2.2.1. TCA Part II Flashcards
Total yield of TCA (Products leading to ATP)
3NADH, 1 GTP, 1 FADH
Total ATP Yield of TCA Cycle per Acetyl-CoA
10 ATP (3NADH = 7.5 ATP, 1 FADH = 1.5 ATP, 1 GTP = 1 ATP)
Where does the TCA Cycle occur in the cell?
The Mitochondrial Matrix
What are the intermediates of the TCA Cycle?
Citrate, IsoCitrate, alpha-Ketoglutarate, Succinyl CoA, Succinate, Fumarate, Malate, Oxaloacetate
(pneumonic: Citrate Is Krebs Starting Substrate For Making Oxaloacetate)
Which enzyme in the TCA cycle is embedded in the inner mitochondrial membrane?
Succinyate Dehydrogenase
(It is involved in making an FADH that interacts with the ETC directly, and FADH is not found as a cytosolic protein because its electron radicals are too unstable)
This is a key regulatory enzyme of the TCA cycle
Isocitrate Dehydrogenase
Tightly regulated via ADP (activates it) and NADH (inhibits it)
Name the cofactors of alpha-ketoglutarate dehydrogenase complex and pyruvate dehydrogenase complex (there are 5)
Thiamine Pyrophosphate (TPP)
Lipoate (or Lipoic Acid)
NAD+
FAD (needs riboflavin)
CoASH
Define the term anaplerotic and its importance to the TCA cycle
Anaplerotic = “fills up” meaning intermediates are added in from processes separate from the TCA cycle
Allows the cell to have flexibility in terms of using the TCA cycle intermediates for other purposes without endangering ATP production
Oxaloacetate is also used for…
Amino acid synthesis
Malate is also used for
Gluconeogenesis (important in the Liver)
Succinyl CoA is also used for…
Heme synthesis (important in Liver)
alpha-ketoglutarate is also used for…
Amino acid synthesis
GABA synthesis (in brain)
Citrate is also used for….
Fatty Acid Synthesis
Tell me about Pyruvate Carboxylase
(Why is it important, what is a coenzyme it uses, where is it?)
Key anaplerotic enzyme
Uses biotin
Found in Liver, Brain, and Adipose (but not muscle!)
Located in Mitochondira and is one of the irreversible enzymes from gluconeogenesis
Which enzyme(s) catalyze the addition of a CoA group onto TCA cycle intermediate(s)?
Citrate Synthase (Acetyl-CoA + OAA –> Citrate)
alpha-KG Dehydrogenase (Alpha-KG + CoA-SH –> Succinyl-CoA)
Which reactions in the TCA cyle involve the loss of a carbon from the TCA intermediate?
Decarboxylation Reactions
Isocitrate DeHydrogenase catalyzing removal of CO2 through Isocitrate –> alpha-KG
alpha-KG Dehydrogenase (alpha-KG –> Succinyl-CoA)
What reaction in the TCA cycle does not use oxidative phosphorylation to generate energy?
The reaction generating GTP (Succinyl Thiokinase’s removal of Co-A from Succinly-CoA to Succinate)
This is an example of substrate-level phosphorylation
What class of Vitamins (think Letter) are the mainstays of the TCA cycle (and metabolism in general?)
Bonus: What are some Vitamins we have seen? (probably don’t need to know the letter and number of each)
B Vitamins
B1 - Thiamine (for TPP)
B2 - Riboflavin (for FAD)
B3 - Niacin (for NAD+)
B5 - Pantothenic Acid (used to synthesize CoA)
B7 - Biotin (used in Pyruvate Carboxylase)
What is the role of the pyruvate carboxylase reaction in the TCA cycle?
Pyruvate Carboxylase adds a CO2 group to Pyruvate to form Oxaloacetate, which is carefully controlled in order to control the rate of the TCA cycle.
Pyruvate Carboxylase activity is enhanced by increased Acetyl-CoA
Glutamate is converted into what intermediate of the TCA cycle?
alpha-ketoglutarate
Aspartate can be transaminated to form what TCA intermediate?
(Asparagine can be made into Aspartate)
Oxaloacetate
Valine, Isoleucine, Methionine, and Threonine can be converted (via several steps) into what TCA cycle intermediate?
Succinyl-CoA
Phenylalanine, Tyrosine, and Aspartate can be made into which TCA cycle intermediate?
Fumarate
When gluconeogenesis is leading to the synthesis of glucose, what two TCA cycle intermediates may be removed from the cycle?
Malate or Oxaloacetate
Glucose can be used to sythesize what two amino acids through oxaloacetate?
Aspartate and Asparagine
Glucose can lead to the synthesis of which amino acids through conversion to alpha-ketoglutarate?
Glutamate, Glutamine, Proline, and Arginine
How can the body switch between amino acids? How is the TCA cycle involved?
Interconversion of amino acids occurs by forming intermediates of the TCA cycle, allowing the cycle to continue, and then pulling another intermediate out for another amino acid’s synthesis.
What are the two major factors regulating the TCA cycle?
The NAD+/NADH ratio (high NAD+ activates TCA)
ADP (allosteric regulator of Isocitrate Dehydrogenase, along with Ca2+, which “activate” the TCA cycle)
When the TCA cycle is slowed down by high ATP or NADH levels, what intermediate builds up and why?
Citrate builds up because NADH allosterically inhibits isocitrate dehydrogenase (converting isocitrate to alpha-KG), leading to a buildup of Isocitrate. However, because the aconitase reaction (citrate to isocitrate) favors the reverse reaction, excess isocitrate is converted to citrate. This citrate then also inhibits citrate synthase, which also slows the TCA Cycle.
What happens to Oxaloacetate when NADH is high? (with regards to TCA cycle intermediates, not it being extracted for Amino Acid synthesis)
OAA is converted to Malate
Which enzyme requires Biotin to form Oxaloacetate?
Pyruvate Carboxylase.
Biotin is needed for the use of CO2 gas as a substrate to be added to the pyruvate. (Recall pyruvate = 3 carbons, OAA=4)
Leigh Syndrome is caused by a deficiency in what protein(s)?
Pyruvate Carboxylase! (or Pyruvate Dehydrogenase Complex)
Why are Leigh Syndrome symptoms principally neuro-motor issues?
The brain depends on glucose metabolism for energy, so any disruption in this process will affect the brain to a more significant degree than other tissues. This is also why this condition is aka “something something necrotizing encephalomyelopathy.”
When does Leigh syndrome present in life, and how severe is it?
Leigh syndrome can be severe, or not as severe depending on its molecular cause. The more severe it is, the earlier its onset is. With very severe cases, it’ll show up immediately after birth and can cause death quickly. Other cases still show up in the pediatric age group, but survival is limited in the best of cases to the teenage years.
What condition does Niacin deficiency cause?
Pellagra
Think the 4 D’s
Diarrhea, Dermatitis, Dementia, and Death
What issues does Riboflavin deficiency cause?
Oral-buccal cavity lesions
What condition does Thiamine deficiency cause?
Beri beri
What issues does Pantothenic acid deficiency cause?
Listlessness, fatigue, and burning feet syndrome
What are the typical causes of Vitamin deficiencies?
Insufficient intake of water-soluble Vitamins (fat-soluble ones last a long time in our bodies)
Insufficient absorption in our GI tract, or increased excretion
Insufficient conversion to its coenzyme form
Reactions catalyzed by the Pyruvate Dehydrogenase Complex are analagous to what other enzyme complex?
alpha-ketoglutarate dehydrogenase complex
What does exercise do to the Pyruvate Dehydrogenase Complex, and how?
Exercise activates this complex by increasing the NAD+/NADH ratio, [Ca2+], and ADP. These changes lead to increased activity of the phosphatase, which removes a phosphate from the complex, greatly increasing its activity.
In general, how is the Pyruvate Dehydrogenase Complex’s activity altered?
Its products (Acetyl-CoA and NADH) inhibit its activity through a kinase
Its substrates (CoA-SH and NAD+) enhance its activity through a phosphatase
What is the structure of Citrate?
What is the structure of Isocitrate?
What is the structure of alpha-ketoglutarate
What is the structure of Succinyl-CoA?
What is the structure of Succinate?
What is the structure of Fumarate?
What is the structure of Malate?
What is the structure of Oxaloacetate?
At physiological conditions, the structure is de-protonated
What enzyme catalyzes the change of Oxaloacetate to Citrate?
Citrate Synthase
What enzyme catalyzes the change of Citrate to Isocitrate
Aconitase
What enzyme catalyzes the change of Isocitrate to alpha-ketoglutarate?
Isocitrate dehydrogenase
What enzyme catalyzes the change of alpha-ketoglutarate to succinyl CoA?
alpha-ketoglutarate dehydrogenase complex
What enzyme catalyzes the change of Succinyl-CoA to Succinate?
Succinyl-CoA Synthetase
(or Succinyl Thiokinase)
What enzyme catalyzes the change of Succinate to Fumarate?
Succinyl Dehydrogenase
What enzyme catalyzes the change of Fumarate to Malate?
Fumarase
What enzyme catalyzes the change of Malate to Oxaloacetate?
Malate Dehydrogenase
How much energy is conserved in the oxidation of Acetyl-CoA via the TCA cycle, and where does the non-conserved energy go?
90%, the rest of it escapes as heat.
