a survey of metabolism - kimika · 2010-05-18 · 3 the study of metabolism allows us to understand...
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ASURVEYOFMETABOLISM
HLeeYuJsuicoJunsay
DepartmentofChemistry
SchoolofScienceandEngineering
AteneodeManilaUniversity1
2
Whydolivingorganismsneedenergy?
1. EnergyformoEon–kineEcenergy2. Maintainhomeostasis–steadystate,potenEal
energy
3. Builduptheorganism’scomponentsfromavailablenutrients–chemicalenergy
4. Removeswaste–chemicalandkineEcenergy5. Respondstoenvironmentalchanges–chemical
energy
6. Removeandregeneratedamagedparts–chemicalenergy
3
Thestudyofmetabolismallowsustounderstandhowallthecell’sprocessaredone!
Insomeway,itisalsoastudyofhowenergyistransformedbytheorganismfromoneformtoanother!
4
AboveandbeyondallcharacterisEcs,itismetabolismthatprovidesthebestworkingdefiniEonoflife.
“ItismetabolismandnotreplicaEonthatprovidesthebestworkingdefiniEonoflife.EvoluEonarybiologistswouldsaythatweexistinordertoreproduce–butwearenot,eventhemostamorousofuse,tryingtoreproducealltheEme.Yet,ifwestopmetabolizing,evenforaminuteortwo,wearedonefor.”
» PhillipBallinStoriesoftheInvisible:AGuidedTourofMolecules,OxfordUniversityPress,2001.
METABOLISM
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6
Organismscanbedividedtomanymetabolism‐basedclasses.
Autotrophvs.Heterotroph
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Organismscanbedividedtomanymetabolism‐basedclasses.
Aerobesvs.Anaerobes
8
Thepathwaybywhichmoleculesdegradeandsynthesizecompoundsiscalledthemetabolicpathway
Astudyofenergytransferfromfoodtobiologicalmolecules
9
Enzymecomplexesprovidethemachineryformetabolism
10
Energyiscarriedfromoneformtoanotherbychemicalcompounds‐METABOLITES.
11
Metabolismiscarriedoutin3stages:
1. DegradaEon/Synthesisofcomplexmetabolites
2. TransformaEonofsimplemetabolites
3. Energypay‐off
12
Organismsmaintainnon‐equilibriumcondiEonsbetweentheselfandthenon‐self:steadystate.
• McKeeandMcKee(1999)Biochemistry:AnIntroducEon.Figure4.2,p.64.
System
Surroundings
EquilibriumSteadyStateNOTatequilibrium
Andwhenwetalkaboutenergyandequilibrium,weusuallylookatthermodynamics.
BIOLOGICALTHERMODYNAMICS
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ThermodyamicsconsiderstheenergeLcsofa
reacLon.
FIRSTLAW:“Youcan’twin.”Energycannotbecreatedordestroyed.Itis
onlytransformedintootherforms
ΔEsystem=–ΔEsurrounding
15
ThermodyamicsconsiderstheenergeLcsofa
reacLon.
SECONDLAW:“Youalwayslose.”Thetotalentropyoftheuniverse(entropyof
system+surrounding)increasesinaspontaneousreacEon
€
ΔStotal = ΔSsystem + ΔSsurroundings > 0
16
ThermodyamicsconsiderstheenergeLcsofa
reacLon.
THIRDLAW:“Youwillnevergetthere/PerfecLonisboring”
Theentropy,S,ofapure,perfectlycrystallinesolidatabsolutezerois0.
17
Gibbsfreeenergy,ΔG,isthemaximum“useful”workthatcanbeproducedbyachemicalreacEon.
ΔG<0ThereacEonisspontaneousintheforwarddirecEon.
ΔG>0ThereacEonisnon‐spontaneousaswrinen.ThereacEonisspontaneousinthereversedirecEon.
ΔG=0ThereacEonisatequilibrium.
€
ΔG = ΔH −TΔS
18
ThermodyamicsconsiderstheenergeLcsofa
reacLon.
ΔGisthemaximum“useful”workthatcanbeproducedbyachemicalreacLon.
19
EnergeEcallyunfavorablereacEonsarecoupledtofavorableonestodrivethemforward.(thisishoworganismswin!)
20
ΔG=+17kJ/mol
ΔG=‐30kJ/mol
EnergeEcallyunfavorablereacEonsarecoupledtofavorableonestodrivethemforward.
CoupledreacEonspassesthroughadifferentmechanismwhoseoverallyieldgiveΔG<0
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CHEMICALSTRATEGIES
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Organismsusecommonchemicalstrategiesinenergymanagement.
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PhosphoryltransferreacEonsyieldverynegaEveΔGmakingthemidealforcouplingwithotherreacEons
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PhosphoryltransferreacEonsyieldverynegaEveΔGmakingthemidealforcouplingwithotherreacEons
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ATPhasintermediatephosphoryltransferpotenEal.
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LessreacLvethanPEP,kineLcallystable.
ATPhasintermediatephosphoryltransferpotenEal.
27
Why do we need an intermediate metabolite as energy carrier?
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Phophoryl transfer molecules are used up in the cells depending on certain conditions
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Phophoryl transfer molecules are used up in the cells depending on certain conditions
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OxidaEon‐reducEonreacEonsneedredoxpartners.
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OxidaEon‐reducEonreacEonsneedredoxpartners.
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Theseredoxpartnersareusuallyelectroncarriers..Toothermoleculesortorespiratoryenzymes
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CASESTUDY:GLYCOLYSISANDTHEFATESOFPYRUVATE
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Glycolysisandthecitricacidcycleareatthecenterofthemetabolicprocessesinlivingorganisms
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Glucosemetabolisminvolvesbothenergyproducing(catabolic,orange)andenergyconsuming(anabolic,green)processes
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WHYGLUCOSE?!
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Theonlyfuelthebrainusesinnon‐starvaEoncondiEons
Theonlyfuelredbloodcellscanuse WHY?
EvoluEonary:probablyavailableforprimiEvesystems(fromformaldehyde)
Lowtendencytoglycosylateproteins,strongtendencytoexistinringform(recall:allequatorial!)
GlycolysisturnsglucosetopyruvatewhichthencanbeuElizedinfermentaEonorthrucompleteoxidaEon.
38
Glycolysisoccursinthreemajorstages:
1. INVESTMENT:Glucosefructose‐1,6‐biphosphate
2. MULTIPLIER:Fructose‐1,6‐biphosphateglyceraldehyde‐3‐phosphate
3. PAYBACK:Glyceraldehyde‐3‐phosphatePyruvate
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STEP1:PhosphorylaEonofglucoseusinghexokinase(orglucokinase)toglucose‐6‐phosphate(G6P)
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• Thisstepisaprimingstep–usesATPtogetmoreATPlater,–VerynegaEveΔG
• Donetokeepglucoseinthecytoplasm
O
OH
OH
OH
HO
OH
hexokinase
ATP ADP
O
OH
OH
OH
-2O3PO
OH
Glucose Glucose-6-phosphate
STEP1:PhosphorylaEonofglucoseusinghexokinase(orglucokinase)toglucose‐6‐phosphate(G6P)
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• Thisstepisaprimingstep–usesATPtogetmoreATPlater,–VerynegaEveΔG
• Donetokeepglucoseinthecytoplasm
STEP2:IsomerizaEonofG6Ptofructose‐6‐phosphate
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• 3rdstepwillbeeasieronaprimaryOH,ratherthanahemiacetal
• ReadiesthecompoundforlatercleavagebetweenC3‐C4
O
OH
OH
OH
-2O3PO
OH
O
OH
OH-2O3PO
HO
OH
phosphogluycoisomerase
Glucose-6-phosphateFructose-6-phosphate
STEP2:IsomerizaEonofG6Ptofructose‐6‐phosphate
43
• 3rdstepwillbeeasieronaprimaryOH,ratherthanahemiacetal
• ReadiesthecompoundforlatercleavagebetweenC3‐C4
STEP3:PhosphorylaEonofF6Ptofructose‐1,6‐bisphosphate(usingPhosphofructokinase,PFK)
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• Thisisanotherprimingstep–UsesATPtogetmoreATPlater,–VerynegaEveΔG
• Thisisthecommibedstep:F‐1,6‐BPisveryreacEve!• PFK,InhibitedbylotsofATP.(ifyoudon’tneedenergy,yourstepwillnotoccur)
O
OH
OH-2O3PO
HO
OH
O
OH
OPO3-2-2O3PO
HO
OH
phosphofructokinase
Fructose-6-phosphate Fructose-1,6-bisphosphate
ATP ADP
RecallSTAGE1:INVESTMENT
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STEP4:Cleavingthe6Cmoleculetotwo3Cmolecules
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• Donebyaldolase(areversealdolcondensaEonreacEon)
O
HO
-2O3PO OPO3-2
OH
Fructose-1,6-bisphosphate
Aldolase
H2C
C O
CH2OH
O P
O
O-
O-
Dihydroxyacetonephosphate(DHAP)
HC
HC OH
CH2O
O
P
O
O-
O-
1
2
3
4
5
6+
Glyceraldehyde-3-phosphate (G-3-P)
1
2
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5
6
STEP4:Cleavingthe6Cmoleculetotwo3Cmolecules
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• Donebyaldolase(areversealdolcondensaEonreacEon)
STEP5:ConvertsDHAPtoG‐3‐P
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• UsesTriose‐phosphateisomerase• ThisreacEonyieldsanoveralltwo(2)G‐3‐Ppermoleculeofglucose
H2C
C O
CH2OH
O P
O
O-
O-
Dihydroxyacetonephosphate(DHAP)
HC
HC OH
CH2O
O
P
O
O-
O-
Glyceraldehyde-3-phosphate (G-3-P)
Triose-phosphate isomerase
STEP5:ConvertsDHAPtoG‐3‐P
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• UsesTriose‐phosphateisomerase• ThisreacEonyieldsanoveralltwo(2)G‐3‐Ppermoleculeofglucose
RecallSTAGE2:MULTIPLIER
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CHECKLIST:
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We’veUSEDUP2ATPmoleculestoprocess1glucosemolecule
Weareleswith2G3Pnow
Timeforenergypayback,thusSTAGE3!
Recallthatstage3happensinparalleltothetwoG3Pmolecules
STEP6:G‐3‐Pisoxidizedto1,3‐bisphosphateglycerate(1,3‐BPG)
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• YieldsNADH,anelectroncarrier!• YieldsahighlyreacEve1,3‐BPG,aphosphorylcarrier!
C
HC OH
CH2O
O
P
O
O-
O-
Glyceraldehyde-3-phosphate (G-3-P)
H
C
HC OH
CH2O
O
P
O
O-
O-
1,3-bisphosphate glycerate(1,3-BPG)
OPO3-2
NAD+ NADH
HPO4-2+
H++G-3-P dehydrogenase
STEP7:1,3‐BPGistransformedto3‐phosphoglycerate(3‐PG)
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• YieldsATPpaybackEme!(rememberforeverystephere,twoareactuallyyieldedduetothetwoG‐3‐Pmoleculesthatwemadeearlier!)
C
HC OH
CH2O
O
P
O
O-
O-
1,3-bisphosphate glycerate(1,3-BPG)
OPO3-2
C
HC OH
CH2O
O
P
O
O-
O-
OH
3-phosphoglycerate(3-PG)
phophoglycerate kinase
ADP ATP
STEP8:3‐PGisconvertedto2‐PG
54
• PlacesphosphatefromC3toC2..ReadiesthemoleculetomakePhosphoenolpyruvate,anotherhighlyreacEvecompound!
C
HC OH
CH2O
O
P
O
O-
O-
OH
3-phosphoglycerate(3-PG)
C
HC O
CH2OH
O
P
O
O-
O-
OH
2-phosphoglycerate(2-PG)
phophoglycerate mutase
STEP9:2‐PGisre‐arrangedtophosphoenolpyruvate(PEP)
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• EnolasecreatesanenollikefuncEonalgroup.
C
HC O
CH2OH
O
P
O
O-
O-
OH
2-phosphoglycerate(2-PG)
C
C O
CH2
O
P
O
O-
O-
OH
Phosphoenol pyruvate(PEP)
enolase
H2O
STEP9:PEPisconvertedtoPyruvate
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• YieldsATPanotherpaybackstep!
C
C O
CH2
O
P
O
O-
O-
OH
Phosphoenol pyruvate(PEP)
ADP + H+ ATP
pyruvate kinase C
C
OHH2C
OHO
C
C
OH3C
OHOketo-enoltautomerization
pyruvate
RecallSTAGE3:PAYBACK
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CHECKLIST:
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Made2NADH(onefromeachG‐3‐P)
Made4ATP(twofromeachG‐3‐P)
OVERALLMassbalance:
Glucose+2Pi+2ADP+2NAD+
2Pyruvate+NADH+2ATP+2H++2H2O
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NADHhastwopossiblefates:fermentaEonorrespiraEon
FermentaLon:IntheabsenceofO2,NADHisusedasachemicalreductantofpyruvatetomakelactate
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NADHhastwopossiblefates:fermentaEonorrespiraEon
RespiraLon:InthepresenceofO2,NADHisusedasaelectroncarriertoharnessenergyinthemitochondria.
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Pyruvatehasthreepossiblefates:lactatefermentaEon,alcoholfermentaEonandcompleteoxidaEon
LactateFermentaLon:IntheabsenceorshortsupplyofO2,pyruvateisconvertedtolactate(vialactatedehydrogenase).Reverseisdonebythesameenzyme.
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Pyruvatehasthreepossiblefates:lactatefermentaEon,alcoholfermentaEonandcompleteoxidaEon
LactateFermentaLon:IntheabsenceorshortsupplyofO2,pyruvateisconvertedtolactate(vialactatedehydrogenase).Reverseisdonebythesameenzyme.
63
Pyruvatehasthreepossiblefates:lactatefermentaEon,alcoholfermentaEonandcompleteoxidaEon
EthanolFermentaLon:Inanaerobicbacteria/yeast,pyruvateisdecarboxylatedthenreducedtoethanol
O
H3C
O
OH
O
H3C
H
H3C C
OH
H
H
CO2
alcoholdecarboxylase
pyruvate acetaldehyde
NADH + H+ NAD+
alcohol dehydrogenase
ethanol
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Pyruvatehasthreepossiblefates:lactatefermentaEon,alcoholfermentaEonandcompleteoxidaEon
RespiraLon:InthepresenceofO2,pyruvateisconvertedtoAcetyl‐CoAwhichwillbefedontothetricarboxylicacidcycle.
O
H3C
O
OH
pyruvate Acetyl-CoA
O
H3C
SCoA
HSCoANAD+
NADH + H+CO2
pyruvate dehydrogenase complex (E1 + E2 + E3)
65
TheenergeEcsofglycolysisrevealsthreeimportantthings:
1. Mostoftheprocessisnotenergyintensiveandarethusreversible
2. Therearethreeirreversiblesteps:1,3and10.
3. ThesestepsarepossiblywhereregulaEoncanhappen
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Othermonosaccharidescanalsoenterglycolysis.
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Thesynthesisofglucosefrompyruvate,lactate,aminoacidsorothermetabolites,iscalledgluconeogenesis.
Occursmainlyinliverandkidneys
Notthemerereversalofglycolysisfor2reasons: EnergeEcsmustchangetomakegluconeogenesisfavorable(deltaGofglycolysis=‐74kJ/mol
ReciprocalregulaEonmustturnoneonandtheotheroff‐thisrequiressomethingnew!
71
Sevenstepsofglycolysisareretained: Steps2and4‐9
Threestepsarereplaced: Steps1,3,and10(theregulatedsteps!)
ThenewreacEonsprovideforaspontaneouspathway(ΔGnegaEveinthedirecEonofsugarsynthesis),andtheyprovidenewmechanismsofregulaEon
MakesureyouknowtheTHREEBYPASSSTEPSofGluconeogenesis!!!
Thesynthesisofglucosefrompyruvate,lactate,aminoacidsorothermetabolites,iscalledgluconeogenesis.
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Thesynthesisofglucosefrompyruvateiscalledgluconeogenesis.
Occursmainlyinliverandkidneys
Notthemerereversalofglycolysisfor2reasons: EnergeEcsmustchangetomakegluconeogenesisfavorable(deltaGofglycolysis=‐74kJ/mol
ReciprocalregulaEonmustturnoneonandtheotheroff‐thisrequiressomethingnew!
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Thesynthesisofglucosefrompyruvate,lactate,aminoacidsorothermetabolites,iscalledgluconeogenesis.
74
Thesynthesisofglucosefrompyruvateiscalledgluconeogenesis.
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Asidefrom(+)and(‐)effectors,hormonescontrolgeneexpression.
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Asidefrom(+)and(‐)effectors,hormonescontrolgeneexpression.
CASESTUDY:TRICARBOXYLICACIDCYCLEANDELECTRONTRANSPORTCHAIN
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Acetyl‐CoAentersacyclethatconvertsittoCO2
andlotsofelectroncarriers
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Acetyl‐CoAentersacyclethatconvertsittoCO2
andlotsofelectroncarriers
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Acetyl‐CoAreactwithOxaloacetateandisconvertedtoCitrate.Thecycleregeneratestheoxaloacete,disposesoftheCO2andyieldlotsofenergycarriers.
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Acetyl‐CoAreactwithOxaloacetateandisconvertedtoCitrate.Thecycleregeneratestheoxaloacete,disposesoftheCO2andyieldlotsofenergycarriers.
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Acetyl‐CoAreactwithOxaloacetateandisconvertedtoCitrate.Thecycleregeneratestheoxaloacete,disposesoftheCO2andyieldlotsofenergycarriers.
84
Acetyl‐CoAreactwithOxaloacetateandisconvertedtoCitrate.Thecycleregeneratestheoxaloacete,disposesoftheCO2andyieldlotsofenergycarriers.
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NADHandFADH2carrieshighenergyelectronwhichcreatesahydrogenpotenEalwhichinturncreatesATP
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NADHandFADH2carrieshighenergyelectronwhichcreatesahydrogenpotenEalwhichinturncreatesATP.1NADH=3ATP,1FADH2=2ATP.
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Glycolysis+Pyruvatedehydrogenase+TCA=lotsofenergy
CASESTUDY:BETA‐OXIDATIONOFFATS
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89
FatsaredegradedbycuungthemupintoC2fragments:Acetyl‐CoAandfedintotheTCA.
90
FatsaredegradedbycuungthemupintoC2fragments:Acetyl‐CoAandfedintotheTCA.
SUMMARY
91
92
Metabolismofnutrientsinvolve
Breakdownfrombiomoleculestosimplemolecules
Simplemoleculesareconvertedtofeedermolecules
Glycolysis, Pyruvatedehydrogenase, B‐oxidaEon
Feedermoleculesarefedtoacyclethatproduceslotsofenergycarriers
TCANADH+FAH2
EnergycarriersareprocessedandcanreleaselotsofATP ElectrontransportChain
THESEPROCESSESARETIGHTLYREGULATED
93
AboveandbeyondallcharacterisEcs,itismetabolismthatprovidesthebestworkingdefiniEonoflife.
“ItismetabolismandnotreplicaEonthatprovidesthebestworkingdefiniEonoflife.EvoluEonarybiologistswouldsaythatweexistinordertoreproduce–butwearenot,eventhemostamorousofuse,tryingtoreproducealltheEme.Yet,ifwestopmetabolizing,evenforaminuteortwo,wearedonefor.”
» PhillipBallinStoriesoftheInvisible:AGuidedTourofMolecules,OxfordUniversityPress,2001.