Biochemistry of Metabolism

Glycolysis

Copyright 1998-2007 by Joyce J. Diwan.

All rights reserved.

6 CH OPO 2
2
3
5
O

H
4

OH

H
OH
3

H
2

H
1

OH

OH

glucose-6-phosphate

Glycolysis takes place in the cytosol of cells.

Glucose enters the Glycolysis pathway by conversion
to glucose-6-phosphate.
Initially there is energy input corresponding to
cleavage of two ~P bonds of ATP.

6 CH2OH
5

H
4

OH

H
OH

H
2

OH

glucose

6 CH OPO 2
2
3
5
O

ATP ADP
H
H
1

OH

Mg2+

OH

H
OH
3

H
2

H
1

OH

Hexokinase H
OH
glucose-6-phosphate

1. Hexokinase catalyzes:
Glucose + ATP glucose-6-P + ADP
The reaction involves nucleophilic attack of the C6
hydroxyl O of glucose on P of the terminal phosphate
of ATP.
ATP binds to the enzyme as a complex with Mg++.

NH2

ATP

adenosine triphosphate
O

P
O

P
O

O
O

P
O

CH2

adenine

OH

H
OH

ribose

Mg++ interacts with negatively charged phosphate

oxygen atoms, providing charge compensation &
promoting a favorable conformation of ATP at the active
site of the Hexokinase enzyme.

6 CH2OH
5

H
4

OH

H
OH

H
2

OH

glucose

6 CH OPO 2
2
3
5
O

ATP ADP
H
H
1

OH

Mg2+

OH

Hexokinase

H
OH
3

H
2

H
1

OH

OH

glucose-6-phosphate

The reaction catalyzed by Hexokinase is highly

spontaneous.
A phosphoanhydride bond of ATP (~P) is cleaved.
The phosphate ester formed in glucose-6-phosphate has
a lower G of hydrolysis.

6 CH2OH

Induced fit:
Glucose binding
to Hexokinase
stabilizes a
conformation
in which:

H
4

OH

H
OH

H
2

OH

6 CH OPO 2
2
3
5
O

ATP ADP
H
H
1

OH

Mg

2+

OH

Hexokinase

glucose

H
OH
3

H
1

H
2

OH

OH

glucose-6-phosphate

glucose

the C6 hydroxyl of the

bound glucose is close to
the terminal phosphate of
Hexokinase
ATP, promoting catalysis.
water is excluded from the active site.
This prevents the enzyme from catalyzing ATP
hydrolysis, rather than transfer of phosphate to glucose.

glucose

Hexokinase

It is a common motif for an enzyme active site to be

located at an interface between protein domains that are
connected by a flexible hinge region.
The structural flexibility allows access to the active site,
while permitting precise positioning of active site
residues, and in some cases exclusion of water, as
substrate binding promotes a particular conformation.

6 CH OPO 2
2
3
5
O

H
4

OH

H
OH
3

H
2

OH

H
1

OH

6 CH OPO 2
2
3

1CH2OH

H
4

OH

HO

3 OH

Phosphoglucose Isomerase
glucose-6-phosphate
fructose-6-phosphate

2. Phosphoglucose Isomerase catalyzes:

glucose-6-P (aldose) fructose-6-P (ketose)
The mechanism involves acid/base catalysis, with ring
opening, isomerization via an enediolate intermediate,
and then ring closure. A similar reaction catalyzed by
Triosephosphate Isomerase will be presented in detail.

Phosphofructokinase
6 CH OPO 2
2
3

1CH2OH

H
4

OH

ATP ADP

HO

3 OH

fructose-6-phosphate

6 CH OPO 2
2
3

Mg2+

1CH2OPO32

H
4

OH

HO

3 OH

fructose-1,6-bisphosphate

3. Phosphofructokinase catalyzes:
fructose-6-P + ATP fructose-1,6-bisP + ADP
This highly spontaneous reaction has a mechanism similar
to that of Hexokinase.
The Phosphofructokinase reaction is the rate-limiting step
of Glycolysis.
The enzyme is highly regulated, as will be discussed later.

1CH2OPO3
2C

HO 3C
H 4C

Aldolase

2
CH
OPO
2
3
3

OH

2C

OH

1CH2OH

2
CH
OPO
2
3
6

fructose-1,6bisphosphate

O
1C

H 2C OH
2
3 CH2OPO3

dihydroxyacetone glyceraldehyde-3phosphate
phosphate

Triosephosphate Isomerase

4. Aldolase catalyzes: fructose-1,6-bisphosphate

dihydroxyacetone-P + glyceraldehyde-3-P
The reaction is an aldol cleavage, the reverse of an aldol
condensation.
Note that C atoms are renumbered in products of Aldolase.

A lysine residue at the active site functions in catalysis.

The keto group of fructose-1,6-bisphosphate reacts with
the -amino group of the active site lysine, to form a
protonated Schiff base intermediate.
Cleavage of the bond between C3 & C4 follows.

1CH2OPO3
2C

HO 3C
H 4C

Aldolase

2
CH
OPO
2
3
3

OH

2C

OH

1CH2OH

2
CH
OPO
2
3
6

fructose-1,6bisphosphate

O
1C

H 2C OH
2
3 CH2OPO3

dihydroxyacetone glyceraldehyde-3phosphate
phosphate

Triosephosphate Isomerase

5. Triose Phosphate Isomerase (TIM) catalyzes:

dihydroxyacetone-P glyceraldehyde-3-P
Glycolysis continues from glyceraldehyde-3-P. TIM's Keq
favors dihydroxyacetone-P. Removal of glyceraldehyde-3-P
by a subsequent spontaneous reaction allows throughput.

Triosephosphate Isomerase
H
H

OH

H H

CH2OPO32

dihydroxyacetone
phosphate

OH
C
C

H H

OH

CH2OPO32

enediol
intermediate

O
C

OH

CH2OPO32

glyceraldehyde3-phosphate

The ketose/aldose conversion involves acid/base catalysis,

and is thought to proceed via an enediol intermediate, as
with Phosphoglucose Isomerase.
Active site Glu and His residues are thought to extract and
donate protons during catalysis.

OH
O

HC

CH2OPO32

CH2OPO32

proposed
enediolate
intermediate

phosphoglycolate
transition state
analog

2-Phosphoglycolate is a transition state analog that

binds tightly at the active site of Triose Phosphate
Isomerase (TIM).
This inhibitor of catalysis by TIM is similar in structure to
the proposed enediolate intermediate.
TIM is judged a "perfect enzyme." Reaction rate is limited
only by the rate that substrate collides with the enzyme.

Triosephosphate Isomerase
structure is an barrel, or
TIM barrel.
In an barrel there are
8 parallel -strands
surrounded by 8 -helices.
Short loops connect alternating
-strands & -helices.

TIM

TIM barrels serve as scaffolds

for active site residues in a
diverse array of enzymes.
Residues of the active site are
always at the same end of the
barrel, on C-terminal ends of
-strands & loops connecting
these to -helices.

TIM

There is debate whether the many different enzymes with

TIM barrel structures are evolutionarily related.
In spite of the structural similarities there is tremendous
diversity in catalytic functions of these enzymes and
little sequence homology.

OH
O

HC

TIM

CH2OPO32

CH2OPO32

proposed
enediolate
intermediate

phosphoglycolate
transition state
analog

Explore the structure of the Triosephosphate Isomerase

(TIM) homodimer, with the transition state inhibitor
2-phosphoglycolate bound to one of the TIM
monomers.
Note the structure of the TIM barrel, and the loop that
forms a lid that closes over the active site after binding

Glyceraldehyde-3-phosphate
Dehydrogenase
H

NAD+

1C

OH

+ Pi

2
CH
OPO
2
3
3

glyceraldehyde3-phosphate

OPO32
+ H+ O
NADH
1C
H

OH

2
CH
OPO
2
3
3

1,3-bisphosphoglycerate

6. Glyceraldehyde-3-phosphate Dehydrogenase
catalyzes:
glyceraldehyde-3-P + NAD+ + Pi
1,3-bisphosphoglycerate + NADH + H+

Glyceraldehyde-3-phosphate
Dehydrogenase
H

NAD+

1C

OH

+ Pi

2
CH
OPO
2
3
3

glyceraldehyde3-phosphate

OPO32
+ H+ O
NADH
1C
H

OH

2
CH
OPO
2
3
3

1,3-bisphosphoglycerate

Exergonic oxidation of the aldehyde in glyceraldehyde3-phosphate, to a carboxylic acid, drives formation of an

acyl phosphate, a "high energy" bond (~P).
This is the only step in Glycolysis in which NAD+ is
reduced to NADH.

1C

H 2 C OH
2
3 CH2OPO3

glyceraldehyde-3phosphate

A cysteine thiol at the active site of Glyceraldehyde3-phosphate Dehydrogenase has a role in catalysis.
The aldehyde of glyceraldehyde-3-phosphate reacts
with the cysteine thiol to form a thiohemiacetal
intermediate.

Enz-Cys

Oxidation to a
carboxylic acid
(in a ~ thioester)
occurs, as NAD+
is reduced to
NADH.

Enz-Cys

OH

HC

CH

SH

OH

OH

CH

CH

CH2OPO32

glyceraldehyde-3phosphate
CH2OPO32

thiohemiacetal
intermediate

NAD+
NADH

Enz-Cys

OH

CH

CH2OPO32

acyl-thioester
intermediate

Pi

Enz-Cys

SH

O3PO

OH

CH

CH2OPO32

1,3-bisphosphoglycerate

The high energy acyl thioester is attacked by Pi to

yield the acyl phosphate (~P) product.

O
C

+
N

NH2

2e + H

NH2

NAD+

NADH

Recall that NAD+ accepts 2 e plus one H+ (a hydride)

in going to its reduced form.

Phosphoglycerate Kinase
O

OPO32 ADP ATP O

O
1C

H 2C OH
2
3 CH2OPO3

1,3-bisphosphoglycerate

Mg

2+

H 2C OH
2
3 CH2OPO3

3-phosphoglycerate

7. Phosphoglycerate Kinase catalyzes:

1,3-bisphosphoglycerate + ADP
3-phosphoglycerate + ATP
This phosphate transfer is reversible (low G), since
one ~P bond is cleaved & another synthesized.
The enzyme undergoes substrate-induced conformational
change similar to that of Hexokinase.

Phosphoglycerate Mutase
O

O
C

O
C

H 2C OH
2
CH
OPO
2
3
3

H 2C OPO32
3 CH2OH

3-phosphoglycerate

2-phosphoglycerate

8. Phosphoglycerate Mutase catalyzes:

3-phosphoglycerate 2-phosphoglycerate
Phosphate is shifted from the OH on C3 to the
OH on C2.

Phosphoglycerate Mutase
O

O
C

O
C

H 2C OH
2
CH
OPO
2
3
3

H 2C OPO32
3 CH2OH

3-phosphoglycerate

2-phosphoglycerate

An active site histidine side-chain

participates in Pi transfer, by
donating & accepting phosphate.
The process involves a
2,3-bisphosphate intermediate.
View an animation of the
Phosphoglycerate Mutase reaction.

O
C

H 2C OPO32
2
3 CH2OPO3

2,3-bisphosphoglycerate

Enolase

O
C

H 2 C OPO32
3 CH2OH

H
O

O
C
C

OH

O
1

OPO32

CH2OH

2C

OPO32

3 CH2

2-phosphoglycerate enolate intermediate phosphoenolpyruvate

9. Enolase catalyzes:
2-phosphoglycerate phosphoenolpyruvate + H2O
This dehydration reaction is Mg++-dependent.
2 Mg++ ions interact with oxygen atoms of the substrate
carboxyl group at the active site.
The Mg++ ions help to stabilize the enolate anion
intermediate that forms when a Lys extracts H+ from C #2.

Pyruvate Kinase
O

O
C
1
C
2

ADP ATP

O
C

OPO32

3 CH2

phosphoenolpyruvate

3 CH3

pyruvate

10. Pyruvate Kinase catalyzes:

phosphoenolpyruvate + ADP pyruvate + ATP

Pyruvate Kinase
O

O
C
1
C
2

ADP ATP

OPO32

3 CH2

phosphoenolpyruvate

O
C

O
1

OH

3 CH2

enolpyruvate

3 CH3

pyruvate

This phosphate transfer from PEP to ADP is spontaneous.

PEP has a larger G of phosphate hydrolysis than ATP.
Removal of Pi from PEP yields an unstable enol, which
spontaneously converts to the keto form of pyruvate.
Required inorganic cations K+ and Mg++ bind to anionic
residues at the active site of Pyruvate Kinase.

glucose
ATP

Glycolysis

Hexokinase

ADP
glucose-6-phosphate

Phosphoglucose Isomerase
fructose-6-phosphate
ATP
Phosphofructokinase
ADP
fructose-1,6-bisphosphate
Aldolase
glyceraldehyde-3-phosphate + dihydroxyacetone-phosphate
Triosephosphate
Isomerase
Glycolysis continued

glyceraldehyde-3-phosphate
NAD+ + Pi
Glyceraldehyde-3-phosphate
Dehydrogenase
NADH + H+

Glycolysis
continued.
Recall that
there are 2
GAP per
glucose.

1,3-bisphosphoglycerate
ADP
Phosphoglycerate Kinase
ATP
3-phosphoglycerate
Phosphoglycerate Mutase
2-phosphoglycerate
Enolase
H2O
phosphoenolpyruvate
ADP
Pyruvate Kinase
ATP
pyruvate

Glycolysis
Balance sheet for ~P bonds of ATP:
How many ATP ~P bonds expended? ________
2
How many ~P bonds of ATP produced? (Remember
4
there are two 3C fragments from glucose.) ________
Net production of ~P bonds of ATP per glucose:
2
________

Balance sheet for ~P bonds of ATP:

2 ATP expended
4 ATP produced (2 from each of two 3C fragments from
glucose)
Net production of 2 ~P bonds of ATP per glucose.
Glycolysis - total pathway, omitting H+:
glucose + 2 NAD+ + 2 ADP + 2 Pi
2 pyruvate + 2 NADH + 2 ATP
In aerobic organisms:
pyruvate produced in Glycolysis is oxidized to CO2 via
Krebs Cycle
NADH produced in Glycolysis & Krebs Cycle is
reoxidized via the respiratory chain, with production of
much additional ATP.

Glyceraldehyde-3-phosphate
Dehydrogenase
H

Fermentation:
Anaerobic
organisms lack a
respiratory chain.

NAD+

1C

OH

+ Pi

2
CH
OPO
2
3
3

glyceraldehyde3-phosphate

OPO32
+ H+ O
NADH
1C
H

OH

2
CH
OPO
2
3
3

1,3-bisphosphoglycerate

They must reoxidize NADH produced in Glycolysis

through some other reaction, because NAD+ is needed for
the Glyceraldehyde-3-phosphate Dehydrogenase reaction.
Usually NADH is reoxidized as pyruvate is converted to
a more reduced compound.
The complete pathway, including Glycolysis and the
reoxidation of NADH, is called fermentation.

Lactate Dehydrogenase
O

O
C
C

NADH + H+ NAD+

O
C
HC

OH

CH3

CH3

pyruvate

lactate

E.g., Lactate Dehydrogenase catalyzes reduction of

the keto in pyruvate to a hydroxyl, yielding lactate, as
NADH is oxidized to NAD+.
Lactate, in addition to being an end-product of
fermentation, serves as a mobile form of nutrient energy,
& possibly as a signal molecule in mammalian organisms.
Cell membranes contain carrier proteins that facilitate
transport of lactate.

Lactate Dehydrogenase
O

O
C
C

NADH + H+ NAD+

O
C
HC

OH

CH3

CH3

pyruvate

lactate

Skeletal muscles ferment glucose to lactate during

exercise, when the exertion is brief and intense.
Lactate released to the blood may be taken up by other
tissues, or by skeletal muscle after exercise, and converted
via Lactate Dehydrogenase back to pyruvate, which may
be oxidized in Krebs Cycle or (in liver) converted to back
to glucose via gluconeogenesis

Lactate Dehydrogenase
O

O
C
C

NADH + H+ NAD+

O
C
HC

OH

CH3

CH3

pyruvate

lactate

Lactate serves as a fuel source for cardiac muscle as

well as brain neurons.
Astrocytes, which surround and protect neurons in the
brain, ferment glucose to lactate and release it.
Lactate taken up by adjacent neurons is converted to
pyruvate that is oxidized via Krebs Cycle.

Pyruvate
Decarboxylase

Alcohol
Dehydrogenase

CO2

NADH + H+ NAD+

O
C
C

CH3

pyruvate

O
C
CH3

acetaldehyde

OH

CH3

ethanol

Some anaerobic organisms metabolize pyruvate to

ethanol, which is excreted as a waste product.
NADH is converted to NAD+ in the reaction
catalyzed by Alcohol Dehydrogenase.

Glycolysis, omitting H+:

glucose + 2 NAD+ + 2 ADP + 2 Pi
2 pyruvate + 2 NADH + 2 ATP
Fermentation, from glucose to lactate:
glucose + 2 ADP + 2 Pi 2 lactate + 2 ATP
Anaerobic catabolism of glucose yields only 2 high
energy bonds of ATP.

Go'
G
kJ/mol kJ/mol
Hexokinase
-20.9 -27.2
Phosphoglucose Isomerase
+2.2
-1.4
Phosphofructokinase
-17.2 -25.9
Aldolase
+22.8
-5.9
Triosephosphate Isomerase
+7.9 negative
Glyceraldehyde-3-P Dehydrogenase
-16.7
-1.1
& Phosphoglycerate Kinase
Glycolysis Enzyme/Reaction

Phosphoglycerate Mutase
Enolase
Pyruvate Kinase

+4.7
-3.2
-23.0

-0.6
-2.4
-13.9

*Values in this table from D. Voet & J. G. Voet (2004) Biochemistry, 3 rd Edition, John
Wiley & Sons, New York, p. 613.

Flux through the Glycolysis pathway is regulated by

control of 3 enzymes that catalyze spontaneous reactions:
Hexokinase, Phosphofructokinase & Pyruvate Kinase.
Local control of metabolism involves regulatory effects
of varied concentrations of pathway substrates or
intermediates, to benefit the cell.
Global control is for the benefit of the whole organism,
& often involves hormone-activated signal cascades.

Liver cells have major roles in metabolism, including

maintaining blood levels various of nutrients such as
glucose. Thus global control especially involves liver.
Some aspects of global control by hormone-activated
signal cascades will be discussed later.

6 CH2OH
5

H
4

OH

H
OH

H
2

OH

glucose

6 CH OPO 2
2
3
5
O

ATP ADP
H
H
1

OH

Mg2+

OH

Hexokinase

H
OH
3

H
2

H
1

OH

OH

glucose-6-phosphate

Hexokinase is inhibited by product glucose-6-phosphate:

by competition at the active site
by allosteric interaction at a separate enzyme site.
Cells trap glucose by phosphorylating it, preventing exit
on glucose carriers.
Product inhibition of Hexokinase ensures that cells will not
continue to accumulate glucose from the blood, if [glucose6-phosphate] within the cell is ample.

6 CH2OH
5

Glucokinase
is a variant of
Hexokinase
found in liver.

OH

H
OH

H
2

OH

6 CH OPO 2
2
3
5
O

ATP ADP
H
H
1

OH

Mg2+

OH

Hexokinase

glucose

H
OH
3

H
1

H
2

OH

OH

glucose-6-phosphate

Glucokinase has a high KM for glucose.

It is active only at high [glucose].
One effect of insulin, a hormone produced when blood
glucose is high, is activation in liver of transcription of
the gene that encodes the Glucokinase enzyme.
Glucokinase is not subject to product inhibition by
glucose-6-phosphate. Liver will take up & phosphorylate
glucose even when liver [glucose-6-phosphate] is high.

 Glucokinase is subject to inhibition by glucokinase

regulatory protein (GKRP).
The ratio of Glucokinase to GKRP in liver changes in
different metabolic states, providing a mechanism for
modulating glucose phosphorylation.

Glycogen

Glucose
Hexokinase or Glucokinase
Glucose-6-Pase
Glucose-6-P
Glucose + Pi
Glycolysis
Pathway

Glucokinase,
with high KM
Glucose-1-P
for glucose,
allows liver to
store glucose
Pyruvate
as glycogen in
Glucose metabolism in liver.
the fed state
when
blood
[glucose] is high. catalyzes hydrolytic release of Pi
Glucose-6-phosphatase
from glucose-6-P. Thus glucose is released from the liver
to the blood as needed to maintain blood [glucose].

The enzymes Glucokinase & Glucose-6-phosphatase, both

found in liver but not in most other body cells, allow the
liver to control blood [glucose].

Pyruvate Kinase
O

Pyruvate Kinase, the

ADP
C
1
last step Glycolysis, is
2
C
OPO
3
controlled in liver partly
2
by modulation of the
3 CH2
phosphoenolpyruvate
amount of enzyme.
O

ATP

O
C

3 CH3

pyruvate

High [glucose] within liver cells causes a transcription

factor carbohydrate responsive element binding protein
(ChREBP) to be transferred into the nucleus, where it
activates transcription of the gene for Pyruvate Kinase.
This facilitates converting excess glucose to pyruvate,
which is metabolized to acetyl-CoA, the main precursor
for synthesis of fatty acids, for long term energy storage.

Phosphofructokinase
6 CH OPO 2
2
3

1CH2OH

H
4

OH

ATP ADP

HO

3 OH

fructose-6-phosphate

6 CH OPO 2
2
3

Mg2+

1CH2OPO32

H
4

OH

HO

3 OH

fructose-1,6-bisphosphate

Phosphofructokinase is usually the rate-limiting step of

the Glycolysis pathway.
Phosphofructokinase is allosterically inhibited by ATP.
At low concentration, the substrate ATP binds only at the
active site.
At high concentration, ATP binds also at a low-affinity
regulatory site, promoting the tense conformation.

60

low [ATP]

PFK Activity

50
40
30

high [ATP]

20
10
0
0

0.5
1
1.5
[Fructose-6-phosphate] mM

The tense conformation of PFK, at high [ATP], has lower

affinity for the other substrate, fructose-6-P. Sigmoidal
dependence of reaction rate on [fructose-6-P] is seen.
AMP, present at significant levels only when there is
extensive ATP hydrolysis, antagonizes effects of high ATP.

Glycogen

Glucose-1-P

Glucose
Hexokinase or Glucokinase
Glucose-6-Pase
Glucose-6-P
Glucose + Pi
Glycolysis
Pathway

Pyruvate
Glucose metabolism in liver.

Inhibition of the Glycolysis enzyme Phosphofructokinase

when [ATP] is high prevents breakdown of glucose in a
pathway whose main role is to make ATP.
It is more useful to the cell to store glucose as glycogen
when ATP is plentiful.