The TCA Cycle Flashcards
a. Define the central role of acetyl CoA in metabolism
- Acetyl CoA has many different roles and pathways that it goes to
- TCA, ketone bodies, sterols and fatty acids
- Most catabolic pathways oxidize fuel to the 2-carbon acetyl portion of acetyl coA
- Pathways “converge” at the acetyl CoA molecule
b. Define the function and the goal of the TCA cycle
- TCA cycle takes acetyl CoA from glycolysis and uses it to make energy compounds (NADH, FADH2, and GTP)
- Those molecules will enter the ETC to create ATP
- Gives off 2 CO2 molecules that are breathed out by the lungs
- Hub of anaerobic metabolism responsible for the oxidation of acetyl CoA to CO2 and H2O
b. Relate the outcome of the TCA cycle in terms of molecules of ATP and GTP produced. Include an accounting of ATP formed per NADH and FADH2.
- TCA gives you 3 NADH molecules, 1 FADH2 molecule, and 1 GTP molecule per cycle
- These molecules go into the ETC in mitochondria and produce ATP by oxidative phosphorylation
- ETC: NET result is (32.5= 7.5) + (11.5=1.5) → 1GTP + 9 ATP per cycle of TCA (10 high energy phosphate molecules)
c. Identify the cofactors that are essential for TCA function.
- TCA requires TPP, FAD/FMN, NADH, coenzyme A, lipoate, and minerals: iron, magnesium, sulfur, and phosphorus
- Increase energy metabolism → increase vitamins B1, B2, B3, B5, lipoic acid, and minerals
e. Relate substrate-level phosphorylation using the formation of GTP during the reaction of succinyl CoA to succinate as an example.
- Substrate level phosphorylation forms GTP from GDP + Pi and releases CoASH
- Formation of a high energy triphosphate compound without the use of O2
f. Relate the term energetically coupled reaction, and relate why it is important to have endothermic reactions coupled to exothermic reactions in the TCA cycle.
- Two reactions at once (chemical coupling)
- Exothermic rxn drives endothermic rxn (energetic coupling)
g. Identify the five molecules of the TCA cycle that lead to other pathways (i.e. efflux reactions).
- TCA requires TPP, FAD/FMN, NADH, coenzyme A, lipoate, and minerals: iron, magnesium, sulfur, and phosphorus
- Increase energy metabolism → increase vitamins B1, B2, B3, B5, lipoic acid, and minerals
h.Define the term “anaplerotic reaction” in terms of the TCA cycle and relate why these reactions are vital for the TCA cycle to function.
TCA intermediates are depleted by other pathways
anaplerotic (i.e., filling) reactions provide TCA intermediates for the cycle
Most important is pyruvate + CO2 to OAA (by pyruvate carboxylase)
Also have amino acid pathways and odd chain fatty acid oxidation intermediates
Key, as always, is balance
Pyruvate normally enters TCA via conversion to Acetyl CoA by pyruvate dehydrogenase
However, due to malate accumulation, OAA level can be low…OR…
If acetyl CoA levels are high, PDH is turned off
Pyruvate can be converted directly to OAA, which replenishes the pool and reacts with the abundant acetyl CoA to drive the cycle = anaplerotic rxn.
i.Identify the various mechanisms used to regulating the enzymes of the TCA cycle.
● Rate-limiting enzymes
○ Allosteric activators and inhibitors
○ Example: NADH is a strong allosteric inhibitor because if there is NADH then we don’t need to make more energy
○ Causes an accumulation of precursors that go off to other pathways
● Feedback inhibition
○ When the product of a reaction builds up and goes back in the reaction chain to inhibit an earlier step resulting in that product not being made anymore
● Irreversible reactions
● Committed steps
○ Enzymes that must generate a constant pool of product
● Compartmentation
● Hormone regulation
● Tissue-dependent controls
j .Identify the function of pyruvate dehydrogenase, and define its function in terms of regulating the flux of pyruvate to acetyl CoA, and therefore regulating the entry of acetyl CoA into the TCA cycle
- Pyruvate dehydrogenase is when PDH get phosphorylated and becomes inactive (uses up an ATP)
- Covalent modification
- During fasting conditions glucagon is high and favors the phosphorylated PDH
- Use pyruvate for glucose synthesis instead
- Regulated by ATP, NADH, acetyl coA, and ADP
k. Identify the regulation of pyruvate dehydrogenase by allosteric modulation and reversible covalent phosphorylation, including the molecules/enzymes involved in these regulatory mechanisms.
● Oxaloacetate → citrate has a large -deltaG
● Reaction will proceed if given acetyl coA
● Inhibited by the product citrate
● Allosteric control of PDH:
○ Stimulate: Py, NAD+, CoA
○ Inhibit: NADH and acetyl coA
○ Signal metabolic state of the cell
L. Identify the two key allosteric modulators that regulate the TCA cycle.
Allosterically activated by ADP and Ca2+ and inhibited by NADH
what product is made by glycolysis that signifies the end of that pathway?
pyruvate
what is one of the fates of pyruvate? What happens if the cell doesn’t have mitochondria, what happens to the pyruvate? What cofactor must be used? So as a result, is pyruvate more oxidized or reduced, is lactate more oxidized or reduced? Why does the cell use NADH to reduce lactate? Why is this important overall?
it is converted to Acetyl-Coa and used in the mitochondria; it turns into lactate and the cell exports it, *lactate produced by lactate dehydrogenase, used with NADH; pyruvate is more oxidized, lactate is more reduced; The cell uses NADH so that it can provide the energy to perform the reaction; it controls how active glycolysis is active overall
what happens if cell has enough mitochondria and not enough oxygen can supply the muscle?
pyruvate builds up, muscle reduces it to lactate and it gets sent out because since mitochondria is backed up, glycolysis is main source of ATP and this needs to be kept running, NAD+ needs to be readily available and pyruvate needs to be removed
what is muscle soreness a result from?
lactate acid in muscle because muscles are not in shape, lactate is made from excessive pyruvate stores and so being in shape allows for more efficient use of pyruvate reducing build up of lactate
what are the cofactors that the TCA cycle requires? For boosting energy?
TPP, FAD/FMN, NADH, coenzyme A, lipoate and the minerals iron, magnesium, sulfur and phosphorus; Increase your dietary intake of vitamins B1, B2, B3, B5, lipoic acid and the above minerals.
succinate dehydrogenase is a member of the electron transport chain AS WELL AS the _____?
the TCA cycle
what can we note about FADH2?
the FADH2 produced is located inside succinate dehydrogenase, so the electrons pass directly into the ETC. FADH2 is not a soluble cofactor and cannot diffuse on its own.
what are three reactions of the TCA cycle that have large negative ΔGo’ values?
formation of citrate
formation of αKG
formation of succinyl CoA
what two reactions have positive ΔGo’ values, and therefore favor the accumulation of subtrate?
Citrate and Malate
Malate is a key crossover metabolite for this potential pathway?
gluconeogenesis, because of this, OAA levels are often low and control Acetyl CoA entry into the cycle
citrate is a key crossover metabolite for this pathway?
fatty acid synthesis pathway.
the efflux of intermediates to the TCA cycle can help with these five pathways, helping to achieve balance.
- amino acid synthesis
- gluconeogenesis
- fatty acid synthesis
- amino acid synthesis/NT for brain
- heme synthesis
what are anaplerotic reactions for the TCA cycle?
this means that TCA intermediates are depleted by other pathways
Most important is pyruvate + CO2 to OAA (by pyruvate carboxylase) because if you have a lot of acetyl CoA you need for OAA and so pyruvate can be directly converted to OAA
what is an important anaplerotic reaction in the TCA cycle?
Pyruvate can be converted directly to OAA, which replenishes the pool and reacts with the abundant acetyl CoA to drive the cycle with CO2 and ATP
what are the two key signals that control the TCA cycle?
ATP / ADP ratio (energy charge) and the NADH / NAD+ ratio (the redox level).
what is the goal of the TCA cycle?
to transfer electrons to NAD+ and the production of ATP following electron transfer by NADH.
if the cell doesn’t need the TCA cycle, the citrate levels are high why?
positive endergonic reactions cause it to pool and negative feedback taking place and therefor controls Acetyl CoA from moving forward
what is the major regulator of the TCA cycle?
NADH, not FADH2 because these immediately go into the ETC so no buildup here
what is negative allosteric modulation in metabolism?
slow down enzyme and a few substrates pass but if removed than inhibition is gone and more product is formed
where does Acetyl CoA come from?
fats and pyruvate among other sources
people with energy metabolism have problems with this enzyme, found in the TCA cycle?
pyruvate dehydrogenase (PDH)
where does the TCA cycle take place again?
inside the mitochondrial matrix
what happens if the TCA cycle is down regulated and pyruvate accumulates?
the cell will convert it to lactate and export the lactate to keep pyruvate from building up.
Cells that don’t have mitochondria must convert pyruvate to lactate…no mito means no TCA cycle
what are the allosteric control modulators for pyruvate dehydrogenase?
Allosteric control of PDH:
Py, NAD+, CoA stimulate, if you have the buildup of Py, then this is converted to lactate to prevent build up
NADH, acetyl CoA inhibit
Signal metabolic state of the cell
what is the effect of fasting on Pyruvate dehydrogenase (PD)?
glucagon is stimulated and signals liver to shutdown PD, PHH kinase becomes active and so Phosphorylation of PDH by PDH kinase in response to glucagon inactivates the PDH.
Removal of the phosphate on PDH by the PDH phosphatase in response to insulin signaling activates PDH and allows it to operate.
what is the effect of ADP on PDH kinase? Ca?
negative allosteric modulator for PDH kinase if ADP levels are high to get more pyruvate to acetyl CoA, therefore ADP will tell the PDH kinase not to inactivate PDH
the PDH phosphatase will be stimulated by cell Ca2+. When Ca2+ levels rise, this is a signal for growth or movement or activity, so the cell will need energy, so PDH needs to be active. Therefore Ca2+ tells the PDH phosphatase to dephosphorylate any PDH to activate it to increase TCA cycle activity overall.
describe mitochondria state for the following:
red blood cells
Skeletal muscles
cardiac/slow twitch muscles
brain
Red Blood Cells – no mitochondria, no TCA activity
Skeletal Muscle: Fast Twitch – less mitochondria, some TCA activity
Cardiac / Slow twitch Muscle – Lots of mitochondria and TCA activity
Brain – Lots of mitochondria and TCA activity
solubility of NADH vs FADH2?
NADH is very soluble and FADH2 is hydrophobic and protein must be used to obtain electrons
what is the goal of the TCA cycle?
to conserve the energy of acetyl CoA(2 carbon molecules can yield 25ish ATP molecules) oxidation in the form of electron transfer from a series of carbon compounds to form NADH and FADH2 (the reduced form of NAD+ and FAD), so that this energy can be used to make ATP.
Estimated that about 90% of the energy produced by the TCA cycle is conserved
What happens to the reduced coenzymes NADH and FADH2?
reoxidized by the electron transport chain in mitochondria, which drives the production of ATP by oxidative phosphorylation.
what is the outcome of the TCA cycle?
Two carbons enter (acetyl group) the cycle and two carbons are released (CO2) during the cycle: no net synthesis occurs (no increase in total carbon content).
what is The net yield of energy-containing compounds for each cycle
3 NADH, 1 FADH2, 1 GTP
how much ATP is produced per NADH and FADH2
2.5 ATP are produced by the oxidation of each NADH
1.5 ATP are produced by the oxidation of each FADH2
add in the one GTP produced
What are the types of reactions carried out by the TCA cycle?
Condensations, isomerizations, oxidative decarboxylations, dehydrogenations, hydrations trough specific enzymes and cofactors
what are condensation reactions? isomerizations? oxidative decarboxylations? dehydrogenations? hydrations?
bringing together of molecules; the rearrangement of molecules; removal of the carboxyl group from a molecule and giving off of electrons; hydrogens removed and electrons (hydride) which gets picked up by NAD; production of water
