TCA Cycle Flashcards
The TCA cycle _____ two carbons of acetate from acetyl CoA and generates NADH and FAD2H. In anabolism, it generates key intermediates for _____, _____, and _____
Oxidizes
Gluconeogenesis
Fatty acid synthesis
Amino acid synthesis
The TCA cycle occurs in the ___ of the mitochondria. The outer membrane is permeable to most molecules. The inner membrane is very ____. This allows a proton concentration gradient to be established across the ____ ___ of the mitochondria
Matrix
Impermeable
Inner membrane
The matrix naturally has ___ proton concentration. The inter-membrane space has naturally ____ proton concentration
Low
High
The electron transport chain requires genes and proteins from both ____ and ____ DNA
Nucleus
Mitochondrial
Mitochondrial DNA is more similar to _____ DNA then nucleus DNA
Prokaryotic
Mitochondrial DNA is _____ because it is naked, and not bound to histones in a chromatin structure. It is exposed to hire concentrations of ____ ____ ____. The mitochondrial DNA polymerase has limited ability to repair DNA damage.
Hypermutatable
Reactive oxygen species
Mitochondrial DNA is dynamic. There are multiple ____ of the mitochondrial DNA to help push back from the hypermutability, especially in energetics cells like ___ cells
Copies
Muscle
Many symptoms of mitochondrial disease are ____ due to energy starvation during fetal development
Neurological
Glycolysis occurs in the ____. Pyruvate, dehydrogenase, and the TCA cycle occur in the _____.
Cytosol
Mitochondria
Pyruvate is transported to the mitochondria via the _____ ____ ____ which acts as a heterodimer of two subunits: ____ and ____
MPC is located on the ____ ____ of the mitochondria.
Mitochondrial pyruvate carrier (MPC)
MPC1 and MPC2
Inner membrane
Inherited mutations in the mitochondrial pyruvate carrier causes ____ _____
Lactic acidosis
____ ____ is the link between glycolysis and the TCA cycle. It has four subunits. E1 subunit is ____ ____, with a thiamine pyrophosphate. E2 is a _____ with Lipoate and CoA. E3 is a ____ with FAD and NAD+. Keto acid dehydrogenase and branch chain ketoacid dehydrogenase share a similar organization.
Pyruvate dehydrogenase
Pyruvate decarboxylase
Transacetylase
Dihydrolipoyl dehydrogenase
Pyruvate dehydrogenase is regulated by reversible _____. When activated the ___ ___ will proceed. When inhibited, pyruvate will be converted into ____.
Phosphorylation
TCA cycle
Lactate
Pyruvate dehydrogenase is regulated by phosphorylation and dephosphorylation of ____ residues in ____ alpha subunits
Serine
E1
Pyruvate is converted into ____ by pyruvate dehydrogenase which then bonds to coenzyme A, forming ____
Acetate
Acetyl CoA
All reactions of the TCA cycle take place in the ____ ____
Mitochondrial matrix
Overview of TCA cycle:
____ ____ is the key rate limiting enzyme in the TCA cycle
Isocitrate dehydrogenase
The reaction from acetyl-CoA to citrate is energy yielding however, the following reaction is not energetically favorable. This allows for ____ to build up and be used as an intermediate for other biosynthetic reactions. This is like wise for ____.
Citrate
Malate
First step:
The enzyme ____ ____ hydrolyzes, the Theoester bond of acetyl CoA to join acetate and oxaloacetate, forming ____. Citrate has three carboxylic acid groups, making it a tricarboxylic acid.
Citrate synthesis
Citrate
Second step:
The enzyme ____ catalyzes a two step isomerization to convert citrate to _____, which is a tricarboxylic acid
Aconitase
Isocitrate
Third step:
____ ____ catalyzes this oxidative decarboxylate, isocitrate is converted into ____. It uses NAD+ and creates____. IDH1 in the cytosol and IDH2 in the mitochondria catalyze the same reaction but use ____ instead
Isocitrate dehydrogenase (IDH3)
Alpha-ketoglutarate
NADH
NADP+
Isocitrate dehydrogenase removes an ____ group from 6 carbon Isocitrate forming the 5 carbon alphaketoglutarate. _____ is a byproduct
Carboxyl
CO2
Fourth step:
_______ _____ catalyzes the final oxidative decarboxylation, forming _______ from alpha ketoglutarate. ____ and ____ are byproducts
This product is then added to acetyl CoA similar to pyruvate dehydrogenase enzyme.
Alpha-ketoglutarate dehydrogenase
succinyl CoA
NADH
CO2
Alpha ketoglutarate dehydrogenase removes a carboxyl group from the ____ carbon alpha-ketoglutarate forming the ___ carbon succinyl CoA.
At this point ___ carbons have been released as carbon dioxide, but not the same carbons that entered as acetyl CoA
5
4
2
Review:
Look at cofactors
Fifth step:
_____ ____ cleaves the Theoester bond, linking succinate and CoA this is a strongly extra Gondek reaction and the enzyme uses the energy to catalyze substrate level phosphorylation of GDP to make GTP. The end product is ____.
Succinate thiokinase
Sixth step:
____ _____ oxidizes succinate to introduce a double carbon-carbon bond forming ____. FAD is reduced to ___. Succinate dehydrogenase is a component of the electron transport chain transferring electrons from FAD2H to _____.
Succinate dehydrogenase
Fumarate
FAD2H
Coenzyme Q
Seventh step:
_____ _____ it’s a proton and hydroxyl from water to fumarate double bond forming ____.
Fumarate hydratase
Malate
Eighth step:
____ ____ oxidizes malate’s hydroxyl to a keto group forming _____ and reducing NAD+ to NADH in the process
Malate dehydrogenase
Oxaloacetate
In the TCA cycle overall,
1 two carbon acetyl group and two waters become 2 carbon dioxides.
The net production goes on to make ___ ____
10 ATP
In the liver, in the fasted and starved states, ____ is high because of fatty acid Beta-oxidation. This prevents acetyl CoA from oxidation in the ____ ___, and drives it towards ketone body synthesis
NADH
TCA cycle
Isocitrate dehydrogenase is the rate limiting step of the TCA cycle, activity is regulated by the ratio of ____ to ____ in the mitochondria. ADP binding to one subunit changes the conformation of other subunits to alter their affinity for substrate.
ADP
ATP
The presence of ADP results in more ___ ____ enzyme activity, up regulating the TCA cycle. ADP is an _____ ____
Isocitrate dehydrogenase
Allosteric activator
_____ acts as an Allosteric activator of NAD+ dependent Isocitrate dehydrogenase (IDH3). This is a ____ ____ regulation
Citrate
Feedforward activation
Which amino acids can be generated from the TCA cycle intermediates through transamination reactions?
Aspartate and glutamate, their side chains can be transaminated, transaminases use vitamin 6 as a cofactor
____ reactions increase the capacity of the TCA cycle. Every time an intermediate leaves the cycle, the capacity decreases. ____ reactions help replenish the TCA cycle
Anaplerotic
Anaplerotic
_____ participates in fatty acid synthesis when it leaves the TCA cycle
_____ participates in amino acid synthesis and is a Neuro transmitter
____ participate in heme synthesis
_____ participates in gluconeogenesis
_____ participates in amino acids synthesis
Citrate
Alpha-ketoglutarate
Succinyl-CoA
Malate
Oxaloacetate
____ ____ is a Anaplerotic reaction that converts pyruvate to oxaloacetate which can then join acetyl CoA to form citrate
Pyruvate carboxylase
______ ____ pathway in muscles is a type of Anaplerotic reaction. When muscle cells are working, they require a lot of ATP. ____ ____ converts a AMP to inosine monophosphate (IMP). This results in an increase in blood _____.
____ _____ takes a carbon from Aspartate to form fumarate, regenerating ____.
Myoadenylate deaminase
Myoadenylate deaminase
Ammonium
Adenylsuccinate
AMP
______ ____ _____ is from inherited mutations in the gene coding the muscle specific AMPD1 isoform of AMP deaminase results in an inactive enzymes. This makes individuals ___ intolerant because the TCA Cycle can’t be replenished in response to work
Myoadenylate deaminase deficiency
Exercise
TCA cycle intermedius influence _____ Gene expression through epigenetic regulation. _____ is the substrate for histone acetyl transferences. ____ and ____ block histone and cytosine demethylases
Nuclear
Acetyl CoA
Succinate
fumarate
If there is a mutation in succinate dehydrogenase, there is a buildup of ____ which promotes the methylation of nuclear DNA leading to changes in transcriptional patterns, which can ultimately lead to ____
Succinate
Cancer
____ ____ is a tumor suppressor.
Succinate dehydrogenase
____ _____ _____ uses molecular oxygen to hydroxylate the methyl carbon from lysine. During this reaction, alpha-ketoglutarate is decarboxylated to ____. Therefore, An increase in succinate promotes the methylation of lysine rather than the demethylation
Jumanji domain demethylases (JHDM)
Succinate
2-hydroxyglutarate is an ______, meaning it interferes with the function of alpha-ketoglutarate utilizing dioxygenase enzymes, sometimes leading to cancer
Oncometabolite
Gain of function mutations in the ____ ____ causes the enzyme to run in reverse reducing alpha-ketoglutarate to 2-hydroxyglutarate
Isocitrate dehydrogenase
2-hydroxyglutarate acts as a ____ ____ for me deoxygenated, as such as the Jumanji domain lysine demethylases, causing _____ within the cell
Competitive inhibitor
Hypermethylation
Inhibition of ____ _____ and ____ ___ causes hypermethylation and changes the transcriptional program of the cell at specific genes that promote proliferation and inhibit differentiation and apoptosis. Leading to uncontrolled cell division and cancer
Lysine demethylases (KDMs)
Cytosine demethylases (TET2)
______ of proline and lysine residues in _____ is also dependent on alpha-ketoglutarate dependent dioxygenases.
Hydroxylation
Collagen
Alpha-ketoglutarate dependent dioxygenases regulate diverse processes with the cell. When mutations in ____ _____ occur, 2-hydroxylglutarate accumulates causing changes in gene expression and oxygen sensor which can contribute to cancer.
Increased ____ inhibits all of these reactions because it is the product of Isocitrate dehydrogenase
Isocitrate dehydrogenase
Succinate
Succinate dehydrogenase acts as a tumor suppressor, it’s substrate, succinate, builds up and inhibits ______ ____ ____ such as HIF prolyl hydroxylase. This stabilizes HIF and promotes a pro survival metabolism
Alpha-ketoglutarate dependent dioxygenases
____ ____ are also alpha-ketoglutarate dependent dioxygenases. In oxygen sensing, _____ is a substrate for prolyl hydroxylation, which signals its destruction in the presence of oxygen
Prolyl hydroxylases (PHDs)
Hypoxia inducible factor HIF
Many ____ ____ inhibit alpha-ketoglutarate dependent dioxygenases. Mutations in the ___ ____ enzymes cause a build up of these oncometabolites and contribute to cancer
Tricarboxylic acids
TCA cycle
Model of pyruvate dehydrogenase cofactors:
Which of the substances below is used as a substrate by lysine methyltransferase enzymes?
Formate, formaldehyde, adenosylmethionine,
Adenosylmethionine
NADH
At low substrate concentration, the presence of ADP results in more enzyme activity
ADP is an _____ ____ of Isocitrate dehydrogenase
Allosteric activator
Citrate changes the ____ of Isocitrate dehydrogenase
Vmax
Citrate is a ____ ____ of Isocitrate dehydrogenase. The Vmax increases when citrate is added
Allosteric activator
Citrate acts as an activator of Isocitrate dehydrogenase, meaning it is a _____ activation
Feedforward
Tumor suppressor
Which oncometabolite below accumulates from a gain of function mutation?
2-hydroxyglutarate
What type of enzymes are inhibited by the oncometabolite 2-hydroxyglutarate?
Dioxygenase
Lysine methyltransferase
The rate limiting step in the TCA cycle is activated by___
ADP
Alpha-ketoglutarate and Succinate
The mother carries the same mutation but at a lower frequency than the child
Elevated glycolysis to compensate for decreased mitochondrial function
There is no chance that you will pass this mutation to offspring, it is only maternally inherited
Zero
2.5 moles
Succinate
Succinate
Dinitrophenol DNP
Cytochrome C
