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Biochemistry > Test 2 (Chapters 12-21) > Flashcards

Test 2 (Chapters 12-21) Flashcards

1
Q

What is the major source of cellular energy?

A

Oxidation of carbon fuels

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2
Q

What is is the function of common intermediates, like NADH, in the oxidation of carbon fuels?

A

Electron carriers - higher affinity for activated group than carbon fuels, but a lower affinity for electrons than O2.

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3
Q

What is the ultimate electron acceptor in the oxidation of carbon fuels?

A

O2

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4
Q

What are five (5) common activated carriers in metabolism, and what is their activated group?

A
  1. ATP (phosphoryl)
  2. NADH (electron)
  3. NADPH (electron)
  4. FADH2 (electron)
  5. CoA (acyl)
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5
Q

What are three (3) mechanisms of metabolic regulation?

A
  1. the amount of enzymes
  2. their catalytic activities
  3. the accessibility of substrates
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6
Q

How is the amount of enzymes regulated?

A

Its rate of synthesis and its rate of degradation; adjusted primarily by its rate of transcription.

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7
Q

What are four (3) ways catalytic activity is regulated?

A
  1. Feedback inhibition (allosteric regulation of the first reaction in a pathway by the ultimate product)
  2. Reversible covalent modification (reduce catalytic activity by structural changes, such as phosphorylation)
  3. Energy status of the cell (measured by energy charge or phosphorylation potential), which is buffered (catabolic reactions take place when there is low amounts of ATP, anabolic reactions take place when there is high amounts of ATP)
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8
Q

What are the activated and deactivated forms of the nicotinamide adenine dinucleotide?

A

Deactivated: NAD+
Activated: NADH

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9
Q

NAD+ is an electron acceptor in what types of reaction? (3 components)

A
  1. a C-H hydride and a C-OH proton are removed forming a C=O bond
  2. NAD+ itself accepts a hydride, forming NADH, and a proton is added to the solvent.
  3. called dehydrogenation because protons accompany the electrons
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10
Q

What are the activated and deactivated forms of the flavin adenine dinucleotide?

A

Deactivated: FAD
Activated: FADH2

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11
Q

FAD is an electron acceptor in what types of reaction? (2 components)

A
  1. C-H hydrogens on adjacent carbons are removed along with two electrons (homolytic) forming C=C bond
  2. FAD accepts two electrons and two protons forming FADH2
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12
Q

What is the structural and functional difference between NADP+ and NAD+?

A

(1) NADP+ uses its electrons for the reductive biosynthesis (anabolism that creates fuels that can later be oxidated). (2) It contains an additional phosphoryl group tag, not on it’s active site, that tells enzymes that it should be used for reductive biosynthesis.

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13
Q

What are three molecules with a higher phosphoryl-transfer potential than ATP?

A
  1. 1,3-BPG (1,3-biphosphoglycerate)
  2. PEP (phosphoenolpyruvate)
    3 Creatine Phosphate
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14
Q

What is Glycolysis?

A

The sequence of reactions that converts one molecule of glucose into two molecules of pyruvate while generating ATP.

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15
Q

What is gluconeogenesis?

A

The sequence of reactions that converts end products of biochemical pathways into glucose.

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16
Q

Where does glycolysis take place?

A

In the cytoplasm

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17
Q

What are three (3) factors that contribute to a high phosphoryl-transfer potential?

A
  1. Electrostatic repulsion of phosphoryl groups (ATP less stable than ADP)
  2. Resonance stabilization (inorganic phosphate resonance more stbale than ATP)
  3. Stabilization due to hydration (hydrogen bonds stabilize ADP and phosphate better than ATP)
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18
Q

How many reactions are in glycolysis?

A

Ten

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19
Q

What are the two stages of Glycolysis?

A
  1. Stage 1 cleaves glucose into two three-carbon aldehyde fragments
  2. Stage 2 oxidizes the each aldehyde to pyruvate while generating two ATP.
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20
Q

List the reactions, including substrates and products, of Stage 1 of glycolysis and the enzymes and cofactors involved.

A
  1. Glucose -> Glucose 6-phosphate [Hexokinase, ATP]
  2. Glucose 6-phosphate Fructose 6-phosphate [Phosphoglucose isomerase]
  3. Fructose 6-phosphate -> Fructose 1,6-biphosphate [Phosphofructokinase, ATP]
  4. Fructose 1,6-biphosphate -> Glyceraldehyde 3-phosphate + Dihydroxyacetone phosphate [Aldolase]
  5. Dihydroyacetone phosphate Glyceraldehyde 3-phosphate [Triose phosphate isomerase]
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21
Q

List the “big picture” steps of Stage 1 of Glycolysis

A
  1. Kinase phosphorylates glucose
  2. Isomerase prepares phosphorylated-glucose to be phosphorylated again
  3. Second phosphorylation occurs
  4. 6-carbon sugar is cleaved into a usable aldehyde and an unusable ketone
  5. Ketone product is converted to aldehyde product by an isomerase.
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22
Q

What is the important step that commits glucose to glycolysis?

A

Phosphorylation by Hexokinase

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23
Q

What irreversible reaction of Stage 1 of glycolysis uses a key regulatory enzyme?

A

Fructose 6-phosphate -> Fructose 1,6-biphosphate [Phosphofructokinase, ATP]

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24
Q

List the reactions, including substrates and products, of Stage 1 of glycolysis and the enzymes and cofactors involved.

A
  1. Glyceraldehyde 3-phosphate 1,3-Biphosphoglycerate + NADH [inorganic phosphate, NAD+, glyceraldehyde 3-phosphate dehydrogenase]
  2. 1,3-Biphosphoglycerate 3-Phosphoglycerate + ATP [ADP, Phosphoglycerate kinase]
  3. 3-Phosphoglycerate 2-Phosphoglycerate [Phosphoglycerate mutase]
  4. 2-Phosphoglycerate Phosphoenolpyruvate + H2O [Enolase]
  5. Phosphoenolpyruvate -> Pyruvate + ATP [Pyruvate kinase]
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25
Q

List the “big picture” steps of Stage 1 of Glycolysis

A
  1. 3-carbon aldehyde transfers electrons to NAD+ and gains a highly active phosphate group
  2. 1,3-BPG phosphorylates ADP to make ATP
  3. remaining phosphate group is moved to a middle carbon so water can be removed from adjacent carbons
  4. water removed from adjacent carbons, forming highly active phosphate group
  5. phosphoenolpyruvate phosphorylates ADP to make ATP and pyruvate remains.
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26
Q

What are the three fates of pyruvate so as to balance the redox potential of the cell? (i.e. replenish NAD+ that is consumed)

A

Pyruvate must be oxidized (1&2 are anaerobic, 3 is aerobic):

  1. Lactic acid fermentation, in which pyruvate is reduced by NADH using lactate dehydrogenase.
  2. Alcoholic fermentation, in which pyruvate is converted to acetaldehyde by pyruvate decarboxylase, which is reduced by NADH using alcohol dehydrogenase.
  3. Combustion of pyruvate into CO2 and H2O by O2
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27
Q

What is the molecular entry-point of the aerobic respiration?

A

Pyruvate is oxidized to (1) acetyl CoA and (2) carbon dioxide by NAD+

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28
Q

What are two (2) ways Fructose enters glycolysis?

A
  1. In most tissues, Fructose is phosphorylated to Fructose 6-phosphate
  2. In the liver (where most fructose metabolizatin occurs), fructokinase phosphorylates to Fructose 1-phosphate, which is split into Glyceraldehyde and Dihydroxyacetone phosphate [which enters glycolysis] and Glyceraldehyde is phorphorylated to Glyceraldehyde 3-phosphate [which enters glycolysis]
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29
Q

What are the four steps that Galactose takes to enter into Glycolysis?

A
  1. Galactose converted to Galactose 1-phosphate
  2. Galactose 1-phosphate converted to UDP-Galactose
  3. UDP-Galactose converted to UDP-Glucose
  4. UDP-Glucose converted to Glucose
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30
Q

What three enzymes are regulated in Glycolysis?

A
  1. Hexokinase
  2. Phosphofructokinase
  3. Pyruvate kinase
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31
Q

What is a committed step?

A

The first irreversible reaction unique to a metabolic pathway.

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32
Q

What is the committed step of glycolysis?

A

Phosphorylation of fructose 6-phosphate to fructose 1,6-biphosphate by phosphofructokinase

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33
Q

What is the most important control element in a metabolic pathway?

A

The enzyme of the committed step.

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34
Q

What are four (4) ways glycolysis helps pancreatic beta cells regulate glucose?

A
  1. Increase ATP concentration
  2. Closing K+ Channel
  3. Opening Calcium Channel
  4. Releasing Insulin
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35
Q

What three irreversible reactions are bypassed in Gluconeogenesis?

A
  1. Glucose -> Glucose 6-phosphate
  2. Fructose 6-phosphate -> Fructose 1,6-biphosphate
  3. Phosphoenolpyruvate -> Pyruvate
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36
Q

How is glucose -> glucose 6-phosphate bypassed in gluconeogenesis?

A

Glucose 6-Phosphotase: Glucose 6-phosphate -> Glucose

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37
Q

How is Fructose 6-phosphate -> Fructose 1,6-biphosphate bypassed in gluconeogenesis?

A

Fructose 1,6-biphosphatase: Fructose 1,6-biphosphate -> Fructoes 6-phosphate

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38
Q

How is Phosphoenolpyruvate -> Pyruvate bypassed in gluconeogenesis? (two steps)

A
  1. Pyruvate carboxylase: pyruvate + ATP -> oxaloacetate + ADP
  2. Phosphoenolpyruvate carboxykinase (PEPCK): oxaloacetate + GTP -> phosphoenolpyruvate + GDP
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39
Q

What are (2) differences between Glycolysis and Gluconeogenesis?

A
  1. Irreversible steps of glycolysis are bypassed by new reactions in gluconeogenesis
  2. Not all reactions in gluconeogenesis occur in cytoplasm
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40
Q

Which enzymes of gluconeogenesis are located outside of cytoplasm, and where are they?

A
  1. Pyruvate carboxylase (mitochondria)

2. Glucose 6-phosphatase (membrane in ER, ONLY IN LIVER! Otherwise, this is used to make glycogen)

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41
Q

What happens to oxaloacetate while it is shuttled from mitochondria to cytoplasm?

A
  1. It is reduced to malate

2. then reoxidized, also generating NADH

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42
Q

What are three allosteric regulators of glycolysis/gluconeogenesis

A
  1. ATP/AMP (energy state)
  2. Citrate (status of citric acid cycle)
  3. High alanine and acetyl CoA
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43
Q

What enzymes are reciprocally regulated between glycolysis and gluconeogenesis, and by what signal molecule?

A
  1. Phosphofructokinase and fructose 1,6-biphosphatase are regulated by fructose 2,6-biphosphate (high concentration favor glycoclysis)
  2. Pyruvate kinase and pyruvate carboxylase regulated by other effectors
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44
Q

Describe the Cori cycle

A

Lactate generated by glycolysis in muscle is released into bloodstream, absorbed by liver and converted into glucose by gluconeogenesis.

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45
Q

Describe the relationship between gluconeogenesis and Type II diabetes

A
  1. PEPCK has insulin resistance
  2. Gluconeogenesis constantly active
  3. Elevated blood glucose, leading to symptoms of diabetes.
46
Q

How many NTP are required to synthesize glucose from two molecules of pyruvate?

A

6 NTP: A net 2 ATP are produced from glucose -> Pyruvate, so there is an extra cost of 4 High-energy Phosphoryl transfer molecules in Gluconeogenesis.

47
Q

Where does the conversion of pyruvate to acetyl CoA occur?

A

Mitochondrial matrix

48
Q

What catalyzes the oxidative decarboxylation of pyruvate?

A

Pyruvate dehydrogenase complex

49
Q

What are the three parts of the pyruvate dehydrogenase complex?

A
  1. E1
  2. E2
  3. E3
50
Q

What are the three reactions in the oxidative decarboxylation of pyruvate?

A
  1. Decarboxylation, forming CO2 (E1)
  2. Oxidation to acetyl and transfer to Lipoamide E1
  3. Formation of Acetyl CoA
51
Q

What are the catalystic coenzymes of pyruvate DH?

A
  1. TPP
  2. Lipoid acid
  3. FAD
52
Q

What are the stoichiometric coenzymes of pyruvate DH?

A
  1. NAD+

2. CoA

53
Q

Can animals form glucose from acetyl CoA, as they can with pyruvate?

A

No

54
Q

What are the two fates of acetyl CoA?

A
  1. Incorporation into Citric Acid Cycle

2. Incorporation into lipid

55
Q

What are two regulatory mechanisms for pyruvate dehydrogenase?

A
  1. High energy ratios (high ATP and NADH) stimulate a kinase and inactive pyruvate DH complex
  2. High ADP and pyruvate inhibit the kinase and Ca2+ stimulates the phosphatase and activates the complex
56
Q

Where is the key active site of regulation?

A

E1

57
Q

What are the two stages of the Citric Acid Cycle?

A
  1. Stage One, two carbon atoms couple to oxaloacetate to form citrate, and two carbons are released as CO2 and citrate is metabolized to a four-carbon molecule.
  2. In Stage Two, the four-carbon molecule is metabolized to regenerated oxaloacetate.
58
Q

What is the reaction that results in Citrate?

A

Oxaloacetate + Acetyl CoA -> Citryl CoA + H20 -> Citrate

59
Q

What enzyme catalyzes the reaction that forms citrate?

A

Citrate Synthase

60
Q

What is the committed step of the citric acid cycle?

A

The Citrate Synthase reaction, which involves sequential binding and induced fit.

61
Q

What are the two decarboxylation reactions that yield CO2 and an energy carrier in the citric acid cycle?

A
  1. Isocitrate is oxidized to prepare it to be decarboxylated to Alpha-ketoglutarate.
  2. Alpha-ketoglutarate is oxidized, decarboxylated and CoA is added to form Succinyl CoA
62
Q

Where does isocitrate come from?

A

Aconitase catalyzes the formation of isocitrate from citrate, which is suitable to be oxidized.

63
Q

What enzyme is used for the first decarboxylation of the citric acid cycle?

A

Isocitrate dehydrogenase

64
Q

What enzyme is used for the second decarboxylation of the citric acid cycle?

A

Alpha-ketoglutarate dehydrogenase

65
Q

What is the first step of the second stage of the citric acid cycle?

A

CoA is cleaved from Succinyl CoA, and the free energy released from the process adds a phosphate to ADP forming ATP.

66
Q

Starting from Succinyl CoA, what are the products of Stage 2 of the citric acid cycle?

A
  1. Succinyl Coa -> Succinate + CoA + ATP
  2. Succinate -> Fumarate + FADH2
  3. Fumarate -> Malate
  4. Malate -> Oxaloacetate + NADH
67
Q

What enzyme is involved in the reaction of Succinyl Coa to form Succinate, CoA and ATP?

A

Succinyl CoA Synthetase

68
Q

What enzyme is involved in the reaction of succinate to form fumarate and FADH2?

A

Succinate Dehydrogenase

69
Q

What enzyme is involved in the reaction of fumarate to form malate?

A

Fumarase

70
Q

What enzyme is involved in the reaction of malate to form oxaloacetate and NADH?

A

Malate Dehydrogenase

71
Q

How many ATP and how many activated electron carriers are formed from one cycle of the citric acid cycle?

A
  1. 3 NADH and 1 FADH2 (4)

2. 1 ATP

72
Q

What is an anapleurotic reaction?

A

A reaction that replenishes cycle components used by another pathway.

73
Q

What is an example of an anapleurotic reaction for the Alcitric acid cycle?

A

Pyruvate carboxylase will replenish Oxaloacetate from Pyruvate (this is the same reaction in gluconeogenesis).

74
Q

What is another source for acetyl CoA if pyruvate is used to make oxaloacetate?

A

Degradation of Fatty Acids

75
Q

What is the purpose of the glyoxylate cycle?

A

Allows the formation of carbohydrates from fats (Acetyl CoA) by bypassing decarboxylation steps. This is a cycle present in plants.

76
Q

What are the three (3) key points of Citric Acid Cycle regulation?

A
  1. Citrate Synthase (inhibited by NADH, citrate, ATP and Succinyl CoA)
  2. Isocitrate dehydrogenase (inhibited by ATP and NADH)
  3. Alpha-ketoglutarate dehydrogenase (inhibited by ATP, succinyl CoA and NADH)
77
Q

What is the electron transport chain?

A

A series of four protein complexes embedded in the inner mitochondrial membrane that result in the reduction of oxygen to water

78
Q

What are the four enzyme complexes of the respiratory chain?

A
  1. NADH-Q Oxidoreductase
  2. Succinate-Q Reductase
  3. Q-cytochrome c oxidoreductase
  4. Cytochrome c oxidase
79
Q

What are the common electron carriers of the four enzyme complexes?

A
  1. FMN
  2. Iron-Sulfur complex
  3. Heme-iron complex (Cytochromes)
  4. mobile carrier CoEnzyme Q
80
Q

Which complexes are proton pumps?

A
  1. NADH-Q Oxidoreductase
  2. Q-cytochrome c oxidoreductase
  3. Cytochrome c Oxidase
    [Succinate-Q Reductase is NOT a proton pump.]
81
Q

What is the first complex that NADH electrons enter and what is the first carrier to recieve them?

A
  1. NADH-Q Oxidoreductase is the complex

2. FMN is the first carrier

82
Q

What is the first complex that FADH2 electrons enter and what is the first carrier?

A
  1. Succinate-Q reductase is the complex

2. First Fe-S and then to ubiquinone (Q)

83
Q

What is the product when Q accepts electrons?

A

QH2

84
Q

The flow of two electrons from NADH to Q results in how many protons being pumped out of the matrix?

A

4

85
Q

what is the function of Q-cytochrome c oxidoreductase?

A

To catalyze the transfer of electrons from QH2 to oxidized cytochrome c (Cyt c) while also pumping out protons.

86
Q

The flow of electrons from QH2 to Cyt c results in how many protons being pumped out of the matrix?

A

2

87
Q

What is the Q cycle?

A
  1. Cytochrome c can only carry one electron, but QH2 carriers two electrons.
  2. QH2 gives cytochrome c one electron and a second Q one electron (forming Qradical) and pumps two proton
  3. A second QH2 gives cytochrome c one electron, and Q radical one electron (forming QH2) and pumps two protons
88
Q

What is the net result of the Q cycle that is related to the proton gradient?

A

4 protons are pumped INTO the intermembrane space, and 2 protons are REMOVED from the mitochondrial matrix, a net result of -6 protons from matrix.

89
Q

What is the function of Cytochrome c oxidase?

A

Catalyze the reduction of molecular oxygen to water

90
Q

What is the net result of cytochrome c oxidase that is Suburelated to the proton gradient?

A
  1. Four protons removed from matrix used to convert O2 to 2H2O
  2. Free energy from conversion of O2 to 2H2O used to pump additional 4 protons
    Net change of -8 protons from matrix.
91
Q

What is ATP Synthase?

A

A protein complex in the mitochondria that converts the proton motive force into ATP

92
Q

What are the two components of the proton-motive force?

A
  1. Chemical gradient

2. Charge gradient

93
Q

Describe the subunits of ATP Synthase

A
  1. Contains F0 and F1 subunits, F0 is embedded in plasma membrane and conducts protons, F1 is in the matrix and is catalytic.
  2. Subunits are connected by the gamma-epsilon stalk.
94
Q

Describe the catalytic activity of the F1 subunit (4 steps)

A
  1. F1 subunit has three beta-subunits that rotate around asymmetric gamma subunit: can be Open, Loose, or Tight depending on orientation relative to gamma.
  2. In the Tight form, ATP is synthesized from ADP and Pi
  3. In the Loose form, ATP or ADP is trapped
  4. In the open form, ATP can be released or ADP can bind.
95
Q

How do the beta subunits switch between O, L and T configurations?

A

The gamma subunit is rotated by the rotating c unit of the F0 subunit when a proton enters the channel. It takes 3 protons for one 360 degree rotation

96
Q

What is the proton/ATP relationship for ATP synthase?

A

Every 120 degree turn, a beta subunit changes from Tight to Open and releases ATP. So one proton = 1 ATP

97
Q

where do protons bind in ATP synthase?

A

An aspartate residue of the c channel

98
Q

How do electrons from cytoplasmic electron carriers reach the impermeable mitochondrial matrix?

A
  1. Glycerol 3-phosphate Shuttle

2. Malate-aspartate shuttle

99
Q

Describe the Glycerol 3-phosphate shuttle (3 steps)

A
  1. Dihydroxyacetone phosphate is converted into Glycerol 3-phosphate through electron transfer from NADH in the cytoplasm
  2. Glycerol 3-phosphate transfers electrons to mitochondrial E-FAD to form E-FADH2
  3. E-FADH2 transfers electrons to Q to form QH2 which can enter matrix.
    .
100
Q

How does ATP from the mitochondrial matrix enter the cell cytosol?

A

ATP-ADP Translocase exchanges 1 mitochondrial ATP for 1 cytoplasmic ADP

101
Q

How many molecules are created from the complete combustoin of glucose?

A

30

102
Q

How many molecules of ATP are created from oxidative phosphorylation?

A

26

103
Q

Where do the additional 4 molecules of ATP come form?

A

Metabolism of glucose to two molecules of pyruvate

104
Q

How many molecules of NADH are formed in glycolysis?

A

2

105
Q

How many molecules of NADH are formed in oxidative decarboxylation of pyruvate into acetyl CoA?

A

2

106
Q

How many molecules of NADH are formed in citric acid cycle?

A

6 (3 * 2 acetyl CoA)

107
Q

How many molecules of FADH2 are formed in citric acid cycle?

A

2 (1*2 acetyl CoA)

108
Q

How many molecules of ATP are made from one NADH in oxidative phosphorylation?

A

2.5

109
Q

How many molecules of ATP are made from one FADH2 in oxidative phosphorylation?

A

1.5

110
Q

What molecule regulates oxidative phosphorylation?

A

ADP (this is called respiratory/acceptor control)

Biochemistry (7 decks)

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