Test Three final review

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  1. carbamoyl phosphate
    involved in denitirification and the urea process
  2. What reaction was done to determine structure of ATCase?
    break the S-S bond; run through cesium chloride; then centrifuge and separate products--> assay

    • before: only one peak
    • after assay: breakdown-- 2 peaks= r2, c3
  3. T versus R.
    T state: it is compact; the two lobes are bound by a hinge and they are held by ionic bonds between the amino acids; no space in the middle; side chains are too far apart

    R state: side chains are farther apart; two lobes close and the substrate fits in, allowing active site to be active; the lobes are held within the intramolecular bonds; pull apart and rotate
  4. adenylyl cyclase
    produces cAMP
  5. How many CAMP molecules bind to PKA?
    four bind to the regulatory sites
  6. What is the final common pathway in clotting?
    thrombin formation from prothrombin, which activates fibrinogen into fibrin, which forms a soft clot by cross-linking of lysine and glutamine by transglutaminase
  7. plasmin
    • responsible for cutting bonds int he alpha helical rods of fibrin
    • contains two kringle domains, a serine protease domain, and a fibrin binding domain
  8. Explain in-depth fibrin activation.
    this is the final step of the cascade

    cleavage of four glycine arginine bonds in the central region is going to release the A and B fibrinopeptides. A fibrinogen without these is a fibrin monomer. 

    The fibrin monomer is now capable of polymerizing into fibrin. The fibrin monomers come together to form fibrin. The homologous B and gamma chains have globular domains and holes at the ends that interact with peptides. A knobs fit into gamma holes to form protofibrils, which can be extended by beta subunits associating with other beta subunits. The newly formed soft clot is stabilized by formation of amide bonds between the side chains of lysine and glutamine
  9. blast cells
    still capable of dividing and proliferating
  10. MyoD
    signals production of transcription factors, which eactivate genes for proliferation and activate all muscle specific proteins; key role in regulating muscle differentiation
  11. Explain in detail the chains of myosin.
    six polypeptide chains

    the elongated chains form alpha helical coiled coil and do not have proline nor do they have kinks. There's a repeat of seven amino acids: ABCDEFG; and And D are hydrophobic, BCFG are charged.

    A and D always end up on the same side, allowing them to hide out int he helix. The charged ones lie on the utside.
  12. What is the function of the light chain in myosin?
    reinforces and gives strength during conformational changes
  13. What does actin use ATP for? 

    What direction is actin? myosin? tubulin?
    uses it to polymerize

    directional with plus and minus end; in sarcomere, it is unidirectional 

    myosin is bipolar

  14. HMM
    region of the myosin which contains the S1 and S2 regions
  15. power stroke
    reorientation of the lever arm
  16. Explain the transmittance of movement through myosin?
    little movement in the Ploop translates into slightly larger movement as switch I and II adhere tightly around the gamma phosphoryl group. This is going to cause conformation change in relay helix and thus movement of the lever arm
  17. Explain the troponin complex.
    t has the TnC, TnI, and TnT regions

    TnT is a tropomyosin-binding subunit which regulates the interaction of troponin complex with thin filaments

    TnI inhibits ATP-ase activity of acto-myosin; interacts with tropomyosin; conformational change leads to movement of tropomyosin away from the binding site that myosin can now bind to

    TnC is a Ca2+-binding subunit, playing the main role in Ca2+ dependent regulation of muscle contraction
  18. Why is the cytoplasm complex?
    gives structure to cell with no cell wall

    railway for communicatin system/ cell unit
  19. Intermediate filaments
    made of keratin; comes together in multisubunit helices like collagen
  20. MTOC
    microtubule organizing center; binding point for first subunit. Individual subunits polymerize outward.
  21. axoneme
    bundle of microtubule fibers and other associated fibers that is continuous with teh membrane; euk flagella is anchored by it
  22. nexin
    connects parts of microtubules to each other in the axoneme
  23. Dynein in axoneme
    the ATPase located all up and down the flagellum
  24. Method of dyneine?
    gets ATP in active site

    reaches out to next MT

    grabs it

    hdrolyzes ATP

    conformational change--> power stroke
  25. Dynein's affinity
    has affinity for MT; affinity changes whether ATP or ADP is in active site
  26. What does the motor domain of kinesin have?
    P loop, switch I and II, relay helix attached to neck linker
  27. What is the effect of chemorepellant to bacteria?
    Chemorepellnt binds to receptor on membrane, triggering a kinase adn overphosphorylation, which causes continuous tumbling.
  28. conformer
    with a conformer, your body will introduce more unsaturated fatty acids
  29. What is the aim when running lipid experiments?
    to develop a permeability scale; if you carry a charge, you don't get through with ease

    Hydrophobic molecules have an easier time
  30. prostaglandin H2 is not __
    a transmembrane protien
  31. What does prostaglandin H2 synthase do?
    it is lodged in the membrane/ detects damage to the membrane 

    • 2 step reaction: cyclooxidase and peroxidase
    • 1) converts fatty acids and all and converts it to hydrophilic molecule that signals pain and swelling associated with damage
  32. What is a third category of protiens?
    GPI anchored proteins? 

    addition of hydrophobic groups to associate the protien to the member (like prenyl groups to help anchor)
  33. What effect does chlesterol have on fluidity?
    It increases the period of time recovering
  34. Why is the membrane polarized?
    due to Na+-K+ concentrations

    • inside: high K concentration
    • outside: high Na concentration
  35. They have  gradient they move with. Once the receptor activates it, what happens?
    Na and K flow through the channel and depolarize the membrane to the point where there is no charge difference.
  36. How are the acetylcholine receptors isolated from the membrane?
    you need to isolate via affinity chromatography; contains snake venom that binds to the receptors and inhibits its funciton
  37. What is the structure of acetylcholine receptor?
    pentamer of four different subunits; 2 alpha, one beta, one gamma, and one sigma
  38. What is special about the alpha helix in acetylcholine receptors?
    side chains associated with the alpha helix extend through the channel and block
  39. Explain the patch clamp experiment.
    You go into the cell that has acetylcholine receptors and use a glass pipette to grab the piece fo membrane with receptors. 

    Another way is going into the cell and poking a hole

    an electrode is stuck inside nad outside the pipette. A voltage is applied and the current is mesured. Depending on resistance, the current will change. 

    Result: when channels close, the current needs to pass through the membrane. High resistance. 

    When the channels open, there is lower resistance and it goes in easiy
  40. When doing the patch clamp method with low resistanceseals, explain the pathway
    Suction leads to a gigaseal forming-->

    1) suction: whole cell mode: everything flows out; we have to supply NT outside of pipette

    2) excised-patch mode: inside out--we're removing other part; clog up the tip of the pipette with top or bottom view; apply NT inside pipette
  41. How do you isolate sodium channels?
    affinity chromatography with tetrodotoxin, which binds th Na channels to prevent function
  42. What happens in the S4 region when depolarization occurs (Na channels)?
    new set of charges as S4 rotates up out of the membrane
  43. What helps aquaporins to be more restrictive?
    there are positively charged side chains ner the constriction site to prevent movement through
  44. What are the two forms of energy?
    concentration gradient: allows diffusion across membranes

    membrane potential: charged disparity--> requires energy input to create charged disparity
  45. What is the key for sodium potassium pumps?
    at the core of the protein is an aspartic acid residue that gets phosphorylated
  46. lactose permease
    protein bacteria use to get lactose in cell

    move lactose against gradient/ requires energy; proton gradient that exists across abcterial cell membrane
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Test Three final review
Test three
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