BIOCHEM Exam 2 Lecture 8

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BIOCHEM Exam 2 Lecture 8
2014-02-15 00:50:27

Examm 2 material
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  1. Catalysts
    increase the rate at which a reaction approaches equilibrium

    promote chemical reactions without undergoing permanent change themselves

    enzymes are biological catalysts

    • most enzymes are proteins but not all
    • -ribozymes (RNA)
  2. active site
    the specific area of the enzyme where the reactions occur

    a 3D cleft or crevice in the enzyme that contains catalytic residues

    active sites have many more amino acids than participate in the reaction --> proper folding
  3. enzymes act on substrates with great specificity ... examples:
    • geometric complementarity
    • electronic complementarity
    • specificity depends on arrangement of atoms in active site
    • substrate binds in active site through weak interactions
  4. Models of Specificity:  Lock and Key
    ???  enzyme and substrate fit together like lock and key....?
  5. Models of Specificity: Induced Fit
    • change occurs in substrate
    • results in some sort of strain in the enzyme and the enzyme changes conformation
  6. apoenzymes and holoenzymes
    • apoenzyme = enzyme w/o cofactor
    • holoenzyme = enzyme w/ cofactor 

    apoenzyme + cofactor --> holoenzyme
  7. transition state
    the transition state is an activate form of a molecule that has undergone a partial chem rxn

    the activation energy delta G ++ is the input of energy need to reach the transition state

    • enzymes work because they lower delta G ++
    • -stabilize transition state
    • -provide alternate mechanism or rxn pathway from reactants to product
  8. Binding energy
    • the energy derived from enzyme - substrate reactions
    • activation energy is lowered due to the binding energy released from formation of enzyme substrate complex
    • holds substrates in the proper orientation to react
  9. what enzymes don't do:
    • enzymes do not effect delta g
    • enzymes do not effect keq
  10. enzyme reaction
    S + E --> E + P
  11. kinetics
    • the study of rates of chemical reactions
    • -rate can be defined as decrease in A over time or increase in P over time (for A-->P)
    • -rate constant k
  12. First Order Reactions
    • single reactant, single product
    • A-->P
    • V=k[A] (units s-1)
  13. Second Order Reactions
    • Two reactants, single product
    • A+B-->P
    • V+k[A][B]
    • k has units of mol x s-1
  14. Enzymes and first order reactions
    • E+S-->E+P
    • [E] is constant
    • velocity depends on S and is hyperbolic
  15. Michaelis-Menten kinetics
    • assumes enzymes reversibly associate to make an enzyme substrate [ES] complex
    • the saturation curve on v vs. [S] curves suggested that an ES exists
    • E+S-->ES, k1 is the rate constant for forming, k-1 is constant for dissociation
    • assuming rapid eq, k1=k-1, product is formed in second step E+S-->ES-->E+P
  16. Briggs and Haldene refined Michaelis Menten with what 2 assumptions?
    • 1. steady state assumption
    • -assumes that [ES] reaches steady state value quickly, that it is formed from E+S as quickly as it is broken down to P
    • 2. initial velocity: [P] is negligible at early times in the rxn
    • -experimentally can measure velocity before P has a chance to accumulate E+P<-->E+S becomes significant, v= v0 = k2[ES]
  17. Michaelis-Menten equation
    • rate eqtn for one substrate enzyme catalyzed rxn
    • v0 = Vmax[S]
    •         km+[S]
    • vmax determined from asymptote
    • km determined from [S] at 1/2 max
  18. Lineweaver-Burke plot
    • double reciprocal plot of 1/vo as a function of 1/[S]
    • 1/vo = (Km/Vmax)*(1/[S])+(1/Vmax)
    • in the form y = mx + b
    • x intercept = -1/km
    • y intercept = 1 /vmax
  19. Km
    • michaelis constant
    • concentration of substrate at 1/2 maximal rxn velocity
    • units = mass/vol, M
    • ratio of rates of diss. (ES break) to rates of assoc. (ES form)
    • km = k-1+k2
    •             k1
    • the constant for a given enzyme and substrate
  20. Vmax
    • the velocity of the reaction when the enzyme is fully saturated
    • vmax =k2[ET] where k2 is rate of ES-->P
    • theoretical max, not measurable
    • units of conc/time (M/sec)
  21. turnover number, kcat
    • the rate of substrate converted to product when the enzyme is fully saturated with enzyme 
    • kcat = Vmax
    •            [ET]
    • units s-1
  22. the specificity constant
    • kcat/km
    • allows the comparison of different enzymes or different substrates of the same enzyme
    • depends on: affitinity of the enzyme for a given substrate, rate of catalysis w/ that substrate
    • measure of catalytic efficiency
    • can be used to compare substrate preference for an enzyme
    • kcat/km near 10or 10M-1sec-1 near limit of diffusion
  23. How do enzyme inhibitors reduce rate of rxn?
    • interfering with substrate binding
    • interfering with substrate turnover
    • reversible inhibitors associate and dissociate rapidly from enzyme 
    • irreversible inhibitors dissociate very slowly, it at all
  24. Competitive inhibitors
    • compete with substrate for active site
    • usually resembles substrate but isn't reactive
    • competitive inhibitors can be overcome by increasing the amount of substrate so that [S] >>[I]
  25. Uncompetitive inhibitors
    • can only bind to ES complex
    • does not affect enzyme substrate binding 
    • cannot overcome inhibition by increasing [S]
  26. Mixed inhibitor
    • can bind to E or ES
    • inhibitor binds at a distinct site other than active site 
    • does not interfere with substrate binding
  27. Kinetics of competitive inhibitors
    • -no change in vmax
    • -km increases
  28. kinetics of uncompetitive inhibitors
    • vmax decreases
    • -1/v intercept does up as inhibitor binds ES complex

    • KM appears to decrease
    • -inhibitor decrease [ES] beacuse ESI is unproductive
    • -appears to need less S to reach 1/2 max velocity
  29. Kinetics of mixed inhibitors
    • vmax decreases
    • -1/v intercept increases in value

    • Km may not change
    • -no change if inhibitor has no impact on substrate binding