Ch 8.3 Lecture

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Ch 8.3 Lecture
2014-10-12 00:09:20
test two
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  1. Determining Km and Vmax
    (1/V)=(1/Vmax)+(Km/Vmax) (1/S) results in a straight line
  2. All of the enzymes that exist have the Km they do because of what?
    • they have evolved to funciton in their physological environments
    • They evolved to function perfectly well with those Km values
  3. 3rd definition of Km
    under certain conditions (like when substrate concentrations are low) the Km value approximates the affinity of the substrate for teh enzyme

    lower Km= higher affinity; don't need a lot of substrate to bind
  4. When we're turning over substrate and making product, what is that?
  5. When the substrate of S is low, what is E?

    What do we want?
    near Et

    we want Vmax to be high; Km we want to be high; so the ratio will be high
  6. What does chymotrypsin have a preference for?
    large hydrophobic side chains
  7. What controlles enzyme rates?
    diffusion; the reactions happen only as quickly as diffusion will allow; it is the limiting facto
  8. Explain the example lactate dehydrogenase.
    two subunits which bind in an ordered sequental way, which is when there is more than one substrate that binds to the enzyme
  9. Ordered sequential
    they have to bind in a particular order; more complicated than a single substarte
  10. Random sequential
    doesn't matter which order they bind; doesn't matter which order they leave
  11. Which enzymes follow MM kinetics? 

    What can't they explain?
    single substrate, non-alloseteric. 

    ordered, random sequential, double displacement, allosteric
  12. Double displacement
    enzyme substrates that will never be in the active site at the same time; one displaces the other
  13. Reversible inhibitors?

    bind to enzyme via weak interacts and can let go

    form covalent bonds and, once that is done, enzyme can no longer react
  14. Reversible: what are the three?
    competitive, uncompetitive, and noncompetitve
  15. Competitive?
    binds in active site and competes with substrate for the active site

    looks like substrate but is not
  16. uncompetitive?
    • doesn't bind in the absence of substrate
    • substrate binds and then the uncompetitive inhibitor binds to the site on the enzyme htat appears only after substrate binds

    If substrate is not there, there is no binding site

    When bound, binding site apears
  17. Noncompetitive
    all weak interactions and position of amino acid side chains doesn't react

    binds in different location at any time--> causes allosteric change in enzyme; so active site no longer properly boinds substrate; can bind at any time
  18. How to tell the difference? Competitive?
    In competitive, the inhibitor does not affect Vmax; Km is affected. Since reversible, substrate can displace inhibitor in active site; adding more inhibitor lowers the rate of the reaction, but Vmax can still be attained

    Competitve inhibitors change the Km for the rxn. Vmax does not change

    Amount of substrate needed to get half of Vmax is different
  19. uncompetitive inhibitor
    we're removing substrate from the environmnet because the enzyme is bound by the inhibitor, causing the substrate to be locked into an inactive enzyme

    • There is a reduction in vmax short of the uninhibited Vmax. 
    • If we have 100 enzymes, for example, and inhibitor inactivates by binding, it's almost as if they don't exist. So, Vmax goes down

    Km changes as well because, as we add inhibitor, it is binding substrate as wel, causing less substrate to be present
  20. Noncompetitive inhibitor
    two things can happen: E+S-->ES or E+I--> EI

    substrate can also bind, creating an ESI complex

    Inhibitor can let go

    Same Km, but Vmax is affected. The number of enzymes put in are not all available when inhibited. Vmax corresponds only to the enzymes that can react

    Substrate unaffeted. Vmax different
  21. What is it possible to do?
    design drugs that bind irreversibly via covalent bonds between inhibitor and enzyme

    recycle enzyme! nothing else to do
  22. What are the three irreversible inhibitors
    • group specific reagents
    • affnity labels
    • suicide inhibtiors
  23. Group specific reagents?
    what matters is that side chain reacts/ exists in active site

    it gets in, and a reaction causes a bond to form, inactivating the enzyme and making it irreversible

    ex: DIPF (inhibitor that reacts with active serine residues)
  24. Affinity lables?
    mimics substrate

    differ from GSR because they work like the substate and mimic it to get into the active site

    Once in, a rxn. occurs such that covalent bond is formed btwen inhibitor and enzyme (reaction is not specific)

    Because it look slike the substrate, it ets into the active site--> covalent bond forms, inactivating enzyme
  25. Suicide inhibitors
    get into active site and begins to react similarly to substrate

    reaction intermediate forms covalent bond--> enzyme inactive-> reaction is specific-- inhibtor prevents this in Parkinson patients.
  26. All irreversible inhibitors result in what?
    an irreversible binding to the enzyme and rendering it inactive
  27. What is an example of a suicinde inhibitor?
  28. Explaint he bacterial cell wall?
    • has sugar groups held together by amino acids
    • repeating units of NAM and NAG
    • protects from osmotic stress 
    • Strung amino acids that are connected via pentaglycine bridges
  29. Glycopeptidase transpeptidase
    enzyme responsible for making cross links, without which the cell wall is useless, not wrapped around
  30. What happens?
    one alanine is cleaved off and the remaining alanine forms a temp cov bond with enzyme

    bring in the second substrate, whcih takes the trapped free energy, transfer to form cross link between glycine and alanine
  31. What does penicillin do?
    fits into the active site and has highly reactive bond that is similar to original substrate

    the bond is broken--> covalent linkage to serine residues like alanine but its not alanine. So, alinie isn't released and there's no room for the second substrate

    Total inactivation of enzyme; no crosslinks are made; no protected cell wall to keep bacteria from suffering from osmotic stress--> lysis--> YOU'RE CURED