Biochem Lect 18-19 Flashcards
what are the two possible fates for pyruvate
it will either become lactate where lactate dehydrogenase reduces it by redox reaction in aneorobic reaction
or pyruvate can continue t become acetyl-CoA and that will require oxygen and mitocondria
how does pyruvate from glycolysis in cytoplasm get to mitochondria for citric acid cycle
by the pyruvate dehydrogenase complex which connects glycolysis and TCA cycle as it si large complex with 3 differenyt subunits and need 5 cofactors for catalysis: three ate prosthetic groups= thoamine pyrophosphate(TPP), lipoamide, and FAD
the rest two are coenzyme= coenzyme A and NAD+
how is pyruvate dehydrogenase complex reaction favourable
this reaction is oxidizing pyruvae and activtaing it, but thid id redox decraboxylation as it gives CO2 and NADH
the large negative delta G means it is facourable anf irreversible
what are the 5 steps reaction of PDC complex
each of the 3 subunits will catalyze different reactions but all 3 linked as they are coupled to each other, each subunit will do as its name
E1= decarboxylation as it is pyruvate dehydrogenase
E2= redox reaction as it is dihydrolipoyl transacetylase
E3= redoz reaction as it is dihydrolipoyl dehydrogenase
what is end product of PDC complex and how PDC complex regulated
end product is acetyl CoA from pyruvate
two ratios will regulate PDC: ATP/ADP or ATP/AMP and NADH/NAD+
high ATP and NADH inhibit PDC cycle
how is PDC controlled by feedback inhivition
also known as product inhibition
when acetyl CoA is high, that causes inhibition of E2
when NADH is high, that will inhibit E3
how is PDC regulated by covalent modification
PDC can also be phosphorylated
if it is phorphorylated by PD kinase, that inactivates the E1 complex which turns the whole complex off
if it is dephosphorylated by PD phosphatatse, that will activate E1 and turn on the complex
how is PDC complex allosterically regulated
by acetyl CoA, NADH, pyruvate, ADP and Calcium can also stimulate PD phosphotase and restore PDC activity
why is acetyl CoA an important and useful moelcule
because all different metabolic fuels can generate acetyl CoA, such as fatty acids, ketone bodym sugars, pyruvatem and ethanol
so it is the center for enrgy metabolism
what is general role of TCA cycle and how is it unique from glycolysis and PDC complex
this cycle is oxidizing fuel one, meaning it links breakdown of fuel molecule to ATP production in oxidative phosphorylation
it is the second phase of respiration where ATP geenration come from oxidative phosphorylation while breakdown of metabolite, such a glycolysis pathway, and PDC are first phase of respiration where it is oxidizing fuel
what is net reaction of 1 round of citric acid cycle
acetyl CoA+Pi+GDP+2H2O+3NAD++1FAD–> 3H++2CO2+3NADH+1FADH2+GTP+CoA
where does CO2 carbons originate
from oxaloacetate
which TCA intermediate can be made from amino acid
by transamination reaction, can make alpha-ketoglutamate from glutamate and oxaloactetae from aspartate
how is isocitrate converted to alpha-ketoglutarate in the TCA cycle
by enzyme isocitrate dehydrogenase and byproducts of this reaction are CO2 and protons
what is overview of TCA cycle
stage 1= known as oxidative decarboxylation where acetyl CoA, which is 2C molecule, combine with oxaloacetate, a 4C molecule, and form citrate which is 6C molecule and this starts TCA cycle
where the 2Cs are oxidized to CO2 and generate oxaloacetate in process
stage 2= regenerate oxaloacetate
this si where GTP is made by substrate level phosphorylatrion and 2 H2O molecules are needed by reactions
4 pairs of electrons are also used to reduce and form 3 NADH and 1FADH2 for oxidative phosphorylation
succinate dehydrogenase is membrane bound protein linking TCA cycle to oxidative phosphorylation
how does succinate in TCA cycle get converted to fumarate
by electron transport chain and that is catalyzed by succinate dehydrogenase reaction which used FAD+ as teh cofactor and oxidize it to FADH2
how is the TCA cycle regulated
similiar to glycolysis
low ATP, or high ADP/AMP, and having calcium will stimulate teh cycle to go
high ATP will cause reduced coenzymes and/or product inhibition to stop cycle
why is TCA cycle considered amphibolic reaction
because it links the anabolic and catabolic pathways by acetyl CoA and TCA intermediates
what are the three complexes of mitochondrial oxidative phosphorylation nd how much proton does each make
complex I, also known as NADH-Q oxidoreductase, which will be teh first to take NADH and will move 4 protons
complex II is the succinate dehydrogenase of TCA cycle and also knwon as succinate-Q- reductase and move no protons but will have the FADH2 go through it
complex III= Q-cytochrome C oxidoreductase and that will move 4 protons and will give that electron to Cyt C and that will then give it to complex IV
complex IV= cytochrome C oxidase and will move 2 protons
what is overall idea behind how energy is made in mitochondrial oxidative phosphorylation
that electron transport chain will ahve tehse elctrons flow and generate proton gradient whihc will be used by ATP synthase to make ATP
what molecules will provide electrons for electron trasnport chain
that will be NADH and FADH2 which will carry electrons to teh electron tarsnport chain
how does elctrons passing from one place to another cause energy
as eletcrons are passed from carrier to carrier, there is change in redox potential generting free energy and since enrgy cannot be created or destroyed as stated by first law of tehrmodynamics, that energy will be used to power conformational change in protein complexes and pump protons from matrix into intermembrane space
since electrons are passing from negative E to positive E, that will result in free enrgy change
how many protons are pumped by NADH and FADH2
since NADH eneters strating from complex I, it will pump 10 protons in total, 4 from complex I+4 from complex III+2 from complex IV
but FADH2 eneters fromc omplex II which pumps no protons so it ends up pumping 6 protons in total, 4 from complex III+2 from complex IV
so in total, 1 FADH2 + 1NADH will pump 16 protons
what are some examples of oxidative phosphorylation inhibitores
retenone and amytal will inhibit electron flow from complex I to CoQ
antimyein A will blovk complex II
cyanide, azide, and CO cna inhibt complex IV
oligomycin will inhibit ATP sythnase, also considered as complex V in oxidative phsophorylation
what is the final electron accpetor in oxidative phosphorylation
that will be the 1/2 O2 molecule which will take that eletron and react with protons to make water molecules and that will occur after electron pass through complex IV
how does ATP synthase relate to oxidative phosphorylation complexes
when the electrons have passed through all complexes and went to oxygen, the protons that will be used tp react with oxygen to make water are pumped by ATP synthase from intermembrane space into matrix and by doing this, it causes synthesis of ATP
so at teh end, ATP is synthesized but water is also made, so it cna be considered as condensation reaction ad it also generate H2O
what are uncouplers and how do they affect ATP synthesis
uncouplers can disrupt proton gradient and affect ATP synthesis as tehy are molecules that ahve hydrophobic groups allowing them to cross membrane and these acidic groups can bind proton and move them from high to low concentration gradient which will disrupt the protein gradient that was made by oxidative phosphorylation and affect ATP synthesis
it is understood that ATP synthase will use the proton gradient to amke ATP, but how exactly
that is when peter mitchelle’s chemiosmotic hypothesis came which said that ATP synthesis arise due to the electrochemical gradient across mitochondrial inner emmbrane and the proton gradient is produced by electrons that are transported using suitable electron donors
the proton motive force is teh driving force behind ADP to ATP conversion
what are characteristics of ATP synthase
it is membrane bound, reversible, and dependant on proton gradient
it has F1 which is peripheral protein that carries out catalytic synthesis of ATP in matrix
the FO is teh integral membrane protein and that anchors enzmye complex in the inner mitochondrial membrane
the proton flow through rotor cause rotation in ring of the C subunit of F0
conformational change in F1 B-subunit are resposnible for ATP synthesis
What is Boyer’s binding change mechanism
each B-subunit function independantly and there are 3 different reactiosn occuring at once
binding of proton in rotor rotates the y-subunit and induces conformational change in b-subunit
each b-subunit undergo conformational change between 3 states:
1- open or empty/exit- where ATP leave
2- loose- where ADP and Pi bind
3- tight- where ATP bind
what is teh number of protons needed for ATP synthesis
since protons flopw is responsible for rotation in y-subunit and causing the confromational changes in b-subunit, 3 protons will be transported for production of 1 ATP and 1 extra proton will be also needed for export of ATP out of matrix by ATP-ADP translocase so around 4 protons are needed for 1 ATP in matrix
why dies ATP have to be exported from matrix of mitochondria
to maintain the change across inner mitochondrial membrane and this will be done by ATP-ADP translocase which needs that one extra proton
what is teh P/O ratio
this tells us how many ATP are made per oxygen reduced to water
since NADH pump 10 ptotons and 4 are needed for 1 ATP: 10/4= 2.5 ATP
FADH2 eneters later and pump 6 protons so: 6/4=1.5 ATP
what is an exception to the P/O ratio
NADH from glycolysis which is in cytosol cannot be imported across inner mitochondrial memebrane for use in ETC so a glycerophosphate shuttle passes electron from NADH in cytosoel to FADH2 in mitochondria
so the P/O ratio fro NADH from cytosol is 1.5 as it equals the FADH2
what is the overall sumamry equation for complete oxidation of glucose
1Glucose+30ADP+30Pi+6O2–> 6CO2+30ATP+30H2O
