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BIOCH 200 > Oxidative Phosphorylation and Glucose Metabolism > Flashcards

Oxidative Phosphorylation and Glucose Metabolism Flashcards

1
Q

What are the purposes of catabolic pathways

A

Breakdown of larger molecules into smaller building units. Release and (temporary) storage of energy in high-energy molecules through ATPS/NTPs and Reduced cofactors (NADH/FADH2)

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2
Q

How are catabolic pathways oxidative

A

Metabolites are oxidized as cofactors are reduced. Re-oxidization of cofactors is used to generate ATP.

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3
Q

What is the overview of Oxidative Phosphorylation

A

Reduced cofactors (NADH, FADH2) from glycolysis and CAC (oxidative catabolism). Which leads to electron transport chain (reoxidation of NADH/FADH2) (reduction of O2 to H2O). Which leads to proton gradient (inner mitochondrial membrane). Which leads to ATP synthesis.

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4
Q

Where does Oxidative Phosphorylation occur

A

Inner mitochondria membrane

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5
Q

What are the components of the electron transport chain

A

Complexes 1-4
Coenzyme Q
Cytochrome C

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6
Q

What are the cofactors in oxidative phosphorylation

A 
Flavin mononucleotide (Prosthetic groups), Iron-sulfur clusters (Prosthetic groups), Copper (Cu2+) (Prosthetic groups), Cytochrome heme groups (Prosthetic groups), Coenzyme Q (Lipid-soluble cofactor).
Each cofactor has a characteristic reduction potential or affinity for electrons.
Electrons move from cofactors will lower reduction potential to those with higher reduction potentials.
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7
Q

What are cytochromes

A

Cytochromes are hemoproteins that carry out electron transport.

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8
Q

What is Coenzyme Q

A

Lipid-soluble molecule. It transports electrons to Complex 3 from Complexes 1 and 2 in the inner mitochondrial membrane (Cosubstrate for all three complexes).

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9
Q

What is the Electron Transport Chain

A

Redox reactions have a free energy change related to reduction potential. Reduction potential is “affinity for electrons.” Higher reduction potential leads to a more negative free energy. Electrons move from compounds with lower reduction potentials to those with higher reduction potentials. Free energy changes from redox reactions can be used to transport protons across the membrane (primary active transport)

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10
Q

What is the number of protons reoxidized by every NADH

A

Every NADH reoxidized results in 10 protons being move out of the matrix

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11
Q

What is the number of protons reoxidized by every FADH2

A

Every FADH2 reoxidized results in 6 protons being moved out of the matrix

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12
Q

What is the overall potential energy converted to

A

Overall, the potential energy of the H+ gradient is converted to the chemical energy in the phosphoanhydride bonds of ATP.

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13
Q

What is FO of ATP Synthase

A

FO: Oligomycin. Transmembrane portion, Protons pass through and Triggers conformational change in F1.

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14
Q

What is F1 of ATP Synthase

A

Catalytic portion and Synthesis of ATP from ADP and Pi.

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15
Q

What is the adenine nucleotide translocase and the Pi H+ support

A

Newly synthesized ATP is export from the mitochondrial matrix into the cytosol where it can be used to “drive” the many energy-requiring processes in the cell. The ADP and Pi produced in the cytosol are then transported back into the mitochondrial matrix.

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16
Q

What is the P:O Ratio

A

P:O Ratio is the amount of ATP made (P) per oxygen atom reduced to water (O): 1 water made for each NADH or FADH2 reoxidized (each 2 electrons)
Non-stoichiometric: P:O ratio is ~2.5 ATP/NADH reoxidized, P:O ration is ~1.5 ATP/FADH2 reoxidized
P:O ratio may vary with uncoupling.

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17
Q

What is the rate of oxidative phosphorylation determined by

A

O2 consumption (via electron transport) is connected to ATP production at the ATP Synthase. Oxygen consumption increases when ADP concentration rises. ADP concentration reflects the energy-consumption of the cell.

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18
Q

What is the coupling of ATP synthesis to electron transport

A

Oxygen consumption increases in isolated mitochondria when ATP synthesis is stimulated (addition of ADP)

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19
Q

What does oxygen consumption increase

A

The presence of an uncoupler. This refers to situations when electron transport occurs without ATP synthesis (and thus, also, when catabolism of fuel molecules occurs without ATP synthesis). The proton gradient is then dissipated faster, and the rate of electron transport increases (O2 consumption goes up). The rate of re-oxidation of reduced electron carriers increases, and the rate of reactions in the citric acid cycle increases.

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20
Q

What is the uncoupling of ATP synthesis to electron transport

A

Oxygen consumption with uncouplers, even in the absence of ATP synthesis.

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21
Q

What is Complex 2

A

Succinate Dehydrogenase (part of the citric acid cycle). An integral membrane protein, Complex II contains FAD as a prosthetic group. Catalyzes oxidation of succinate to fumarate as part of the citric acid cycle. Electrons from succinate are ultimately transferred to coenzyme Q in the membrane. No protons are moved across the membrane at Complex II

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22
Q

What do uncoupled systems allow

A

Uncoupled systems allow protons to enter the matrix without ATP synthesis. Protons may enter matrix through a separate process, generating heat instead of ATP

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23
Q

How does oxygen consumption increase in the presence of an uncoupler.

A

This refers to situations when electron transport
occurs without ATP synthesis (and thus, also, when
catabolism of fuel molecules occurs without ATP
synthesis). The proton gradient is then dissipated faster, and the rate of electron transport increases (O2 consumption goes up). The rate of re-oxidation of reduced electron carriers increases, and the rate of reactions in the citric acid cycle increases.

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24
Q

How does affect uncoupling of ATP synthesis to electron

A

Oxygen consumption with uncouplers, even in the absence of ATP synthesis

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25
Q

What is glycolysis

A

Catabolic pathway. Conversion of 1 molecule of glucose into two molecules of pyruvate. Generates ATP directly and NADH from oxidation of metabolites

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26
Q

What are the major pathways of Glucose Metabolism

A

Glucose to Glycogen is glycogen synthesis
Glycogen to the main pathway is glycogenolysis
Glucose to pyruvate is glycolysis
Pyruvate to glucose is gluconeogenesis

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27
Q

What are the structures of glucose

A

Glucose is a six-carbon compound with one aldehyde group and five hydroxyl groups, aldose, hexose and aldohexose, which cyclizes to form a 6-membered ring.

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28
Q

What is Glycolysis

A

Anaerobic pathway for ATP generation. It is ancient. It is conserve. It can operate aerobically in a manner of NADH reoxidation. 10 enzyme-catalyzed reactions occur in the cytosol. One glucose is broken down to 2 pyruvate.

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29
Q

What are the Stages of Glycolysis

A

Stage 1: Energy Investment

Stage 2: Energy Payout

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30
Q

What is Stage 1 of Glycolysis

A

Energy Investment. Glucose needs to be activated. Energy (ATP) is consumed. Involved “hexose” (6 carbons) sugars

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31
Q

What is Stage 2 of Glycolysis

A

Energy Payout. Energy is harvested in the form of ATP. NADH also generated. Involves “triose” (3 carbon) sugars.

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32
Q

What are the energy investment steps of glycolysis

A

Glucose to Glucose-6-phosphate to Fructose-6-phosphate to Fructose-1,6-biphosphate to Dihydroxyacetone phosphate

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33
Q

What are the energy payout steps of glycolysis

A

Glyceraldehyde-3-phosphate to 1,3-biphosphoglycerate to 3-phosphoglycerate to 2-phosphoglycerate to phosphoenolpyruvate to pyruvate

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34
Q

What are the important enzymes involved in glycolysis

A

Hexokinase, Phosphofructokinase-1, Glyceraldehyde 3-phosphate dehydrogenase, and Pyruvate kinase

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35
Q

What step is Hexokinase involved in

A

Glucose to Glucose-6-phosphate

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36
Q

What step is Phosphofructokinase-1 involved in

A

Fructose-6-phosphate to Fructose-1,6-biphosphate

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37
Q

What step is glyceraldehyde-3-phosphate dehydrogenase

A

Glyceraldehyde-3-phosphate to 1,3-biphosphateglycerate

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38
Q

What step is pyruvate kinase

A

Phosphoenolpyruvate to pyruvate

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39
Q

How much ATP is consumed for glucose to glyceraldehyde-3-phosphate (GAP) x2

A

2 ATP are consumed for every glucose

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40
Q

What occurs during the Glucose to Glucose-6-phosphate reaction

A

Irreversible, Exergonic, Coupled reaction (ATP used), Phosphate transfer reaction, Catalyzed by hexokinase. It is regulated but not rate limiting

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41
Q

What occurs during the fructose-6-phosphate to fructose-1,6-biphosphate reaction

A

Irreversible. Exergonic. Coupled reaction (ATP used). Phosphate transfer reaction. Catalyzed by phosphofructokinase-1. Regulated. Rate limiting step.

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42
Q

What is the production of two molecules of glyceraldehyde-3-phosphate

A

Via two separate reactions, two molecules of glyceraldehyde-3-phosphate are produced from one molecule of fructose-1,6-biphosphate. Every reaction described from GAP to pyruvate happens twice per glucose.

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43
Q

How much ATP are produced from Glyceraldehyde-3-phosphate x2 to pyruvate x2

A

4 ATP are generated for every glucose

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44
Q

What is the Glyceraldehyde-3-phosphate to 1,3-bisphosphoglycerate reaction

A

Oxidation. Reversible. “Energy capture” step. Catalyzed by GAPDH

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45
Q

What is 1,3-bisphosphoglycerate (1,3-BPG)

A

1,3-BPG is a “high-energy” intermediate because it is an acyl phosphate (phosphates attached to carboxylates). This chemical group has a large, negative delta G of hydrolysis (both products are stabilized by resonance). 1,3-BPG has a large phosphate transfer potential.

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46
Q

What is the reaction of 1,3-biphosphoglycerate to 3-phosphoglycerate

A

Reversible. Couple (ATP synthesis). “Energy capture” step (ATP). Substrate-level phosphorylation. This reaction is a coupled reaction, a phosphate-transfer reaction, and specifically, a substrate-level phosphorylation reaction.

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47
Q

What is the reaction of 3-phosphoglycerate to 2-phosphoglycerate

A

Isomerization. Reversible.

48
Q

What is the reaction of 2-phosphoglycerate to phosphoenolpyruvate

A

This is a dehydration reaction. Reversible. Phosphoenolpyruvate (PEP) is a high-energy intermediate.

49
Q

What the reaction that creates pyruvate

A

Phosphoenolpyruvate to enolpyruvate to pyruvate. In this reaction, large amounts of free energy are released during the conversion of enolpyruvate to pyruvate

50
Q

What is the reaction of phosphoenolpyruvate to pyruvate

A

Irreversible. Coupled (ATP synthesis). Substrate-level phosphorylation. Catalyzed by pyruvate kinase (regulated). 2 ATP made per glucose (Net yield: 2 ATP)

51
Q

Why is glycolysis regulated

A

Ensures energy needs are met. Glucose is not wasted when ATP is abundant. Intermediate may be used in other processes and reactions.

52
Q

How is the rate of metabolic pathways regulated

A

Substrate availability
Alteration of enzyme activity
Alteration of amount of enzyme
Compartmentation

53
Q

How does substrate availability regulated in glycolysis

A

Glucose import (transporters)

54
Q

How does enzyme regulation regulated in glycolysis

A

Hexokinase, Phosphofructosekinase-1 and Pyruvate kinase

55
Q

What is Hexokinase regulation

A

Glucose-6-phosphate (G6P) is an inhibitor. G6P acts as a negative allosteric effector for hexokinase. Product inhibition

56
Q

What phosphofructokinase-1 regulation

A

PFK-1 is allosterically regulated buy ADP/AMP and PEP. The concentration of ADP/AMP in a cell is a good indicator of the need for ATP. Elevated PEP levels signal that the products of glycolysis are not being consumed.

57
Q

What is pyruvate kinase regulation

A

Allosteric enzyme. Inhibited by ATP (product inhibition). Pyruvate kinase is part of the reciprocal of regulation (glycolysis and gluconeogenesis). Activated by fructose-1,6-biphosphate. Occurs in yeast. Feed forward activation

58
Q

What is the effect of F-1,6-BP on Pyruvate Kinase

A

In some tissues, and in yeast, pyruvate kinase is activated by fructose-1,6-biphosphate. “Heteroallosteric activator” “Feed forward activation”

59
Q

What are PFK-1 and PK both inhibited by

A

Both inhibited by ATP. Most enzymes catalyze reversible reactions. Synchronous regulation of irreversible reactions.

60
Q

What are the ATP investment reactions in glycolysis

A

Glucose to Glucose-6-phosphate

Fructose-6-phosphate to Fructose-1,6-biphosphate

61
Q

What are the isomerization reactions in glycolysis

A

Glucose-6-phosphate to Fructose-6-phosphate
DHAP to GAP
3-phosphglycerate to 2-phosphoglycerate

62
Q

What is the lysis reaction in glycolysis

A

Fructose-1,6-biphosphate to GAP + DHAP

63
Q

What is the oxidation followed by phosphorylation reaction in glycolysis

A

GAP to 1,3-biphosphoglycerate

64
Q

What are the substrate level phosphorylation (SLP) reactions in glycolysis

A

1,3-biphosphoglycerate to 3-phosphoglycerate

Phosphoenolpyruvate to Pyruvate

65
Q

What is the dehydration reaction in glycolysis

A

2-phosphoglycerate to phosphoenolpyruvate

66
Q

What is glycogen metabolism

A

Glycogen is synthesized from glucose-6-phosphate. Breakdown of glycogen uses inorganic phosphate to break glycosidic bonds. No ATP is used to generate glucose-6-phosphate from glycogen. Increases NET yield of ATP (1 more unit)

67
Q

Why is an anaerobic fate for pyruvate required?

A

To generate NAD+ for the oxidation reaction in glycolysis under anaerobic conditions

68
Q

What is pyruvate metabolism

A

Glycolysis produces: 2 pyruvate, 2 NADH, Net of 2 ATP. NADH needs to reoxidized to NAD+ for glycolysis to continue. Oxidative phosphorylation (aerobic). Pyruvate (anaerobic)

69
Q

What is the production of lactate

A

Lactate is not an acid. Lactate is a “dead-end” product in skeletal muscle during anaerobic activity.

70
Q

What does lactate do

A

Hydrolysis of ATP by myosin during vigorous muscle contraction can cause acidotic damage to muscle fibers. Lactate is a metabolic fuel for cardiac tissue.

71
Q

What is the production of ethanol

A

Anaerobic fate of pyruvate. Does not occur in vertebrates. Occurs in yeast. Two steps: decarboxylation and reduction. Final products include CO2, ethanol and NAD+

72
Q

What is the pyruvate dehydrogenase reaction

A

Catalyzed by pyruvate dehydrogenase complex. Links glycolysis to the citric acid cycle. Occurs inside mitochondria, in the matrix

73
Q

How is pyruvate transported into the mitochondria

A

Glycolysis generates pyruvate in the cytosol. Pyruvate is converted to acetyl-CoA in the mitochondrial matrix. Transport across the inner mitochondrial membrane requires the transporter protein pyruvate translocase. A proton is transported with the pyruvate

74
Q

What is acetyl-coA

A

Acetyl group attached via thioester bond. Coenzyme A is a derivative of vitamin B5 linked to an adenosine nucleotide. The “functional” portion of the molecule is the terminal, reaction sulfhydryl group (thiol), which forms a thioester bond with acetyl groups.

75
Q

What is the formation of acetyl-CoA

A

The formation of acetyl-CoA is a key irreversible step in carbohydrate metabolism

76
Q

What is the pyruvate dehydrogenase reaction

A

Oxidative decarboxylation. Transacetylation. Irreversible. Catalyzed by Pyruvate Dehydrogenase Complex (PDH) which requires 5 cofactors including: NAD+, FAD, and CoA

77
Q

What is the pyruvate dehydrogenase complex

A

Multienzyme complex that contains: multiple copies of three catalytic enzymes: decarboxylate, transfer to CoA and oxidation. 5 cofactors including NAD+, FAD and CoA. Regulated by kinases and phosphatases.

78
Q

What are the advantages of multienzyme complexes

A

Speeds up reaction times, limits number of side reactions, and enzymes controlled as a single unit.

79
Q

How is the pyruvate dehydrogenase complex regulate

A

Highly regulated. Irreversible. Acetyl-CoA cannot be used to make glucose in mammals. Sensitive to ATP requirements. Regulated by: NAD+/NADH ratio, Ca2+ concentration and Acetyl-CoA

80
Q

How does NAD+/NADH regulation occur in PDH

A

Substrate/Product effect. NADH inhibits (regulates) PDH. Allostery. Protein kinase activator (phosphorylation of PDH)

81
Q

How does Acetyl-CoA regulation occur in PDH

A

Inhibitor. Protein kinase activation (phosphorylation of PDH)

82
Q

How does Ca2+ regulation occur in PDH

A

Activator. Protein phosphatase activation. Dephosphorylation of PDH

83
Q

How is PDH regulated in reversible phosphorylation

A

Switched off when energy levels are high. Phosphorylation (via a kinase) switches off the activity of the complex. Dephosphorylation (via a phosphatase) activates the complex.

84
Q

What is the result of the inhibition of the pyruvate dehydrogenase complex

A

NADH and acetyl-CoA

85
Q

What is the result of activation of the pyruvate dehydrogenase complex

A

NAD+ and HS-CoA

86
Q

What are the sources of Acetyl-CoA

A

Acetyl-CoA comes from many sources like carbohydrates, fatty acid, and amino acid catabolism

87
Q

What are the products of the reactions of the citric acid cycle

A

Acetyl-CoA (2 C) condenses with oxaloacetate (4 C) to make citrate (6 C)
Two carbons are oxidized to CO2
Oxaloacetate is regenerated
3 NADH, 1 FADH2/QH2 and 1 GTP are made (high-energy products) for each acetyl-CoA

88
Q

What is the Citric Acid Cycle

A

Occurs in mitochondrial matrix (eukaryotes). Oxidizes acetyl-CoA to CO2. Generates high-energy products: NADH, FADH2/QH2, GTP (NTP). Aerobic (O2 reduction to reoxidize NADH, FADH2). Cyclic. Acetyl-CoA generated by metabolism of many compounds: carbohydrates, fats and protein. Amphibolic: intermediates can be used in anabolic reactions

89
Q

What is the reaction of citrate synthase

A

Acetyl-CoA and oxaloacetate to create citrate. Irreversible reaction. Catalyzed by citrate synthase. Not regulated (physiologically)

90
Q

What is the reaction of aconitase

A

Citrate to Isocitrate. Isomerization. Reversible.

91
Q

What is the reaction of isocitrate dehydrogenase

A

Isocitrate to alpha-ketoglutarate. Oxidative decarboxylation. Irreversible. Energy capture step (NADH). Catalyzed by isocitrate dehydrogenase. Regulated

92
Q

What is the reaction of alpha-ketoglutarate dehydrogenase complex

A

Alpha-Ketoglutarate to Succinyl CoA. Oxidative decarboxylation. Irreversible. Energy capture step (NADH). Catalyzed by alpha-ketoglutarate dehydrogenase. Similar to PDH reaction. Regulated. Succinyl CoA is a high-energy intermediation (thioester)

93
Q

What is the reaction of the Succinyl CoA synthetase

A

Succinyl CoA to Succinate. Reversible reaction. Energy capture (NTP). Substrate-level phosphorylation

94
Q

What is the reaction of the Succinate dehydrogenase complex

A

Succinate to Fumarate. Oxidation. Reversible. Catalyzed by succinate dehydrogenase. FAD/FADH2 oxidation of C-C single bond. Integral membrane protein (Complex 2)

95
Q

Explain the details of the reversible reaction of succinate and fumarate

A

FADH2 is reoxidized by donating electrons to coenzyme Q (ubiquinone reduced to ubiquinol). QH2 is reoxidized in the electron transport chain. Succinate dehydrogenase is a membrane-bound enzyme and is part of Complex 2 in the electron transport chain

96
Q

What is the reaction of fumarase

A

Fumarate to L-Malate. Reversible. Hydration

97
Q

What is the reaction of malate dehydrogenase

A

L-Malate to Oxaloacetate. Oxidation. Reversible. Energy capture step (NADH). Regenerates oxaloacetate

98
Q

What is the regulation of the citric acid cycle

A

No rate-limiting reactions per se because it is cycle. It is affected by NAD+/NADH ratio (product/substrate). Regulated enzymes. Affected by concentrations of intermediates.

99
Q

What are the regulated enzymes of the citric acid cycle

A

Isocitrate dehydrogenase and alpha-ketoglutarate dehydrogenase

100
Q

What are the inhibitors of the Citric Acid Cycle

A

NADH and ATP

101
Q

What are the activators of the Citric Acid Cycle

A

ADP and Ca2+

102
Q

How can we slow down the pyruvate dehydrogenase complex and the Citric Acid Cycle

A 
Lower ADP in the matrix
Lower activity of ATP synthase
Increase H+ gradient across IMM
Lower the rate of electron transport
Lower the oxidation of NADH
Lower the NAD+/NADH ratio
103
Q

How can we speed up the pyruvate dehydrogenase complex and the Citric Acid Cycle

A 
Increase the ADP in the matrix
Increase the activity of ATP synthase
Decrease the H+ gradient across IMM
Increase the rate of electron transport
Increase the oxidation of NADH
Increase the NAD+/NADH ratio
104
Q

Is the citric acid cycle catabolic or anabolic

A

It is both catabolic and anabolic so it makes it amphibolic. Citric acid cycle intermediates can be used in synthesis of amino acids, carbohydrates, fats, nucleotides and other compounds

105
Q

What are the anaplerotic reactions in the Citric Acid Cycle

A

Replenish citric acid cycle intermediates. Intermediates may be consumed in other processes. Must be adequate intermediates to continue the citric acid cycle. Many reactions may be anaplerotic: amino acid breakdown and pyruvate carboxylase

106
Q

What are the functions of the Citric Acid Cycle

A

Provide biosynthetic precursors. An important step in the generation of ATP for cellular needs.

107
Q

How much ATP does the Citric Acid Cycle generate for each acetyl-CoA

A

Approximately 10

108
Q

How much ATP do 3 NADH produce in the Citric Acid Cycle

A

7.5 ATP

109
Q

How much ATP does 1 FADH2 produce in the Citric Acid Cycle

A

1.5 ATP

110
Q

How much ATP does 1 GTP produce in the Citric Acid Cycle

A

1 ATP

111
Q

How much ATP does a complete aerobic oxidation of glucose yield

A

32 ATP

112
Q

How much ATP does anaerobic glycolysis generate

A

2 ATP

113
Q

What reaction links glycolysis to the citric acid cycle

A

Pyruvate to Acetyl-CoA

114
Q

What reactions in glycolysis and the citric acid cycle are decarboxylation reactions

A

Pyruvate to Acetyl-CoA
Isocitrate to Alpha-ketoglutarate
Alpha-ketoglutarate to Succinyl-CoA

115
Q

What reactions in glycolysis and the citric acid cycle are energy capture steps (NADH, FADH2, GTP)

A 
Pyruvate to Acetyl-CoA
Isocitrate to Alpha-ketoglutarate
Alpha-ketoglutarate to Succinyl-CoA
Succinyl-CoA to Succinate
Succinate to Fumarate
Malate to Oxaloacetate
116
Q

What reactions in glycolysis and the citric acid cycle are oxidation (redox) reactions

A 
Pyruvate to Acetyl-CoA
Isocitrate to Alpha-ketoglutarate
Alpha-ketoglutarate to Succinyl-CoA
Succinate to Fumarate
Malate to Oxaloacetate
117
Q

What reaction in glycolysis and the citric acid cycle are regulated reactions

A

Pyruvate to Acetyl-CoA
Isocitrate to Alpha-ketoglutarate
Alpha-ketoglutarate to Succinyl-CoA
(Possibly Acetyl-CoA to Citrate if we include citrate inhibition; rather ambiguous)

BIOCH 200 (8 decks)

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