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OBJECTIVES
At the end of the lecture, the student should be
able to:
1. Define the following:
a. Enzymes
b. Apoenzyme
c. Coenzyme
d. Holoenzyme
e. Metalloenzyme
f. Regulatory enzyme
g. Active site of the enzyme
h. Allosteric site of the enzyme
i. Substrate
2. Discuss the helpers (cofactors) of enzymes.
OBJECTIVES
3. Enumerate the six major classes of enzymes.
4. Discuss the characteristics of enzymes.
5. Explain the models of enzyme-substrate
complex.
6. Explain enzyme kinetics.
a. Factors that affect enzyme activity or
reaction velocity.
b. Ways of expressing enzyme activity.
7. Discuss the operation and plots used to
illustrate enzyme kinetics.
a. Michaelis-Menten kinetics
b. Lineweaver-Burke Double Reciprocal Plot
c. Michaelis constant and its significance
OBJECTIVES
8. Discuss enzyme inhibition and its effect on
reaction velocity.
a. Reversible
b. Irreversible
9. Discuss the different ways of regulating enzyme
activity.
10. Explain the factors affecting enzyme activity.
11. Elucidate uses and clinical application of
enzymes.
ENZYMES
Specialized protein catalysts
that accelerate chemical
reactions
DEFINITION OF TERMS
APOENZYME
APOENZYME
APOENZYME
Coenzyme
Prosthetic
group
Metal
ion
HOLOENZYME
Protein
part
Cofactor
(Nonprotei
part)
ENZYME COFACTORS
A. Coenzyme
Enzyme
Chemical
Groups
Transferred
Vitamin
Precursor
Aldehydes
Thiamine
(Vit B1)
Thiamine
Pyrophosphate
(TPP)
Pyruvate dehydrogenase,
Isocitrate dehydrogenase, ketoglutarate dehydrogenase,
Transketolase, -Ketoacid
dehydrogenase
Flavin Adenine
Dinucleotide
(FAD)
Electrons
Riboflavin
(Vit B2)
Nicotinamide
Adenine
Dinucleotide (NAD)
Lactate dehydrogenase;
Other dehydrogenases
Hydride ion
(:H-)
Nicotinic acid
(Niacin; B3)
Amino groups
Pyridoxine
(Vit B6)
Electrons and
acyl groups
Not required
in diet
Pyridoxal
Phosphate (PLP)
Lipoate
Glycogen phosphorylase,
-ALA synthase, Histidine
decardoxylase, Alanine
aminotransferase
Pyruvate dehydrogenase
-Ketoglutarate dehydrogenase
ENZYME COFACTORS
A. Coenzyme
Enzyme
Coenzyme A
(CoASH)
Acetyl CoA
carboxylase
Biocytin
Pyruvate
carboxylase,
Acetyl CoA
carboxylase,
Propionyl CoA
carboxylase
Chemical
Groups
Transferred
Acyl groups
Vitamin
Precursor
Pantothenic
acid & other
compounds
CO2
Biotin
5deoxycobalamin
Methylmalonyl
mutase
H atoms and
alkyl groups
Vit B12
One-carbon
groups
Folic acid
Tetrahydrofolalate
Thmidylate
synthase
CLASSES OF COENZYMES
CLASS
EXAMPLES
Activation-Transfer
Coenzymes
TPP
Coenzyme A
Biotin
PLP
Oxidation-Reduction
Coenzymes
NAD+
FAD
Vit E, Vit C
Marks Medical Biochemistry, 3rd ed.
1. Pantothenic acid-derived,
co-factor of several
enzymes like acetyl CoA
carboxylase.
2. Takes part in reactions of
the CAC, FA synthesis and
oxidation, acylations and
cholesterol synthesis.
CH3
O
H
I
II
C-CH2-CH2-N-C-CC-CH2O
I
II I I
NH
O OH CH3
O = P OI
I
CH2
O
O
I
II
NH2
I
CH2
N
N
O = P OH
I
I
SH
N
N
H
O
O
HH
Active
sulfhydryl
group that form
thioesters with
acyl groups
OH
O
I
O = P OI
O-
ENZYME COFACTORS:
COENZYME A
-Ketoglutarate Dehydrogenase
Complex
Coenzymes:
COOH1. TPP
2. Lipoic Acid
|
3. FAD
CH2 4. NAD+
5. CoASH
|
CH2
|
C=O
|
CoASH
COO-
-Ketoglutarate (C5)
Pyruvate decarboxylase
Dihydrolipoyl transacetylase
Dihydrolipoyl dehydrogenase
NAD
NADH
+ H+
CO2
G0 = - 8.0 kcal
COO|
CH2
|
CH2
|
C=O
|
S ~ CoA
ENZYME COFACTORS:
COENZYME A
Pyruvate Dehydrogenase Complex
COO|
C=O
|
CH3
Pyruvate decarboxylase
TPP
Lipoate Dihydrolipoyl transacetylase
Dihydrolipoyl dehydrogenase
FAD
Pyruvate CoASH
NADH+ +
+
NAD
(C3)
H+
CO2
G0 = - 8.0 kcal/mole
S ~ CoA
|
C=O
|
CH3
Acetyl CoA
(C2)
Pyruvate
I
H-O-C-H
I
Functional
3 CH3
2
group
O
II
C NH2
Nicotinamide
ring
H
C
Lactate
dehydrogenase
N1
O CH2 O
P
H H
H
H
O
O
OH OH
O
P
2
5
O CH2 O
4
1
H H
H3 2 H
3
2
OH
OH
Ribose
ring
O
II
C NH2
N
I
R
NH2
5
4
1N
3 2
Adenine
ring
NADP+ contains a P
on this 2-hydroxyl
AMP
Keto
group
1 COO-
Dissociates
as H+
COOI
C=O + H+
I
CH3
COO
|
HO - C H
|
CH3
L-Lactate
Lactate
dehydrogenase
NAD+
NADH+ + H+
COOI
C=O
I
CH3
Pyruvate
COENZYME:
BIOTIN
O
II
H-N
H
N-H
IIIIIIIIIIIIIII
IIIIIIIIIIIIIII
I
III
III
III
II
Biotin
R
III
H
Protein portion of enzyme:
Acetyl CoA carboxylase
Propionyl CoA carboxylase
Pyruvate carboxylase
N
H
O
O
IIII
H-N
NH
=O
N-H
IIIIIIIIII
Lysyl
residue
Biotin
III
III
CO2
H IIIIIIIIIIIIIII
attachment
site
C
II
O
III
II
COENZYME: BIOTIN
BIOTIN
COOI
C =O
I
CH3
Pyruvate
COO|
C= O
|
CH2
|
COO-
CO2
ATP
ADP + Pi
Pyruvate
carboxylase
Oxaloacetate
Gluconeogenesis
COENZYME:THIAMINE PYROPHOSPHATE
Reactive
carbon atom:
carrier of aldehyde
groups
H
Dissociable
proton
H3C
NN S
NH2
N
C
C
N
N
H
CH2
Coenzyme
binding
site
CNH2 C
CH3
O-
O-
H
C
H
C-C-OH
H
H3C
Thiamine Pyrophosphate
(TPP; Vit B1-derived)
AMP
PYRUVATE (C3)
NAD
Pyruvate
Malate
dehydrogenase
(C4) MALATE
Fumarase
CITRATE (C6)
H2O
Aconitase
H2O
NAD
ISOCITRATE (C6)
NAD
H2O
E
T
C
ATP
Oxid.
Phospho
(C4) FUMARATE
TPP
NADH + H+
CO2
KETOGLUTARATE (C5)
FADH2
Succinate
dehydrogenase
FAD
(C4) SUCCINATE
CoA
Isocitrate
dehydrogenase
NAD
(ATP)
GTP ADP + Pi
- ketoglutarate
dehydrogenase
Mg+
COENZYME: FAD
NH2
H3C
H3C
H3C
Ribitol
N
N
NH
N
Isoalloxacin ring
CH2
From ATP
I
H-C-OH
I
H-C-OH
I
N
H-C-OH O
O
I
II
II
CH2-O-P O P
P O-CH2 N
I
O
O
O
NH2
N
N
OH OH
COENZYME: FAD
ROLE OF FAD IN THE CITRIC ACID CYCLE
Succinate
dehydrogenase
COOH
|
CH2
|
CH2
|
FAD
COOH(C4)
Succinate
FADH2
H -COOH
|
HC
||
CH
|
H -COOH
Fumarate (C4)
COENZYME: FAD
NH2
+ I
H2N = C
I
NH
I
CH2
I
CH2
I
CH2
+
I
H3N C H
I
COO-
Arginine
NADP+
+ H2 O
NO +
Nitric oxide synthase
FAD, FMN, Heme
Tetrahydrobiopterin
NH2
I
C=O
I
NH
I
CH2
I
CH2
I
CH2
+
I
H3N C H
I
COO-
Citrulline
COENZYME:PLP
Reactive aldehyde group
involved in the transfer
of amino groups.
O
O C HH
-
OH
O3PO-CH2
+
N
CH3
Pyridoxal
Phosphate
A Vit. B6-derived coenzyme involved in
carbohydrate, amino acid and
neurotransmitter synthesis.
COENZYME: PLP
ROLE OF PLP IN CARBOHYDRATE METABOLISM:
GLYCOGENOLYSIS
Glycogen
chain
HO
OH
O
OH
H
HO
O
OH
OH
O-PO
OH
Glucose 1-P
O
OH
HO
=
3
HO
O
OH
OH
HO
O
OH
H OH
OH
Glygogen
phosphorylase
PLP
OH
OH
H
Pi
HO
O
HO
OH
H
OH
O
OH
OH
HO
O
O
OH
H
Remaining glycogen
H
OH
OH
COENZYME: PLP
ROLE OF PLP AS A COENZYME IN AMINO
ACID METABOLISM: HEME SYNTHESIS
Glycine +Succinyl CoA
-Aminolevulenate
synthase
PLP
-Aminolevulenic acid
(ALA)
several
reactions
Heme
(Fe protoporphyrin IX)
COENZYME: PLP
ROLE OF PLP IN AMINO ACID METABOLISM:
HISTAMINE SYNTHESIS
H
|
CH2 C COO|
NH3
Histidine
PL
P
Histidine
decarboxylase
CO2
CH2 CH2 NH3
HISTAMINE
COENZYME: PLP
ROLE OF PLP IN AMINO ACID METABOLISM:
TRANSAMINATION
COO|
Alanine
CH2
aminotransferase
|
(transaminase)
NH3+
CH2
|
|
O
+
- +
CH3 C C COO
C=O
||
|
|
CH3 C COOPLP
H
COOPyruvate
Alanine
-Ketoglutarate
COO|
CH2
|
CH2
|
H C NH3+
|
COOGlutamate
ENZYME COFACTORS
Cofactor
Enzyme
Cu+2
Cytochrome oxidase
Mn+2
Mg+2
Ni+2
Urease
Mo
Nitrate reductase
Se
Glutathione peroxidase
Mn+2
Superoxide dismutase
K+
Glucose
Hexokinase
Glucokinase
Mg+2
ATP
ADP
+ Pi
O
||
C1 - H
|
H - C2 - OH
|
OH - C3 - H
|
H - C4 - OH
|
H - C5 - OH
|
H - C6 - O P
|
H
Glucose 6-PO4
GLYCOLYSIS
ENZYME COFACTORS: K+
O
||
C1 O |
C2 O ~ P
|
H C3
|
H
Pyruvate kinase
Phosphoenol Pyruvate
(PEP)
K+
ADP
ATP
COO|
C2 = O
|
CH3
Pyruvate
G0 = - 6.1 kcal/mole
Carbonic anhydrase
CO2 + H2O
H2CO3
Zn+2
METALLOENZYMES
Enzymes that require
a metal in their
composition
SUBSTRATE
The molecule acted upon
by the enzyme
to form a
product
ATP AS A CO-SUBSTRATE
O
||
C1 - H
|
H - C2 - OH
|
OH - C3 - H
|
H - C4 - OH
|
H - C5 - OH
|
H - C6 OH
|
H
Glucose
O
||
C1 - H
|
H - C2 - OH
|
OH - C3 - H
|
H - C4 - OH
|
H - C5 - OH
|
Hexokinase/
Glucokinase
Mg+2
ATP
ADP
G0 = - 4.0 kcal/mole
H - C6 - O P
|
H
Glucose 6-Phosphate
CHYMOTRYPSIN:ACTIVE SITE
His 57
Ser 195
ALLOSTERIC SITE
Substrate
Substrate sites
Enzyme
Allosteric site
REGULATORY ENZYME
The enzyme that catalyzes the
rate-limiting or committed
step of a metabolic
pathway.
REGULATORY ENZYME
Phosphofructokinase I
H
|
H - C1 - OH
|
C2 = O
|
OH - C3 - H
|
H - C4 - OH
|
H - C5 - OH
|
H - C6 - O P
|
H
H
|
H - C1 - O - P
|
ATP
ADP + Pi
C2 = O
|
OH - C3 - H
|
H - C4 - OH
Phosphofructokinase I
|
H - C5 - OH
+
|
ATP
H - C6 - O P
AMP
Citrate
|
F 2,6 bisPO4
+
H
H
Fructose 6phosphate
Glycolysis
Fructose 1,6bisphosphate
REGULATORY ENZYME
Acetyl CoA Carboxylase
Citrate
Insulin
High CHO
Low Fat
High Prot.
O
||
CH3 C S CoA
Malonyl CoA
Palmitoyl CoA
Epinephrine
Glucagon
High Fat
Fasting
ATP
ADP + Pi
H2O
O
O
\
||
C CH2 C S CoA
//
MALONYL CoA
O
REGULATORY ENZYME
HMG Coa Reductase
Insulin, T3
Glucocorticoids
Cholesterol
Bile acids
Mevalonate
Glucagon
Statins
O
II
+
OC
I
HMG CoA reductase
CH2
I
OH C CH2
I
C S CoA NADPH
NADPH
CoA
II
+ H+
O
HMG CoA
C1OO|
C2H2
|
HO C3 CH3
|
C4H2
|
C5H2OH
Mevalonate
Cholesterol Synthesis
REGULATORY ENZYME
Glucose 6-Phosphate
Dehydrogenase
H
|
C1 = O
|
H C2 OH
|
HO C 3 H
|
H C4 OH
|
H C 5 OH
|
C6H2OPO32-
Glucose 6-phosphate
NADP
NADPH
+ H+
Glucose 6-phosphate
dehydrogenase
O
||
C1
|
H C2 OH
|
HO C3 H
|
H C4 OH
|
H C5
|
C6H2OPO32-
6-phosphogluconolactone
ISOENZYME
Different structural forms of an
enzyme which catalyze the same
chemical reactions act on the
same substrate(s) and produce the
same product(s) but exhibit differing
degrees of efficiency.
Different isoenzymes are expressed in
specific tissues of the body.
ISOENZYMES OF LACTATE
DEHYDROGENASE
Lactate dehydrogenase
(LDH) catalyzes the
reversible conversion of
pyruvate to lactate.
Tetramer consisting of 2
subunits: M (found in
skeletal muscles and
liver) & H (heart).
5 distinct isoenzyme forms
(from combination of M &
H isozymes).
An increase of H4 in the blood
indicates tissue damage
as in heart attack.
Enzymes can therefore serve
as markers for disease.
EXAMPLE
Oxidoreductases
Transferases
Hydrolases
Lyases
Isomerases
Ligases
Synthetases, Carboxylases
OXIDOREDUCTASES
Transfer of electrons and hydrogen
atoms from donors (or reductants,
hence oxidized to acceptors (or
oxidants, hence reduced).
COO
|
HO C H + NAD+
|
CH3
-
L-Lactate
Lactate
dehydrogenase
COO|
C = O + NADH + H+
|
CH3
Pyruvate
TRANSFERASES
Transfer functional groups (like C-, N-, or
P-) from donors to acceptors; utilize 2
substrates to produce 2 products.
COOAlanine
COOCOOtransaminase
|
|
|
H3N C H + C = O
C = O + H3N C O
|
|
|
|
PLP
CH3
(CH2)2
CH3
(CH2)2
L-Alanine
|
Pyruvate
|
(amino acid)
(keto acid)
COOCOOsubstrate -Ketoglutarate
product
L-Glutamate
(keto acid)
(amino acid)
substrate
product
TRANSFERASES
VI.
Reactions:
GLYCOLYSIS
Kinase
- transfers the
functional group
phosphate from ATP to an acceptor
O
||
C1 - H
|
H - C2 - OH
|
OH - C3 - H
|
H - C4 - OH
|
H - C5 - OH
|
H - C6 OH
|
H
Glucose
Hexokinase
Glucokinase
Mg+2
ATP
(donor)
ADP + Pi
(product)
G0 = - 4.0 kcal/mole
O
||
C1 - H
|
H - C2 - OH
|
OH - C3 - H
|
H - C4 - OH
|
H - C5 - OH
|
H - C6 - O P
|
H
Glucose 6phosphate
(product)
TRANSFERASES
Glycosyltransferase if the transferred
group is a carbohydrate residue
OH
I H
CH-C=C-(CH2)12-CH3
H
0
II
R1-C-N-CH
I H
CH2OH
Galactosyl
transferase
Ceramide
UDP-galact- UDP
ose
Fatty
acid
OH
I H
0
CH-C=C-(CH2)12-CH3
H
II
R1-C-N-CH
I H
O
CH2
O
HOCH2
HO H
OH
H
H
Galactose
H
OH
Cerebroside
(Galactocerebroside;
a glycosphingolipid)
HYDROLASES
Catalyze cleavage of chemical bonds by
addition of H2O, producing 2 products
Phosphate bond
O
O
Pyrophosphatase
||
||
O P ~ O P ~ O- + HOH
|
|
O
OPyrophosphate
(PPi)
O
||
2 HO P O|
O
Phosphate
2 (Pi)
HYDROLASES
Thiolase
Acetyl CoA
CoA
O
||
CH3-C-S-CoA
CH3-(CH2)12-C-S-CoA
Fatty acyl CoA (2 carbons shorter)
LYASES
Cleave C-C, C-O, C-N bonds by means
other than hydrolysis or oxidation
O O\\ /
C
|
C = O H+
|
CH3
Pyruvate
Pyruvate
decarboxylase
H O
\ //
C
|
CH3
+ O=C=O
Carbon
dioxide
(CO2)
Acetaldehyde
LYASES
Cleave C-C, C-O, C-N bonds by means other
than hydrolysis or oxidation
4
HO
CH2 CH COOI
NH3+
OH
3,4-Dihydroxyphenylalanine (DOPA)
PLP
DOPA decarboxylase
CO2
+
CH2 CH2 NH3
HO
OH
Dopamine
LYASES
Cleave C-C, C-O, C-N bonds by means other
than hydrolysis or oxidation
H
|
CH2 C COO|
NH3
Histidine
PLP
Histidine
decarboxylase
CO2
HISTAMINE
GLYCOLYSIS
LYASES
Catalyze C-C bond cleavage in a reversible reaction
P
P
|
|
O O H
OH OH O
|
||
|
|
|
|
H - C1 C2 C3 - C4 - C5 - C6 - H
|
|
|
|
|
H
OH H
H H
Fructose 1,6-Bisphosphate
O
||
H C1 H
|
H C2 OH
|
H C3 O P
|
H
Glyceraldehyde
3 Phosphate (GADP)
G0 = + 5.73 kcal/mole
Aldolase A
O
||
H C4 O P
|
H C5 OH
|
H C6 OH
|
H
Dihydroacetone
Phosphate (DHAP)
LYASES
Synthase catalyzes a physiologically important
reaction that favors the formation of a C-C bond
C1OO|
C2= O
|
C3H2
H2O
|
C4OOOxaloacetate (C4)
S~CoA
|
C1 = O
|
C2H3
Acetyl CoA (C2)
HS-CoA
Citrate synthase
C1OO|
C2H2
|
HO C3 C4OO|
C5H2
|
C6OOCitrate (C6)
LYASES
Synthase catalyzes a physiologically important
reaction that favors the formation of a C-C bond
CH2OH
I
HC-NH3+
I
COOSerine
H2O
PLP
HS-CH2-CH2-CH-COOI
Cystathionine synthase
NH3+
Homocysteine
S
CH2
CH2
I
I
CH2
H -C-NH3+
I
I
CH-NH3+
COOI
COO-
Cystathione
LYASES
Hydratase add H2O to a susbtrate
C1OO|
H C2
||
C3 H
|
C4OO-
Fumarate
H2O
Fumarase
(or fumarate hydratase
C1OO|
HO C2 H
|
H C3 H
|
C4OO-
Malate
ISOMERASES
Transfer of functional groups or double
bonds within the same molecule
C1OO|
H3N C2 H
|
C3H3
L-Alanine
Alanine
racemase
C1OO|
H C2 NH3
|
C3H3
D-Alanine
ISOMERASES
GLYCOLYSIS
Transfer of functional groups or double
bonds within the same molecule
O
||
H C1 H
|
H C2 OH
|
H C3 O P
|
H
Glyceraldehyde
3 Phosphate (GADP)
Triosephosphate
isomerase
O
||
H C1 O P
|
H C2 OH
|
H C3 OH
|
H
Dihydroacetone
Phosphate (DHAP)
ISOMERASES
Transfer of functional groups or double
bonds within the same molecule
O
||
C1 - H
|
H - C2 - OH
|
OH - C3 - H
|
H - C4 - OH
|
H - C5 - OH
|
H - C6 - O P
|
Glucose H
6-Phosphate
(Aldose)
Aldehyde group
Keto group
ATP
H
ADP
|
H C1 - OH
|
C2 = O
|
Phosphohexoisomerase
OH - C3 - H
|
H - C4 - OH
|
H - C5 - OH
|
H - C6 - O P
|
H
Fructose 6-Phosphate
(Ketose)
ISOMERASES
Transfer of functional groups or double
bonds within the same molecule
O
||
C1 O|
H C2 OH
|
H C3 O P
|
H
3-Phosphoglycerate
Phosphoglycerate mutase
Mg+2
G0 = + 1.06 kcal/mole
O
||
C1 O|
H C2 O - P
|
H C3 OH
|
H
2-Phosphoglycerate
ISOMERASES
Transfer of functional groups or double
bonds within the same molecule
C1H2OH
I
C2=O
I
HOC3H
I
HC4OH
I
H2C5OPO32-
Epimerase
D- Xylulose 5-phosphate
C1H2OH
I
C2=O
I
HC3OH
I
HC4OH
I
H2C5OPO32-
D- Ribulose 5-phosphate
C-3 Epimers
LIGASES
Catalyze the joining of
substrates in the presence of ATP.
CH3
ATPADP + Pi
Pyruvate carboxylase
|
C=O
|
COO- BiotinPyruvate
CO2
ATP
ADP
+ Pi
COO|
CH2
|
C=O
|
COO-
Oxaloacetate
CHARACTERISTICS OF
ENZYMES
They are not changed by the
reaction they catalyze.
CHARACTERISTICS OF
ENZYMES
CHARACTERISTICS OF
ENZYMES
Free energy, G
(catalyzed)
Substrates
or
+
Reactants
(e.g. CO2 + H2O)
G
for the
reaction
Products
(H2CO3)
Reaction progress
CHARACTERISTICS OF
ENZYMES
They are highly specific for
the reactants or substrates
they act on and catalyze
only one type
of chemical
reaction.
ENZYME SPECIFICITY
Carbonic
anhydrase
CO2 + H2O
H2CO3
ENZYME SPECIFICITY
Catalase
2 H2O2
2 H2O
ENZYME SPECIFICITY
COO|
HO - C H
|
CH3
L-Lactate
COO|
H - C OH
|
CH3
D-Lactate
Lactate
dehydrogenase
NAD+
NADH+ + H+
COOI
C OH
I
CH3
Pyruvate
ENZYME SPECIFICITY
O
||
C1 - H
|
H - C2 - OH
|
OH - C3 - H
|
H - C4 - OH
|
H - C5 - OH
|
H - C6 OH
|
H
Glucose
Glucokinase
Mg+2
ATP
ADP + Pi
O
||
C1 - H
|
H - C2 - OH
|
OH - C3 - H
|
H - C4 - OH
|
H - C5 - OH
|
H - C6 - O P
|
GlucoseH6-phosphate
CHARACTERISTICS OF
ENZYMES
PEPTIDE BOND
H
H
I
I
R C CO NH C R
I
I
NH2
COOH
Maximal velocity
ENZYME-SUBSTRATE COMPLEX
CYTOCHROME P450-CAMPHOR
Camphor
Cytochrome P-450
E+S
k1
k-1
Substrate
binding
ES
k2
k-2
Catalytic
step
E+P
MICHAELIS-MENTEN EQUATION
Vmax [S]
Vo =
{Km + [S]}
Vo = Velocity at any time (moles/time)
Vmax = Maximal velocity (or reaction rate)
Km = Michaelis constant for the particular
enzyme under investigation
= (K-1 + K2)/K1
[S] = Substrate concentration (molar)
MICHAELIS-MENTEN
SATURATION CURVE
Zero order
Vmax
A
Km
A = [S] < Km
B = [S] = Vmax/2
Vmax
First order
C = [S] > Km
= Vo is maximal
(Vmax)
REPRESENTATION OF AN ENZYME IN
THE PRESENCE OF A SUBSTRATE
S=
E=
[S] < Km
[S] = Vmax/2
[S] > Km
SIGNIFICANCE OF KM
1. It is the substrate concentration at
which half of the active sites of the
enzyme are filled up.
2. It is an inverse measure of the affinity
of the substrate for the enzyme:
a. The lower the Km, the higher is
the
affinity.
b. The higher the Km, the lower is
KM AND PHYSIOLOGICAL
VI. Reactions:
GLYCOLYSIS
UTILIZATION OF GLUCOSE
O
||
C1 - H
|
H - C2 - OH
|
OH - C3 - H
|
H - C4 - OH
|
H - C5 - OH
|
H - C6 - O P
|
mM
H
Glucose
6-
Hexokinase
O
(Extrahepatic cells, RBCs)
||
C1 - H
Glucokinase
|
(Liver, Pancreatic -cells
H - C2 - OH
|
OH - C3 - H
|
Mg+2
H - C4 - OH
|
H - C5 - OH
ATP
ADP + Pi
|
H - C6 OH
Km for hexokinase = 0.1
|
phosphate
H Km for glucokinase = 5 mM
Glucose
1
V
Km
Slope =
Vmax
Intercept 1
on X-axis =
-
Km
1
Intercept on Y-axis =
Vmax
1
[S]
LINEWEAVER-BURKE DOUBLE
RECIPROCAL PLOT:SAMPLE PROLEM
Y intercept
55
50
45
4
0
35
30
25
- .12
Km
Vmax
Slope =
20
Y intercept =
15
Vmax
10
X intercept =
I
1
Km
.05
.1
.
.
1/[S]1(mM-1) 2
5
.25
.
3
LINEWEAVER-BURKE DOUBLE
RECIPROCAL PLOT: SAMPLE PROBLEM
Y intercept =
X intercept =
Vmax
Km
Vmax =
Y intercept
Vmax =
Km =
1
20
Km =
Km =
1
X intercept
1
.12
8.33 (mM-1)
INHIBITION OF ENZYMATIC
REACTIONS
Reversible
a. Competitive
b. Non-competitive
c. Uncompetitive
Irreversible
REVERSIBLE INHIBITION
REVERSIBLE INHIBITON
Inhibitor Type
Competitive
Inhibitor
Noncompetitive
Inhibitor
Uncompetitive
Inhibitor
Kinetic Effect
Vmax unchanged;
Km increased to
reach a given
velocity.
Vmax decreased
proportionately to
inhibitor
concentration; Km
unchanged (since
substrate can still
bind to the
enzyme).
Competitive
inhibitor
1
[V]
Uninhibited
enzyme
1
Vmax
-1
Km
1
[S]
1
[V]
Uninhibited
enzyme
1
Vmax
1
Km
1
[S]
1
[V]
Uninhibited
enzyme
1
Vmax
1
Km
1
[S]
Vmax
Same
Noncompetitive
inhibitor
Competitive
inhibitor
Uncompetitiv
inhibitor
Km
Competitive
1
[V]
Same
Noncompetitive
Uninhibited
enzyme
1
Vmax
Uncompetitive
-1
Km
1
[S]
IRREVERSIBLE INHIBITION
Diisopropylphosphofluoridate (DIPF)
O
II
+
H3C-C- O-CH2-CH2-N(CH3)3
Acetylcholine
O
II
+
HO- CH2-CH2-N(CH3)3
OH
I
Enz-Ser
Choline
O
II
O- C CH3
I
Enz-Ser
H2O
+ H3C-C-OAcetate
OH
I
Enz-Ser
OH
I
Enz-Ser +
CH3 O
CH3
I
II
I
H-C-O - P - O-C-OI
I
I
CH3 F
CH3
(Enz acetylcholinesterase)
F- , H +
CH3 O
CH3
I
II
I
H-C-O - P - O-C-O- Inactive
enzyme
I
I
I
CH3 O
CH3
Enz-Ser
Strained peptide
bond
Bacterial enzyme
I
C=O
I
H-N H
CH3
I
S
H-C C
C
CH3
I
C
O=C N
II H
H COO
O
I
Ser
Glycopeptide
transpeptidase
ENZYME TARGET
DISEASE
Amrubicin
Topoisomerase II
CA chemotherapy
Antabuse
Aldehyde
dehydrogenase
Alcoholism
Captopril
Angiotensinconverting enzyme
Hypertension
Celebrex
Cyclooxyenase-2
Arthritis
Digoxin
Na+-K+-ATPase pump
Heart problem
HIV protease
Acquired
Immunodeficiency
Syndrome (AIDS)
Lipitor
Hypercholesterolemia
Viagra
Phosphodiesterase
Erectile dysfunction
Agenerase
Angiotensin I
(decapeptide, 10 AAs)
Renin
(JG cells,
placenta)
Angiotensin
converting
enzyme (ACE)
Angiotensin II
(octapeptide, 8 AAs)
Arteriolar
vasoconstriction
BP
Aldosteronemediated renal
Na+ & H2O
reabsorption
ACE Inhibitor
(Captopril,
Functions/
Amlodipine)
Effects
2 NADP+
CoA
O
OH
II
|
O C CH2 C CH2 CH2OH
|
CH3
MEVALONATE (C6)
Statins
Atorvastatin
(Ex. Lipitor)
CHOLESTEROL
GTP
cGMP
Pi
Phosphodiesterase
Viagra (Sildenafil
citrate)
GMP
cGMP
Smooth muscle
relaxation
and vasodilation
in penile
blood vessels
SUSTAINED ERECTION
NSAIDS
(ASA,
Indomethacin)
5-Lipoxygenase
5-HPETE
Peroxidase
Prostaglandin
H2 synthase
Spontaneous
Glu
COX-2
COX-1
Prostaglandin
H2 synthase
Pain and
inflammation
5-HETE
LTA4
Leukotriene
(Leukotriene A4)
synthase
Leukotriene
synthase
Glutathione
(Glu-Gly-Cys)
LTC4
LTD4
Phospholipase A2
-NSAIDS
-Selective
COX-2
inhibitors
(Ex. Celebrex)
Cyclooxygenase
PGG2
(Prostaglandin G2)
Peroxidase
LTB4
PGI2
Prostacyclin
(Prostacyclin) synthase
LTE4
Gly
PGE2
PGH2
(Prostaglandin H2)
Thromboxane
synthase
Isomerase
Reductase
EICOSANOID SYNTHESIS
PGF2
TXA2
(ThromboxaneA2)
Alcohol dehydrogenase
NADH + H+
CH3 - OH
Acetaldehyde
Aldehyde dehydrogenase
_
Acetate
Antabuse
Acetyl CoA
KINETICS FOR AN
ALLOSTERIC ENZYME
REGULATION OF ENZYME
ACTIVITY
Feedback Inhibition
Allosteric (Non-covalent)
Modification
Covalent Modification
Zymogen Activation
Induction or Repression
of Enzyme Synthesis
FEEDBACK INHIBITION
Original Precursor(s)
Enzyme 1
1
Enzyme 2
2
Enzyme 3
3
Enzyme 4
4
Enzyme 5
Final Products
FEEDBACK INHIBITION
Carbamoyl PO4 + Aspartate
Aspartate transcarbamoylase
(ATCase)
Carbamoyl aspartate
series of
reactions
Acetyl
CoA
Acetoacetyl
CoA
2N
A
+ DP
2H +
+
2N
A
+ DP
2H H
+
HMG CoA
Acetyl
CoA
> 25 steps
Feedback
inhibition
Cholesterol
ALLOSTERIC MODIFICATION
Allosteric modulator (activator or inhibitor)
Binds to regulatory or allosteric site
Conformational change in the
regulatory enzyme
Effect is transmitted to the active site
Change in shape of the active site
Altered activity
ALLOSTERIC MODIFICATION:
Phosphofructokinase I
COVALENT MODIFICATION
ATP Protein ADP
kinase
ENZYME-
ENZYME-
Ser -- OH
HPO4=
H2O
Phosphoprotein
phosphatase
Ser O PO32-
COVALENT MODIFICATION
OF THE ENZYME
2 ATP
2 ADP
Phosphorylase
kinase
P
Phosphoprotein
2 Pphosphatase 2 H2O
ATP
and/or
G6P
AMP
Glucose
P
Phosphorylase b
(inactive)
Phosphorylase a
(active)
Glycogen phosphorylase
Pyruvate
dehydrogenase
kinase
Pyruvate
dehydrogenase
ADP
Pyruvate
dehydrogenase
(active)
(inactive)
Pi
Pyruvate
dehydrogenase
phosphatase
H2O
ENZYMES
Low activity
High activity
EP
Glycogen synthase
EP
Pyruvate dehydrogenase
EP
EP
Glycogen phosphorylase
EP
Citrate lyase
EP
Phosphorylase b kinase
EP
EP
E = Dephosphorylated
EP = Phosphoenzyme
ZYMOGEN ACTIVATION
Chymotrypsinogen
ZYMOGEN ACTIVATION:
BLOOD COAGULATION
Clotting Factors
Ca+2
Prothrombin
Thrombin
Fibrinogen
Fibrin
INDUCTION OR REPRESSION
OF ENZYME SYNTHESIS
Blood glucose Blood glucose levels
levels
(Starvation)
(Well-fed state)
Insulin
Synthesis of
key enzymes involved
in glucose degradation
Glucagon
Synthesis of
key enzymes involved
in glucose synthesis
FACTORS AFFECTING
ENZYME ACTIVITY
Temperature
pH
Substrate
concentration
Co-factors
EFFECT OF TEMPERATURE
Optimum T
Increasing
enzyme
activity
Heat
inactivation
of the
enzyme
10
20
30
40
50
60
Temperature (oC)
70
80
EFFECT OF pH
Optimum
pH
OPTIMUM pH OF VARIOUS
ENZYMES
EFFECT OF CO-FACTORS:
Chlorides, Bromides, Iodides
Cofactors increase the rate of
enzyme-catalyzed reactions
EFFECT OF SUBSTRATE
CONCENTRATION
Vmax
Aspartate
aminotransferase
QUESTION 1
Which of the following is TRUE when a substrate
concentration equals km in an enzyme-catalyzed
reaction?
A. A few of the enzyme molecules are present
as ES complex.
B. Majority of the enzyme molecules are present
as ES complex.
C. Half of the enzyme molecules are present as
ES complex.
D. All of the enzyme molecules are present as
ES complex.
QUESTION 1
Which of the following is TRUE when a substrate
concentration equals km in an enzyme-catalyzed
reaction?
A. A few of the enzyme molecules are present
as ES complex.
B. Majority of the enzyme molecules are present
as ES complex.
C. Half of the enzyme molecules are present as
ES complex.
D. All of the enzyme molecules are present as
ES complex.
QUESTION 2
Competitive inhibition can be relieved by
increasing which of the following?
A. Enzyme concentration
B. Inhibitor concentration
C. Enzyme-substrate concentration
D. Substrate concentration
QUESTION 2
Competitive inhibition can be relieved by
increasing which of the following?
A. Enzyme concentration
B. Inhibitor concentration
C. Enzyme-substrate concentration
D. Substrate concentration
QUESTION 3
Which of the following enzymes requires
biotin as a coenzyme?
A. PEP carboxykinase
B. Pyruvate carboxylase
C. Phosphofructokinase I
D. Pyruvate dehydrogenase
QUESTION 3
Which of the following enzymes requires
biotin as a coenzyme?
A. PEP carboxykinase
B. Pyruvate carboxylase
C. Phosphofructokinase I
D. Pyruvate dehydrogenase
QUESTION 4
An enzyme with a low Km indicates
which of the following?
A. High affinity for the substrate.
B. Requires increased amount of
substrate to become saturated.
C. Vmax can be reached at high
substrate concentration.
D. Less enzyme-substrate complexes
are formed.
QUESTION 4
An enzyme with a low Km indicates
which of the following?
A. High affinity for the substrate.
B. Requires increased amount of
substrate to become saturated.
C. Vmax can be reached at high
substrate concentration.
D. Less enzyme-substrate complexes
are formed.
QUESTION 5
Enzymes can be regulated when
phosphorylated. This type of regulation
is called:
A. Allosteric control
B. Feed back regulation
C. Covalent modification
D. Enzyme induction
QUESTION 5
Enzymes can be regulated when
phosphorylated. This type of regulation
is called:
A. Allosteric control
B. Feed back regulation
C. Covalent modification
D. Enzyme induction
REFERENCES
Lehningers Principles of Biochemistry, Nelson,
D.L., Cox, M.M., 5th ed., pp. 183-220.
Harpers Illustrated Biochemistry, Murray, R. K.,
et. al., 29th ed., pp. 62-82.
Biochemistry with Clinical Correlations, Devlin, M.
T., 7th ed., pp. 378-421.
Biochemistry, Lippincotts Illustrated Reviews,
Champe, P.C., Harvey, R.A., 4th ed., pp. 53- 67.
Principles of Biochemistry, Horton, H.R., et al.,
4th ed., pp. 129-156.
Marks Basic Medical Biochemistry: A Clinical
Approach, Lieberman, M., Marks, A.D., 3rd ed.,
pp. 116-154.
THANK YOU
THANK
YOU
THANK YOU