The Citric Acid Cycle Flashcards
introduction
How does TCA cycle use pyruvate (product of glycolysis)
abstracts electrons from pyruvate which is dumped to electron carriers NAD+ and FAD. Pyruvate enter as acetyl-CoA
Introduction
What happens in the first phase of TCA cycle?
- Where most energy harnessing takes place
- Fusion of acetyl unit with oxaloacetate producing citrate and tricarboxylic acid
- Net step involves isomerization
- next two steps sequentially remove two C-atoms as CO2
Introduction
What happens in the second phase of TCA cycle?
remaining 4C molecule is processed to regenerate oxaloacetate
Introduction
How many times can the TCA cycle run from a molecule of oxaloacetate?
Infinite number of times
Introduction
It is said that the TCA cycle is one of the most important metabolic pathway. What is one reason that supports this?
The TCA cycle intermediates are precursors for the biosynthesis of other products. For example;
1. some amino acids can generate oxaloacetate for gluconeogenesis via TCA cycle
2. reduction of NAD+ and FAD to NADH and FADH2
Pyruvate to Acetyl-CoA
What bond is formed when acetyl group combines with CoA
thioester bond
Pyruvate to acetyl-CoA
What important part of CoA is used to bond with acetyl group?
β-mercapto-ethylamine part which contains the thiol group
Pyruvate to Acetyl-CoA
Pyruvate Dehydrogenase Complex is a multienzyme complex involved in creating acetyl-CoA. What are the advantages of a multienzyme complex?
- distance is minimized which increases efficency and reaction rate.
- It reduces the chances for side reactions due to the distance which also minimizes interactions with other substances
- can be coordinately controlled as a single molecule can regulate 3 reactions
Pyruvate to Acetyl-CoA
There are 3 enzyme components of the multienzyme complex. Pyruvate dehydrogenase (E1), dihydrolipoyl transacetylase (E2), and?
Pyruvate Dehydrogenase Complex
dihydrolipoyl dehydrogenase (E3)
Pyruvate to Acetyl-CoA
What happens in pyruvate dehydrogenase?
Pyruvate Dehydrogenase Complex
oxidative decarboxylation of pyruvate in the presence of TPP
Pyruvate to Acetyl-CoA
Dihydrolipoyl transacetylase is the second enzyme in the complex. It requires the presence of 1?, a prosthetic group. It catalyzes the 2? of 3? to 4?. CoA is a substrate of E2 which accepts 5? from 6?.
Pyruvate Dehydrogenase Complex
- lipoamide or lipoic acid
- transfer
- acetyl group
- CoA
- acetyl group
- lipoamide
Pyruvate Dehydrogenase Complex
There are 3 domains in the multienzyme complex. Acetyltransferase domain, binding domain, and lipoyl domain. What is the significance of these domains and how are they connected?
Acetyltransferase domain is the site of catalysis. Binding domain is responsible for interaction of E2 with E1 and E3. Lipoyl domain is where the lipoic acid is covalently bound to E2. These domains are conncected by flexible polypeptide linkers.
Pyruvate Dehydrogenase Complex
This enzyme requires the covalently bound (to E3) FAD prosthetic group. Name the enzyme, the substrate involved, and what it catalyzes.
dihydrolipoyl dehydrogenase has NAD+ as its substrate. It catalyzes the regeneration of oxidized form lipoamide in E2.
Pyruvate Dehydrogenase Complex
Name the overall reaction of this complex.
Pyruvate + CoA + NAD+ → acetyl CoA + CO2 + NADH + H+
Process of TCA Cycle
this reaction is unfavorable due to formation of methane-by-product?
Direct oxidation
Process of TCA Cycle
Why are carbonyl groups essential in cell processes?
They serve as electrophilic centers readily attacked by any nucleophile
Process of TCA Cycle
There are 2 stages in the TCA cycle. Briefly discuss each one.
Stage 1: most energy is harnessed (steps 1-4)
Stage 2: regeneration of oxaloacetate (steps 5-8)
Process of TCA Cycle
Enzyme, substrate/s, and products/s of step 1?
Step 1: citrate cynthase
2C (Acetyl-CoA) + 4C (oxaloacetate) → citrate + CoA
Process of TCA Cycle
In step 1, name the intermediate formed and the mechanism the enzyme employed.
citroyl-CoA, employed ordered sequential mechanism
Process of TCA Cycle
Why is the hydrolysis of citroyl-CoA thioester bond favorable?
highly exergonic reaction
Process of TCA Cycle
What happens if acetyl-CoA will bind first instead of oxaloacetate?
Premature cleavage of acetyl unit from CoA
Process of TCA Cycle
Enzyme, substrate/s, and products/s of step 2?
Aconitase, citrate → isocitrate
Process of TCA Cycle
In step 2, what sub-steps are employed by the enzyme and what intermediate is formed?
dehydration (loss of H2O) followed by hydration (gain of H2O), cis-Aconitrate
Process of TCA Cycle
In step 2, the enzyme undergoes “moonlighting”. Briefly discuss.
Moonlighting is when some proteins can perform more than one function. In the case of aconitase, it has an iron-sulfur cluster that acts with aconitase. If iron levels are too low, aconitase functions without this cluster and instead becomes an iron regulatory protein.
Process of TCA Cycle
Enzyme, substrate/s, and products/s of step 3?
isocitrate dehydrogenase, isocitrate + NAD+ forming α-ketoglutarate expelling NADH and CO2 in the process
Process of TCA Cycle
A substrate in step 3 (oxodative decarboxylation) requires ________ ions as cofactors which act in the formation of ________ intermediate.
Mg/Mn ions, oxalosuccinate
Process of TCA Cycle
Enzyme, substrate/s, and products/s of step 4?
α-ketoglutarate dehydrogenase, α-ketoglutarate + NAD+ + CoA → succinyl-CoA + NADH + CO2
Process of TCA Cycle
The enzyme in step 4 has similar structure and mechanism with?
Pyruvate Dehydrogenase since it is also a multienzyme complex
Process of TCA Cycle
Enzyme, substrate/s, and products/s of step 5?
succinyl-CoA synthetase, Succinyl-CoA + GDP + Pi → Succinate + GTP + CoA-SH
Process of TCA Cycle
The enzyme of step 5 was found to have α- and β-subunits. What are their roles for the enzyme?
α-subunit (N-terminal): Rossman fold which is the binding site for succinyl-CoA
β-subunit: has ATP grasp where ADP binds and transformed to ATP
Process of TCA Cycle
Enzyme, substrate/s, and products/s of step 6?
succinate dehydrogenase, succinate + FAD → fumarate + FADH2
Process of TCA Cycle
What makes enzyme of step 6 special?
enzyme is also complex II of ETC which direclty links the TCA cycle to ETC
Process of TCA Cycle
Enzyme of step 6 has its downsides. Another substrate can bind with the enzyme which can be fatal since it affects both the TCA cycle and the ETC. Name this substrate and what it does.
Malonate, structurally similar to succinate. Competetive inhibition
Process of TCA Cycle
Enzyme, substrate/s, and products/s of step 7?
fumarase, fumarate → L-malate
Process of TCA Cycle
In step 7, an intermediate is formed. What is the intermediate.
Carbanion transition state
fumarate + OH- → carbanion transition state + H+ → L-malate
Process of TCA Cycle
Can the enzyme of step 7 produce D-malate?
No. The enzyme is highly specific to fumarate producing L-malate.
Process of TCA Cycle
Enzyme, substrate/s, and products/s of step 8?
L-malate dehydrogenase, L-malate + NAD+ → Oxaloacetate + NADH
