The TCA cycle Flashcards
Overall purpose of TCA cycle
8 step reaction.
Oxididize Acetyl CoA into 2 molecules of Co2, while conserving eenrgy in reduced compounds.
Cycle oxidizes Acetyl coA produced from any sources
Overall reaction of the TCA cycle
Acetyl-CoA + 3NAD+ + 1FAD+ + 1ADP + Pi + 2H2O -> 2CO2 + 3 NADH + 1FADH2 + 1 ATP + CoA
Is Malate to Oxaloacetate reduction or oxidation?
Oxidation
Is NAD+ to NADH+ oxdiation or reduction?
Reudction
Enzymes that catalyze redox reactions are called
oxidoreductases or dehydrogenases
how many redox reactions are there in the TCA cycle
4.
What compounds are produced from the TCA cycle, per pyruvate Acetyl CoA
3 NADH, 1 FADH2 , 2 Co2
How does the structure of citrate syntehase help with the condensation of OAA with acetyl CoA
Citrate synthease exists as a homono dimer. Controlled by induced fit. OAA binds first -> conformational change that generates Acetyl CoA binding
How does the Aconitaste work
Eliminate water (forom the OAA), than add water
OH and H groups switch
Dehyadration, followed by hydatioj
Why does the OH and H group need to change positons?
Position of OH group in citrate is not conducvie to oxidative decarboxylation.
The decarboxylation enzyme needs OH at a specific position in the subtrate
What is the whole process in the TCA cycle
Oxdiative DEcarboxylation
How does aconitase work?
H is removed, OH removed.
Enzyme doesn’t move, substrate rotates so enzyme can deposit the H back
Which carbon (from OAA or Acetyl CoA) is removed for the oxdiative decarboxylation reactions?
From OAA. carbon from Acetyl CoA is preserved
Which enzyme has a similar complex to PDH
alpha-ketoglutarate dehydrogenase with the same cofactors
If there was a label from Acetyl CoA, after the action of alpha-ketoglutarate dehydrogenase, where would the label be?
be in succinyl coA
Pyruvate dehydrogenase and alpha ketoglutarate dehydrogenase is likely similar due to
evolution in gene duplication
How does the succinyl CoA synthase work? thermodynamically? this step.
Cleavage of the thioester group of the succinyl CoA is coupled with the phosphorylation of nucleoside diphosphate.
This is an example of substrate level phosphorylation.
Which enzyme from the TCA cycle is involved in the electron transport chain?
Succinate dehydrogenase is not located in the mitochondrial matrix, but is embeeded in the inner mitochondrial membrane. It is part of the electron transport chain.
Why is the hydrogen acceptor FAD at the succinate dehydrogenase step>?
Because the free energy change isn’t enoguh to reduce NAD+
What does blocking a step in the TCA cycle do
Leads to accumulation of intermediates that are usually present at very low concentrations
Effect of exogenous Fluroacetate, targets which enzyme
Aconitase
Effect of exogenous Arsenite/mercury
blocks alpha ketoglutarate and PDH
Effect of exogenous malonate
effects succinate dehydrogenase
What are the irreversible steps in TCA cycle/regulatory steps
Citrate synthase, isocitrate dehydrogenase and alpha-ketoglutarate dehydrogenase multi enzyme complex
How is citrate synthase regulated? Any exceptions?
controlled by subrtate and product concentrations.
In bacteria: citrate synthase is controlled by ATP (allosteric inhibitor)
(+) Acetyl CoA
(-) Citrate
Before the TCA cycle, what is regulated? Why do we need other control points for other enzymes?
Before the TCA cycle, the pyruvate dehydrogenase complex is a crucial site of control, which modulates the conversion of glucose-derived pyruvate into acetyl coA.
However, pyruvate isnt the only source of acetyl coA -> so the cycle itself also needs to be precisely controlled to meet an aminal’s need for ATP.
=> hence, the control points of isocitrate dehydrognease and alpha ketoglutarate dehydrogenase
What are regulators of isocitrate dehydrogenase
(+) ADP (signals need for more energy)
(-) NADH (presence of high transfer potential electrons and ultimate end product)
(-) ATP (ultimate end product)
What are regulators of alpha ketoglutarate dehydrogenase
(-) NADH (presence of high-transfer potential electrons and ultimate end product
(-) ATP (ultimate end product)
(-) Succinyl CoA (product of the reaction)
How is the TCA cycle regulated differently between the liver and in the the muscles?
In the liver: TCA operates at a constant rate with “fine tuning: because it needs to provide intermediates for other processes
In the muscles: rate of TCA can change 100 fold during exercise
TCA and glycolysis coordination. What happens when you inhibit isocitrate dehydrogenase
- INhibition of isocitrate dehydrogenase
- Build up of citrate
- Citrate accumulation signals PFK and F-1,6-BPase
- Inhbiition of isocitrate dehydrogenase inhibits glycolysis and stimultes gluconeogeneesis
How is citric acid made in real life? What bacteria?
Aspergillus niger
How to increase citric acid production in Aspergillus niger?
- Make more acetyl CoA, OAA
- Produce proteins with lower Km -> higher affinity
- Deactivation of aconitase and/or isocitrate dehydrogenase.
- Look for strains of Aspergillus that have citrate insensitive PFK
- PFK inhibition by citrate can be avoided by buildiing up other positve effectors.
What is a catabolic reaction?
- Degradation, release energy
What is an anabolic reaction?
syntehsize, make precursors
Is TCA catabolic or anabolic?
TCA is both (Amphibolic)
Its not just about making energy, it also biosyntehsizes, producing intermediates for other processes
What are anaplerotic reactions?
Replenishing reactions such as pyruvate carboxylase (Pyr -> Oxa)
What are cataplerotic reactions?
reactions that drain the TCA cycle
such as gluconeogenesis (take away TCA cycle)
Fatty acid biosysntheiss, amino acid biosynthesis
Examples of anaplerotic reactions that replenish the cycle
- Replensihment of OAA (from pyruvate carboxylase)
- Replenishment of succinyl CoA (from specific fatty acids)
- Replenishment of OAA and alpha ketoglutarate with some amino acds
How is OAA replensished?
If you need glucose -> OAA will be diverted into gluconeogensis and the TCA cycle will operate at a reduced rate
An anaplerotic reaction will occur:
Pyruvate carboxylase will make more OAA. this reaction is used in gluconeogenesis as well. dependent on Acetyl coA
Acetyl CoA presents a feedforward activation. Its accumulation promotes more OAA to be made, and utilizatioon trhoguh TCA.
is cancer a metabolic disease?
yes
How does Cancer and the TCA relate?
Mutant in isocitrate dyhydrogenase leads to unrestrained growth.
Other defects in the enzymes contribute to use of aerobic glycolysis by canceer cells.
-> try to force cancer cells to use oxidative phosphorylation
What is a variation of the TCA cycle?
Glyoxylate cycle
Why do seeds store energy
cuz they cant do photosynthesis, so they cannot fix carbon
Purpose of glycoxylate cycle in plants and bacteria
to syntehsize carbohydrates from fats.
The glyoxylate cycle is prominent in oil-rich seeds.
MIcroorganisms use acetyl coA as carbon source when glucose is not available
to allow conversion of Acetyl CoA to succinate for the syntehsis of other carbohydrates
Can humans turn fat into glucose
No
In plants, how is fat turned into glucsoe, what cycles do they utilize
the TCA cycle and glyoxylate cycle
How many acetyl coA is used in glyoxylate
2
How does the glyoxylate cycle make glucose from fat
it bypasses the 2 decarboxylation steps, to gain succinate, whereas in the TCA cycle, 2 Co2 is gaine
What are the enzymes unique to the glyoxylate cycle?
Isocitrate lyase and malate synthase
Which enzyme goes from isocitrate -> glyoxylate and succinate
Isocitrate lyase
Where does glyoxylate take place in the cell
Takes place in glyoxysomes, found in specialized peroxisomes in plants. Right next to the mitochondria. Glyoxysomes are found right next to lipid bodies in seed
