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NADPH
G6P
Ru5P
Xu5P
G3P Su7P
F6P E4P Xu5P
G3P
R5P
F6P
Pentose Phosphate Pathway
Glycolysis
DNA, RNAATP
Coordinate Regulation of Glycolysis and Gluconeogenesis
O P OO
O
OOPO
O
OH OH
OH
O
OOPO
O
OH OH
OH
O
OH
OOPO
O
OH OH
OH
O
OH
OOPO
O
OH OH
O
OH
O PO
O
O
OOPO
O
OH OH
O
OH
O PO
O
O
Glycolysis Gluconeogensis
ATP ADP
Pi
PFK2-bPase
complex
phosphatase
kinase
PFKF-1,6-bPase
F2,6bP glucose
ATP F2,6bPglucose
ATP
Glycogen Phosphorylase Regulation
ab
ATP ADP
ActiveR
Conformationalchange
InactiveT
Muscle; b state responds to energy charge
bR
bT aT
aRbR
bT aT
aR
High [ATP], [G6P] High [AMP]
Liver; a state responds to glucose levels
bR
bT aT
aRbR
bT aT
aR
Low [glucose]High [glucose]
Pancreatic β cell glucose sensing mechanism.
(portal vein)
ATP
GlucoseGlucose
K+
Ca2+
K +
Ca2+
glycolysis, TCA cycle and ox-phos
Hi ATP:ADP ratio inhibits K+ efflux pump, depolarizes cell.
Depolarization induces Ca2+ influx
Ca2+ spike causes exocytosis of insulin
cAMP ATP
O N
N
NO
OP
O
O
OH
NH2
+ +
Adenylate cyclase
Glucagonreceptor and G-coupled protein
PKAi PKAaATP ADP
PKAi PKAa
ATP ADP
Phosphorylasekinase
Glycogen phosphorylase
b a
Protein Kinase A
Glycogenbreakdown
+
++
+ PKA exists as C2R2tetramer in inactive form. cAMP binding causes dissociation into two active C monomers that phosphorylate other proteins.
Glucagon activates cAMP cascade in the liver
PKA coordinately regulates carbohydrate metabolism
PKAa
glycogen
Glc
G1P
G6P F6P F1,6bP
pyruvate
Phosphorylate PFK2-F2,6bPase complex;stimulates F-2,6-bPase activity and inactivates the kinase; activates gluconeogenesis
Phosphorylateglycogen
phosphorylase:stimulates glycogen
breakdown; phosphorylate
glycogen synthase: inhibits
glycogen synthesis.
Glucose is secreted into the blood.
Liver cell
TCA cycle and related metabolism
Ala,Val,Leu,IlePhe,Tyr,
Pyr
AcCoA
Succ-CoA
OAA
Fatty acids
Asp,Asn citrate
isocit
α-kg
Succ
fum
mal
PEPGlycolysisGluconeogenesis
NADH + H+NADH + H+
Glu, Gln
NADH + H+
FADH2Part of Ox-Phos
ATP
Redox Shuttling in Mitochondria
NAD+
NADH+ H+
NAD+
NADH+ H+
Q
2e- 2e-
2e- 2e-
Succ
FumOH OPO3
OH
OH OPO3
O
Glycerol 3-phosphate
DHAP
Glycerol 3-phosphate dehydrogenase
Succinatedehydrogenase
Complex 1; NADH
Dehydrogenase
NAD+
NADH+ H+
CytosolicNADH
dehydrogenase
matrix cytoplasm
FADH2 FADH2
Inner mitochondrial membrane
Mal-Asp Shuttle in Mitochondria
matrix cytoplasm
αkg αkg
Asp
Mal
NADH+ H+
Asp
MalNAD+
Inner mitochondrial membrane
Glu
OAA
Glu
OAA
NAD+
NADH+ H+
Aspartate-glutamate
carrier
α-kg –malatecarrier
β-Oxidation of fatty acids.
R
O
CoA
O
CoA
R
O
CoA
R
O
CoA
OH
R
O
CoA
O
R
O
CoA
FADH2
NADH
Citrate – Malate – Pyruvate Transport System
Mito Cyto
Cit Cit
PiPi
MalMal
CoASH
OAA Ac-CoA
Pyr
ATP ADP
NADH + H+
NAD+
NADPH + H+
Ac-CoA
OAA
NADP+NAD+
NADH + H+
ATP
ADP
Pyr
1
2
3
45
6
FattyAcids
Enzymes:1. Citrate synthase2. ATP-citrate lysase3. Malate dehydrogenase4. Malic enzyme5. Pyruvate carboxylase6. Malate dehydrogenase
Carriers:Citrate transported by two pumps, both are co-transporters. One co-transports orthophosphate, the other malate. Pyruvate transported by a separate pump.
CO2
Regulating Fatty Acid Synthesis and Degradation
cAMP
Insulin receptorGlucagon receptor
PKAactive PKAinactive
ACCaseACCase
FA FANADH, FADH2
β-Ox TCAFAS
AcCoAPyrCitCit
AcCoAMalCoA
AMP Glucose
Pyr
PPP
NADPH
triglycerides
FA
+
+
+
+
mitochondria
Cytochrome Oxidase Cycle
O=OO2
Fe Cu
2 H2O
OH
-OH
O-OOH
=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-ATPasewith a geometry that differs from that of the F1F0ATPase 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 electrostaticallywith an Arg sidechain. The electrostatic repulsion drives the charges apart, leading to rotational motion.
Copyright ©1999 by the National Academy of Sciences
Dimroth, Peter et al. (1999) Proc. Natl. Acad. Sci. USA 96, 4924-4929
Z-scheme in Photosynthesis
Photophosphorylation
Oxidative metabolism of arachidonic acid
O
CO2-
OH
O
O
O
CO2-
OH
O
O
CO2-
OOH
CO2-
2O2
Other PG’s
PGG2
PGH2
TXA2
Thromboxane synthase
cyclooxygenase
peroxidase
Inhibited by NSAIDs
CO2-OOH
OCO2-
lipoxygenase
O2
Cyclooxygenase and peroxidase activities in one enzyme called prostaglandin synthase
5-HPETE
LTA4
Other LT’s
Lipoproteins : lipid and cholesterol transport in the blood.
• Lipids transported– Triglycerides, phospholipids, cholesterol, and
cholesteryl esters• Proteins in lipoproteins
– Structural proteins– enzymes
• Nomenclature of lipoproteins– Electrophoretic mobility
α: highest mobility; HDL particlesβ: lowest mobility; LDL particlesPre−β: intermediate mobility; VLDL
– Density, size Protein Particle Function
C=chylomicron; H=HDL; VL=VLDL; L=LDL; I=IDL
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
PL>>CE>>TG~PL30-50<20HDL
CE>>PL>TG~C21~20LDL
CE>TG~PL>CE10~25IDL
TG>PL~CE>C8~50VLDL
TG>>PL>CE>C1100’sChyl
Lipids% ProteinD, nmParticle
Lipoprotein Biochemistry: Generation of lipoprotein particles
Chylomicrons
VLDLs& LDLs
HDLs
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
PII PII
Glu Gln
ATPα-kg
ATP + NH4+ ADP
ADP
PPi Pi
UTP PPi
H2OUMP
PII
AT
PII
AT
GS
GS
UT
inactive
active
AT
Uridylylated PII binds to AT and
activates the deadenylylation of
GS
Non-uridylylated PII converts AT into an adenylylating form that inactivates GS
AT inhibited by α-kg; activated by Gln
Regulation of Glutamine Synthetase
AMP
De-adenylylationadenylylation
UT inhibited by Gln,Activated by α-kg and ATP
Self-mutiliation inLesch-Nyhan syndrome
Gout: excess uric acid
Folate and Purine Biosynthesis
N
N
NH
N
NHR
NH2
O
N
N
NH
N
NHR
NH2
O
HH
N
N
NH
N
NHR
NH2
O
HH
H
H
NADPH+ H+
NADP+
NADPH+ H+
NADP+
NADPH+ H+
NADP+
N
N
NH
N
NHR
NH2
O
H
CH3
Met
HCysDHFR catalyzes these reactions
N
N
NH
N
NR
NH2
O
H
H
O
Formate+
ATP
ADP +Pi
5
10
5
10
5
105
10
5
10
Ribonucleotide reductase mechanism.1. The free radical of ribonucleotide reductase
eliminates a hydrogen atom from carbon 3' of the substrate, generating a free radical.
2. One of the thiol groups of the enzyme donates a proton to oxygen on C2'.
3. A water molecule is eliminated. 4. The carbocation on C2' is reduced by the
second sufhydryl group. 5. 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 dinuclearFe cluster in the enzyme. O2 is the oxidant that converts the Fe(II)-Fe(II) form into the Fe(III)-Fe(II) form.
Fe(II) Fe(II) Fe(III) Fe(II)
O2
From: http://www.med.unibs.it/~marchesi/ndp_reductase.html
Ribonucleotide reductase structural biology
R1 dimerR1 hexamer
http://opbs.okstate.edu/~leach/biochem203folder/bioch203%20classes/b203c19/dndp.htm
Model for Ribonucleotide Reductase Activity
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
R1 R12 R14a R16
Low population states
Most active
R14bS site Reduced
ATP or dATP CDP UDP
dTTP GDP CDP UDP
dGTP ADP CDP GDP UDP
Inactive active
From: Cooperman & Kashlan (2003) Adv. Enzym. Regul. 43, 167-182.
Regulating Transcription
A. Negative Regulation: derepressionexample: lac repressor; ligand = galactose
C. Positive Regulation: inductionexample: CAP; ligand = cAMP
Regulation of lac operon
1. Glucose: well-fed state lowers [cAMP]means no induction; system C on left of equilibriumif low [Galactose], system A on left; lac genesrepressed; 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 genessystem insensitive to whether Galactose hi or lo
B. Negative Regulation: repressionexample: trp repressor; ligand = tryptophannot involved in lac gene regulation.