Chemistry 2100
Lecture 11
Protein Functions
Binding
P
+
L
PL
Catalysis
Structure
Why Enzymes?
•
•
•
•
Higher reaction rates
Greater reaction specificity
Milder reaction conditions
Capacity for regulation
COO
-
COO
NH2
O
OH
COO
OH
COO
• Metabolites have many
potential pathways of
decomposition
Chorismate
mutase
COO
OOC
O
NH2
-
-
O
COO
COO
OH
-
• Enzymes make the
desired one most
favorable
Specificity: Lock-and-Key Model
• Proteins typically have high specificity: only certain substrates bind
• High specificity can be explained by the complementary of the binding site
and the ligand.
•Complementarity in
– size,
– shape,
– charge,
– or hydrophobic / hydrophilic character
•“Lock and Key” model by Emil Fisher (1894) assumes that complementary
surfaces are preformed.
+
Specificity: Induced Fit
• Conformational changes may occur upon ligand binding
(Daniel Koshland in 1958).
– This adaptation is called the induced fit.
– Induced fit allows for tighter binding of the ligand
– Induced fit can increase the affinity of the protein for a
second ligand
• Both the ligand and the protein can change their
conformations
+
Apoenzyme + Coenzyme = Holoenzyme
Apoenzyme + Coenzyme = Holoenzyme
Apoenzyme + Coenzyme = Holoenzyme
Apoenzyme + Coenzyme = Holoenzyme
Enzymatic Activity
Potential Energy
• increase [reactant]
• increase temperature
• add catalyst
Reactants
Products
Reaction
TS
Potential Energy
• increase [reactant]
• increase temperature
• add catalyst
Reactants
Products
Reaction
TS
• increase [reactant]
Potential Energy
Ea
• increase temperature
• add catalyst
Reactants
Products
Reaction
TS
• increase [reactant]
Potential Energy
Ea
• increase temperature
• add catalyst
Reactants
Products
Reaction
TS
• increase [reactant]
Potential Energy
Ea
• increase temperature
• add catalyst
Reactants
Products
Reaction
TS
• increase [reactant]
Potential Energy
Ea
• increase temperature
• add catalyst
Reactants
Products
Reaction
TS
• increase [reactant]
Potential Energy
Ea
• increase temperature
Ea'
• add catalyst
Reactants
Products
Reaction
How to Lower
Enzymes organizes
reactive groups into
proximity

G ?
How to Lower

G ?
Enzymes bind transition states best
Potential Energy
H2O
+
CO2
HOCO2–
H2O + O C O
O
HO
Reaction
C O– + H+
+
H+
Potential Energy
H2O
+
CO2
H2O + O C O
Reaction
HOCO2–
+
H+
Potential Energy
H2O
+
CO2
HOCO2–
+
H2O + O C O
O
HO
Reaction
C O– + H+
H+
Potential Energy
H2O
+
CO2
HOCO2–
+
H2O + O C O
O
HO
Reaction
C O– + H+
H+
H2O
+
CO2
HOCO2–
H
Potential Energy
H O
+
O
C O
H2O + O C O
O
HO
Reaction
C O– + H+
H+
H2O
+
CO2
HOCO2–
H
H O
+
O
C O
Potential Energy
Ea
H2O + O C O
O
HO
Reaction
C O– + H+
H+
H2O
+
CO2
HOCO2–
H
H O
+
O
C O
Potential Energy
Ea
Ea'
H2O + O C O
O
HO
Reaction
C O– + H+
H+
s u crose
+
s u crase
[ s u crose-s u crasecomple x ]
H2O
glu cose
+
fru ctos e
+
s u crase
s u crose
+
s u crase
[ s u crose-s u crasecomple x ]
H2O
glu cose
+
fru ctos e
+
s u crase
s u crose
+
s u crase
[ s u crose-s u crasecomple x ]
H2O
glu cose
+
fru ctos e
+
s u crase
s u crose
+
s u crase
[ s u crose-s u crasecomple x ]
H2O
glu cose
+
fru ctos e
+
s u crase
s u crose
+
s u crase
[ s u crose-s u crasecomple x ]
H2O
glu cose
+
fru ctos e
+
s u crase
s u crose
+
s u crase
[ s u crose-s u crasecomple x ]
H2O
glu cose
+
fru ctos e
+
s u crase
s u crose
+
s u crase
[ s u crose-s u crasecomple x ]
H2O
glu cose
+
fru ctos e
+
s u crase
s u crose
+
s u crase
[ s u crose-s u crasecomple x ]
H2O
glu cose
+
fru ctos e
+
s u crase
How to Do Kinetic
Measurements
Enzyme Activity
Figure 23.3 The effect of enzyme concentration on
the rate of an enzyme-catalyzed reaction. Substrate
concentration, temperature, and pH are constant.
Enzyme Activity
Figure 23.4 The effect of substrate concentration on
the rate of an enzyme-catalyzed reaction. Enzyme
concentration, temperature, and pH are constant.
Enzyme Activity
Figure 23.5 The effect of temperature on the rate of
an enzyme-catalyzed reaction. Substrate and enzyme
concentrations and pH are constant.
Enzyme Activity
Figure 23.6 The effect of pH on the rate of an
enzyme-catalyzed reaction. Substrate and enzyme
concentrations and temperature are constant.
What equation models this
behavior?
Michaelis-Menten Equation
O
(C H3 ) 3 N C H2
C H2
ace tylcholine
O C C H3
+
H2 O
AChE
O
(ACh)
(C H3 ) 3 N C H2 C H2
c holine
(Ch)
OH
+
HO C C H3
ace tic acid
O
(C H3 ) 3 N C H2
C H2
ace tylcholine
O C C H3
+
H2 O
AChE
O
(ACh)
(C H3 ) 3 N C H2 C H2
c holine
(Ch)
OH
+
HO C C H3
ace tic acid
O
(C H3 ) 3 N C H2
C H2
ace tylcholine
O C C H3
+
H2 O
AChE
O
(ACh)
(C H3 ) 3 N C H2 C H2
c holine
(Ch)
OH
+
HO C C H3
ace tic acid
O
(C H3 ) 3 N C H2
C H2
ace tylcholine
O C C H3
+
H2 O
AChE
O
(ACh)
(C H3 ) 3 N C H2 C H2
c holine
(Ch)
OH
+
HO C C H3
ace tic acid
Ser
C H2
Glu
Asp
CO O
H
CO OH
(C H3) 3N
His
O
C H2
C H2
O
H
•
•
C
C H3
O
N
NH
Ser
C H2
Glu
Asp
CO O
H
CO OH
(C H3) 3N
His
O
C H2
C H2
O
H
•
•
C
C H3
O
N
NH
Ser
C H2
Glu
Asp
CO O
H
CO OH
(C H3) 3N
His
O
C H2
C H2
O
H
•
•
C
C H3
O
N
NH
Ser
C H2
Glu
Asp
CO O
H
CO OH
(C H3) 3N
His
O
C H2
C H2
O
H
•
•
C
C H3
O
N
NH
Ser
C H2
Glu
Asp
CO O
H
CO OH
(C H3) 3N
His
O
C H2
C H2
O
H
•
•
C
C H3
O
N
NH
Ser
C H2
Glu
Asp
CO O
H
CO OH
(C H3) 3N
His
O
C H2
C H2
O
H
•
•
C
C H3
O
N
NH
Ser
C H2
Glu
Asp
CO O
H
CO OH
(C H3) 3N
His
O
C H2
C H2
O
H
•
•
C
C H3
O
N
NH
Ser
C H2
Glu
Asp
CO O
H
CO OH
(C H3) 3N
His
O
C H2
C H2
O
H
•
•
C
C H3
O
N
NH
Ser
C H2
Glu
Asp
CO O
H
CO OH
(C H3) 3N
His
O
C H2
C H2
O
H
•
•
C
C H3
O
N
NH
Ser
C H2
Glu
Asp
CO O
His
O
H
CO OH H
H
(C H3) 3N
C H2
C H2H
O
O
•
•
C
C H3
O
N
NH
Ser
C H2
Glu
Asp
CO O
His
O
H
CO OH H
H
(C H3) 3N
C H2
C H2H
O
O
•
•
C
C H3
O
N
NH
Ser
C H2
Glu
Asp
CO O
His
O
H
CO OH H
H
(C H3) 3N
C H2
C H2H
O
O
•
•
C
C H3
O
N
NH
Ser
C H2
Glu
Asp
CO O
His
O
H
CO OH H
H
(C H3) 3N
C H2
C H2H
O
O
•
•
C
C H3
O
N
NH
Ser
C H2
Glu
Asp
CO O
His
O
H
CO OH H
H
(C H3) 3N
C H2
C H2H
O
O
•
•
C
C H3
O
N
NH
Ser
C H2
Glu
Asp
CO O
His
O
H
CO OH H
H
(C H3) 3N
C H2
C H2H
O
O
•
•
C
C H3
O
N
NH
Ser
C H2
Glu
Asp
CO O
His
O
H
CO OH H
H
(C H3) 3N
C H2
C H2H
O
O
•
•
C
C H3
O
N
NH
Ser
C H2
Glu
Asp
CO O
His
O
H
CO OH H
H
(C H3) 3N
C H2
C H2H
O
O
•
•
C
C H3
O
N
NH
Ser
C H2
Glu
Asp
CO O
His
O
H
CO OH H
H
(C H3) 3N
C H2
C H2
O
•
•
C
C H3
O
N
NH
Ser
C H2
Glu
Asp
CO O
His
O
H
CO OH H
H
(C H3) 3N
C H2
C H2
O
•
•
C
C H3
O
N
NH
O
(C H3 ) 3 N C H2
C H2
ace tylcholine
O C C H3
+
H2 O
AChE
O
(ACh)
(C H3 ) 3 N C H2 C H2
c holine
(Ch)
OH
+
HO C C H3
ace tic acid
Inhibitors
• Reversible inhibitors
– Temporarily bind enzyme and prevent activity
• Irreversible inhibitors
– Permanently bind or degrade enzyme
Reversible Inhibition
Irreversible Inhibition
Acetylcholinesterase
Ser
C H2
Glu
CO O
Asp
His
O
H
CO OH
•
•
N
NH
Ser
C H2
Glu
Asp
CO O
His
O
H
CO OH
F
•
•
CH3
CH
CH3
O
P
CH3
O
N
NH
Ser
C H2
Glu
Asp
CO O
His
O
H
CO OH
F
•
•
CH3
CH
CH3
O
P
CH3
O
N
NH
Ser
C H2
Glu
Asp
CO O
His
O
H
CO OH
F
•
•
CH3
CH
CH3
O
P
CH3
O
N
NH
Ser
C H2
Glu
Asp
CO O
His
O
H
CO OH
F
•
•
CH3
CH
CH3
O
P
CH3
O
N
NH
Ser
C H2
Glu
Asp
CO O
His
O
H
CO OH
CH3
CH
CH3
O
F
P
CH3
•
•
O
N
NH
I
N
CH N OH
CH3
Pyr idine
aldoxime
met hiodide ( PAM)
Br
Br
(C H3 ) 3 N–CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 CH2 –N(C H3 ) 3
dec amet honium
O
(C H3 ) 3 N
bromide
O
CH2 CH2 OCCH2 CH2 COCH 2 CH2 N(C H3 ) 3
succ inylcholine
Commercial Enzymes
• lactase
• rennin
• papain
• high-fructose corn syrup
• pectinase
• clinical assays
• lactase
• rennin
• papain
• high-fructose corn syrup
• pectinase
• clinical assays
• lactase
• rennin
• papain
• high-fructose corn syrup
• pectinase
• clinical assays
• lactase
• rennin
• papain
• high-fructose corn syrup
• pectinase
• clinical assays
s tarch
-amylase
de xtrins
gluc oamylase
glucose
gluc ose
isome rase
fructos e
s tarch
-amylase
de xtrins
gluc oamylase
glucose
gluc ose
isome rase
fructos e
s tarch
-amylase
de xtrins
gluc oamylase
glucose
gluc ose
isome rase
fructos e
• lactase
• rennin
• papain
• high-fructose corn syrup
• pectinase
• clinical assays
• lactase
• rennin
• papain
• high-fructose corn syrup
• pectinase
• clinical assays
• lactase
• rennin
• papain
• high-fructose corn syrup
• pectinase
• clinical assays