BAHAN KULIAH BIOKIMIA POWER POINT BAGIAN 1 /BIOCHEMISTRY POWER POINT LECTURES PART 1 | Karya Tulis Ilmiah
Glycolysis
5/9/03
Glycolysis
The conversion of glucose to pyruvate to yield 2ATP
molecules
•10 enzymatic steps
•Chemical interconversion steps
•Mechanisms of enzyme conversion and intermediates
•Energetics of conversions
•Mechanisms controlling the Flux of metabolites
through the pathway
Historical perspective
Winemaking and baking industries
1854-1865 Louis Pasture established that microorganisms were
responsible for fermentation.
1897 Eduard Buchner- cell free extracts carried out fermentation
no “vital force” and put fermentation in the province of
chemistry
1905 - 1910 Arthur Harden and William Young
•
inorganic phosphate was required ie. fructose-1,6bisphosphate
•
zymase and cozymase fractions can be separated by
diaylsis
Inhibitors were used. Reagents are found that
inhibit the production of pathway products, thereby
causing the buildup of metabolites that can be
identified as pathway intermediates.
Fluoride- leads to the buildup of 3-phosphoglycerate
and 2-phosphoglycerate
1940 Gustav Embden, Otto Meyerhof, and Jacob
Parnas put the pathway together.
Pathway overview
1. Add phosphoryl groups to activate glucose.
2. Convert the phosphorylated intermediates into high energy
phosphate compounds.
3. Couple the transfer of the phosphate to ADP to form ATP.
Stage I A preparatory stage in which glucose is phosphorylated
and cleaved to yield two molecules of glyceraldehyde-3phosphate - uses two ATPs
Stage II glyceraldehyde-3-phosphate is converted to pyruvate
with the concomitant generation of four ATPs-net profit is
2ATPs per glucose.
Glucose + 2NAD+ + 2ADP +2Pi 2NADH +
2pyruvate + 2ATP + 2H2O + 4H+
Oxidizing power of NAD+ must be recycled
NADH produced must be converted back to NAD+
1. Under anaerobic conditions in muscle NADH
reduces pyruvate to lactate (homolactic fermentation).
2. Under anaerobic conditions in yeast, pyruvate is
decarboxylated to yield CO2 and acetaldehyde and the
latter is reduced by NADH to ethanol and NAD+ is
regenerated (alcoholic fermentation).
3. Under aerobic conditions, the mitochondrial
oxidation of each NADH to NAD+ yields three ATPs
Hexokinase
CH2OH
H
O
H
OH
Mg++
H
+ ATP
H
OH
OH
H
OH
Glucose
CH2OPO32H
O
H
OH
H
+ ADP + H+
H
OH
OH
H
OH
Glucose-6-phosphate
Isozymes: Enzymes that catalyze the same reaction but
are different in their kinetic behavior
Tissue specific
Glucokinase- Liver controls blood glucose levels.
Hexokinase in muscle - allosteric inhibition by ATP
Hexokinase in brain - NO allosteric inhibition by ATP
Hexokinase reaction mechanism is
RANDOM Bi-Bi
Glucose
ATP
ADP
Glu-6-PO4
When ATP binds to hexokinase without glucose it does not
hydrolyze ATP. WHY?
The binding of glucose elicits a structural change that puts
the enzyme in the correct position for hydrolysis of ATP.
The enzyme movement places the ATP in close
proximity to C6H2OH group of glucose and excludes
water from the active site.
H
O
H
H
OH
OH
H
OH
-D-Xylose
There is a 40,000 fold
increase in ATP hydrolysis
upon binding xylose which
cannot be phosphorylated!
Yeast hexokinase, two lobes are gray and green.
Binding of glucose (purple) causes a large
conformational change. A substrate induced
conformational change that prevents the unwanted
hydrolysis of ATP.
Phosphoglucose Isomerase
CH2OPO32H
O
H
OH
H
O3POCH2
H
H
OH
OH
H
-2
OH
O
CH2OH
HO
H
OH
H
OH
Uses an “ ene dione intermediate
1) Substrate binding
2) Acid attack by H2N-Lys opens the ring
3) Base unprotonated Glu abstracts proton from C2
4) Proton exchange
5) Ring closure
Uncatalyzed isomerization of Glucose
Phosphofructokinase
-2
O3POCH2
H
O
CH2OH
HO
H
OH
H
+ ATP
OH
Fructose-6-PO4
-2
O3POCH2
Mg++
H
O
CH2OPO3-2
HO
H
OH
H
+ ADP
OH
Fructose-1,6-bisphosphate
1.) Rate limiting step in glycolysis
2.) Irreversible step, can not go the other way
3.) The control point for glycolysis
Aldolase
CH2OPO3-2
CH2OPO3-2
C
O
HO
C
H
H
C
OH
H
C
OH
HO
C
O
C
H
H
+
O
H
CH2OPO3-2
H
Fructose -1,6-bisphosphate
(FBP)
Dihydroxyacetone
phosphate (DHAP)
C
OH
Glyceraldehyde-3phosphate (GAP)
CH2OPO3-2
Aldol cleavage (retro aldol condensation)
There are two classes of Aldolases
Class I animals and plants - Schiff base intermediate
Step 1 Substrate binding
Step 2 FBP carbonyl groups reacts with amino LYS to
form iminium cation (Schiff base)
Step 3. C3-C4 bond cleavage resulting enamine and
release of GAP
Step 4 protonation of the enamine to a iminium cation
Step 5 Hydrolysis of iminium cation to release DHAP
CH2OPO3-2
C14
CH2OH
+
NH
CH2OPO3-2
(CH2)4
Lys
+ NaBH4
H
C14
CH2OH
NH3
(CH2)4
Lys
Class II enzymes are found in fungi and algae and
do not form a Schiff base. A divalent cation usually
a Zn+2 polarizes the carbonyl intermediate.
CH2OPO32-
CH2OPO3-2
C
HO
C
O
-
-
O
C
Zn2+
HO
Zn2+
H
H
Probably the occurrence of two classes is a metabolic
redundancy that many higher organisms replaced
with the better mechanism.
Aldolase is very stereospecific
When condensing DHAP with GAP four possible
products can form depending on the whether the proS or pro R hydrogen is removed on the C3 of DHAP
and whether the re or si face of GAP is attacked.
CH2OPO3
H
H
H
OH
OH
CH2OPO3
D-Fructose
1,6 bisphosphate
2-
CH2OPO32-
O
O
O
HO
CH2OPO32-
CH2OPO32-
2-
O
H
OH
HO
H
H
H
OH
HO
H
HO
H
OH
H
CH2OPO32D-Psicose
1,6 bisphosphate
OH
CH2OPO32-
D-Tagatose
1,6 bisphosphate
H
OH
H
OH
CH2OPO32-
D-Sorbose
1,6 bisphosphate
Triosephosphate isomerase
DHAP
GAP
GAP
1
2
K eq
4.7 x10
DHAP
96
TIM is a perfect enzyme which its rate is diffusion
controlled.
A rapid equilibrium allows GAP to be used and
DHAP to replace the used GAP.
TIM has an enediol intermediate
H
H
H
O
C
H
OH
H
OH
CH2OPO32-
H
C
OH
CH2OPO3
2-
C
OH
C
O
CH2OPO32-
GAP
enediol
DHAP
Transition state analogues Phosphoglycohydroxamate (A) and
2-phosphoglycolate (B) bind to TIM 155 and 100 times stronger
than GAP of DHAP
HO
B.
A.
OH
O
H
N
O
C
-
CH2OPO3
2-
O32-POH2C
O
O32-POH2C
O-
TIM has an extended “low barrier”
hydrogen bond transition state
Hydrogen bonds have unusually strong interactions and
have lead to pK of Glu 165 to shift from 4.1 to 6.5 and the
pK of
Geometry of the eneolate intermediate
prevents formation of methyl glyoxal
Orbital symmetry prevents double bond formation
needed for methyl glyoxal
Glyceraldehyde-3-phosphate
dehydrogenase
The first high-energy intermediate
H
O
H
C
OPO32-
O
OH + NAD+ + Pi
CH2OPO32-
H
C
OH + NADH
CH2OPO32-
Uses inorganic phosphate to create 1,3 bisphosphoglycerate
Reactions used to elucidate GAPDH’s mechanism
Mechanistic steps for GAPDH
1. GAP binds to enzyme.
2. The nucleophile SH attacks aldehyde to make a
thiohemiacetal.
3. Thiohemiacetal undergoes oxidation to an acyl
thioester by a direct transfer of electrons to
NAD+ to form NADH.
4. NADH comes off and NAD+ comes on.
5. Thioester undergoes nucleophilic attack by Pi to
form 1,3 BPG.
The acid anhydride of phosphate in a high energy
phosphate intermediate
Arsenate uncouples phosphate formation
O
O
3PG
O
As
O
O
GAP DH
+
H
H
C
OH
O-
O
O
O
O
O
H
O
As
C
H
C
OH
OH
CH2OPO32-
CH2OPO32-
+
O
CH2OPO32O
As
O
O
5/9/03
Glycolysis
The conversion of glucose to pyruvate to yield 2ATP
molecules
•10 enzymatic steps
•Chemical interconversion steps
•Mechanisms of enzyme conversion and intermediates
•Energetics of conversions
•Mechanisms controlling the Flux of metabolites
through the pathway
Historical perspective
Winemaking and baking industries
1854-1865 Louis Pasture established that microorganisms were
responsible for fermentation.
1897 Eduard Buchner- cell free extracts carried out fermentation
no “vital force” and put fermentation in the province of
chemistry
1905 - 1910 Arthur Harden and William Young
•
inorganic phosphate was required ie. fructose-1,6bisphosphate
•
zymase and cozymase fractions can be separated by
diaylsis
Inhibitors were used. Reagents are found that
inhibit the production of pathway products, thereby
causing the buildup of metabolites that can be
identified as pathway intermediates.
Fluoride- leads to the buildup of 3-phosphoglycerate
and 2-phosphoglycerate
1940 Gustav Embden, Otto Meyerhof, and Jacob
Parnas put the pathway together.
Pathway overview
1. Add phosphoryl groups to activate glucose.
2. Convert the phosphorylated intermediates into high energy
phosphate compounds.
3. Couple the transfer of the phosphate to ADP to form ATP.
Stage I A preparatory stage in which glucose is phosphorylated
and cleaved to yield two molecules of glyceraldehyde-3phosphate - uses two ATPs
Stage II glyceraldehyde-3-phosphate is converted to pyruvate
with the concomitant generation of four ATPs-net profit is
2ATPs per glucose.
Glucose + 2NAD+ + 2ADP +2Pi 2NADH +
2pyruvate + 2ATP + 2H2O + 4H+
Oxidizing power of NAD+ must be recycled
NADH produced must be converted back to NAD+
1. Under anaerobic conditions in muscle NADH
reduces pyruvate to lactate (homolactic fermentation).
2. Under anaerobic conditions in yeast, pyruvate is
decarboxylated to yield CO2 and acetaldehyde and the
latter is reduced by NADH to ethanol and NAD+ is
regenerated (alcoholic fermentation).
3. Under aerobic conditions, the mitochondrial
oxidation of each NADH to NAD+ yields three ATPs
Hexokinase
CH2OH
H
O
H
OH
Mg++
H
+ ATP
H
OH
OH
H
OH
Glucose
CH2OPO32H
O
H
OH
H
+ ADP + H+
H
OH
OH
H
OH
Glucose-6-phosphate
Isozymes: Enzymes that catalyze the same reaction but
are different in their kinetic behavior
Tissue specific
Glucokinase- Liver controls blood glucose levels.
Hexokinase in muscle - allosteric inhibition by ATP
Hexokinase in brain - NO allosteric inhibition by ATP
Hexokinase reaction mechanism is
RANDOM Bi-Bi
Glucose
ATP
ADP
Glu-6-PO4
When ATP binds to hexokinase without glucose it does not
hydrolyze ATP. WHY?
The binding of glucose elicits a structural change that puts
the enzyme in the correct position for hydrolysis of ATP.
The enzyme movement places the ATP in close
proximity to C6H2OH group of glucose and excludes
water from the active site.
H
O
H
H
OH
OH
H
OH
-D-Xylose
There is a 40,000 fold
increase in ATP hydrolysis
upon binding xylose which
cannot be phosphorylated!
Yeast hexokinase, two lobes are gray and green.
Binding of glucose (purple) causes a large
conformational change. A substrate induced
conformational change that prevents the unwanted
hydrolysis of ATP.
Phosphoglucose Isomerase
CH2OPO32H
O
H
OH
H
O3POCH2
H
H
OH
OH
H
-2
OH
O
CH2OH
HO
H
OH
H
OH
Uses an “ ene dione intermediate
1) Substrate binding
2) Acid attack by H2N-Lys opens the ring
3) Base unprotonated Glu abstracts proton from C2
4) Proton exchange
5) Ring closure
Uncatalyzed isomerization of Glucose
Phosphofructokinase
-2
O3POCH2
H
O
CH2OH
HO
H
OH
H
+ ATP
OH
Fructose-6-PO4
-2
O3POCH2
Mg++
H
O
CH2OPO3-2
HO
H
OH
H
+ ADP
OH
Fructose-1,6-bisphosphate
1.) Rate limiting step in glycolysis
2.) Irreversible step, can not go the other way
3.) The control point for glycolysis
Aldolase
CH2OPO3-2
CH2OPO3-2
C
O
HO
C
H
H
C
OH
H
C
OH
HO
C
O
C
H
H
+
O
H
CH2OPO3-2
H
Fructose -1,6-bisphosphate
(FBP)
Dihydroxyacetone
phosphate (DHAP)
C
OH
Glyceraldehyde-3phosphate (GAP)
CH2OPO3-2
Aldol cleavage (retro aldol condensation)
There are two classes of Aldolases
Class I animals and plants - Schiff base intermediate
Step 1 Substrate binding
Step 2 FBP carbonyl groups reacts with amino LYS to
form iminium cation (Schiff base)
Step 3. C3-C4 bond cleavage resulting enamine and
release of GAP
Step 4 protonation of the enamine to a iminium cation
Step 5 Hydrolysis of iminium cation to release DHAP
CH2OPO3-2
C14
CH2OH
+
NH
CH2OPO3-2
(CH2)4
Lys
+ NaBH4
H
C14
CH2OH
NH3
(CH2)4
Lys
Class II enzymes are found in fungi and algae and
do not form a Schiff base. A divalent cation usually
a Zn+2 polarizes the carbonyl intermediate.
CH2OPO32-
CH2OPO3-2
C
HO
C
O
-
-
O
C
Zn2+
HO
Zn2+
H
H
Probably the occurrence of two classes is a metabolic
redundancy that many higher organisms replaced
with the better mechanism.
Aldolase is very stereospecific
When condensing DHAP with GAP four possible
products can form depending on the whether the proS or pro R hydrogen is removed on the C3 of DHAP
and whether the re or si face of GAP is attacked.
CH2OPO3
H
H
H
OH
OH
CH2OPO3
D-Fructose
1,6 bisphosphate
2-
CH2OPO32-
O
O
O
HO
CH2OPO32-
CH2OPO32-
2-
O
H
OH
HO
H
H
H
OH
HO
H
HO
H
OH
H
CH2OPO32D-Psicose
1,6 bisphosphate
OH
CH2OPO32-
D-Tagatose
1,6 bisphosphate
H
OH
H
OH
CH2OPO32-
D-Sorbose
1,6 bisphosphate
Triosephosphate isomerase
DHAP
GAP
GAP
1
2
K eq
4.7 x10
DHAP
96
TIM is a perfect enzyme which its rate is diffusion
controlled.
A rapid equilibrium allows GAP to be used and
DHAP to replace the used GAP.
TIM has an enediol intermediate
H
H
H
O
C
H
OH
H
OH
CH2OPO32-
H
C
OH
CH2OPO3
2-
C
OH
C
O
CH2OPO32-
GAP
enediol
DHAP
Transition state analogues Phosphoglycohydroxamate (A) and
2-phosphoglycolate (B) bind to TIM 155 and 100 times stronger
than GAP of DHAP
HO
B.
A.
OH
O
H
N
O
C
-
CH2OPO3
2-
O32-POH2C
O
O32-POH2C
O-
TIM has an extended “low barrier”
hydrogen bond transition state
Hydrogen bonds have unusually strong interactions and
have lead to pK of Glu 165 to shift from 4.1 to 6.5 and the
pK of
Geometry of the eneolate intermediate
prevents formation of methyl glyoxal
Orbital symmetry prevents double bond formation
needed for methyl glyoxal
Glyceraldehyde-3-phosphate
dehydrogenase
The first high-energy intermediate
H
O
H
C
OPO32-
O
OH + NAD+ + Pi
CH2OPO32-
H
C
OH + NADH
CH2OPO32-
Uses inorganic phosphate to create 1,3 bisphosphoglycerate
Reactions used to elucidate GAPDH’s mechanism
Mechanistic steps for GAPDH
1. GAP binds to enzyme.
2. The nucleophile SH attacks aldehyde to make a
thiohemiacetal.
3. Thiohemiacetal undergoes oxidation to an acyl
thioester by a direct transfer of electrons to
NAD+ to form NADH.
4. NADH comes off and NAD+ comes on.
5. Thioester undergoes nucleophilic attack by Pi to
form 1,3 BPG.
The acid anhydride of phosphate in a high energy
phosphate intermediate
Arsenate uncouples phosphate formation
O
O
3PG
O
As
O
O
GAP DH
+
H
H
C
OH
O-
O
O
O
O
O
H
O
As
C
H
C
OH
OH
CH2OPO32-
CH2OPO32-
+
O
CH2OPO32O
As
O
O