introduction to enzymes biological catalysts. life process = chemical reactions enzymes abcdef...
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Introduction to Enzymes
Biological Catalysts
Life Process = Chemical Reactions
Enzymes
A B C D E FEnzyme 1 Enzyme 2 Enzyme 3 Enzyme 4 Enzyme 5
Chemical Reactions
Spontaneous and Fast
Spontaneous but Slow
Na+ + Cl- + H2OHCl + NaOH
2 H2O
ADP + Pi
2 H2 + O2
ATP + H2O
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
105 molecules CO2 per enzyme molecule per second
107 x uncatalyzed reaction
H2CO3CO2 + H2O
Table 11-1
Catalytic Power of Some Enzymes
Mild Reaction Condition
• Physiological pH = ~7.3
• Temperature = ~37°C
Table 11-1
Greater Reaction Specificity
Glucose + ATP Glucose-6-P + ADP
Hexokinase
Fructose + ATP Fructose-6-P + ADP
Mannose + ATP Mannose-6-P + ADP
Glucose + ATP Glucose-6-P + ADP
Glucokinase
ONLY
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)
H3C CH
OH
COOH H3C C
O
COOH + NADH + H+
PyruvateLactate
+ NAD+
Lactate Dehydrogenase
L-Lactate:NAD Oxidoreductase
Enzyme Nomenclature(Common Name versus Systematic
Name)
H3C CH
OH
COOH H3C C
O
COOH + NADH + H+
PyruvateLactate
+ NAD+
Lactate Dehydrogenase
L-Lactate:NAD Oxidoreductase
Enzyme Catalysis
Substrate(s) Product(s)
Reaction Pathway (Coordinate)
Br
H
H
HO C
H
Br
H
HO C
H
H
CH3Br + OH-
CH3OH + Br-
OH- + + Br
-
Reactants "Transition State" Products
CH
H
H
Transition State Diagram
Stabilizing the transition state
Catalysts
Pathway of Enzyme Catalysis
E + S [E–S]Binding Catalysis
E + P
Enzyme–Substrate
Complex
Active Site
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
Page 325
Aconitase Reaction
Prochiral Substrate Chiral Product
Figure 11-2
Stereospecificity in Substrate Binding
Enzymes Vary in Geometric Specificity
(Alcohol Dehydrogenase)
Ethanol ——> Acetaldehyde
Methanol ——> Formaldehyde
Isopropanol ——> Dimethylketone
RATE: Ethanol > Methanol > Isopropanol
Trypsin and Chymotrypsin
NH CH C
R1
NH
O
CH
R2
C
O
NH CH C
R1
O
O
CH
R2
C
O
H3N+
+_
H2O
Trypsin
NH CH C NH
O
N C
complementary binding or posit ioning site
"SPECI FI CI TY"_
+
arginine or lysine
"long + side chain"
H2O
Long positively charged side chain
Chymotrypsin
NH CH C NH
O
N C
"aromatic side chain"
"SPECI FI CI TY"
complementary binding or posit ioning site
phenylalaninetyrosinetryptophan
Hydrophobic Pocket
H2O
O Aromatic side chain
Some Enzymes Require Cofactors
Cofactors
• Simple Proteins (no cofactor)
• Protein plus Cofactor
– Apoenzyme: protein only
– Holoenzyme: protein plus cofactor
Apoenzyme + cofactor Holoenzyme
(inactive) (active)
Figure 11-3
Types of Cofactors
Organic Cofactor
PermanentlyAssociated
Transiently
Associated
Metal Ions
Figure 11-4
Coenzymes: Cosubstrates[NAD(P)+ ——> NAD(P)H + H+]
NADP+
N
OCH2
OH OH
O
OCH2
OH OPO3=
AOP
O
O–
P
O
O–
O
CNH2
O
Nucleotide
Nucleotide
NADPH
N
R
CNH2
OH H
Page 327
Coenzymes: Cosubstrates(Alcohol Dehydrogenase)
Coenzymes: Prosthetic Groups
(Cytochromes)
Cytochrome•Heme(Fe3+)
Cytochrome•Heme(Fe2+)
e–e–
Coenzymes Must be Regenerated
NAD+ NADH + H+
2H+ + 2e–
2H+ + 2e–
Heme(Fe3+) Heme(Fe2+)
e–
e–
Alcohol Dehydrogenase
Cytochromes
Cosubstrate:Different enzyme
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
PP
PP
4 ATP
4 ADP4 H2O
Phosphorylase a "active"
Phosphorylase b "inactive"
+
Phosphorylase Phosphatase
Phosphorylase Kinase4 Pi
(glucose)n-1 + glucose-1-PPhosphorylase
(glucose)n + Pi
Non-covalent Modification
Effectors or Ligands
Negative Effectors
"active"
Regulatory Site
Active Site
"inactive" orless active
I
I
+
Positive Effectors
+
"active" ormore active
"inactive" orpoorly active
++
Allosteric Proteins
positive ef f ector
negative ef f ector
no ef f ectorVo
[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