6. ENZIM.ppt

Chapter 2
computing
Presentation copyright © 2002 David A Bender and some images copyright © 2002 Taylor & Francis Ltd
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Enzymes

Activation energy of a thermoneutral
reaction
computing
Presentation copyright © 2002 David A Bender and some images copyright © 2002 Taylor & Francis Ltd 
Activation energy of a chemical reaction
the energy needed to break a chemical bond
initial
excited
final
energy
level
thermoneutral
In a thermoneutral reaction, the same energy is released
when the new bond is formed

Activation energy of an exothermic reaction
computing
In an exothermic reaction, more energy than the activation energy
is released when the new bond is formed
an exothermic reaction proceeds with an output of energy
initial
excited
final
energy
level
exothermic

Activation energy of an endothermic
reaction
computing
In an endothermic reaction, less energy than the activation energy
is released when the new bond is formed
an endothermic reaction requires an input of energy to proceed
initial
excited
final
energy
level
endothermic

Enzymes are proteins that catalyse
reactions
computing
Enzymes are proteins that catalyse chemical reactions.
Folding of the protein
into its tertiary structure
brings side-chains of
various amino acids
that may be far apart
in the primary sequence
into close juxtaposition,
forming an active site.

Enzymes lower the activation energy
computing
An example of enzyme catalysis:
the serine proteases, chymotrypsin, trypsin and elastase
initial
excited
final
+ enzyme
non-enzymic
energy
level
In vitro
10 – 12 hours in 12 mol /L HCl at 105ºC, random hydrolysis of peptide bonds
In vivo
1 – 2 hours at 37ºC, specific bonds hydrolysed
Enzymes lower the activation energy of the reaction

Specificity of the serine proteases - 1
computing
Bonds hydrolysed:
trypsin
esters of basic aa
chymotrypsin
esters of aromatic aa
elastase
esters of small neutral aa


Specificity of the serine proteases - 2
computing
substrate sits in a groove
on the enzyme surface
bond to be cleaved
lies over catalytic site


Specificity - trypsin
computing
-
Gly
Gly
Asp
-
+
peptide in groove on enzyme surface
trypsin
Bonds hydrolysed:
trypsin
esters of basic amino acids
chymotrypsin
esters of aromatic amino acids
elastase
esters of small neutral amino acids

Specificity - chymotrypsin
computing
Gly
Gly
Ser
chymotrypsin
Bonds hydrolysed:
trypsin
chymotrypsin
elastase

Specificity - elastase
computing
Val
Thr
Gly
elastase
Bonds hydrolysed:
trypsin
chymotrypsin
elastase

Enzyme specificity – D- and L-isomers
computing
Enzyme specificity
distinguishing between D- and L-isomers
Because of multiple interactions in binding to the active site,
enzymes can readily distinguish between stereo-isomers
C
C
OH
O
H
H
CH2OH
C
COO-
CH3
NH3
+
H
D-glyceraldehyde D-alanine
C
C
H
O
H
HO
CH2OH
C
COO-
CH3
H
+
H3N
L-glyceraldehyde L-alanine

Enzyme specificity – cis- and trans- isomers
computing
Enzyme specificity
distinguishing between cis- and trans-isomers
Because of multiple interactions in binding to the active site,
enzymes can readily distinguish between isomers
cis
trans

Stages in an enzyme catalysed reaction
computing
Stages in an enzyme-catalysed reaction
Enz + S Enz-S
Enz-S Enz-P
Enz-P Enz + P
Enz + S Enz-S Enz-P Enz + P
Binding of the substrate to the enzyme to form the enzyme-substrate complex
Reaction of the enzyme-substrate complex to form the enzyme-product complex
Breakdown of the enzyme-product complex and release of product
Overall


Factors that affect the activity of enzymes
computing
 pH of incubation or environment
 temperature
 concentration of enzyme
 concentration of substrate
 covalent modification of enzyme
 inhibitors and activators
Factors that affect the activity of enzymes

pH dependence of an enzyme-catalysed
reaction
computing
pH dependence of an enzyme-catalysed reaction
0
0.2
0.4
0.6
0.8
1
1 2 3 4 5 6 7 8 9 10 11 12
pH
relative
activity
Enzyme A Enzyme B


Temperature dependence of an enzyme-
catalysed reaction
computing
Temperature dependence of an enzyme-catalysed reaction
0 20 40 60 80 100
temperature (°C)
rate
of
reaction
(µmol
/min)
10 minute incubation . . . . . . . . 1 minute incubation


The effect of varying the amount of enzyme
present - 1
computing
The effect of varying the amount of enzyme present
enzyme concentration
relative
activity
enzyme concentration
relative
activity
predictable linear increase
in product formation with
increasing amount of enzyme
non-enzymic formation of product
or product already present in
tissue sample

present - 2
computing
concentration of enzyme
relative
activity
enzyme has multiple subunits
monomer is inactive
or has low activity
active dimer dissociates
at low concentration

present - 3
computing
concentration of enzyme
relative
activity
monomer is active
enzyme associates to
less active dimer at
high concentration

Substrate dependence
computing
[substrate]
rate
Vmax
½ Vmax
Substrate dependence of an enzyme-catalysed reaction
enzyme ± saturated
little change in rate with increasing substrate
sharp
increase
in
rate
with
increasing
substrate
Km

The relevance of Km
computing
[substrate], mmol /L
rate
The relevance of Km:
two enzymes “competing” for substrate S
S
P
X
enzyme A
enzyme B
enzyme A
low Km
enzyme B
high Km

Experimental determination of Km
computing
Experimental determination of Km and Vmax
The Lineweaver-Burk double reciprocal plot
1 / [substrate]
1
/
rate
-1 / Km
1 / Vmax


Enzymes with two substrates – ordered
reaction
computing
Enzymes with two substrates
A + B C + D
Ordered reaction – each substrate binds in turn
A + Enz A-Enz
A-Enz + B A-Enz-B C-Enz-D C-Enz + D
C-Enz Enz + C
1 / [substrate A]
1
/
rate
varying
concentration
of
substrate
B
converging lines

Enzymes with two substrates – ping-pong
reaction
computing
Enzymes with two substrates
A + B C + D
Ping-pong reaction – one substrate reacts, and modifies enzyme,
then second substrate reacts with modified enzyme
A + Enz A-Enz C-Enz* C + Enz*
B + Enz* B-Enz* D-Enz D + Enz
1 / [substrate A]
1
/
rate
varying
concentration
of
substrate
B
parallel lines

Transamination – an example of a ping-pong
reaction
computing
pyridoxal phosphate
pyridoxamine phosphate
C COOH
R1
H
NH2
C COOH
R1
O
N
C
OH
CH3
CH2
H O
O
P
O
OH
OH
N
OH
CH3
CH2
O
P
O
OH
OH CH2 NH2
C COOH
R2
H
NH2
C COOH
R2
O
An example of a ping-pong reaction:
the reaction of transamination (see §9.3.1.2)

Enzymes with cooperative substrate binding
computing
Enzymes with cooperative substrate binding
– allosteric enzymes (see also §10.2.1)
[substrate]
rate
of
reaction

Enzyme inhibitors as drugs
computing
Enzyme inhibitors as drugs
 reversible inhibitors
 non-covalent (equilibrium) binding to enzyme
 many are relatively unspecific
 irreversible inhibitors
 bind to enzyme covalently
 many are substrate analogues
 undergo part of reaction
 transition state covalent intermediate does not break down
 mechanism-dependent (suicide) inhibitors
 highly specific for target enzyme
 so-called rational drug design
 based on studies of enzyme mechanism

Reversible versus irreversible inhibitors as
dugs
computing
Reversible versus irreversible inhibitors as drugs
Reversible inhibitors diffuse onto and off the enzyme
 therefore undergo metabolism and excretion
 dose may be required several times per day
Irreversible inhibitors are covalently bound
 inactivate a molecule of enzyme permanently
 dose required only daily or less often
 (depending on rate of enzyme protein synthesis)
 it may take a long time to adjust the patient’s dose
Omeprazole is used to treat gastric ulcers
 irreversible inhibitor of proton pump in gastric mucosa
 dose required only once per day
 overdose would not matter because aim is to inhibit acid
secretion more or less completely to permit ulcer to heal

Dialysis to determine if an inhibitor is
reversible or irrevserible
computing
Dialysis to determine if an inhibitor is reversible or irreversible
small molecules
equilibrate
across the membrane
proteins are too large
to cross the membrane
semi-permeable membrane

computing
small molecules
equilibrate
across the membrane

computing
small molecules
equilibrate
across the membrane
inhibitor removed
activity restored


computing
small molecules
equilibrate
across the membrane
inhibitor not removed
activity not restored


Competitive reversible inhibition
computing
Competitive reversible inhibition
[substrate]
rate
of
reaction
increasing
[inhibitor]
1 / [substrate]
1
/
rate
of
reaction
Vmax is unchanged, Km is increased
if enough substrate is added, it overcomes the inhibitor
Enz + S + I Enz-I
Enz + S + I Enz-S Enz-P Enz + P
increasing
[inhibitor]

Non-competitive reversible inhibition
computing
Non-competitive reversible inhibition
[substrate]
rate
of
reaction
1 / [substrate]
1
/
rate
of
reaction
Km is unchanged, Vmax is decreased
adding more substrate has no effect on the rate of reaction
Enz + S + I Enz-S + I Enz-S-I Enz-P-I Enz + P + I
slow
increasing
[inhibitor]
increasing
[inhibitor]

A competitive or non-competitive inhibitor
as a drug - 1
computing
A competitive or non-competitive inhibitor as a drug
A
B
C
D
Do you want to:
 increase the concentration of B in the cell ?
 decrease the concentration of D in the cell ?
drug inhibits this enzyme

as a drug - 2
computing
A
B
C
D
Do you want to:
with a competitive inhibitor:
as [B] increases, so rate of reaction increases
when [B] rises high enough
rate of reaction = Vmax
rate of formation of D is unchanged

as a drug - 3
computing
A
B
C
D
Do you want to:
with a non-competitive inhibitor:
as [B] increases, rate of reaction is unchanged
no matter how much B accumulates
rate of formation of D is lower than normal

Prosthetic groups and coenzymes
computing
In addition to reactive groups from amino acids
proteins may contain non-protein molecules:
Prosthetic group – covalently bound organic molecule or metal ion
Coenzyme – tightly but not covalently bound organic molecule
If an enzyme requires a prosthetic group of coenzyme:
Enzyme + prosthetic group or coenzyme
= holo-enzyme – catalytically active
Enzyme protein without prosthetic group or coenzyme
= apoenzyme – catalytically inactive

“Coenzymes” that are really cosubstrates
computing
Some compounds referred to as coenzymes
are really cosubstrates
 They are present in µmolar concentrations
 (most substrates are present in mmolar concentrations)
 They undergo rapid turnover
 the total body content of ATP is ~ 10g
 total daily turnover of ATP is ~ body weight (~70 kg)
 They are shared between several enzymes
 NAD+ is reduced to NADH by many different enzymes
 NADH is used as a reducing agent by many other enzymes

The major coenzymes
computing
The major coenzymes
precursor functions
ATP adenosine triphosphate adenine energy metabolism
CoA coenzyme A pantothenate acyl transfer
FAD flavin adenine dinucleotide vitamin B2 redox
FMN flavin mononucleotide vitamin B2 redox
NAD nicotinamide adenine dinucleotide niacin redox

The adenine nucleotides
computing
The adenine nucleotides: AMP, ADP and ATP
adenosine monophosphate (AMP)
adenosine diphosphate (ADP)
adenosine triphosphate (ATP)
N
N
NH2
N
N
CH2 O P OH
O
OH
O
OH OH
N
N
NH2
N
N
CH2 O P O
O
OH
P OH
O
OH
O
OH OH
N
N
NH2
N
N
CH2 O P O
O
OH
P O
O
OH
P OH
O
OH
O
OH OH

Coenzyme A
computing
Coenzyme A
O
OH
O
P
OH
HO O
CH2
O
P
O
P
O
CH2
OH
O
OH
O
C
H3C
CHOH
CH3
C
NH
O
CH2
CH2
C NH CH2 CH2 SH
O
N
N
N
N
NH2
H
coenzyme A (CoASH)
-SH group forms thio-esters with fatty acids

Riboflavin and the flavin coenzymes
computing
H3C
H3C N
N
N O
O
N
CH2 CH CH CH CH2OH
OH OH OH
H3C
H3C N
N
N O
O
N
CH2 CH CH CH CH2
OH OH OH
O P OH
OH
O
H3C
H3C N
N
N O
O
N
CH2 CH CH CH CH2
OH OH OH
O P O P O
OH
O
OH
O
CH2 O
OH OH
N
N
NH2
N
N
riboflavin
riboflavin monophosphate
(flavin mononucleotide, FMN)
flavin adenine dinucleotide (FAD)
Riboflavin and the flavin coenzymes

Oxidation and reduction of flavin coenzymes
computing
Oxidation and reduction of the flavin coenzymes
NH
N
N
N
O
O
H3C
H3C
CH2 CH
OH
CH
OH
CH
OH
CH2OH
oxidized riboflavin
riboflavin semiquinone radical
NH
N
N
N
O
O
H3C
H3C
CH2 CH
OH
CH
OH
CH
OH
CH2OH
H
NH
N
N
N
O
O
H3C
H3C
CH2 CH
OH
CH
OH
CH
OH
CH2OH
H
H
fully reduced riboflavin
2H
H
H

The nicotinamide nucleotides
computing
The nicotinamide nucleotide coenzymes, NAD and NADP
O
OH OH
N
N
N
N
NH2
OH
OH
O
CH2 O P O
O
OH
P O
OH
O
CH2
N
CONH2
phosphorylated in NADP
nicotinamide adenine dinucleotide (NAD)
N
CONH2
N
CONH2
H H
XH2
X
oxidized coenzyme
NAD
+
or NADP
+
reduced coenzyme
NADH or NADPH
+ H+

Classification of enzymes - 1
computing
The classification of enzymes by the reaction catalysed
1) Oxidation and reduction reactions
2) Transfer of a reactive group from one substrate to another
3) Hydrolysis of bonds
4) Addition across carbon-carbon double bonds
5) Rearrangement of groups within a single molecule of substrate
6) Formation of bonds between two substrates

Classification of enzymes - 2
computing
The classification of enzymes by the reaction catalysed
1) Oxidoreductases: oxidation and reduction reactions
dehydrogenases addition or removal of H
oxidases two-electron transfer to 02 forming H2O2
two-electron transfer to ½ O2 forming H2O
oxygenases incorporate 02 into product
hydroxylases incorporate ½ O2 into product as -OH and form H20
peroxidases use as H202 as oxygen donor, forming H20
2) Transferases: transfer a chemical group from one substrate to another
kinases transfer phosphate from ATP onto substrate
3) Hydrolases: hydrolysis of C-O, C-N, O-P and C-S bonds
(e.g. esterases, proteases, phosphatases, deamidases)
4) Lyases: addition across a carbon-carbon double bond
(e.g. dehydratases, hydratases, decarboxylases)
5) Isomerases: intramolecular rearrangements
6) Synthetases: formation of bonds between two substrates
frequently linked to utilization of ATP

The metabolism of ethanol
computing
The metabolism of ethanol
NAD
NADH
NAD
NADH
alcohol dehydrogenase
aldehyde dehydrogenase
9 enzyme-catalysed reactions
(the citric acid cycle)
ethanol
acetaldehyde
acetate
O2
3
mitochondrial electron
transport chain
CH2 OH
CH3
HC O
CH3
COOH
CH3
2 CO2 + 3 H2O
+ 29 kJ /gram
O2
3
ethanol
combustion of ethanol
CH2 OH
CH3
2 CO2 + 3 H2O
+ 29 kJ /gram

Linear and branched pathways
computing
ABCD
A linear pathway


PQR
XYZ
A branched pathway
substrate concentration
rate

Looped, spiral or repeating pathways
computing
Looped, spiral or repeating pathways
The substrate undergoes a series of reactions resulting in
a homologous product (eg 2 carbons longer or shorter);
this undergoes the same sequence of reactions.
oxidation
to C=C

hydration
to CH-OH

cleavage

oxidation
to C=O


A cyclic biosynthetic pathway
computing
A cyclic biosynthetic pathway
The product is built up on a carrier molecule
that is unchanged at the end

add-on-a-bit


add
add
 on-a
add-on-a
add-on-a


bit
add-on-a
add-on-a-bit

A cyclic catabolic pathway
computing
A cyclic catabolic pathway
The product is broken down on a carrier molecule
that is unchanged at the end

add
 bit
add-on-a
add-on-a


on-a
add
add


add-on-a-bit
add-on-a-bit

End
computing
End of presentation
The enzyme assay simulation on the CD accompanies this Chapter

6. ENZIM.ppt

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