T05 - TCA and OxPhos Flashcards
Pyruvate dehydrogenase catalyzes what reaction?
catalyzes the following irreversible reaction:
pyruvate + CoA + NAD+ → acetyl-CoA + CO2 + NADH
Which reaction/enzyme serves as the key control point for entry of carbon into the TCA cycle?
pyruvate dehydrogenase reaction (which converts pyruvate to acetyl-CoA)
The pyruvate dehydrogenase enzyme is a critical control point for which processes? (3)
entry of carbon into TCA cycle
activation of gluconeogenesis
glucose → fat conversion
Where in the cell is the pyruvate dehydrogenase complex located?
mitochondria
Differentiate between fatty acid synthesis and oxidation in terms of where these processes occur.
fatty acid synthesis = cytosol
fatty acid oxidation = mitochondria
The pyruvate dehydrogenase conversion of pyruvate to acetyl-CoA can be broken down into how many steps?
3
What happens in the first reaction of the pyruvate dehydrogenase complex?
E1 oxidizes hydroxyethyl group of thiamine pyrophosphate (coenzyme form of vit B1) and transfers group to lipoamide
What happens in the second reaction of the pyruvate dehydrogenase complex?
E2 transfers acetyl group from lipoamide to acetyl-CoA
What happens in the third reaction of the pyruvate dehydrogenase complex?
E3 regenerates oxidized lipoamide, using FADH2 and NADH as cofactors
The pyruvate dehydrogenase complex requires what five cofactors?
thiamine pyrophosphate (TPP, a form of vit B1)
FAD (vit B2/riboflavin)
NAD (vit B3/niacin)
lipoamide
CoA
Describe how the pyruvate dehydrogenase complex is regulated.
PDH kinase → phosphorylates E1 → inhibits/reduces activity of PDH
PDH phosphatase → dephosphorylates E1 → restores PDH activity
What stimulates and inhibits PDH kinase?
stimulates — high ATP:AMP/ADP ratio, high NADH:NAD+ ratio, high acetyl-CoA:CoASH ratio [these ultimately inhibit PDH activity]
inhibits — ADP, NAD+
What stimulates and inhibits PDH phosphatase?
stimulates — insulin, Ca2+
How is the outer membrane of the mitochondria unusual?
small molecules (i.e. metabolites) can readily cross the bilayer, but larger molecules such as proteins can’t cross
Describe the permeability of the inner membrane of the mitochondria.
semipermeable such that charged molecules cannot cross the inner membrane except via transporter proteins
What does the TCA cycle ultimately do to the acetyl-CoA that is fed in?
acetyl-CoA is oxidized into CO2 + H2O
Where are the enzymes of the TCA cycle located?
in the mitochondrial matrix
Draw out the TCA cycle.
Describe the features of the citrate synthase reaction of the TCA cycle. (2)
irreversible (because of very negative ΔG value)
important regulatory control point
What inhibits the citrate synthase reaction of the TCA cycle?
high ATP:ADP
What is the limiting reagenet in the citrate synthase reaction of the TCA cycle?
oxaloacetate — concentration is extremely low and is tightly controlled by several factors
What are the activators and inhibitors of isocitrate dehydrogenase?
activators = ADP
inhibitors = NADH, ATP
How does an increasing NADH/NAD+ ratio affect the malate dehydrogenase reaction?
increasing NADH/NAD+ shifts equilibrium to favor malate over oxaloacetate, which decreases [oxaloacetate] and therefore slows down citrate synthase
Citrate, as a TCA intermediate, can be shunted to produce which biosynthetic molecules? (2)
fatty acids
sterols
Alpha-ketoglutarate, as a TCA intermediate, can be shunted to produce which biosynthetic molecules? (3)
glutamate
AAs
purines
Succinyl-CoA, as a TCA intermediate, can be shunted to produce which biosynthetic molecules? (2)
porphyrins
heme
Oxaloacetate, as a TCA intermediate, can be shunted to produce which biosynthetic molecules? (4)
aspartate
AAs
purines
pyrimidines
Differentiate between cataplerotic and anaplerotic reactions.
cataplerotic = draining TCA intermediates toward biosynthetic pathways
anaplerotic = repleneshing TCA intermediates from other nutrients/metabolites
Is the reduction of O2 to H2O exergonic or endergonic?
extremely exergonic
Where does oxidative phosphorylation take place?
in inner mitochondrial membrane
Describe the structure of quinones.
variable number of isoprene units
Where in the body are quinones found?
found in all tissues
Describe how quinones are reduced.
reduced by one electron to both semiquinone and hydroquinone → act as both electron and proton carriers
reduced by two electrons (hydride ion)
Are quinone reductions reversible?
Yes, both reduction by one electron and two electrons is reversible.
Flavoproteins are derivatives of
riboflavin (vitamin B2)
What are the two predominant forms of flavoproteins?
FMN
FAD
What is the function of flavoproteins in the context of oxidative phosphorylation?
funnel electrons removed from a variety of sources into the respiratory chain
Describe the composition of iron-sulfur proteins.
contain Fe (not part of heme) in association w/ S atoms in the form of sulfides and cysteines
How do iron-sulfur proteins function as electron carriers?
oscillate between Fe2+ and Fe3+ states
What are cytochromes?
hemeproteins found in close association with both inner mitochondrial membrane and cytoplasmic face of ER
Describe how the heme in cytochromes differ from the heme in hemoglobins.
heme in cytochromes = electron carrier (alternating between Fe2+ and Fe3+)
heme in hemoglobin = oxygen carrier
Name the following complexes in the mitochondrial respiratory chain:
Complex I
Complex II
Complex III
Complex IV
Complex I = NADH-Q oxidoreductase
Complex II = succinate-Q-reductase
Complex III = Q-cytochrome c oxidoreductase
Complex IV = cytochrome c oxidase
What is the significance of Complex II in the mitochondrial respiratory chain?
Complex II (a.k.a. succinate-Q-reductase) is part of the TCA cycle
it is the only complex that doesn’t transport H+ across the inner membrane
What is the ratio of NADH oxidized to ATP produced?
for every 1 NADH oxidized (i.e. 2 electrons transferred to O2), 3 ATP produced
[results from highly exergonic oxidation of NADH coupled to slightly endergonic synthesis of ATP]
Describe the stoichiometry and mechanism of protons crossing the mitochondrial respiratory chain complexes.
4 H+ extruded into intermembrane space as electrons pass through Complexes I and IV
2 H+ extruded into intermembrane space as electrons pass through Complex III
Describe the composition of Complex I/NADH-Q oxidoreductase.
FMN-bound NADH dehydrogenase
Fe-S proteins
Write out the mechanism of the Complex I/NADH-Q oxidoreductase reaction. (6)
transfers NADH 2e- → FMN → series of Fe-S clusters → CoQ → QH2 → QH2 leaves and diffuses through membrane
CoQ in Complex I/NADH-Q oxidoreductase can exist in what three forms?
fully oxidized state (Q)
semiquinone (QH•)
ubiquinol (QH2)
(T/F) Electron flow through Complex I/NADH-Q oxidoreductase alone is capable of driving ATP synthesis.
True.
Describe what occurs in Complex II/succinate-Q reductase of the mitochondrial respiratory chain.
e- from TCA cycle shuttled from protein-found FADH2 → Fe-S clusters → CoQ
Complex II/succinate-Q reductase shuttles electrons from the TCA from FADH2 to CoQ without extrusion of protons. What two other enzymes are also capable of accomplishing this?
glycerol phosphate dehydrogenase
fatty acyl CoA dehydrogenase
Broadly speaking, what is the function of Complex III/Q-cytochrome c oxidoreductase?
to relocate electrons from QH2 to oxidized cytochrome c
Describe the composition of complex III/Q-cytochrome c oxidoreductase.
contains multiple cytochrome proteins, each with different electron affinities
Is cytochrome c a one-electron or two-electron carrier?
cytochrome c is a one-electron carrier (electrons to it are handed off by a two-electron carrier)
What is the function of Complex IV/cytochrome c oxidase?
transfer cytochrome c electrons to O2
Describe the composition of Complex IV/cytochrome c oxidase. (2)
contains:
multiple heme-containing cytochromes
Cu+ → Cu2+ oscillating copper-bound proteins
Describe the stoichiometry of the Complex IV/cytochrome c oxidase reaction.
4 H+ taken up from matrix to reduce 1 equivalent of O2, generating 2 H2O
What were the three underlying observations of the chemiosmotic hypothesis postulated by Peter Mitchell?
(1) there are 3 sites of energy conservation
(2) ATP synthase requires intact inner mitochondrial membrane
(3) uncouplers of oxidation from phosphorylation were small molecules that could equilibrate a proton gradient across a membrane
Three complexes of the mitochondrial respiratory chain pump protons across the inner membrane, creating an energized proton gradient. How is the energy contained in this gradient conserved? (2)
conserved through ADP + Pi → ATP synthesis, mediated by ATP synthase enzyme
[H+] is equilibrated across the membrane in the process
In the context of chemiosmosis, what are uncouplers? Give three examples.
compounds that disrupt the proton gradient by increasing permeability of membrane to protons
examples of uncouplers: dinitrophenol, FCCP, valinomycin
What is another name for the ATP synthase enzyme?
F1-ATP synthase
Describe the conformational change that leads to ATP synthesis in F1-ATP synthase.
H+ flow down gradient → rotation of dimers w/ respect to stalk → conformational change from open (release ATP) → loose (ADP + Pi) → tight (dissociation and formation of ATP)
Respiration and phosphorylation are well coupled in most mitochondria. What is an exception to this trend?
not well coupled in mitochondria of brown adipose tissue
How is respiratory control measured?
ratio of rate of oxygen consumption in presence of ADP to rate of oxygen consumption in absence of ADP
the higher the ratio with a specified substrate, the more tightly coupled the mitochondria
Uncoupling proteins cause a short-circuit in the proton gradient necessary to drive ATP synthesis, but are still clinically important. Why?
in short-circuiting the proton gradient, uncoupling proteins such as thermogenin generate heat → method for generating heat to maintain body temperature
In a healthy cell, how do ATP and ADP levels compare?
ATP levels exceed that of ADP by factor of 4-10
(T/F) NADH/NAD+ are transported into the mitochondrial matrix using a specific carrier.
False. There is no means to transport NAD+ or NADH across the mitochondrial inner membrane.
What is the purpose of the malate-aspartate shuttle?
to get NADH from the cytosol into the mitochondrial matrix
Write out the pathway of the malate-aspartate shuttle.
OAA reduced to malate in cytosol using NADH → malate exchanged for a-KG → travels to mitochondrial matrix → mitochondrial malate dehyrogenase oxidizes malate back into OAA, producing NADH
Describe what happens in ethanol metabolism. (8)
ethanol oxidation → buildup of NADH → cells reduce pyruvate to lactate → less pyruvate for gluconeogenesis → acetate from ethanol oxidation converted to acetyl-CoA → can’t be oxidized via TCA because not enough NAD+ → converted to fat → fatty liver
Isocitrate dehydrogenase and cancer: location, mutation, and disease
location = mitochondria/cytoplasm
mutation = dominant
disease = glioma, acute myeloid leukemia
Succinate dehydrogenase and cancer: location, mutation, and disease
location = mitochondria
mutation = dominant
disease = several
Fumarase and cancer: location, mutation, and disease
location = mitochondria
mutation = dominant
disease = renal cell cancer
What are the allosteric inhibitors of pyruvate dehydrogenase?
ATP
Acetyl-CoA
NADH
What are the allosteric activators of pyruvate dehydrogenase?
AMP
CoA
NAD+
What are the covalent activators of pyruvate dehydrogenase?
activation by dephosphorylation
What are the covalent inhibitors of pyruvate dehydrogenase?
phosphorylation of E1 (pyruvate dehydrogenase)
Write out the equation for complete oxidation (i.e. via TCA/OxPhos) of one glucose molecule.
glucose + 32 Pi + 32 ADP + 32 H+ + 6 O2 → 6 H2O + 32 ATP + 6 CO2
