G6P
Pentose Phosphate Pathway
NADPH
Ru5P
DNA, RNA
ATP
Glycolysis
R5P
Xu5P
G3P
Su7P
F6P
E4P
Xu5P
F6P
G3P
Coordinate Regulation of Glycolysis and Gluconeogenesis
Glycolysis
Gluconeogensis
O
O
O P O
O
O
HO
O P O
O
OH
O
O P
OO
OH
ATP
ADP
kinase
O
HO
OH
O
O P
OO
OH
PFK2bPase
complex
O
O P O
O
O
O P O
O
Pi
OH
HO
O
phosphatase
OH
OH
O
OH
OH
HO
PFK
F2,6bP
glucose
ATP
F-1,6-bPase
O
O
O P O
O
O P O
O
O
OH
HO
OH
F2,6bP
glucose
ATP
OH
Glycogen Phosphorylase Regulation
a
b
ATP
ADP
Active
R
Conformational
change
T
Inactive
Muscle; b state responds to energy charge
bR
aR
bR
aR
bT
aT
bT
aT
High [ATP], [G6P]
High [AMP]
Liver; a state responds to glucose levels
bR
aR
bR
aR
bT
aT
bT
aT
High [glucose]
Low [glucose]
Pancreatic β cell glucose sensing mechanism.
(portal vein)
Glucose
Glucose
glycolysis, TCA cycle
and ox-phos
Hi ATP:ADP ratio inhibits
K+ efflux pump,
depolarizes cell.
ATP
K+
Ca2+
Ca2+ spike causes
exocytosis of insulin
Depolarization induces
Ca2+ influx
Ca2+
K+
Adenylate cyclase
NH2
N
+
Glucagon
receptor and Gcoupled protein
Protein
Kinase A
PKAi
Phosphorylase
kinase
O
cAMP ATP
ATP
O
OH
O
PKAi
PKAa
+ ADP
+
b
N
+ +
+ ADP
Glycogen
phosphorylase
N
P
PKAa
ATP
O
O
Glycogen
breakdown
a
Glucagon activates cAMP cascade in the liver
PKA exists as C2R2
tetramer in inactive
form. cAMP binding
causes dissociation
into two active C
monomers that
phosphorylate other
proteins.
PKA coordinately regulates carbohydrate metabolism
Liver cell
glycogen
Phosphorylate
glycogen
phosphorylase:
stimulates
glycogen
breakdown;
phosphorylate
glycogen
synthase: inhibits
glycogen
synthesis.
PKAa
G1P
G6P
Glc
F6P
Phosphorylate PFK2F2,6bPase complex;
stimulates F-2,6-bPase
activity and inactivates the
kinase; activates
gluconeogenesis
F1,6bP
Glucose is
secreted into
the blood.
pyruvate
TCA cycle and related metabolism
Glycolysis
Gluconeogenesis
PEP
Pyr
Ala,Val,Leu,Ile
Phe,Tyr,
AcCoA
Asp,
Asn
Fatty acids
citrate
OAA
isocit
NADH + H+
NADH + H+
mal
α-kg
Glu, Gln
NADH + H+
fum
Part of
Ox-Phos
FADH2
Succ-CoA
Succ
ATP
Redox Shuttling in Mitochondria
NADH
+ H+
NADH
+ H+
matrix
2e-
cytoplasm
2e-
Cytosolic
NADH
dehydrogenase
NAD+
NAD+
Complex 1;
NADH
Dehydrogenase
Q
DHAP
O
Succ
FADH2
2e-
FADH2
2e-
OPO3
OH
OH
NAD+
Fum
OH
Succinate
dehydrogenase
NADH
+ H+
OPO3
Glycerol 3-phosphate
Glycerol 3-phosphate
dehydrogenase
Inner mitochondrial membrane
Mal-Asp Shuttle in Mitochondria
α-kg –
malate
carrier
matrix
αkg
NAD+
NADH
+ H+
cytoplasm
αkg
Mal
Mal
NAD+
OAA
OAA
NADH
+ H+
Asp
Asp
Glu
Aspartateglutamate
carrier
Inner mitochondrial membrane
Glu
β-Oxidation of fatty acids.
O
FADH2
CoA
R
O
O
CoA
R
CoA
R
O
CoA
O
R
OH
O
CoA
NADH
R
O
CoA
Citrate – Malate – Pyruvate Transport System
Mito
Pi
Pi
Ac-CoA
Cyto
CoASH
ATP
ADP
2
1
Cit
Cit
OAA
OAA
NADH + H+
Mal
5
ADP
Enzymes:
1. Citrate synthase
2. ATP-citrate lysase
3. Malate dehydrogenase
4. Malic enzyme
5. Pyruvate carboxylase
6. Malate dehydrogenase
NADH + H+
3
6
Mal
Ac-CoA
NAD+
4
NAD+
NADP+
Pyr
ATP
Pyr
NADPH + H+
CO2
Carriers:
Citrate transported by two pumps, both
are co-transporters. One co-transports
orthophosphate, the other malate.
Pyruvate transported by a separate pump.
Fatty
Acids
Regulating Fatty Acid Synthesis and Degradation
Insulin receptor
Glucagon receptor
cAMP
triglycerides
+
FA
+
PKAactive
+
AMP
PKAinactive
Glucose
PPP
ACCase
ACCase
NADPH
MalCoA
AcCoA
Pyr
+
Cit
Pyr
Cit
FAS
AcCoA
β-Ox
FA
TCA
FA
NADH, FADH2
mitochondria
O
O2
=O
Cytochrome Oxidase Cycle
Fe
Cu
OH
O
OH
-O
2 H2O
-OH
=O
H+
F1F0 ATPase structure
From the ATPase Group at Univeristat Freiburg: http://www.atpase.de/
Ion binding and rotary motion in ATPase
This particular figure is
drawn for a Na-ATPase
with a geometry that differs
from that of the F1F0
ATPase in ox-phos, but the
phyisico-chemical principles
are very similar. In fact,
since this protein is much
easier to work with, it is
generally used as a model
system for the more
complex F1F0 ATPase.
Ions enter channel from
one side of rotor and are
forced to the “bottom” by
low dielectric environment.
Once the cation is at the
bottom of the channel, it
interacts electrostatically
with an Arg sidechain. The
electrostatic repulsion
drives the charges apart,
leading to rotational
motion.
Dimroth, Peter et al. (1999) Proc. Natl. Acad. Sci. USA 96, 4924-4929
Copyright ©1999 by the National Academy of Sciences
Z-scheme in Photosynthesis
Photophosphorylation
Oxidative metabolism of arachidonic acid
CO2-
lipoxygenase
O2
2O2
cyclooxygenase
OOH
CO2-
O
CO2-
Inhibited by
NSAIDs
PGG2
O
OOH
5-HPETE
peroxidase
O
CO2-
O
CO2-
Cyclooxygenase and
peroxidase activities in
one enzyme called
prostaglandin synthase
PGH2
O
OH
Thromboxane synthase
LTA4
CO2-
O
O
Other LT’s
Other PG’s
TXA2
OH
Lipoproteins : lipid and cholesterol
transport in the blood.
•
Lipids transported
–
•
Proteins in lipoproteins
–
–
•
Triglycerides, phospholipids, cholesterol, and
cholesteryl esters
Structural proteins
enzymes
Nomenclature of lipoproteins
–
Electrophoretic mobility
α: highest mobility; HDL particles
β: lowest mobility; LDL particles
Pre−β: intermediate mobility; VLDL
–
Density, size
Particle D, nm % Protein
Lipids
Chyl
100’s
1
TG>>PL>CE>C
VLDL
~50
8
TG>PL~CE>C
IDL
LDL
HDL
~25
~20
<20
10
21
30-50
CE>TG~PL>CE
CE>>PL>TG~C
PL>>CE>>TG~PL
Protein
Particle
Function
A-I
C,H
Ligand for HDL receptor; activates LCAT
A-II
C,H
Inhibitor of A-I
A-IV
C,H
???
B-100
L,VL,I
VL synthesis; Ligand for receptor
B-48
C
C synthesis
C-I
VL,H,C
Activator of LCAT?
C-II
VL,H,C
Activate lipoprotein lipase
C-III
VL,H,C
Inhibit C-II
D
Some H
Lipid transfer protein?
E
All
Ligand for receptors
C=chylomicron; H=HDL; VL=VLDL; L=LDL; I=IDL
Lipoprotein Biochemistry: Generation of lipoprotein particles
Chylomicrons
HDLs
VLDLs
& LDLs
Figures from Harper’s Biochemistry, 25th Edition
Regulation of Glutamine Synthetase
Metabolic fates of glutamine
From Purdue University: http://www.hort.purdue.edu/rhodcv/hort640c/hort640c.htm
Regulation of Glutamine Synthetase
ATP + NH4+
ADP
Gln
Glu
α-kg
ATP
AT inhibited by
α-kg; activated
by Gln
ADP
GS
active
adenylylation
AT
AT
AMP
PII
Non-uridylylated PII
converts AT into an
adenylylating form
that inactivates GS
AT
PII
GS
PPi
Uridylylated PII
binds to AT and
activates the
deadenylylation of
GS
Pi
inactive
UMP
De-adenylylation
H2O
PII
PII
UT
UTP
PPi
UT inhibited by Gln,
Activated by α-kg and ATP
Self-mutiliation in
Lesch-Nyhan syndrome
Gout: excess uric acid
Folate and Purine Biosynthesis
Formate
+
ATP
NADPH
+ H+
H
H2N
N
N
NADPH
+ H+
R
NADP+
N
N
N
N
H
5
H
N
O
10
HN
R
5
HN
N
O
10
N
H
O
O
H
HN
10
R
Met
DHFR catalyzes
these reactions
H
HCys
H2N
N
N
5
HN
N
5
HN
N
N
NADPH
+ H+
NADP+
H2N
10
HN
O
N
HN
N
H2N
H
H2N
H
5
HN
NADP+
H
ADP +
Pi
O
CH3 HN
10
R
R
Ribonucleotide reductase mechanism.
1.
2.
3.
4.
5.
The free radical of ribonucleotide reductase
eliminates a hydrogen atom from carbon 3' of
the substrate, generating a free radical.
One of the thiol groups of the enzyme
donates a proton to oxygen on C2'.
A water molecule is eliminated.
The carbocation on C2' is reduced by the
second sufhydryl group.
The enzyme donates a hydrogen atom to C3'
to form the deoxyribonucleotide. The enzyme
in converted in its radical form and must be
reduced to its starting disulfhydryl form.
The initial free radical is generated via a dinuclear
Fe cluster in the enzyme. O2 is the oxidant
that converts the Fe(II)-Fe(II) form into the
Fe(III)-Fe(II) form.
O2
Fe(II) Fe(II)
Fe(III) Fe(II)
From: http://www.med.unibs.it/~marchesi/ndp_reductase.html
Ribonucleotide reductase structural biology
R1 dimer
R1 hexamer
http://opbs.okstate.edu/~leach/biochem203folder/bioch203%20classes/b203c19/dndp.htm
Model for Ribonucleotide Reductase Activity
R1
R12
R14a
R16
Low population states
Most active
Hexamer site
• binds ATP, makes hexamer
Adenosine site
• binds ATP (KM= 100 µM) or dATP (KM=0.3 µM)
• dATP binding changes R1 to inactive tetramer
Specificity site
S site
Reduced
ATP or dATP
CDP UDP
dTTP
GDP CDP UDP
dGTP
ADP CDP GDP UDP
R14b
Inactive active
From: Cooperman & Kashlan (2003) Adv. Enzym. Regul. 43, 167-182.
Regulating Transcription
A. Negative Regulation: derepression
example: lac repressor; ligand = galactose
C. Positive Regulation: induction
example: CAP; ligand = cAMP
Regulation of lac operon
1.
Glucose: well-fed state lowers [cAMP]
means no induction; system C on left of equilibrium
if low [Galactose], system A on left; lac genes
repressed;
if high [Galactose], system A on right; lac gene
expression de-repressed, i.e. express lac genes
2.
Glucose: starvation raises [cAMP];
system C shifted to right; express lac genes
system insensitive to whether Galactose hi or lo
B. Negative Regulation: repression
example: trp repressor; ligand = tryptophan
not involved in lac gene regulation.