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Introduction to Enzymes
Biological Catalysts
Life Process = Chemical Reactions
Enzymes
A
Enzyme 1
B
Enzyme 2
C
Enzyme 3
D
Enzyme 4
E
Enzyme 5
F
Chemical Reactions
Spontaneous and Fast
HCl + NaOH
Na+ + Cl- + H2 O
Spontaneous but Slow
2 H2 + O2
ATP + H 2O
2 H2 O
ADP + Pi
Types of Reactions
• Spontaneous Reactions: thermodynamically
or energetically favorable
• Kinetically Unfavorable Reactions
• Requirement for Catalysts
– Protein Catalysts: Enzymes
– RNA Catalysts: Ribozymes
General Properties of Enzymes
• Higher reaction rates (catalytic power)
• Milder reaction conditions
• Greater reaction specificity
• Capacity for regulation
Higher Reaction Rates
Carbonic Anhydrase
CO2 + H2O
H2 CO3
105 molecules CO2 per enzyme molecule per second
107 x uncatalyzed reaction
Catalytic Power of Some Enzymes
Table 11-1
Mild Reaction Condition
• Physiological pH = ~7.3
• Temperature = ~37°C
Greater Reaction Specificity
Hexokinase
Glucose + ATP
Fructose + ATP
Mannose + ATP
Glucose-6-P + ADP
Fructose-6-P + ADP
Mannose-6-P + ADP
Glucokinase
Glucose + ATP
Table 11-1
ONLY
Glucose-6-P + ADP
Capacity for Regulation
• Allosteric (Regulatory) Enzymes
• Covalent Modification
– Irreversible
– Reversible
• Non-covalent Modification
Enzyme Classes
• Oxidoreductases: oxidation-reduction reactions
• Transferases: transfer of functional groups
• Hydrolases: hydrolysis reactions (cleavage and
introduction of water)
• Lyases: group elimination to form double bond
• Isomerases: isomerization (intramolecular
rearrangements
• Ligases (synthases): bond formation coupled with
ATP hydrolysis
Enzyme Nomenclature
(Usual usage: often use suffix –ase)
• Common Name:
– Useful but sometimes ambiguous
• Examples: Urease/Arginase
• Exceptions to the –ase suffix:
– Trypsin/Chymotrypsin
• Systematic Name:
– Substrate(s) Type of reaction-ase
Enzyme Nomenclature
(Common Name versus Systematic Name)
Aconitase
Aconitate Hydratase
EC 4.2.1.3
Enzyme Nomenclature
(Common Name versus Systematic Name)
Aconitase
Aconitate Hydratase
EC 4.2.1.3
Enzyme Nomenclature
(Common Name versus Systematic Name)
O
OH
H3C
CH
COOH
Lactate
+
NAD+
H3C
C
COOH +
Pyruvate
Lactate Dehydrogenase
L-Lactate:NAD Oxidoreductase
NADH
+
H+
Enzyme Nomenclature
(Common Name versus Systematic Name)
O
OH
H3C
CH
COOH
Lactate
+
NAD+
H3C
C
COOH +
Pyruvate
Lactate Dehydrogenase
L-Lactate:NAD Oxidoreductase
NADH
+
H+
Enzyme Catalysis
Substrate(s)
Product(s)
Reaction Pathway (Coordinate)
CH3Br
H
OH
-
+ H
+ OH
-
CH3OH
H
Reactants
Br
HO
Br
-
H
H
C
+
C
Br
H
"Transition State"
H
HO
C
H
H
Products
+ Br
-
Transition State Diagram
Stabilizing the transition state
Catalysts
Pathway of Enzyme Catalysis
E+S
Binding
[E–S]
Catalysis
Enzyme–Substrate
Complex
Active Site
E+P
Substrate Specificity
• Active Site
– Lock and Key Model
– Induced Fit Model
• Stereospecificity: 3-point attachment
• Geometric Specificity: e.g. trypsin and
chymotrypsin
Principle of Complementarity
• Geometric (physical) complementarity
• Electronic (chemical) complementarity
Enzyme-Substrate Complex
Binding Site
Models of Complementarity
Lock and Key
Induced Fit
Enzymes are Stereospecific
Aconitase Reaction
Prochiral Substrate
Page 325
Chiral Product
Stereospecificity in Substrate
Binding
Figure 11-2
Enzymes Vary in Geometric
Specificity
(Alcohol Dehydrogenase)
Ethanol ——> Acetaldehyde
Methanol ——> Formaldehyde
Isopropanol ——> Dimethylketone
RATE: Ethanol > Methanol > Isopropanol
Trypsin and Chymotrypsin
H2O
O
NH CH
C
O
NH
R1
R1
C
R2
O
NH CH
CH
C
_
O
+
+
H 3N
O
CH
R2
C
Trypsin
H2O
O
N
NH
arginine
or
lysine
CH
+
C
NH
C
Long
"long +positively
side chain"charged
side chain
complementary binding
or positioning site
_
"SPECIFICITY"
Chymotrypsin
H2O
O
N
NH
phenylalanine
tyrosine
tryptophan
CH
C
O
NH
C
"aromatic side
chain"
Aromatic
side
chain
complementary binding
or positioning site
Hydrophobic
Pocket
"SPECIFICITY"
Some Enzymes Require Cofactors
Cofactors
• Simple Proteins (no cofactor)
• Protein plus Cofactor
– Apoenzyme: protein only
– Holoenzyme: protein plus cofactor
Apoenzyme + cofactor
(inactive)
Holoenzyme
(active)
Types of Cofactors
Organic
Cofactor
Transiently
Associated
Figure 11-3
Permanently
Associated
Metal Ions
Coenzymes: Cosubstrates
[NAD(P)+ ——> NAD(P)H + H+]
Figure 11-4
NADP+
O
C
O
P O CH2
O–
O
N
OH
Nucleotide
O
OH
O
P O CH2
O–
NH2
OH
O
A
Nucleotide
OPO3=
NADPH
H O
C
H
N
R
NH2
Coenzymes: Cosubstrates
(Alcohol Dehydrogenase)
Page 327
Coenzymes: Prosthetic Groups
(Cytochromes)
Cytochrome•Heme(Fe3+)
e–
e–
Cytochrome•Heme(Fe2+)
Coenzymes Must be Regenerated
2H+ + 2e–
NAD+
e–
NADH + H+
2H+ + 2e–
Alcohol Dehydrogenase
Cosubstrate:
Different enzyme
Heme(Fe3+)
Heme(Fe2+)
e–
Cytochromes
Prosthetic group:
Same enzyme
Control of Enzyme Activity
Irreversible Covalent Modification
• Zymogen Activation
• Proteolysis
– Lysosomes
– Proteosomes (ubiquitin)
Zymogen Activation
H2O
+
"Inactive"
"Active"
Reversible Covalent Modification
(glucose)n
Phosphorylase
Phosphatase
+
Phosphorylase
Pi
(glucose)n-1
P
P
P
P
glucose-1-P
Phosphorylase a
"active"
4 H2 O
4 ADP
4 Pi
4 ATP
+
+
Phosphorylase
Kinase
Phosphorylase b
"inactive"
Non-covalent Modification
Effectors or Ligands
Negative Effectors
+
Active
Site
I
I
Regulatory
Site
"active"
"inactive"
or
less active
Positive Effectors
+
+
+
"inactive"
or
poorly active
"active"
or
more active
Allosteric Proteins
no effector
Vo
negative effector
positive effector
[S]
General Properties of Enzymes
• Biological Catalysts
– Not used up in the reaction (Regenerated)
– Higher reaction rates (catalytic power)
• Within a biologically relevant time frame
– Milder reaction conditions
• Biologically appropriate conditions
– Greater reaction specificity
– Capacity for regulation
• Control of substrate and product availability