BIBC 102 Metabolic Biochemistry Randy Hampton

Metabolic Biochemistry BIBC 102 BIBC 102 Web Site http://courses.ucsd.edu/rhampton/bibc102/ IA/TA sections start Monday Oct 8 IA/TA office hours (1 per wk) Posted soon My office hours 2130 Pacific Hall Tue 5-6

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Energy map of a reaction fig6-2 DG‡ is the activation energy

altering rate by catalysis enzymes alter DG‡. period fig6-3

how enzymes alter reactions: no enzyme fig6-5

how enzymes alter reactions: plus enzyme fig6-5

covalent intermediates Main Enzymatic Catalytic Mechanisms entropy reduction acid-base catalysis metal ion catalysis covalent intermediates other, stranger things… rh

Main Enzymatic Catalytic Mechanisms entropy reduction rh

entropy reduction: reaction 1 fig6-7

entropy reduction: reaction 2 about 105 times faster fig6-7

entropy reduction: reaction 3 about 108 times faster fig6-7

entropy reduction: Off the CHAIN!

entropy reduction acid-base catalysis Main Enzymatic Catalytic Mechanisms entropy reduction acid-base catalysis rh

recall from O-chem... acids and bases enhance rates of reactions like this

fig6-9

entropy reduction acid-base catalysis metal ion catalysis Main Enzymatic Catalytic Mechanisms entropy reduction acid-base catalysis metal ion catalysis rh

ions as cofactors table 6-1

covalent intermediates Main Enzymatic Catalytic Mechanisms entropy reduction acid-base catalysis metal ion catalysis covalent intermediates rh

covalent intermediates Main Enzymatic Catalytic Mechanisms entropy reduction acid-base catalysis metal ion catalysis covalent intermediates other, stranger things… rh

“UN-REQUIRED” READING not required, but interesting

Activation energy and reaction rate fig 6-2

Activation energy and reaction rate fig 6-3

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

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

Activation energy and reaction rate designate blue terms as constants

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

Lowering activation energy …

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

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

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

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

Ligand Binding rh

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

Binding isotherm rectangular hyperbola rh

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

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

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

fig 6-11

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

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

action of a competitive enzyme inhibitor fig 6-15

action of a uncompetitive inhibitor fig 6-15

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

CHYMOTRYPSIN: a protease

CHYMOTRYPSIN: a protease fig 6-18

catalytic triad fig 6-21

fig 6-21

fig 6-21

fig 6-21

fig 6-21

fig 6-21

fig 6-21

fig 6-21

fig 6-21