Mitochondria and CAC Flashcards
What are the three main function of the citric acid cycle?
- produce NADH and FADH2
- produce organic intermediates used in biosynthesis
- eliminate surplus organic compounds as CO2
is the citric acid cycle aerobic or anaerobic?
aerobic but doesn’t consume O2 directly
does the citric acid cycle generate energy?
the energy generated is stored in form of high energy electrons in NADH and FADH2
what CAC intermediate does the CO2 come from?
acetyl-CoA and oxaloacetate
what are the high energy intermediates of the CAC?
succinyl-CoA (generates GTP), and acetyl-CoA (generates C-C bond)
what confers the directionality of the CAC?
the three irreversible steps
what is the relative concentrations of malate to oxaloacetate?
much more malate than oxaloacetate
What is the deltaG of the malate dehydrogenase reaction? How does it move forward?
It is positive, making it endergonic but since the next reaction is highly exergonic, once coupled with this reaction, the free energy becomes about 0
How much ATP can be produced per glucose?
20 per glucose (so 10 per acetyl-CoA)
What are the mechanisms by which the CAC is regulated?
- substrate availability
- product inhibition
- competitive feedback inhibition
- allosteric activation
- allosteric inhibition
How is citrate synthase regulated?
- substrate availability (of acetyl CoA and oxaloacetate): in vivo these do not saturate the enzyme and acetyl-CoA is controlled by PDC
- product inhibition: citrate, which is a competitive inhibitor of oxaloacetate
- competitive feedback: succinyl-CoA competes with acetyl-CoA
- allosteric inhibition: NADH
- allosteric activation: ADP
How is isocitrate dehydrogenase regulated?
- product inhibition: NADH, which displaces NAD+
- allosteric activation: ADP and Ca++
- when the enzyme is off, citrate and isocitrate is in equilibrium and citrate goes into the citoplasm
- citrate in the cytoplasm activates fatty acid synthesis and inhibits PFK which inhibits glycolysis
How is alpha-ketoglutarate dehydrogenase regulated?
- product inhibition: NADH and succinyl-CoA
- allosteric activation: Ca++
What is the role of pyruvate carboxylase and how does it fit it the CAC regulation?
- it converts pyruvate to oxaloacetate
- accumulation of acetyl-CoA indicates that there is a need of oxaloacetate to restart the CAC
What is amphibolic?
anabolism and catabolism
are the CAC intermediates at the start or end of anabolic and catabolic reactions?
- anabolic: start
- catabolic: end
What do cataplerotic reactions do to the CAC?
deplete the CAC intermediates (used for anabolism)
what do anaplerotic reactions do to the CAC?
replenish the depleted CAC intermediates (used for catabolism)
What are the different Cataplerotic reactions?
- fatty acid biosynthesis (ATP citrate lyase)
- amino acid biosynthesis (glutamate dehydrogenase)
- glucose biosynthesis (PEPCK)
what are the different anaplerotic reaction?
- oxaloacetate production (pyruvate carboxylase)
what is an amphiplerotic reaction?
a reaction that can either be cataplerotic or anaplerotic
what are the different amphiplerotic reactions?
- amino acid synthesis or breakdown (glutamate transaminase and alanine/aspartate transaminase)
- supplies malate/makes pyruvate + NADH (malic enzyme)
where is pyruvate usually located?
in the cytosol
how is pyruvate transported into the mitochondria?
VDAC (voltage-gated anion channel) for outer membrane and MPC (mitochondrial pyruvate channel) for inner membrane
name the two methods to shuttle cytosolic NADH to the mitochondria.
- DHAP/G3P shuttle
- malate/aspartate shuttle
how is NADH transported using the DHAP/G3P shuttle?
- NADH reduces DHAP into G3P (glycerol-3-phosphate)
- G3P can go through the mitochondrial membrane and delivers the electron to FAD+
- DHAP can go back into the cytosol
how is NADH transported using the malate/aspartate shuttle?
- oxaloacetate is reduced to malate
- malate can go through the mitochondrial membrane, where it it oxidated back into oxaloacetate, which makes an NADH
- oxaloacetate converted to aspartate by transaminase, which can cross the membrane
- aspartate can then be converted back into oxaloacetate by transaminase
how does the ATP/ADP translocator work?
- it will allow ADP and ATP to be transported across the membrane following the concentration gradient (and you need ADP in the mitochondria in order to make ATP)
- there is low ADP in the mitochondria since ATP synthase keeps using it up, and there is high ATP in the mitochondria since ATP synthase is making some
- so will transport ADP inside and ATP outside
is the electron transport chain endergonic or exergonic?
exergonic
How does the ETC transport electrons?
metals and other molecules transiently accept electrons and bring it from low to high potential
what are other pathways than CAC/glycolysis that reduces coenzyme Q?
the oxidation of fatty acids bring FAD
why are there so many chemical reaction in the ETC?
to store the chemical energy that is released
how does a proton wire work?
proton wire is way to transport protons by passing a proton from one molecule to another until it goes to the end, where it is released
how many protons does complex 1 pump per NADH?
4
how does complex 1 work?
the subunits which are not membrane bound accept the electron and eventually reduces coenzyme Q (is doubly reduced Q –> 2Q), when it is reduced, the “arm” (part that is membrane bound) sense it and causes conformational change that opens up the proton channels
how many protons does complex II pump?
none
what is the role of complex II?
it generates a membrane potential which allows complex 3 and 4 to pump protons
what provides electrons to complex II?
succinate (not FADH2 since it is part of the complex)
how many protons does complex III pump?
4
how does Complex III work?
cytochrome C is bound it it so can receive 1 electron and then bring it to complex IV
explain the Q cycle?
- 1 QH2 gets fully oxidized to Q
- One Q is partially reduced to QH+
- then another QH2 is fully oxidized
- QH+ gets a second electron from the free electron from step 3
how many protons does complex IV pump?
2
what does complex IV require and what does it generate?
- requires 4 Cyt C (cytochrome C)
- generates 2 H2O
is ATP synthesis and exergonic or endergonic process?
endergonic
what provides the energy for ATP synthesis?
the proton motor force
what is the F1 and the F0 component of ATP synthase?
- F1: the non-membrane bound
- F0: the membrane bound rotating subunits
explain the binding change mechanism for ATP synthase?
- there are 3 sites: open (empty site, where ATP is released), loose (where ADP and Pi bind), and tight (where ATP is formed)
- the subunits rotate and go from open, to loose, to tight
how is Pi transported into the mtochondria?
by a Pi/H+ co-transporter that transports H+ inside due to concentration gradient
what is the P/O ratio?
calculation of the amount of phosphate incorporated into ATP per one oxygen reduced
how many ATPs are produced in one complete rotation of Fo?
3
how many protons are returned to the matrix for one complete rotation of Fo (explain how it is calculated)?
3 (1 proton enters mitochondria for every ATP produced) + 8 (number of c-subunits which may change with the organism) = 11
how many protons are required to synthesize 1 ATP?
protons/ ATPs produced
here: 11/3 = 3.7 protons/ATP
how do you calculate the P/O ratio for different proton donor?
- NADH: we know that it pumps 10 protons and that we require 3.7 protons/ATP so P/O = 2.7 ATP/NADH (~2.5)
- FADH2: we know that it pumps 6 protons so P/O = 1.6 ATP/FADH2 (~1.5)
what is the evidence for Chemi-osmotic coupling?
- respiratory chain can function in the absence of phosphate
- the # moles of ATP generated through NADH oxidation was not an integer
- an intact inner mitochondrial membrane (imm) is required
- key electron transport proteins span the imm
- generating an artificial proton gradient permits ATP synthesis without electron transport
- uncouplers such as DNP inhibits ATP synthesis
what is a chemical uncoupler and how does it work?
DNP, which is a weak acid that can diffuse through the membrane and takes protons from the cytosol and bring it into the matrix, which reduces the proton gradient
what is an endogenous uncoupler and how does it work?
- UCP1, which is in brown adipose tissue
- is a channel that allows protons to be pumped back in of the mitochondrion so that the energy can be dissipated as heat
