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-1,6-
bisphosphate
• 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-3-
phosphate - 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 CH2OPO32-
O H
Mg++
H H O H
H H
OH H + ATP OH H + ADP + H+
OH OH OH
OH
H OH H OH

Glucose 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
There is a 40,000 fold
increase in ATP hydrolysis
OH OH upon binding xylose which
H OH cannot be phosphorylated!
-D-Xylose
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
CH2OPO32-
-2
O H O3POCH2 CH2OH
H
H O
OH H H HO

OH OH H OH
OH H
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 -2
O3POCH2 CH2OH O3POCH2 CH2OPO3-2
O O
H HO Mg++ H HO
+ ATP + ADP
H OH H OH
OH H OH H

Fructose-6-PO4 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 Dihydroxyacetone
C O
HO C H phosphate (DHAP)
HO C H
H
OH
H C
+
H C OH
H O

CH2OPO3-2 Glyceraldehyde-3-
H C OH
phosphate (GAP)
Fructose -1,6-bisphosphate CH2OPO3-2
(FBP)

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 CH2OPO3-2

C14
+
NH (CH2)4 Lys H C14 NH3 (CH2)4 Lys

CH2OH + NaBH4 CH2OH

 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
-
O Zn2+
C O Zn2+

HO C - HO 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 pro-
S or pro R hydrogen is removed on the C3 of DHAP
and whether the re or si face of GAP is attacked.
CH2OPO32- CH2OPO32- CH2OPO32-
2-
CH2OPO3
O O O
O
H OH HO H H OH
HO H
H OH HO H HO H
H OH
H OH H OH H OH
H OH
CH2OPO32- CH2OPO32- CH2OPO32-
2-
CH2OPO3
D-Psicose D-Tagatose D-Sorbose
D-Fructose 1,6 bisphosphate
1,6 bisphosphate 1,6 bisphosphate
1,6 bisphosphate
 Triosephosphate isomerase

DHAP GAP

K eq 
 GAP  4.7 x10 2

1
 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 OH
H O
H C OH
H C OH H C OH C O

CH2OPO32- CH2OPO32- 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
OH A. -
B.
O H
N - C O O-
O

2- O32-POH2C O32-POH2C
CH2OPO3
 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

O H
O OPO32-

H C OH + NAD+ + Pi H C OH + NADH

CH2OPO32-
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
3PG
O As O O

O As O O O-
GAP DH O O
+ O H C OH

O H H C OH
CH2OPO32-
CH2OPO32-
H C OH +
CH2OPO32- O

O As O