PHRD5025 Biochem - Lecture 5 Enzymes I

  1. -substrate for an enzyme
    -used up during a reaction
  2. -non-protein groups that bind to the enzyme
    -required for activity
    -not used up during a reaction
  3. example of a coenzyme
    • tetrahydrofolate
    • - coenzyme for thymidylate synthase (dUMP->dTMP)
  4. example of a cofactor
    • Mg2+ 
    • -required for ATPases like motor protein kinesin
  5. organic molecules that serve as cofactors (2)
    • 1) flavin
    • 2) heme
  6. class of enzyme that catalyzes the transfer of electrons
  7. class of enzyme that catalyzes group transfer reactions
  8. class of enzyme that catalyzes hydrolysis reaction (transfer of functional groups to water)
  9. class of enzyme that catalyzes the addition of groups to double bonds, or formation of double bonds by removal of groups
  10. class of enzyme that catalyzes the transfer of groups within molecules to yield isomeric forms
  11. class of enzyme that catalyzes the formation of C-C, C-S, C-O, and C-N bonds by condensation reactions coupled to ATP cleavage
  12. catalyst that speeds up chemical reactions so that they occur at a useful rate
  13. is the enzyme consumed during the reaction?
  14. "pocket" of the enzyme in which the reaction takes place
    active site
  15. molecule that binds within the active site of an enzyme
  16. 2 features that distinguish the active site amino acids
    • 1) they specifically recognize the substrate
    • 2) they accelerate the chemical reaction
  17. catalyzes the conversion of glyceraldehyde-3-phosphate into dihydroxyacetone phosphate
    triose phosphate isomerase
  18. first order/unimolecular reaction equation
  19. V0=k[S]
    • rate of formation of P, or, rate of depletion of S
    • S->P (at rate of k)
  20. when the rate at which the substrate is taken up by the active site is equal to the rate at which product is released by the active site
    (flux in = flux out)
    steady state
  21. when V0=0.5*Vmax
  22. small Km
    enzyme needs less substrate to engage half of the active sites (stronger affinity)
  23. large Km
    enzyme needs more substrate to engage half of the active sites (weaker affinity)
  24. when [S]=___ , exactly 50% of active sites are converting S to P
  25. Michaelis-Menten Equation
    V0=Image Upload 1
  26. Vmax=
  27. average amount of time for the substrate to go through the active site

  28. affinity of the substrate for the enzymes active site in the steady state
  29. second order/bimolecular reaction equation
  30. V0=k[E][S]
    rate of formation of ES, or, rate of depletion of E or S
  31. 2 requirements for bimolecular reactions
    • 1) collision of molecules
    • 2) chemistry to form ES complex
  32. rate limiting step for enzymes in which kcat/km is close to the diffusion-controlled limit
  33. diffusion-controlled limit
    rate at which E and S can diffuse together in an aqueous solution
  34. do catalysts alter the equilibrium of the reaction?
  35. how do catalysts speed up chemical reactions?
    by stabilizing the transition state (TS)
  36. 3 requirements for enzyme recognition of substrate
    • 1) active site formed with AAs that form many weak, non-covalent interactions w/ substrate
    • 2) substrate must have correct shape
    • 3) all H-bonding donors/acceptors & charged groups must have precisely positioned partners within the active site
  37. example of enzyme that utilizes the induced fit mechanism
  38. 3 types of chemistry used by enzymes
    • 1) general acid/base catalysis
    • 2) metal ion catalysis
    • 3) covalent catalysis
  39. requirements for covalent catalysis (2)
    • 1) catalyst must be better nucleophile than water
    • 2) covalent intermediate must be less stable to hydrolysis than the substrate
  40. how much is is the Image Upload 2G0 affected by enzyme catalysis?
  41. example of an enzyme that utilizes covalent catalysis
    chymotrypsin (serine protease)
  42. enzymes that contain multiple active sites that communicate with one another and can be influenced by effector molecules
    allosteric enzymes
  43. homoallostery
    active sites communicate with each other
  44. heteroallostery
    active sites are affected by other molecules
  45. location of positive effector binding in allosteric enzymes
    regulatory (R) domain
  46. location of substrate binding in allosteric enzymes
    catalytic (C) domain
  47. homotropic cooperativity
    an allosteric enzyme can be activated by its own substrate
  48. type of velocity curve for allosteric enzyme homotropic cooperativity
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PHRD5025 Biochem - Lecture 5 Enzymes I