Citric acid cycle Flashcards
how many energy capture steps are there in the CAC?
5
What classifies a reaction as aerobic?
O2 doesn’t have to be a part of the pathway but must be needed to drive the pathway
what classifies a step as an energy capture step?
if a high energy molecule is made and exits the pathway to be used elsewhere
how many CO2 are generated from the CAC? where?
6 due to the 6C contained in glucose
1) conversion of pyruvate to acetyl-coA
2) conversion of isocitrate to alpha-ketoglutarate
3) conversion of alpha-ketoglutarate to succinyl-coA
what are the 3 irreversible steps in the CAC?
1) synthesis of citrate (citrate synthase)
2) synthesis of alpha-ketoglutarate (isocitrate dehydrogenase)
3) synthesis of succinyl-coA (alpha-ketoglutarate dehydrogenase)
what 3 classes of molecules can give us acetyl-coA?
Carbs
fatty acids
amino acids
how does citrate synthase join acetyl coA to citrate? what bond is used to produce the energy needed to form this new bond?
uses water to hydrolyze thioester bond and use the energy to form citrate
what makes the citrate synthase rxn exergonic?
hydrolysis of thioester
-water cleaves coA
why does citrate have be converted to isocitrate? why is the water in this reaction not counted to the net water use?
citrate is a tertiary alcohol which makes braking the C-C bond more difficult, conversion to isocitrate makes it a secondary alcohol and breaking the
bonds is easier
-water is removed and added back in
why does citrate typically not build up in the mitochondrial matrix?
if the CAC slows down, citrate is taken to the cytosol and converted into FA
how does isocitrate get converted into α-ketoglutarate?
oxidative decarboxylation
1) isocitrate is oxidized to form an intermediate
2) the intermediate has a CO2 removed (first release of CO2)
- release of CO2 associated with H+ uptake
what the isocitrate intermediate has a CO2 removed, where is this CO2 group located?
2C away from the carbonyl group
why is Mg2+ essential to convert isocitrate to α-ketoglutarate?
Mg+ pulls electron density away from the carbonyl group to aid in decarboxylation
why are there 2 forms of isocitrate dehydrogenase? what are these 2 forms?
NAD+-dependent enzyme in the matrix (CAC)
-needed for the ETC
NADP+-dependent enzyme in the cytosol
-electrons in NADPH are used in synthesis due to reducing power
what is an enzyme that can produce NADPH? (it has 2 forms)
isocitrate dehydrogenase
explain the structure of an α-keto acid:
contains a keto group and carboxylic acid group attached to the same carbon
what 3 major things occur when α-ketoglutarate is converted to succinyl-coA? where else is this seen?
1) oxidation
2) decarboxylation
3) generation of high energy thioester
seen in pyruvate dehydrogenase
how is the α-kotoglutarate dehydrogenase complex regulated? how does this differ from the pyruvate dehydrogenase complex?
regulated only through allostery, therefore it is not as tightly regulated
-it is not regulated through phosphorylation / dephosphorylation unlike PDHC
how do arsenic compounds affect the pyruvate dehydrogenase complex and the α-ketoglutarate dehydrogenase?
arsenic compounds interact with the sulfur hydride groups on lipoamide and prevent it from being reduced to dihydrolipoamide
-binds bacteria to arsenic more tightly but still binds to lipoamide
what type of bond is broken and what bond is formed when converting succinyl-coA to succinate?
breaking thioester and forming phosphoanhydride in the form of GTP through substrate level phosphorylation
what is a synthetase?
an enzyme that joins 2 molecules with the participation of an ATP or NTP
-look at forward and reverse
why is the conversion of succinyl-coA to succinate considered a substrate level phosphorylation? what enzyme catalyzes this rxn?
GDP is needed in order for the reaction to occur which gets regenerated using SLP to remove a phosphate group from GTP and add it to ADP
- NDK catalyzes this rxn
what 3 steps are involved in the succinyl-coA Synthetase rxn (production of GTP)?
1) formation of succinyl phosphate which is high energy acyl phosphate
-mixed anhydride
2) formation of phosphoryl-His (high energy intermediate)
3) Phosphoryl transfer to GDP forming GTP
when molecule breaks the mixed anhydride (succinyl-phosphate) which forms succinate and another high energy intermediate?
Enzyme with a His group
what molecule carries the phosphate group that is transferred to GDP to form GTP?
phosphoamide, which forms a phosphoanhydride bond in GTP
how many high energy bonds are formed in the conversion of succinyl-coA to succinate? what are they
4
-thioester
-mixed anhydride
-phosphoamide
-phospho anhydride
what 2 reactions use water in the CAC?
1) citrate synthesis (hydrolysis of thioester)
2) hydrolysis to convert fumarate to malate
in the CAC, what is the overall goal of the last 3 rxn’s?
convert the CH2 to a C=O in OAA
how is FAD typically involved in reactions that have alkanes?
they typically oxidize alkanes to alkenes
how is NAD typically involved reactions that have OH?
oxidized to carbonyl
what are the 3 alpha-keto acids in the CAC?
pyruvate, OAA and alpha-ketoglutarate
what are the high energy intermediates of the CAC?
3 NADH
1FADH
1GTP
PER Acetyl-coA
doubled for
why can mammals not convert FA to glucose?
because they are broken down into Acetyl-coA
what carbons in FA are broken down into Acetyl-coA? how doe s this affect FA metabolism?
every carbon except the last 3C in an uneven chain
the last 3C on a FA chain can be used to make glucose
when Acetyl-CoA comes into the CAC, how many C are free to make extra molecules?
none
-by the time the cycle reaches succinyl-CoA, both of the carbons from acetyl-CoA have been lost as CO₂, leaving no carbons from acetyl-CoA that can be used to synthesize glucose through gluconeogenesis
what conditions must be met for TCA intermediates to undergo gluconeogenesis once they enter the CAC?
Intermediates after (step 3) α-ketoglutarate (such as succinate, fumarate, malate, and oxaloacetate and Glutarate) have at least 4C that can be used to regenerate oxaloacetate
-there is a formation of a brand new OAA
-only one decarboxylation following this
-OAA is a key intermediate in gluconeogenesis, allowing them to contribute to glucose synthesis
what are catabolic and anabolic processes of the CAC?
catabolic: oxidative catabolism of carbs, FA and amino acids
anabolic: provision of precursors for aa synthesis, purine and pyrimidine biosynthesis, gluconeogenesis, FA and sterol synthesis and heme biosynthesis
what is the difference between catapleurotic vs anaplerotic?
-Anaplerotic reactions are those that refill the TCA cycle with intermediates, ensuring that the cycle can continue to function efficiently
-Cataplerotic reactions, on the other hand, siphon off intermediates for biosynthetic needs
what is the most important anaplerotic rxn in mammals? what cofactor is needed? what is the most important allosteric activator?
pyruvate carboxylase to regenerate OAA
-biotin is cofact
-Acetyl-coA
what are all the reasons why Acetyl-coA is the most important activator of the pyruvate carboxylase reaction?
1) regulates CAC- OAA is needed for the CAC and acetyl-coA will signal to replenish it so citrate can be formed
2) High levels of Acetyl-coA signal the body that fat is being broken down as a fuel source, the body prefers to use glucose so high levels of Acetyl coA will stimulate gluconeogenesis and the conversion to OAA
3) inhibition of PDHC- reduces Acetyl-coA production and shifting pyruvate formation to OAA
what is the purpose of transaminases? what is a common example of this?
take amino group from AA and transfer to an alpha-keto acid
transfer of Pyruvate and Glutamate to α-ketoglutarate alanine
what is pyruvates corresponding amino acid following a transamination?
alanine
what is what is α-ketoglutarate corresponding amino acid following a transamination?
Glutamate
what is OAA corresponding amino acid in a transamination rxn?
Aspartate
when we have large amounts of FA, how does this affect Acetyl-coA, PDHC and pyruvate carboxylase?
high levels of FA will breakdown to form Acetyl-coA
Acetyl coA will:
1) inhibit PDHC
2) activate Pyruvate carboxylase
during starvation, what is acetyl coA converted to? why does this occu?
Acetyl coA is converted into ketone bodies
-during starvation, gluconeogenesis is stimulated by the oxidation of fat which produces Acetyl coA (inhibits PDHC and activates pyruvate carboxylase), the activation of gluconeogenesis means that the CAC is slowed down as OAA is not being used there. This causes a build up of Acetyl coA and instead of going into the CAC, it is converted into ketones
during exercise, where is pyruvate coming from? where does OAA go and why?
Glucose (we are not starving)
-OAA goes into the CAC to make energy
during starvation, where does pyruvate come from?
AA and lactate
True or False: the activity of the CAC controls the activity of the ETC
FALSE
The energy of the ETC controls the energy of the CAC
what are the 2 most important factors that regulate the CAC? what are the 2 other factors?
1) Energy state of the cell
-ATP:ADP
2) Redox state of the cell
-NADH:NAD+
3) Product inhibition
-NADH, Succinyl-coA, citrate
4) Substrate availability
-NAD+, acetyl-coA and OAA
what are 2 reasons why ADP doesn’t typically build up in the cytosol?
1) will be used in the adenylate kinase rxn to create ATP and AMP (activates AMP-dependent kinase)
2) ADP is taken into the matrix
how does ADP activate the CAC?
1) affects activity of ATP synthase
2) allosteric activator of Isocitrate dehydrogenase
