Molecular Biochemistry I

Gluconeogenesis;
Regulation of Glycolysis & Gluconeogenesis

Copyright © 1999-2007 by Joyce J. Diwan.

All rights reserved.
Gluconeogenesis occurs mainly in liver.
Gluconeogenesis occurs to a more limited extent in
kidney & small intestine under some conditions.
Synthesis of glucose from pyruvate utilizes many of the
same enzymes as Glycolysis.
Three Glycolysis reactions have such a large negative DG
that they are essentially irreversible.
 Hexokinase (or Glucokinase)
 Phosphofructokinase
 Pyruvate Kinase.
These steps must be bypassed in Gluconeogenesis.
Two of the bypass reactions involve simple hydrolysis
reactions.
 Glucose-6-phosphatase
6 CH OPO 2 CH2OH
2 3
5 O O
H H H H
H H2O H
4
OH H 1
OH H + Pi
OH OH OH OH
3 2
H OH H OH
glucose-6-phosphate glucose

Hexokinase or Glucokinase (Glycolysis) catalyzes:

glucose + ATP  glucose-6-phosphate + ADP
Glucose-6-Phosphatase (Gluconeogenesis) catalyzes:
glucose-6-phosphate + H2O  glucose + Pi
 Glucose-6-phosphatase
6 CH OPO 2 CH2OH
2 3
5 O O
H H H H
H H2O H
4
OH H 1
OH H + Pi
OH OH OH OH
3 2
H OH H OH
glucose-6-phosphate glucose

Glucose-6-phosphatase enzyme is embedded in the

endoplasmic reticulum (ER) membrane in liver cells.
The catalytic site is found to be exposed to the ER lumen.
Another subunit may function as a translocase, providing
access of substrate to the active site.
 Phosphofructokinase 
6 CH OPO 2 1CH2OH 6 CH OPO 2 1CH2OPO32
2 3 2 3
O ATP ADP O
5 H HO 2 5 H HO 2

H 4 3 OH H 4 3 OH
Pi H2O
OH H OH H
fructose-6-phosphate fructose-1,6-bisphosphate
 Fructose-1,6-biosphosphatase

Phosphofructokinase (Glycolysis) catalyzes:

fructose-6-P + ATP  fructose-1,6-bisP + ADP
Fructose-1,6-bisphosphatase (Gluconeogenesis) catalyzes:
fructose-1,6-bisP + H2O  fructose-6-P + Pi
Bypass of Pyruvate Kinase:
Pyruvate Kinase (last step of Glycolysis) catalyzes:
phosphoenolpyruvate + ADP  pyruvate + ATP
For bypass of the Pyruvate Kinase reaction, cleavage of
2 ~P bonds is required.
 DG for cleavage of one ~P bond of ATP is insufficient
to drive synthesis of phosphoenolpyruvate (PEP).
 PEP has a higher negative DG of phosphate hydrolysis
than ATP.
 Pyruvate Carboxylase PEP Carboxykinase
O O
O O C
O O
C ATP ADP + Pi C O GTP GDP C
C O CH2 C OPO32
CH3 HCO3 C CO2 CH2
O O
pyruvate oxaloacetate PEP

Bypass of Pyruvate Kinase (2 enzymes):

Pyruvate Carboxylase (Gluconeogenesis) catalyzes:
pyruvate + HCO3 + ATP  oxaloacetate + ADP + Pi
PEP Carboxykinase (Gluconeogenesis) catalyzes:
oxaloacetate + GTP  PEP + GDP + CO2
 Pyruvate Carboxylase PEP Carboxykinase
O O
O O C
O O
C ATP ADP + Pi C O GTP GDP C
C O CH2 C OPO32
CH3 HCO3 C CO2 CH2

O O
pyruvate oxaloacetate PEP

Contributing to spontaneity of the 2-step process:

Free energy of one ~P bond of ATP is conserved in the
carboxylation reaction.
Spontaneous decarboxylation contributes to
spontaneity of the 2nd reaction.
Cleavage of a second ~P bond of GTP also contributes
to driving synthesis of PEP.
 N subject to O
carboxylation
Pyruvate C
Carboxylase HN NH
lysine
uses biotin CH CH residue
as prosthetic O O C
H2C CH
group. S (CH2)4 C NH (CH2)4 CH

biotin NH
lysine
H

H3N+ C COO Biotin has a 5-C side chain whose terminal

CH2
carboxyl is in amide linkage to the e-amino
group of an enzyme lysine.
CH2

CH2 The biotin & lysine side chains form a long

CH2
swinging arm that allows the biotin ring to

swing back & forth between 2 active sites.
NH3
 O
-O C
C N NH lysine
O
CH CH residue
O O
O O C
 H2C CH
O P O C O
S (CH2)4 C NH (CH2)4 CH
OH
carboxyphosphate carboxybiotin NH

Biotin carboxylation is catalyzed at one active site of

Pyruvate Carboxylase.
ATP reacts with HCO3 to yield carboxyphosphate.
The carboxyl is transferred from this ~P intermediate to
N of a ureido group of the biotin ring. Overall:
biotin + ATP + HCO3  carboxybiotin + ADP + Pi
At the other O
active site of O O
C -O C
Pyruvate C N NH
Carboxylase the C O O carboxybiotin
CH CH
activated CO2 is CH3
H2C CH O
transferred from pyruvate
S (CH2)4 C NH R
biotin to pyruvate:
carboxybiotin O O O
C
+ pyruvate C
 C O HN NH
biotin
biotin + CH2 CH CH

oxaloacetate C H2C CH O

O O S (CH2)4 C NH R
View an oxaloacetate
animation.
Pyruvate Glucose-6-phosphatase
glucose-6-P glucose
Carboxylase
(pyruvate  Gluconeogenesis Glycolysis
oxaloactate) pyruvate
is allosterically fatty acids
activated by acetyl CoA ketone bodies
acetyl CoA.
oxaloacetate citrate
[Oxaloacetate]
tends to be
Krebs Cycle
limiting for
Krebs cycle.
When gluconeogenesis is active in liver, oxaloacetate is
diverted to form glucose. Oxaloacetate depletion hinders
acetyl CoA entry into Krebs Cycle. The increase in [acetyl
CoA] activates Pyruvate Carboxylase to make oxaloacetate.
Avidin, a protein in egg whites with a b
barrel structure, tightly binds biotin.
Excess consumption of raw eggs can
cause nutritional deficiency of biotin.
The strong avidin-to-biotin affinity is avidin
used by biochemists as a specific "glue." with bound biotin

If it is desired to bind 2 proteins together for an

experiment, biotin may be covalently linked to one
protein and avidin to the other.
Explore with Chime the biotinyl domain of a
carboxylase and the avidin-biotin complex.
 O
O PEP Carboxykinase Reaction
C O O O
GTP GDP O
C O C C
CH2 C O C OPO32
CO2
C CH2 CH2
O O
oxaloacetate PEP

PEP Carboxykinase catalyzes GTP-dependent

oxaloacetate  PEP. It is thought to proceed in 2 steps:
 Oxaloacetate is first decarboxylated to yield a
pyruvate enolate anion intermediate.
 Phosphate transfer from GTP then yields
phosphoenolpyruvate (PEP).
 Mn++
In the bacterial enzyme, ATP is
Pi donor instead of GTP. ATP pyruvate
In this crystal structure of an Mg++
E. Coli PEP Carboxykinase,
PEP Carboxykinase
pyruvate is at the active site as active site ligands PDB 1AQ2
an analog of PEP/ oxaloacetate.

A metal ion such as Mn++ is required for the PEP

Carboxykinase reaction, in addition to a Mg++ ion that
binds with the nucleotide substrate at the active site.
Mn++ is thought to promote Pi transfer by interacting
simultaneously with the enolate oxygen atom and an
oxygen atom of the terminal phosphate of GTP or ATP.
The source of pyruvate and oxaloacetate for
gluconeogenesis during fasting or carbohydrate
starvation is mainly amino acid catabolism.
Some amino acids are catabolized to pyruvate,
oxaloacetate, or precursors of these.
Muscle proteins may break down to supply amino acids.
These are transported to liver where they are deaminated
and converted to gluconeogenesis inputs.
Glycerol, derived from hydrolysis of triacylglycerols in
fat cells, is also a significant input to gluconeogenesis.
 glyceraldehyde-3-phosphate
NAD+ + Pi Glyceraldehyde-3-phosphate
NADH + H+ Dehydrogenase
1,3-bisphosphoglycerate
ADP
Summary of Phosphoglycerate Kinase
ATP
Gluconeogenesis 3-phosphoglycerate
Pathway: Phosphoglycerate Mutase
2-phosphoglycerate
Gluconeogenesis
enzyme names in H2O Enolase
red. phosphoenolpyruvate
CO2 + GDP
Glycolysis enzyme PEP Carboxykinase
GTP
names in blue. oxaloacetate
Pi + ADP
Pyruvate Carboxylase
HCO3 + ATP
pyruvate Gluconeogenesis
 glucose Gluconeogenesis
Pi
Glucose-6-phosphatase
H2O
glucose-6-phosphate
Phosphoglucose Isomerase
fructose-6-phosphate
Pi
Fructose-1,6-bisphosphatase
H2O
fructose-1,6-bisphosphate
Aldolase

glyceraldehyde-3-phosphate + dihydroxyacetone-phosphate
Triosephosphate
Isomerase
(continued)
Glycolysis & Gluconeogenesis are both spontaneous.
If both pathways were simultaneously active in a cell, it
would constitute a "futile cycle" that would waste energy.
Glycolysis:
glucose + 2 NAD+ + 2 ADP + 2 Pi 
2 pyruvate + 2 NADH + 2 ATP
Gluconeogenesis:
2 pyruvate + 2 NADH + 4 ATP + 2 GTP 
glucose + 2 NAD+ + 4 ADP + 2 GDP + 6 Pi
Questions:
1. Glycolysis yields how many ~P ? 2
2. Gluconeogenesis expends how many ~P ? 6
3. A futile cycle of both pathways would waste how many
~P per cycle ? 4
 Phosphofructokinase 
6 CH OPO 2 1CH2OH 6 CH OPO 2 1CH2OPO32
2 3 2 3
O ATP ADP O
5 H HO 2 5 H HO 2

H 4 3 OH H 4 3 OH
Pi H2O
OH H OH H
fructose-6-phosphate fructose-1,6-bisphosphate
 Fructose-1,6-biosphosphatase

To prevent the waste of a futile cycle, Glycolysis &

Gluconeogenesis are reciprocally regulated.
Local Control includes reciprocal allosteric regulation
by adenine nucleotides.
 Phosphofructokinase (Glycolysis) is inhibited by
ATP and stimulated by AMP.
 Fructose-1,6-bisphosphatase (Gluconeogenesis) is
inhibited by AMP.
The opposite effects of adenine nucleotides on
 Phosphofructokinase (Glycolysis)
 Fructose-1,6-bisphosphatase (Gluconeogenesis)
insures that when cellular ATP is high (AMP would then
be low), glucose is not degraded to make ATP.
When ATP is high it is more useful to the cell to store
glucose as glycogen.
When ATP is low (AMP would then be high), the cell
does not expend energy in synthesizing glucose.
Global Control in liver cells includes reciprocal
effects of a cyclic AMP cascade, triggered by the
hormone glucagon when blood glucose is low.
Phosphorylation of enzymes & regulatory proteins in
liver by Protein Kinase A (cAMP Dependent Protein
Kinase) results in
 inhibition of glycolysis
 stimulation of gluconeogenesis,
making glucose available for release to the blood.
Enzymes relevant to these pathways that are
phosphorylated by Protein Kinase A include:
 Pyruvate Kinase, a glycolysis enzyme that is
inhibited when phosphorylated.
 CREB (cAMP response element binding protein)
which activates, through other factors, transcription
of the gene for PEP Carboxykinase, leading to
increased gluconeogenesis.
 A bi-functional enzyme that makes and degrades
an allosteric regulator, fructose-2,6-bisphosphate.
Reciprocal regulation by fructose-2,6-bisphosphate:
 Fructose-2,6-bisphosphate stimulates Glycolysis.
Fructose-2,6-bisphosphate allosterically activates
the Glycolysis enzyme Phosphofructokinase.
Fructose-2,6-bisphosphate also activates
transcription of the gene for Glucokinase, the liver
variant of Hexokinase that phosphorylates glucose
to glucose-6-phosphate, the input to Glycolysis.
 Fructose-2,6-bisphosphate allosterically
inhibits the gluconeogenesis enzyme
Fructose-1,6-bisphosphatase.
Recall that Phosphofructokinase, the rate-limiting step
of Glycolysis, is allosterically inhibited by ATP.
At high concentration, ATP binds at a low-affinity
regulatory site, promoting the tense conformation.

60

50 low [ATP]
Sigmoidal PFK Activity
40
dependence of
reaction rate on 30
high [ATP]
[fructose-6- 20

phosphate] is 10
observed at 0
high [ATP]. 0 0.5 1 1.5 2
[Fructose-6-phosphate] mM
 60

50 low [ATP]
PFK activity in

PFK Activity
the presence of the 40

globally controlled 30

allosteric regulator 20
high [ATP]
fructose-2,6- 10
bisphosphate is 0
similar to that at 0 0.5 1 1.5 2
[Fructose-6-phosphate] mM
low ATP.

Fructose-2,6-bisphosphate promotes the relaxed state,

activating Phosphofructokinase even at high [ATP].
Thus activation by fructose-2,6-bisphosphate, whose
concentration fluctuates in response to external hormonal
signals, supersedes local control by [ATP].
 PFK2/FBPase2 homodimer PDB
2BIF

PFK-2
The allosteric regulator domain
fructose-2,6-bisphosphate
is synthesized & degraded
by a bi-functional enzyme FBPase-2
that includes 2 catalytic domain
with bound
domains: fructose-6-P
in active site

Phosphofructokinase-2 (PFK2) domain catalyzes:

Fructose-6-phosphate + ATP  fructose-2,6-bisphosphate + ADP
Fructose-Biophosphatase-2 (FBPase2) domain catalyzes:
Fructose-2,6-bisphosphate + H2O  fructose-6-phosphate + Pi
Bifunctional PFK2/FBPase2 assembles into a homodimer.
 PFK2/FBPase2 homodimer PDB
2BIF

PFK-2
domain

FBPase-2
domain
with bound
fructose-6-P
in active site
Adjacent to the PFK-2 domain in each copy of the liver
enzyme is a regulatory domain subject to
phosphorylation by cAMP-dependent Protein Kinase.
Which catalytic domains of the enzyme are active depends
on whether the regulatory domains are phosphorylated.
 (active as Phosphofructokinase-2)
Enz-OH
ATP ADP

fructose-6-P fructose-2,6-bisP

Pi View an
Enz-O-PO32 animation.
(active as Fructose-Bisphosphatase-2)

cAMP-dependent phosphorylation of the bi-functional

enzyme activates FBPase2 and inhibits PFK2.
[Fructose-2,6-bisphosphate] thus decreases in liver
cells in response to a cAMP signal cascade, activated by
glucagon when blood glucose is low.
 (active as Phosphofructokinase-2)
Enz-OH
ATP ADP

fructose-6-P fructose-2,6-bisP
Downstream
effects of Pi
the cAMP Enz-O-PO32
cascade: (active as Fructose-Bisphosphatase-2)

Glycolysis slows because fructose-2,6-bisphosphate is

not available to activate Phosphofructokinase.
Gluconeogenesis increases because of the decreased
concentration of fructose-2,6-bisphosphate, which would
otherwise inhibit the gluconeogenesis enzyme Fructose-
1,6-bisphosphatase.
 Glycogen Pyruvate

X Gluconeogenesis

Glucose-1-P Glucose-6-P Glucose + Pi

Glucose-6-Pase
X

Glycolysis
Pathway

Summary of effects of glucagon-cAMP cascade in liver:

 Gluconeogenesis is stimulated.
 Glycolysis is inhibited.
 Glycogen breakdown is stimulated.
 Glycogen synthesis is inhibited.
 Free glucose is formed for release to the blood.
The Cori Cycle operates during exercise.
For a brief burst of ATP utilization, muscle cells utilize
~P stored as phosphocreatine.
Once phosphocreatine is exhausted, ATP is provided
mainly by Glycolysis, with the input coming from
glycogen breakdown and from glucose uptake from the
blood.
(Aerobic fat metabolism, discussed elsewhere, is more
significant during a lengthy period of exertion such as a
marathon run.)
 Cori Cycle
Liver Blood Muscle

Glucose Glucose
2 NAD+ 2 NAD+
2 NADH 2 NADH
6 ~P 2 ~P

2 Pyruvate 2 Pyruvate
2 NADH 2 NADH
2 NAD+ 2 NAD+
2 Lactate 2 Lactate

Lactate produced from pyruvate passes via the blood to

the liver, where it may be converted to glucose.
The glucose may travel back to the muscle to fuel
Glycolysis.
 Cori Cycle
Liver Blood Muscle

Glucose Glucose
2 NAD+ 2 NAD+
2 NADH 2 NADH
6 ~P 2 ~P

2 Pyruvate 2 Pyruvate
2 NADH 2 NADH
2 NAD+ 2 NAD+
2 Lactate 2 Lactate

The Cori cycle costs 6 ~P in liver for every 2 ~P made

available in muscle. The net cost is 4 ~P.
Although costly in ~P bonds, the Cori Cycle allows the
organism to accommodate to large fluctuations in energy
needs of skeletal muscle between rest and exercise.
The equivalent of the Cori Cycle also operates during
cancer.
If blood vessel development does not keep pace with
growth of a solid tumor, decreased O2 concentration
within the tumor leads to activation of signal processes
that result in a shift to anaerobic metabolism.
 Liver Blood Cancer Cell

Glucose Glucose
2 NAD+ 2 NAD+
2 NADH 2 NADH
6 ~P 2 ~P

2 Pyruvate 2 Pyruvate
2 NADH 2 NADH
2 NAD+ 2 NAD+
2 Lactate 2 Lactate

Energy dissipation by the Cori Cycle, which expends

6 ~P in liver for every 2 ~P produced via Glycolysis for
utilization within the tumor, is thought to contribute to
the weight loss that typically occurs in late-stage cancer
even when food intake remains normal.