in membrane studies
  3. Structure of phospholipid bilayers
  4. Membrane fluidity & factors influencing it; experiments to study fluidity
  5. Compositional symmetry of membranes & vectorial labeling experiments
  6. Types of membrane proteins; solubilization experiments
  7. Proteins of the erythrocyte membrane
  8. Bacteriorhodopsin
  9. Lateral mobility of membrane proteins; experiments demonstrating lateral mobility
  10. Restricted lateral mobility with intestinal epithelial cells/glucose transport system as an example
  11. Definitions of glycocalyx and glycoproteins
  12. Simple diffusion, facilitated diffusion, active transport
  13. Gated ion channels
  14. Mechanism of the Na+K+ ATPase pump
  15. Na+glucose cotransport pump and the mechanism of glucose transport in intestinal epithelial cells
  16. Gated ion channels
  17. Mechanism of a nerve impulse

B. Cytomembrane system

  1. Pathways of protein trafficking; posttranslational & cotranslational import of proteins; chart showing paths of protein trafficking
  2. Roles in protein trafficking of endoplasmic reticulum, golgi apparatus, transport vesicles, secretory vesicles, endocytotic vesicles, lysosomes
  3. Experiments: pulse-chase with autoradiography or green fluorescent protein; viral models for cytomembrane system; differential staining; cell fractionation; genetic mutational analysis
  4. Structure of the ER; functions of smooth & rough ER
  5. Mechanism of cotranslational import in rough ER; formation of integral membrane proteins; synthesis of N-linked oligosaccharide in ER; lipid synthesis in ER and generation of lipid compositional asymmetry
  6. Structure & functions of the golgi apparatus
  7. Modification of N-linked oligosaccharide in golgi; phosphorylation of mannose in cis golgi of proteins destined for lysosomes; sorting of proteins for lysosomes in the trans golgi
  8. Coat proteins COPII, COPI, clathrin
  9. v-snares and t-snares and the targeting of vesicles to specific locations; synaptobrevin and syntaxin as examples
  10. Retrieval of proteins to compartments, with the KDEL receptor system as an example
  11. Exocytosis and the formation of the plasma membranes
  12. Endocytosis (phagocytosis, pinocytosis, coated pit), endosomes, and lysosome formation
  13. LDL cholesterol as an example of coated-pit endocytosis

C. The cytoskeleton

  1. Definition; types of cytoskeleton fibers; monomers of microfilaments & microtubules
  2. Concept of dynamic polymerization & depolymerization; measurment of polymerization by measuring viscosity
  3. Concept of molecular moters
  4. Study of cytoskeleton by visualization methods, genetic methods, biochemical approaches
  5. Details of microtubule structure from ppt & diagrams
  6. Microtubule associated proteins
  7. Details of microtubule functions from ppt & diagrams
  8. Inhibitors of microtubule polymerization or depolymerization & experiments using them as given in ppt
  9. General properties of molecular motors; details of kinesin, KLPs, and dynein as given in ppt & diagrams
  10. Details of microtubule organizing centers, centrioles, gamma tubulin, and assembly of microtubules, as given in ppt and diagrams
  11. Details of the dynamic properties of microtubules; role of GTP; as given in ppt & diagrams
  12. Details of ciliary/flagellar structure & motility given in the ppt & diagrams

D. Cell signaling

  1. Types of cell signaling covered in ppt, diagrams, & lecture notes
  2. Paracrine, endocrine, synaptic signaling
  3. Gap junctions
  4. Degradation of signaling molecules & its importance
  5. Intracellular (steroid) receptors vs cell surface receptors & the difference in their mechanisms
  6. Structure of steroid hormone receptors
  7. How steroid hormones act to produce changes in gene expression; primary response genes & proteins; secondary response genes and proteins
  8. Chick oviduct experiments on steroid hormone mechanism
  9. Three classes of cell surface receptors and how they differ
  10. Concept of a protein phosphorylation cascade in metabolic regulation
  11. Protein kinases and phosphatases
  12. Complete mechanism of G-linked protein receptors, including all enzymes involved, in detail as given in the ppt, lecture notes, and diagrams
  13. cAMP and calcium as second messengers
  14. Mechanism of epinephrine-mediated regulation of glycogen hydrolysis as given in the ppt, lecture notes, and diagrams.

Exam 1, version C: Answer key posted separately on Biology 4410 page. Correct mc choices are highlighted in yellow (you'll need word or openoffice to see it).

Exam 2 answers (1st version, not makeup):

A. Multiple matching: Spit-back, see notes.

B. Essay questions

1.  (a) The sequence deleted from site “B” was the signal peptide sequence that targeted the envelope protein to the er. When it was deleted, the envelope protein stayed in the cytoplasm.

(b) Take the sequence deleted from site “B” and splice it into site “A” You should see the capsid protein synthesized in the ER.

Spit-back, see notes & text diagram

Specific mannose residues on N-linked glycoproteins in lysosomal proteins are phosphorylated in cis-golgi to form mannose-6 phosphate. In the trans-golgi, these proteins are recognized by mannose 6-phosphate receptors that sort the proteins into vesicles destined for lysosomes.

4.  Scramblase enzyme in ER; flippase enzymes in plasma membrane (also in ER).

5. Spitback, see notes & ppt