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BIOCH 310 > Citric acid cycle > Flashcards

Citric acid cycle Flashcards

1
Q

how many energy capture steps are there in the CAC?

A

5

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2
Q

What classifies a reaction as aerobic?

A

O2 doesn’t have to be a part of the pathway but must be needed to drive the pathway

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3
Q

what classifies a step as an energy capture step?

A

if a high energy molecule is made and exits the pathway to be used elsewhere

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4
Q

how many CO2 are generated from the CAC? where?

A

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

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5
Q

what are the 3 irreversible steps in the CAC?

A

1) synthesis of citrate (citrate synthase)

2) synthesis of alpha-ketoglutarate (isocitrate dehydrogenase)

3) synthesis of succinyl-coA (alpha-ketoglutarate dehydrogenase)

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6
Q

what 3 classes of molecules can give us acetyl-coA?

A

Carbs
fatty acids
amino acids

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7
Q

how does citrate synthase join acetyl coA to citrate? what bond is used to produce the energy needed to form this new bond?

A

uses water to hydrolyze thioester bond and use the energy to form citrate

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8
Q

what makes the citrate synthase rxn exergonic?

A

hydrolysis of thioester
-water cleaves coA

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9
Q

why does citrate have be converted to isocitrate? why is the water in this reaction not counted to the net water use?

A

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

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10
Q

why does citrate typically not build up in the mitochondrial matrix?

A

if the CAC slows down, citrate is taken to the cytosol and converted into FA

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11
Q

how does isocitrate get converted into α-ketoglutarate?

A

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

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12
Q

what the isocitrate intermediate has a CO2 removed, where is this CO2 group located?

A

2C away from the carbonyl group

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13
Q

why is Mg2+ essential to convert isocitrate to α-ketoglutarate?

A

Mg+ pulls electron density away from the carbonyl group to aid in decarboxylation

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14
Q

why are there 2 forms of isocitrate dehydrogenase? what are these 2 forms?

A

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

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15
Q

what is an enzyme that can produce NADPH? (it has 2 forms)

A

isocitrate dehydrogenase

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16
Q

explain the structure of an α-keto acid:

A

contains a keto group and carboxylic acid group attached to the same carbon

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17
Q

what 3 major things occur when α-ketoglutarate is converted to succinyl-coA? where else is this seen?

A

1) oxidation
2) decarboxylation
3) generation of high energy thioester

seen in pyruvate dehydrogenase

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18
Q

how is the α-kotoglutarate dehydrogenase complex regulated? how does this differ from the pyruvate dehydrogenase complex?

A

regulated only through allostery, therefore it is not as tightly regulated
-it is not regulated through phosphorylation / dephosphorylation unlike PDHC

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19
Q

how do arsenic compounds affect the pyruvate dehydrogenase complex and the α-ketoglutarate dehydrogenase?

A

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

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20
Q

what type of bond is broken and what bond is formed when converting succinyl-coA to succinate?

A

breaking thioester and forming phosphoanhydride in the form of GTP through substrate level phosphorylation

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21
Q

what is a synthetase?

A

an enzyme that joins 2 molecules with the participation of an ATP or NTP
-look at forward and reverse

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22
Q

why is the conversion of succinyl-coA to succinate considered a substrate level phosphorylation? what enzyme catalyzes this rxn?

A

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

23
Q

what 3 steps are involved in the succinyl-coA Synthetase rxn (production of GTP)?

A

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

24
Q

when molecule breaks the mixed anhydride (succinyl-phosphate) which forms succinate and another high energy intermediate?

A

Enzyme with a His group

25
Q

what molecule carries the phosphate group that is transferred to GDP to form GTP?

A

phosphoamide, which forms a phosphoanhydride bond in GTP

26
Q

how many high energy bonds are formed in the conversion of succinyl-coA to succinate? what are they

A

4
-thioester
-mixed anhydride
-phosphoamide
-phospho anhydride

27
Q

what 2 reactions use water in the CAC?

A

1) citrate synthesis (hydrolysis of thioester)

2) hydrolysis to convert fumarate to malate

28
Q

in the CAC, what is the overall goal of the last 3 rxn’s?

A

convert the CH2 to a C=O in OAA

29
Q

how is FAD typically involved in reactions that have alkanes?

A

they typically oxidize alkanes to alkenes

30
Q

how is NAD typically involved reactions that have OH?

A

oxidized to carbonyl

31
Q

what are the 3 alpha-keto acids in the CAC?

A

pyruvate, OAA and alpha-ketoglutarate

32
Q

what are the high energy intermediates of the CAC?

A

3 NADH
1FADH
1GTP

PER Acetyl-coA
doubled for

33
Q

why can mammals not convert FA to glucose?

A

because they are broken down into Acetyl-coA

34
Q

what carbons in FA are broken down into Acetyl-coA? how doe s this affect FA metabolism?

A

every carbon except the last 3C in an uneven chain

the last 3C on a FA chain can be used to make glucose

35
Q

when Acetyl-CoA comes into the CAC, how many C are free to make extra molecules?

A

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

36
Q

what conditions must be met for TCA intermediates to undergo gluconeogenesis once they enter the CAC?

A

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

37
Q

what are catabolic and anabolic processes of the CAC?

A

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

38
Q

what is the difference between catapleurotic vs anaplerotic?

A

-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

39
Q

what is the most important anaplerotic rxn in mammals? what cofactor is needed? what is the most important allosteric activator?

A

pyruvate carboxylase to regenerate OAA

-biotin is cofact
-Acetyl-coA

40
Q
A
40
Q

what are all the reasons why Acetyl-coA is the most important activator of the pyruvate carboxylase reaction?

A

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

41
Q

what is the purpose of transaminases? what is a common example of this?

A

take amino group from AA and transfer to an alpha-keto acid

transfer of Pyruvate and Glutamate to α-ketoglutarate alanine

42
Q

what is pyruvates corresponding amino acid following a transamination?

A

alanine

43
Q

what is what is α-ketoglutarate corresponding amino acid following a transamination?

A

Glutamate

44
Q

what is OAA corresponding amino acid in a transamination rxn?

A

Aspartate

45
Q

when we have large amounts of FA, how does this affect Acetyl-coA, PDHC and pyruvate carboxylase?

A

high levels of FA will breakdown to form Acetyl-coA

Acetyl coA will:
1) inhibit PDHC
2) activate Pyruvate carboxylase

46
Q

during starvation, what is acetyl coA converted to? why does this occu?

A

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

47
Q

during exercise, where is pyruvate coming from? where does OAA go and why?

A

Glucose (we are not starving)
-OAA goes into the CAC to make energy

48
Q

during starvation, where does pyruvate come from?

A

AA and lactate

49
Q

True or False: the activity of the CAC controls the activity of the ETC

A

FALSE

The energy of the ETC controls the energy of the CAC

50
Q

what are the 2 most important factors that regulate the CAC? what are the 2 other factors?

A

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

51
Q

what are 2 reasons why ADP doesn’t typically build up in the cytosol?

A

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

52
Q

how does ADP activate the CAC?

A

1) affects activity of ATP synthase

2) allosteric activator of Isocitrate dehydrogenase

BIOCH 310 (11 decks)

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