Chapter 3
Enzymes
What is an enzyme?
§ High molecular weight (15,000<MW<10
6Daltons)
Naming of enzymes
§ Isozymes
§ Enzymes having different molecular forms but catalyzing the same reaction
Coenzymes and cofactors
n Nonprotein components essential to enzyme activity
n Many enzymes carry out their function relying solely on their protein structure
n Many others require nonprotein component, called cofactors and coenzymes
§
Provide proteins with chemically versatile functions not found in amino acid side chains§
Cofactors : metal ions + coenzymes§
Coenzymes : organic molecules (e.g., NAD, FAD, CoA, and some vitamines)§
Serving as intermediate carriers of functional groups in the enzyme reactionn Nonprotein components essential to enzyme activity
n Many enzymes carry out their function relying solely on their protein structure
n Many others require nonprotein component, called cofactors and coenzymes
§
Provide proteins with chemically versatile functions not found in amino acid side chains§
Cofactors : metal ions + coenzymes§
Coenzymes : organic molecules (e.g., NAD, FAD, CoA, and some vitamines)§
Serving as intermediate carriers of functional groups in the enzyme reactionCofactors and coenzymes
Coenzymes
Apoenzyme and Holoenzyme
n Apoenzyme
§ Protein part of enzyme
n Holoenzyme
§ An enzyme containing a nonprotein group
§ Holoenzyme = apoenzyme + cofactor
n Apoenzyme
§ Protein part of enzyme
n Holoenzyme
§ An enzyme containing a nonprotein group
§ Holoenzyme = apoenzyme + cofactor
Classification of Enzymes
n Classification by 6 catalytic functions
n “ATP : glucose phosphotransferase”
§
ATP + D-glucose à ADP + D-glucose 6-phosphate§
Enzyme Commission number (E.C. number) : 2.7.1.1§
2 : class number (transferase)§
7 : subclass (phosphotransferase)§
1 : hydroxyl group as acceptor§
1 : glucose as acceptorn Classification by 6 catalytic functions
n “ATP : glucose phosphotransferase”
§
ATP + D-glucose à ADP + D-glucose 6-phosphate§
Enzyme Commission number (E.C. number) : 2.7.1.1§
2 : class number (transferase)§
7 : subclass (phosphotransferase)§
1 : hydroxyl group as acceptor§
1 : glucose as acceptorClassification of Enzymes
n Oxidoreductases
§
lactate dehydrogenasen Transferase
§
transaminasen Hydrolase
§
nitrilasen Oxidoreductases
§
lactate dehydrogenasen Transferase
§
transaminasen Hydrolase
§
nitrilaseClassification of Enzymes
n Lyase
§
aspartate ammonia lyasen Isomerases
§
alanine racemasen Ligases
§
DNA ligase (Consult your bio book!) n Lyase§
aspartate ammonia lyasen Isomerases
§
alanine racemasen Ligases
§
DNA ligase (Consult your bio book!)Enzyme as catalyst
n Enzyme is unchanged and can repeat the process
Enzyme
(sucrase) Active site
1
Substrate (sucrose)
Enzyme available with empty active site 4
Glucose Fructose
2 3
Enzyme available with empty active site
Substrate binds to enzyme with induced fit Substrate is
converted to products Products
are released
How does substrate bind to enzyme ?
n Active site
§
place of enzyme where substrate bindsn Enzyme and substrate molecules recognize each other through structural complementarity
n The substrate binds to the enzyme through relatively weak forces
§
H bonds, ionic bonds, and van der Waals interactionHow do enzymes make the reaction faster?
How to reduce activation energy?
n Non-covalent interactions between enzyme and substrate
n Binding energy, DG
B§
The energy derived from enzyme-substrate interactionn Binding energy lowers activation energy
How to reduce activation energy?
How to reduce activation energy?
n Enzyme must be complementary to not the substrate, but the transition state
§
Binding energy offsets the activation energy à lower a net activation energyBinding energy contributed by formation of weak noncovalent interactions between substrate and
enzyme in transition state Binding energy contributed by formation of weak noncovalent interactions between substrate and
enzyme in transition state
Enzyme affects reaction rate
A+B → C+D -rA = kCAαCBβ k(T) = Ae-E/RT
Enzyme kinetics
f(S) = ?
?
?
Enzyme kinetics
?
Michaelis-Menten Kinetics
Determination of K
mand V
mDetermination of K
mand V
mDetermination of K
mand V
mKm
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