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BMSC 230 Metabolism > Roesler Section > Flashcards

Roesler Section Flashcards

1
Q

Where does most of the ATP come from in cellular respiration?

A

Not in glycolysis, will be in oxidative reactions instead (Citric acid cycle and electron transport chain)

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2
Q

3 stages of cellular respiration (not including glycolysis)

A

Catabolism of pyruvate to acetyl CoA
Citric acid cycle
Oxidative phosphorylation

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3
Q

Give an overview of the Pyruvate dehydrogenase complex

A

3 enzymes, that catalyze 5 biochemical reactions
requires 5 cofactors, oxidative decarboxylation
Irriversible reaction
present in mitochondria

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4
Q

What are the three enzymes in the PDH?

A

E1 - pyruvate dehydrogenase
E2- Dihydrolipoyl Transacetylase
E3 - Dihydrolipoyl Dehydrogenase

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5
Q

What is the MPC?

A

Mitochondrial Pyruvate transporter
Moves pyruvate from cytoplasm after glycolysis into the inner mitochondrial membrane

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6
Q

What do cofactors do? 5 points

A

Helper molecules
non protein
bound to an enzyme (either tightly or loosely)
required for catalysis
does not catalyze reactions

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7
Q

What are the 5 PDH cofactors?

A
  1. Thiamine Pyrophosphate (TPP)
  2. Lipolic Acid
  3. Coenzyme A
  4. FAD (flavin adenine dinucleotide) - electron carrier
    5.NAD+ (nicotinamide adenine dinucleotide) - electron carrier

*Lipolic acid is not derived from B vitamins

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8
Q

How many high energy electrons are gained in the citric acid cycle?

A

8

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9
Q

What does pyruvate release when it is converted into actetyl CoA?

A

Releases CO2

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10
Q

Where does Acetyl CoA lead into after being made from pyruvate?

A

Citric acid cycle

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11
Q

What is TPP derived from, where is it bound, what does it accept and what is it known as?

A

Derived from vitamin B1 (thiamine)
Bound to E1 of PDH
Accepts 2 carbon backbone of acetyl CoA after decarboxylation ( hydroxyethyl TPP intermediate)
Known as a transient carbon carrier

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12
Q

Where does glycolysis occur?

A

Cytosol

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13
Q

Where does the citric acid cycle occur?

A

Mitochondrial matrix

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14
Q

Why does the body use protein complexes instead of separate enzymes?

A

makes the overall process faster because if the enzymes are already associated the product does not need lots of time to find the next enzyme

From slides - local concentration of substrates around enzymes is kept high - rate of reaction is not limited by diffusion of substrates to each subunit of PDH

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15
Q

What is lipolic acid a cofactor of? What two special groups does it have and what can happen to them? What is its function? What does it accept?

A

Lipolic acid is a cofactor of the E2 subunit

Has 2 thiol groups which can be oxidized, reduced or acetylated

It carries electrons and acyl (carbon) groups

It accepts hydroxyethyl intermediates from TPP as an acetyl groups

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16
Q

What are NADH and FADH2? What is the main difference between them?

A

They are electron carriers and can exist in oxidized or reduced states
They each carry 2 electrons
NADH is a mobile carrier while FADH2 is a protein bound carrier

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17
Q

Give a 5 point summary of the PDH reaction

A

Pyruvate is converted to acetyl coa by PDH complex
PDH - 3 enxymes - 5 reactions and 5 cofactors (coenzymes / prosthetic groups
E1 - oxidative decarboxylation of pyruvate and transfer of 2 carbon unit (hydroxyethyl intermediate to E2)
E2 - transfer of acetyl group to CoA to synthesize Acetyl CoA
E3 - regenerates oxidizes lipoyl group of E2 and transfers protons and electrons first to FAD and then to NAD+ to complete the reaction cycle

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18
Q

How is the PDH regulated?

A

Allosterically- by NADH, Acetyl CoA and ATP as inhibitors
- Pyruvate and ADP as allosteric activators

Post-translational modification- by Phosphorylation/ dephosphorylation - above inhibitors activate PDH Kinase which inhibits PDH
- Above activators activate PDH phosphatase which activates the PDH
- ATP adds phosphate group to form ADP

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19
Q

Why is acetyl CoA so important for metabolic activity?

A

Acts as a metabolic shipping and receiving department for all classes of biomolecules and is a major source of metabolic energy.

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20
Q

Why does it make sense for a high-energy molecule like ATP to inhibit glycolytic reactions?

A

Because the high energy molecules (ATP) are also products meaning the reaction does not need to produce more ATP because the amount is already sufficient

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21
Q

What 3 amino acids can be phosphorylated?

A

Serine, threonine and tryosine

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22
Q

Where does the TCA cycle occur?

A

Mitochondrial matrix

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23
Q

What substrate formed in the first reaction of the TCA cycle is regenerated in the last step of the TCA cycle?

A

Oxaloacetate 4 carbon molecule

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24
Q

What is the first step of the TCA cycle that uses Acetyl CoA from the pyruvate dehydrogenase reactions?

A

C2 molecule of Acetyl CoA joins with Oxaloacetate (C4) to become Citrate (C6) via the enzyme citrate synthase

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25
Q

How many ATP are produced per cycle of the TCA cycle?

A

only 1, but many high transfer potential electrons to make wayyy more ATP in the electron transport chain

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26
Q

What are the three steps in forming Citrate using citrate synthase?

A
  1. oxaloacetate binds to citrate synthase
  2. induces a conformational change in citrate synthase
  3. generates the acetyl CoA binding site
  4. Acetyl CoA binds (duh)
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27
Q

How many carbon dioxide are lost in one cycle of the TCA cycle?

A

2 carbon dioxide are lost, turning Citrate from a 6C molecule to a 5C molecule to a 4C molecule which returns back to the 4C molecule that binds to the C2 Acetyl CoA to create the C6 used in the first place

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28
Q

How many high energy electron carriers are produced in one cycle of the TCA cycle?

A

3 NADH and 1 FADH2

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29
Q

What does citrate become and what causes the reaction in the TCA cycle?

A

Citrate is isomerized into Isocitrate via the enzyme Aconitase
Aconitase catalyzes the formation of isocitrate from citrate (isomerization), reaction favours isocitrate not citrate formation

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30
Q

What does isocitrate become and what causes the reaction in the TCA cycle?

A

Isocitrate is oxidized and decarboxylated to A-Ketoglutarate via Isocitrate dehydrogenase which catalyzes the oxidative decarboxylation of isocitrate forming a-ketoglutarate and capturing high energy electrons as NADH

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31
Q

What does A-ketoglutarate become and what causes the reaction in the TCA cycle?

A

A-ketoglutarate is oxidated and decarboxylated to succinyl CoA via the A-Ketoglutarate dehydrogenase complex which catalyzes the synthesis of succinyl CoA from a-ketoglutarate, generating NADH
- this enzyme and reaction are structurally and mechanistically similar to the pyruvate dehydrogenase complex

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32
Q

What is succinyl CoA become and what causes the reaction in the TCA cycle?

A

Succinyl CoA becomes Succinate via Succinyl CoA synthetase.
Succinyl CoA synthetase catalyzes the cleavage of thioester linkage and forms ATP

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33
Q

What does succinyl CoA synthetase do?

A
  • Cleaves the high energy thioester bond of succinyl CoA turning it to Succinate
  • energy released drives synthesis of the high energy gtp pr ATP - it is an energy conserving reaction
  • substrate level phosphorylation – direct transfer of phosphate to ADP or GDP
34
Q

What step is the main point in regulation for the TCA cycle?

A

The step where Succinyl CoA is formed by the oxidative decarboxylation of A-Ketoglutarate - when the A-Ketoglutarate complex catalyzes the synthesis of succinyl CoA from A-ketoglutarate, generating NADH

35
Q

What does succinate become and what causes the reaction?

A

Succinate is oxidized to become fumarate via succinate dehydrogenase by introducing a double bond in trans configuration, generates FADH2

36
Q

What is special abount succinate dehydrogenase?

A

Only membrane bound enzyme of the TCA cycle

37
Q

What does fumarate become and what causes the reaction?

A

Fumarate is hydrated to become malate, catalyzed by fumarase

38
Q

What does malate become and what causes the reaction?

A

Malate is oxidized by malate dehydrogenase to become oxaloacetate, regenerating the starting material of the cycle

39
Q

Why can the reaction between 2glyceraldehyde3-phosphate to 2 1,3-bisphosphoglycerate have either 3 or 5 atp produced?

A

Depends on the type of NADH shuttle used to get it from the cytoplasm to the mitochondria
-Glycerol 3-phosphate shuttle generates 3 atp
-Malate/aspartate shuttle generates 5 atp

40
Q

How is the TCA cycle regulated?, which enzymes are regulated?

A

There are two TCA cycle enzymes that are regulated and both are by allosteric mechanisms
- Isocitrate dehydrogenase - stimulated by ADP and inhibited by NADH and ATP
- aKetoglutarate dehydrogenase (catalyzes rate limiting step) - no activators - inhibited by products of its reaction- succiny CoA and NADH (and ATP)

41
Q

What happens to the TCA cycle when at rest?

A

ATP and NADH are higher, inhibiting Isocitrate dehydrogenase, don’t need to make more ATP if enough is present

42
Q

When fats are broken down what is an important product of that?

A

Acetyl CoA

43
Q

Can we make glucose from fats?

A

No, we can make fats from glucose but not the other way around, not enough carbons.

44
Q

What are replenishing reactions for intermediates of the TCA cycle called?

A

Reactions that replenish and provide intermediates for the pathway are called ANAPLEROTIC reactions

45
Q

Why is fluoroacetate poisonous?

A

Because fluoroacetate is converted to fluoroacetyl CoA and then to fluorocitrate which can inhibit aconitase and therefore the formation of isocitrate, blocking the TCA cycle - cannot continue under that condition

46
Q

What is an analogous cycle in plants and bacteria?

A

The glyoxylate cycle

47
Q

How is the glyoxylate cycle similar to the citric acid cycle?

A

Main difference is it bypasses the two decarboxylation steps, allowing the synthesis of carbs from fats

48
Q

Where does the glyoxylate cycle occur in plants?

A

In the glyoxysome of plants

49
Q

What is the main product of the glyoxylate cycle?

A

Succinate (which can be converted into oxaloacetate and then glucose)

50
Q

Why can mammals not synthesize glucose from acetyl CoA?

A

Because the input is 2 carbons in Acetyl CoA and the two carbons are lost as CO2

51
Q

Why do plants use the glyoxylate cycle?

A

For plants when germinating as seeds, the seeds have fat stores and it converts the fats into glucose for energy before the plant can begin photosynthesizing

52
Q

Give a general overview of oxidative phosphorylation

A

Metabolic pathway that uses energy released by the oxidation of nutrients to produce ATP
- ATP is synthesized as electrons pass from electron donor to electron acceptor
- Energy that is released during electron transport drives ATP synthesis
- the final electron acceptor is O2
- occurs in the mitochondria inner membrane - electron transport chain

53
Q

What are the 5 main parts of the electron transport chain?

A

5 main protein complexes + cytochrome C
- 4 complexes for electron transport - bucket brigade
- 1 complex for ATP synthesis

54
Q

What is chemiosmotic theory?

A

Energy is released as electrons flow thru transport chain
- energy is used to transport protons across the inner membrane
- this generates potential energy - pH gradient across membrane
- protons flow back down across the membrane and down the gradient through enzyme ATP synthase
- ATP synthase uses energy to ATP

55
Q

Which complex in the electron transport chain does not act as a proton pump?

A

Complex II - succinate dehydrogenase

56
Q

Name the 5 ETC complexes

A

I - NADH dehydrogenase
II - succinate dehydrogenase
III - Ubiquinone:cytochrome C oxidoreductase
- Cytochrome C
IV - Cytochrome oxidase

57
Q

What part of the ETC is soluble?

A

Cytochrome C

58
Q

What are the 5 electron carriers used in the ETC?

A
  1. NADH and FADH2 from TCA
  2. Coenzyme Q
  3. Cytochromes A,B,C
  4. Iron-sulfur center-containing proteins
  5. Copper-sulfur center-containing proteins
59
Q

What is Coenzyme Q?

A

Lipid soluble electron carrier
- moves in lipid bilayer - inner mito membrane
- moves e- between less mobile e- carriers in mem
moves 2e-

60
Q

What are cytochromes?

A

Proteins that function as electron carriers
- cytochrome C is soluble - carries 1e-
- outer surface of mito membrane
- has heme group that has a Fe bound by 4 N, iron is what accepts and donates the electrons

61
Q

What are proteins with iron sulfur centers?

A

2 iron joined by 2 sulfur - linked to protein by CYS
- can carry electrons
- proteins can have multiple centers

62
Q

What is complex I in the ETC?

A

NADH dehydrogenase
- 1st reaction of ETC
- several iron-sulfur centers
-L shaped, part in matrix part in membrane
- 2 electron reduction by coenzyme Q
- 4 protons moved from matrix to intermembrane space

63
Q

What is complex II in the ETC?

A

Succinate dehydrogenase
- 2nd point of entry into ETC
- takes in FADH2
- oxidizes succinate to fumarate - transfers electrons to CoQ- QH2
- electrons go from succinate to FAD to iron sulfur centers to CoQ to QH2

  • NO H are moved across membrane - does not contribute to formation of H gradient
64
Q

What is complex III in the ETC?

A

Cytochrome C oxioreductase
- in inner mito mem
transfers electrons from QH2 - cytochrome C
- uuses heme and F/S centers
transports 4 protons from matrix to intermembrane space
- contributes to proton gradient
-

65
Q

What is complex IV in the ETC?

A

Cytochrome c oxidase
- final complex
- inner mito mem
- carries electrons from cyt c to O2 which is reduced to water
- pumps 2 H across per electron pair
O2 is final e- acceptor (requires 4 electrons)

66
Q

Where do the electrons from NADH and FADH2 converge in the ETC?

A

complex q

67
Q

What is proton motive force?

A

the electrochemical energy that drives ATP synthesis as protons flow back down the gradient into the matrix which provides the energy for atp synthase to work

68
Q

What is ATP synthase?

A

catalyzes formation of ATP from ADP and Pi
- protons re enter the matrix by passing thru atp synthase
- creates enough energy to couple a phosphate group to ADP forming ATP

69
Q

What are the F0 and F1 regions of ATP synthase?

A

F0 - pore that spans membrane - protns flow thru F0 pore

F1 - in the matrix of mitochondria - spherical head which phosphorylation of ADP occurs

70
Q

How many A and B subunits are there in ATP synthase? How are they arranged?

A

3 pairs of alternating A and B subunits

71
Q

How are cristae formed in the mitochondria?

A

due to the dimerization of ATP synthase
- cristae help organize proton pumps in a smaller space to increase concentration of protons near ATP synthase

72
Q

What are the three conformations of the catalytic B subunits of the F1 complex in ATP synthase?

A

L - loose form - B subunit traps ADP and Pi
T - tight form - ATP is synthesized from ADP and Pi
O - open form - B subunit has low affinity for ATP - releasing it from B subunit so another ADP and Pi can bind

73
Q

Explain how the three different B subunits interact with each other?

A

The B subunits are always in different conformations and rotates between the three.
- When 3 protons pass through the pore, Y rotates which changes conformation of B
- Open conformation changes to loose to bind an ADP and Pi
- loose confirmation changes to tight - condenses and makes ATP from ADP and Pi
-Tight conformation changes to Open - releasing ATP so the cycle starts again
1

74
Q

How many protons are needed to turn the subunit 120 degrees?

A

1 ATP is produced for every 3 protons that re enter mitochondria thru ATP synthase (takes 3 protons to crank that shit)

75
Q

How many protons does it take to make an ATP?

A

4 (why? - 3 to turn, 1 to move Pi into matrix)

76
Q

How is ATP moved into the cytosol after being produced in the mitochondria?

A

Via the ATP-ADP translocase

77
Q

How does NADH that is generated in the cytosol make it into the mitochondria?

A

2 diff shuttles that transport NADH from cytoplasm to matrix
- Malate-aspartate shuttle (2.5ATP/NADH) - liver / heart
-glycerol-3-phosphate shuttle (1.5 ATP/ NADH) - muscle - mimics complex II ***

78
Q

How do different poisons affect oxidative phosphorylation?

A

Rotenone - prevents e- transfer from complex I to CoQ
Cyanide / Carbon Monoxide - inhibit cytochrome C oxidase (complex IV) - binds to iron in the heme group preventing transfer of electrons to O2

79
Q

What is brown fat?

A

Brown adipose tissue that is present in hibernating rodents and newborn humans - has many mitochondria that dissipate energy instead of storing it
- via uncoupling the electron transport chain from ATP synthesis heat is generated - bypasses ATP synthase energy is turned into heat

80
Q

What is the advantage of using a protein complex? (PDH)

A

Substrate channeling - local concentrations of substrates around enzymes is kept high

81
Q
A

BMSC 230 Metabolism (7 decks)

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