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EXAM 4 Flashcards

1
Q

Why is the Citrate Cycle considered a hub of metabolism?

A

It is central to aerobic metabolism and ATP production by generating a bulk of NADH and FADH2.

It links the oxidation of various metabolic fuels (carbs, fatty acids, and proteins) to ATP synthesis through shared intermediates and provides metabolites for numerous biosynthetic pathways.

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2
Q

How is the Citrate Cycle linked to the Electron Transport Chain?

A

The Citrate cycle is linked to the electron transport chain by using shared NADH and FADH2 as intermediates for the ETC and ATP Synthase Complex.

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3
Q

Where do most of the reactions of the amino acids and fatty acid metabolism happen?

A

In the mitochondrial matrix.

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4
Q

The citrate cycle__________________ (oxidizes/reduces) __________________________ (acetyl-CoA/pyruvate) to produce ___________________________________ (3 biomolecules):

A

Oxidizes acetyl-CoA to produce GTP, NADH, and FADH2.

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5
Q

What are the four things that the citrate cycle accomplishes for the cell?

A
  • Transfers 8 electrons from acetyl-CoA to the coenzymes NAD+ and FAD to form 3NADH and 1 FADH2 that will be oxidized by ETS to generate ATP by oxidative phosphorylation.
  • Generates 2 CO2 as waste products and uses substrate level phosphorylation to make 1 GTP which is converted to ATP by diphosphate kinase.
  • Supplies metabolic intermediates (like regenerating oxaloacetate) for amino acid and porphyrin biosynthesis.
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6
Q

How can the citrate cycle be seen as a metabolic engine?

A

The citrate cycle uses acetyl-CoA as a fuel, the exhaust is CO2 and the work is transferring electrons using a series of linked redox reactions.

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7
Q

Why do we call the Krebs cycle the Citrate cycle?

A

We call Krebs cycle the citrate cycle because the citrate cycle reflects that all 3 carboxylate groups on citrate are deprotonated at physiologic pH and therefore are not acid in cells.

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8
Q

What is the overall net reaction of the citrate cycle?

A

Acetyl-CoA + 3NAD+ + FAD + GDP + Pi + 2H2O —> CoA + 2CO2 + 3NADH + 3H+ + 1FADH2 + GTP.

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9
Q

What are the key regulated enzymes in the citrate cycle?

A
  • Pyruvate dehydrogenase: regulates the flux of acetyl-CoA and can be inhibited by acetyl-CoA, ATP, and NADH.
  • Citrate synthase: catalyzes the first reaction and is inhibited by citrate, succinyl CoA, NADH, and ATP.
  • Isocitrate dehydrogenase: catalyzes oxidative decarboxylation and transfers 2 electrons to NAD+ to make NADH.
  • Alpha ketoglutarate dehydrogenase: similar to pyruvate, has multi-subunit as well and does oxidative decarboxylation.
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10
Q

What role do redox reactions play in metabolism?

A

Redox reactions are a form of energy conversion which transfers electron pairs to other molecules.

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11
Q

The more electrons a carbon atom has available to donate, the more __________________ (reduced/oxidized) it is.

A

reduced.

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12
Q

What kind of E’ values do oxidants have? Reductants?

A

Reductants will have electrons that move to E’ values that are negative; oxidants will have electrons that have positive E’ values.

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13
Q

What is the role of pyruvate dehydrogenase?

A

Pyruvate dehydrogenase converts pyruvate into acetyl-CoA which is used for complete oxidation by the citrate cycle or for fatty acid synthesis.

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14
Q

What are the five coenzymes for PDH?

A
  • NAD+
  • FAD
  • CoA
  • TPP
  • Lipoamide
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15
Q

What is NAD+?

A

NAD+ is derived from niacin (vitamin B3) and is a critical component in the alpha-ketoglutarate complex.

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16
Q

What is FAD?

A

It is derived from riboflavin (Vitamin B2) and functions in the redox reaction involving dihydrolipoamide.

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17
Q

What is CoA?

A

CoA is derived from pantothenic acid (vitamin B5) and functions as an acetate carrier in the E2 catalytic site.

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18
Q

What is TPP?

A

TPP is derived from thiamine (vitamin B1) and is an important enzyme in PDH and alpha-ketoglutarate dehydrogenase reaction.

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19
Q

What is lipoamide?

A

Lipoamide uses a reactive disulfide to participate in redox reactions within the enzyme active site.

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20
Q

What is the stoichiometry of the E1:E2:E3 subunits?

A

22:60:6 which have 60 active sites.

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21
Q

What is the role of lipoamide in the E2 subunit?

A

It acts as a bridge between the E1 and E3 subunits.

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22
Q

What role does Arsenite play in the PDH?

A

Arsenite is the inhibitor of lipoamide because it blocks the lipoamide catalytic activity.

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23
Q

What are the five steps of the PDH complex?

A
  • The E1 subunit binds pyruvate and catalyzes a decarboxylation reaction to form hydroxyethyl-TPP and CO2 release.
  • The hydroxyethyl-TPP of E1 reacts with the disulfide of the lipoamide group of E2 to generate acetyl-dihydrolipoamide.
  • The E2 lipoamide group carries acetyl group from the E1 to the E2 catalytic site.
  • The dihydrolipoamide group swings to E3 subunit where it is reoxidized to the disulfide and transfers two electrons and 2 protons to E3 linked FAD to make FADH2.
  • The E3 FADH2 coenzyme is reoxidized to transfer two electrons to NAD+ producing NADH and H+.
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24
Q

What are the two things that can happen to Acetyl-CoA after it has been produced?

A
  • Be metabolized in the citrate cycle, converting redox energy to ATP by oxidative phosphorylation.
  • Used as a form of stored energy to fatty acids which are transported to adipose tissue as triglycerides.
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25
How is the PDH complex inhibited?
PDH complex is inhibited by phosphorylation of a serine residue on the E1 subunit by PDK. NADH, Acetyl-CoA, and ATP activate PDK.
26
How does pyruvate carboxylase play a role in balancing the input of acetyl-CoA and oxaloacetate?
Pyruvate carboxylase plays a critical role in balancing the input of acetyl-CoA and oxaloacetate by maintaining flux when fatty acid oxidation is the main source of energy.
27
What is PDH activated by?
PDH is activated by CoA-SH to stimulate acetyl-CoA production.
28
What is Pyruvate Carboxylase activated by?
Acetyl-CoA to maintain OAA for citrate synthesis.
29
What is a scenario where pyruvate carboxylase will be turned on?
When there are high levels of acetyl-CoA so it is stored as fatty acid oxidation as an energy.
30
Where does the majority of citric acid come from?
Aspergillus niger cultures, NOT lemon juice.
31
What happens when you inhibit the citrate cycle?
Inhibition of the citrate cycle leads to increased citrate export into the culture medium.
32
The citrate cycle is _______________________________ (amphibolic/anaplerotic):
Amphibolic.
33
The pyruvate carboxylase reaction is ___________________________ (amphibolic/anaplerotic):
Anaplerotic.
34
How does biotin play a role in the pyruvate carboxylase reaction?
Biotin is used to catalyze ATP dependent reactions and replenishes oxaloacetate.
35
What is the Chemiosmotic Theory?
The Chemiosmotic Theory states that the energy from the redox reactions translates to the potential energy in form of proton gradient across a proton-impermeable membrane.
36
What is the basic idea of chemiosmosis?
It is the energy from redox reactions or light that is coupled to electron transfer in membrane bound proteins to translocate protons across the membrane.
37
What are the key elements of Chemiosmotic Theory?
* Oxidation of NADH and FADH2 in the mitochondrial matrix by the ETS links redox energy to make ATP. * H+ flow back into the proton gradient via ATP Synthase Complex in response to chemical and electrical differences.
38
What does an uncoupler protein do to the proton gradient?
Uncoupler proteins short-circuit the protons, allowing them to leak into the membrane without making ATP.
39
What does oligomycin do to the proton flow?
Oligomycin inhibits flow of protons into the ATP synthase complex, leading to a high proton gradient and membrane potential.
40
What does ETS/Oxidative Phosphorylation do for the cell?
* Generates ATP derived from oxidation of metabolic fuels for 28 out of 32 ATP obtained from glucose catabolism. * The tissue-specific UCP1 in brown adipose short circuits the ETS and produces thermogenesis.
41
What is the overall net reaction of ETS/Oxidative Phosphorylation?
2NADH + 2H+ + 5ADP + 5Pi + O2 -----> 2NAD+ + 5ATP + 2H2O.
42
What are the key enzymes in the oxidative phosphorylation pathway?
* ATP synthase complex * NADH dehydrogenase (Complex 1) * Ubiquinone-cytochrome c oxidoreducase (Complex 3) * Cytochrome C oxidase (Complex 4)
43
What are examples of oxidative Phosphorylation in everyday biochemistry?
Cyanide.
44
What are the key enzymes in the oxidative phosphorylation pathway?
ATP synthase complex, NADH dehydrogenase (Complex 1), Ubiquinone-cytochrome c oxidoreducase (Complex 3), Cytochrome C oxidase (Complex 4) ## Footnote NADH dehydrogenase oxidizes NADH and moves 4H+ to the transmembrane space.
45
What is an example of oxidative phosphorylation in everyday biochemistry?
Cyanide which binds to the heme group on Complex 4 and blocks ETS ## Footnote This prevents the reduction of oxygen to form H2O.
46
What is the redox reaction of the ETS?
The oxidation of NADH and FADH2 in the inner mitochondrial membrane coupled to the reduction of O2 to form H2O.
47
What is proton translocation dependent on?
Proton translocation is dependent on the redox loop (Q cycle) or conformational change in protein complex due to changes in pKa.
48
How many electrons start the ETS redox reaction?
2 electrons from NADH oxidation enter the ETS at complex 1 ## Footnote Total of H+ translocated is 10.
49
What are the four steps in Complex 1: NADH Ubiquinone?
1) NADH is oxidized and loses 2 electrons transferred to FMN. 2) 2 electrons transferred from carrier to another carrier. 3) Electrons donated to coenzyme Q along with 2H+ to form QH2. 4) 4 H+ translocated and 2E- and 2H+ reduce coenzyme Q.
50
What are the three functions of CoQ?
1. Mobile electron carrier transporting electrons from Complex 1 to Complex 3. 2. Entry point of ETS for 2 electrons from citrate cycle, fatty acid oxidation, and glycerol 3P dehydrogenase. 3. Converts 2E- transport of Complex 1 and 2 to 1 electron transport in Complex 3.
51
What leads to the name CoQ10?
The hydrocarbon tail of human CoQ contains 10 units.
52
What happens in Complex 2?
Complex 2, called Succinate Dehydrogenase, catalyzes the oxidation of succinate to fumarate using FAD.
53
What is happening in Complex III?
Complex 3, Ubiquinone-Cytochrome C, transfers electrons one at a time to cytochrome c and translocates 4 H+ across the inner mitochondrial membrane.
54
What are the two functions of the Q cycle?
1. Mobile electron carrier and transformer converting 2e- transport system into 1e- transport system. 2. Requires two QH2 molecules oxidized by complex 3.
55
How does the Q cycle convert a two-electron translocation process into two one-electron transfers?
1. First QH2 oxidized at Qp site. 2. Oxidized Q moves from Qp to Qn. 3. Q in Qn site reduced forming a semiquinone. 4. Second QH2 binds to QP site and is oxidized.
56
What is the role of Cytochrome C?
Transfers one electron at a time from Complex 3 to Complex 4 using iron heme prosthetic group.
57
How does Complex IV accept electrons?
Complex IV accepts electrons one at a time from cytochrome c and donates them to oxygen to form water.
58
What does ATP Synthase Complex respond to?
Undergoes conformational change in response to proton force across the inner mitochondrial membrane.
59
What are the main three pieces of ATP Synthase Complex?
1) Rotor. 2) Catalytic Headpiece. 3) Stator.
60
What is the binding change mechanism?
Conformational changes in the Beta subunit of the catalytic headpiece control ATP synthesis by cycling O ---> L ----> T.
61
Where is the catalytic site for ATP synthase?
On the Beta subunit. Mg2+ ions are required for the enzyme reaction.
62
What happens during a 360-degree rotation of the gamma subunit?
Produces 3 ATP with 9 H+.
63
What are ATP translocase and phosphate translocase?
Critical in the exchange of ATP synthesis product ATP for reactants ADP + Pi.
64
What happens when you add ADP + Pi to the system?
Low rate of O2 reduction and ATP synthesis.
65
What is the role of DNP?
Dissipates the proton gradient, lowers energy barrier for proton translocation, and wastes energy as heat.
66
What are UCPI?
Uncoupling proteins, also known as thermogenin, lead to heat production by diverting redox energy.
67
What is the reason why DNP is bad to ingest?
DNP dissipates the proton gradient and severely reduces ATP synthesis, causing liver damage.
68
Why can't individuals with beriberi metabolize pyruvate into acetyl-CoA?
They lack pyruvate dehydrogenase coenzyme TPP, leading to a build-up of pyruvate.
69
What happens when you add fumarate to the system?
Increases O2 consumption.
70
How does adding citrate increase oxaloacetate?
Increases the ability of the citrate cycle to metabolize acetyl-CoA by increasing intermediates.
71
How many ATP are produced per pyruvate that metabolizes 3 CO2?
12.5.
72
How does adding citrate increase oxaloacetate?
Adding citrate increased the ability of the citrate cycle to metabolize acetyl-CoA by increasing intermediates, oxaloacetate.
73
What effect does adding acetyl-CoA have on oxaloacetate?
Adding acetyl-CoA has no effect on oxaloacetate because oxaloacetate levels were limiting.
74
How many ATP are generated per pyruvate that metabolizes 3 CO2?
12.5
75
What happens if there is an inhibitor of the citrate cycle?
The citrate in the cytosol isn't being exported, inhibiting phosphofructo-kinase, which shuts down glycolysis.
76
What is the consequence of Cytochrome C being in the cytosol?
High levels of Cyt C in the cytosol indicate that the mitochondria isn't functioning properly and may lead to apoptosis.
77
Why does the ATP exchange ratio in mitochondria count 4H+ translocated for every ATP synthesized?
Phosphate Translocase needs 1H+ to accompany Pi into the matrix.
78
Fill in the blank: Cystolic NADH in muscle donates 2e- to ______ by glycerol 3P shuttle.
FADH2
79
How much ATP is produced by mitochondrial FADH2 oxidation?
1.5 ATP/NADH or 3 ATP/2NADH
80
True or False? High levels of ATP and NADH decrease the flux through the citrate cycle.
True
81
How many ATP does the citrate cycle generate?
20
82
True or False? ATP synthase uses substrate-level phosphorylation to produce ATP.
False
83
What does ATP Synthase use to produce ATP?
Oxidative phosphorylation
84
Why are mitochondrial shuttles important for glycolysis?
They regenerate NAD+ when pyruvate is oxidized in mitochondria.
85
What is the role of cytosolic NADH in liver cells under aerobic conditions?
Cytosolic NADH provides electrons to reduce oxaloacetate to malate, which is transported into the mitochondria to produce NADH.
86
What is Oxidative Phosphorylation?
Oxidative Phosphorylation is responsible for generating the majority of ATP derived from glucose.
87
Fill in the blank: Oxidative Phosphorylation converts NADH and ______ into ATP.
FADH2

Biochemistry (44 decks)

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