Chapter 10 Lecture 2

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DesLee26
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286175
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Chapter 10 Lecture 2
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2014-11-09 21:42:54
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Sam
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BIC
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Test Three
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  1. Explain promoters and enzzymes.
    Promoters bind to very specific sequences within the promoter. If we affect sequences in oriniterm we affect the binding of proteins or whether it is n or off
  2. At promoter, what happens.
    different proteins accumulate

    • many involve direct contact of DNA
    • Everything is replicated
  3. Mutations cant what?
    tell the difference between exons and introns. They just cause mutations. If within exons, the Km and Vmax can be affected, altering amino acid associated with active site--> reaction mechanism is affected or the binding affinity of substrate is affected
  4. Isozymes
    cells can use this for regulation. 

    Evolutionarily speaking, the gene for an enzyme existed--> gene replicated--> if it mutated, different variations of the gene arise--> same function of enzyme withdifferent structure
  5. Explain the lactate dehydrogenase example.
    lactate dehydrogenase coverts pyruvate to lactate

    Circles are the M version and squares are the H version. 

    As a fetus, the circles are more occupied, whcih represent a lower affinity for pyruvate, because the fetus gets oxygen from mom. As they get older (even when still in the womb and preparing for birth), signals in the womb cause change to squares to signal that the environment will change. The squares have a better affinity for pyrute and works better under aerobic conditions

    in heart?
  6. What is a cascade?
    when you take a little tiny signal and amplify it
  7. What are some modifications of protein activity?
    we're inside cells; a captive supply of ATP allows a phosphate group to be added to or removed from Ser, Thr, and Tyr. After conformation of prootein--> can turn it on
  8. Explain the phosphorylation process.
    Take the -OH group, bring in ATP, pop off the gamma phosphoryl group and add it to protein--> phosphorylation (done by glycogen phosphorylase)

    Use protein phosphatase to remove it
  9. Explain phosphorylation in terms of proteins and phosphates.
    Free energy increases and is highest when the protein is not phosphorylated; ATP has all three phosphates

    Protein-P has higher energy than just protein (net loss of energy between ATP and ADP; there is loewr energy in ADP, but protein now has a higher free energy associated with it (when the phosphate is attached)

    Protein and free phosphate have lowest energy
  10. What is cAMP?
    second messenger and helps transmit signal from membrane to cytoplasm; produced by adenylyl cyclase; taking ATP and making cAMP
  11. Protein kinase A?
    four olypeptide chains (2 catalytic and 2 regulatory);

    • key aspect lies in the regulatory subunits and has two features that can regulate PKA
    • 1) binding sites for cAMP
    • 2) ???
  12. PKA is a what?
    serine, threonine kinase; it finds specific serine and threonines that are in the sequence: Arg-ARg-x-S/T-Z, where x is the small and Z is the large hydrohphobic one
  13. Binding site for cAMP
    camp incerases, it readily diffuses and binds to regulatory site--> conformational change--> causes regulatory subunit to let go of catalytic subunit
  14. What is the sequence in PKA called?
    consensus sequence, which is a generic term to describe any protien sequecne that you find over and over again doing the same thing
  15. What does an inhibitor do?
    provides a pseudosubstrate. 

    It replaces Ser/ Thr with another amino acid; so, everything binds, but no reaction is catalyzed because the alanine (or replacement amino acid) replaces the Ser/Thr). Can't get phosphorylated because there is no Ser/ Threonine
  16. In proteolytic activation, what is not an option?

    What are some examples of this?
    reversibility

    digestive and blood clotting
  17. Explain the process in summary.
    Zymogens are secreted into the intestine; we don't want tem active within cells; so, they are packaged into membrane bound vesicles in proenzyme force. Signal comes--> granules fuse to membrane and zymogens are released, but must be activated.
  18. Proenzyme versus zymogen.
    • proenzyme: inactive form of an enzmye
    • zymogen: inactive form of a protein
  19. Explain activation of chymotrypsin.
    it exists as a 245 amino acid protein 

    there is cleavage between the 15th and 16th protein to create pi-chymotrypsin, which acts on other pi-chymotrypsins to cleave into three polypeptide chains, which is the functional one
  20. Explain the conformational change of chymotrypsin.
    it comes right after the first cut. Isoleucine is originally on the surface, but goes inside the protein once cut. It also has a positively charged amino termnus that attracts Asp 194

    Movement of one drags the whole chain with it, producing a hydrophobic pocket that makes the active site and positions the catalytic triad so that they function properly
  21. Explain activation of zymogens for the stomach?
    in the stomach, they must all be activated, but are not all active int eh cell. 

    Enteropeptidase activates trypsin, which is the master protease, activating all the proteases and itself.
  22. Proteins can begin doing what to each other? To prevent this, what happens?
    digesting each other

    inhibitors are released with the enzymes
  23. Trypsin inhibitor?
    has a lysine residue to fit into the active site

    when it binds, its half life is long--> stays bound for a long times and inactivates the enzyme--> doesn't function
  24. Amount released is proportional to the amount of __.
    enzyme released (irreversible inhibitor)
  25. Explain elastin.
    has a random conformation and is found in tissues that regularly change shape

    target of elastase: released to desgrade damaged elastin and remodel
  26. What does elastin have?
    has an inhibitor- alpha antiproteinase to inhibit it
  27. When will the inhibitor not work?
    when there is a mutation in the inhibitor gene and change in charge

    proactively damaged by smoking (oxidation reaction prevents binding of inhibitor on elastase, whcih goes crazy, digesting elastin) Body replaces it with collagen
  28. Blood clotting...

    what are clots?
    Platelets embedded in a mesh of cross-linked fibrin
  29. Reasons for clot:
    • stop bleeding
    • temp. shield over wound surface
    • matrix through which new cells repair the wound [scaffolding matrix]
  30. Two pathways that lead to a clot that differ by teh __.
    sources o damage

    intrinsic: exposure to an unnatural surface; broken skin

    extrinsic: blunt forced trauma
  31. What are the clots done by?
    thrombin and fibrin 

    prothrombin adn fibrinogen are the precursors
  32. It is a __ and keeps the response __.
    cascade

    localized
  33. Fibrinogen

    - structure
    three pairs of polypeptide chains

    present in blood in high concentrations (3 mg/ml)
  34. What is the key to fibrinogen?
    • 1) stays soluble
    • 2) stays monomers (not polymers)
  35. What is not important? They just need a lot of negative charges to __
    sequence

    • help keep them soluble
    • help them repel each other to prevent polymerization
  36. Once activated, there is a __ at either end to __.
    • binding site
    • allow activation
  37. Thrombin does what? 

    Those polymerized molecule are cross linked by __
    activates fibrinopeptides, allowing polymers to form: FIBRIN!

    transglutaminase: glutamine and lysine
  38. How does cross linking occur?
    by fibrin
  39. Explain thrombin.
    • a serine protease
    • starts at 582 amino acid zymogens
    • 2 cuts for activation
    • --> short polypeptide and long polypeptide held by ionic bonds, no disulfide bonds
  40. Other domains on thrombin.
    Gla: has alot of glutamic acid; post-translational modification

    Kringle: connectors
  41. Purpose of domains of thrombin
    since thrombin needs to get to the site, platelets participate

    prothrombin arrives at a wound site riding on platelets
  42. The glutamate residues get __. 

    Enzymes that do this require __.
    modified to carboxyglutamate

    Vitamin K as a cofactor
  43. What hapens if Ca can't bind?
    can't bind to prothrombin, it can't attach to plate membrane
  44. __ and __ anchors self in platelets. 

    As platelets accumulate, what happens?
    gla domain

    calcium binding

    athe protein is there adn is modified, activated, leading to clot formation
  45. Clot forms causing __.
    small signal--> large signal
  46. Cut cross links to __. 

    - Another protease: __

    Responsible for what?
    release from surface of new skin

    plasmin (plasminogen)

    cutting links to release scabs
  47. Structure of thrombin
    serine protease domain

    kringle domain

    fibrin binding
  48. A clot has __--> attracts __, which is cleaved-? activates it--> clot breaks free.
    fibrin

    plasminogen

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