1. BIBC 102 ANNOUNCEMENTS Randy’s bipartite office hours Tue 3-4 pm
Thr 3-4 pm
2130 Pacific Hall
BIBC 102 Web Site
Soft Reserves lecture slides are
available. Near Hi Thai.

2. BIBC 102 ANNOUNCEMENTS

3. BIBC 102 ANNOUNCEMENTS Principles of Biochemistry,6th ed
Lehninger, Nelson and Cox
Will be on reserve at the Biomedical
Library, but not Geisel Library

4. Activation energy and reaction rate
fig 6-2

5. Activation energy and reaction rate
fig 6-3

6. What is the relation between changes in activation energy
and reaction rate?

7. S P k dS/dt = k[S] Activation energy and reaction rate blue terms are
constant when
temperature is
constant...

8. Activation energy and reaction rate
designate blue terms as constants

9. Activation energy and reaction rate
call DG‡ = A for simplicity

10. Lowering activation energy …

11. Lowering activation energy …
when DG‡ is lowered by this amount: d
the rate constant is increased by this factor:
note the following features:
lowering DG‡ makes reaction faster
identical effect on both directions

12. how big a deal is this?
recall that C2 = RT
at body temp, RT= 2573 J/mole
so if DG‡ changes by the value of one
hydrogen bond (~20 kJ/mole)
rate enhancement is e7.8 = 2440

13. If you have not already
please read
LIGAND BINDING
and
ENZYME CATALYSIS

14. If you have not already
please read
LIGAND BINDING
and
ENZYME CATALYSIS

15. Ligand Binding rh

16. Does this form make intuitive sense?
when there is no L, LB is also 0
as L gets big, LB approaches B
saturable rh

17. Binding isotherm
rectangular hyperbola rh

18. Enzyme kinetics: binding and beyond
when there is no S, reaction rate is 0
as S gets big, rate reaches a maximum
saturable rh

19. Vmax S Km + S Vo = Michaelis-Menten Equation
Maud
Menten
again, a rectangular hyperbola rh

20. Vmax S Km + S Vo = Michaelis-Menten Equation
when there is no S, V0 is also 0
as S gets big, V0 approaches Vmax
saturable rh

21. fig 6-11

22. how fast can an enzyme “do” a reaction?
Vmax = kcat[E]T
table 6-7

23. Competition for binding
remember to tell
them about I and Y
feature of saturability rh

24. action of a competitive enzyme inhibitor
fig 6-15

25. action of a uncompetitive inhibitor
fig 6-15

26. a “suicide” inhibitor
catalytic action of enzyme causes
permanent covalent inhibition
fig 6-16

27. CHYMOTRYPSIN: a protease

28. CHYMOTRYPSIN: a protease
fig 6-18

29. catalytic
triad
fig 6-21

30. fig 6-21

31. fig 6-21

32. fig 6-21

33. fig 6-21

34. fig 6-21

35. fig 6-21

36. fig 6-21

37. fig 6-21

40. Why do we need these details? an example:
The HIV Protease: cleaves single HIV-encoded
polypeptide into various proteins needed for
viral replication
Specific inhibitors of the HIV protease were
developed by an intimate understanding of the
structure and mechanism of the enzyme
amprenavir
Agenerase®

41. Now many HIV protease inhibitors
fig 6-30

42. amprenavir in HIV protease active site

43. hexokinase reaction
pg 212

44. hexokinase
fig 6-22

45. hexokinase
induced fit
fig 6-22

46. site of Pi
transfer
fig 6-22

47. C6
ATP
glucose
transfer of P
from ATP
ATP
xyulose
hydrolysis of
ATP

48. Regulation by phosphorylation: general case
fig 6-35

49. Regulation by phosphorylation: general case
switchable changes in activity
can activate or diminish activity

50. phosphorylation of glycogen phosphorylase
dephosphorylated
enzyme less
active
phosphorylated
enzyme more
active
fig 6-36 ish

51. Many covalent modifications

52. Many covalent modifications

53. COOPERATIVITY
and
ALLOSTERIC
REGULATION

54. Simple binding:
one K describes whole curve rh

55. Cooperative binding: hemoglobin vs. myoglobin
K is NOT
constant rh

56. sigmoidal (“s-ish”) curve shape
Cooperative binding
sigmoidal (“s-ish”) curve shape
“K” is a function of ligand concentration
protein has multiple subunits (4o structure)*
myoglobin
hemoglobin
*empirical
observation rh

57. S P XXX enzyme with tertiary structure: single subunit
enzyme with quaternary structure: multiple subunits
this sort of structure allows
the concentration of S to
alter the the action of the
enzyme on S...
XXX

58. single subunit shows M&M kineticsP Vo S
multiple subunits allows sigmoidal kinetics
cooperativity Vo
when S is high
E gets busy!! S

59. A non-cooperative system…rh

60. Cooperative enzyme
sigmoidal (“s-ish”) curve shape
“Km” is a function of substrate concentration
not a constant!!
protein has multiple subunits (4o structure)
allows regulation by substrate or
by unrelated molecules rh

61. Cooperative enzyme: sigmoidal rate curve
no constant
Km for this
curve!!
fig 6-34

62. Effect of cooperativity: from sluggish to steep
(table 15-2)

63. S S P R S this sort of structure allows the concentration of S to
alter the the action of the
enzyme on S... S P S
this sort of structure allows the concentration of R to alter the the action of the enzyme on S... R S

64. fig 6-31

65. Allosteric regulators
activator
inhibitor
fig 6-34

66. Allosteric
regulation Le
deuxième
secret de
la vie !!
Jacques Monod rh

67. Aspartate transcarbamoylase
regulatory
catalytic
fig 6-32

68. fig 6-32

69. chorismate mutase:
a simple allosteric enzyme
branch point in aromatic aa
metabolism...

70. chorismate mutase: branch point in aa metabolism
tryptophan
tyrosine

71. chorismate mutase Vo no regulator [chorismate] plus tryptophan plus
tyrosine
[chorismate]

72. CM chorismate mutase: branch point in aa metabolism tryptophan
activates CM
tyrosine
inhibits CM

73. chorismate mutase: a homodimer
active
site
regulator
binding
4o structure is required for allostery!

74. chorismate mutase
small spatial differences in
structure underlie regulation

75. chorismate mutase
small spatial differences in
structure underlie regulation