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Biochemistry 501 > Unit 3 > Flashcards

Unit 3 Flashcards

1
Q

Oxidation of which of the following bonds result in energy production by candles, cars, mice, and us?

A

C-H and C-C

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2
Q

What characterizes an oxidation reaction in terms of gain/loss?

A

loss of electrons, gain of oxygen, or loss of hydrogen

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3
Q

What characterizes a reduction reaction in terms of gain/loss?

A

gain of electrons, loss of oxygen, or gain of hydrogen

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4
Q

In what direction do reactions go?

A

NET reactions go towards equilibrium; e.g., if equilibrium = 1.8 M of A and 0.2 M of B and we start with 1.9 M of A and 0.1 M of B, reaction will proceed in the forward direction to reach equilibrium

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5
Q

negative deltaG

A

exergonic reaction, meaning if reaction occurs, will proceed in forward direction; energetically favorable

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6
Q

positive deltaG

A

endergonic reaction, meaning if reaction occurs, will proceed in reverse direction; not energetically favorable

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7
Q

0 deltaG

A

reaction is at equilibrium

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8
Q

enthalpy change (deltaH)

A

difference in bond energies between reactants and products; negative deltaH is exothermic (more stable), positive deltaH is endothermic (less stable)

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9
Q

relationship between deltaH and deltaG

A

exothermic (-deltaH) contributes to favorable deltaG (-deltaG)

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10
Q

entropy change (deltaS)

A

change in “randomness;” positive deltaS is favorable

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11
Q

relationship between deltaS and deltaG

A

positive deltaS contributes to favorable deltaG (-deltaG)

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12
Q

relationship between deltaG and Keq

A

as Keq increases, deltaG becomes more favorable (more negativE); large Keq (>1) means forward reaction is favored and thus deltaG is negative, while small Keq (<1) means reverse reaction is favored and thus G is positive

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13
Q

What do the sign and magnitude of deltaG indicate?

A
  1. Sign of deltaG reveals direction
  2. Magnitude of deltaG indicates how far from equilibrium/how much energy will be released as reaction proceeds to equilibrium
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14
Q

Does thermodynamics (deltaG) predict the rate of a reaction?

A

No, thermodynamics does not predict how rapidly equilibrium is approached, but rather how far a reaction is from equilibrium and the direction it will proceed to get there

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15
Q

Do enzymes change deltaG or Keq?

A

No, enzymes only change deltaGDD (double dagger), which is the activation energy of the transition state

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16
Q

How does ATP provide energy to substrates?

A

Going from less stable to more stable releases more energy, and ATP –> ADP is a massive increase in stability (lots of energy released, large -deltaG); subtrate coupling to this ATP breakdown renders amine formation available

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17
Q

yield of glycolysis

A

From one glucose molecule:
2 net ATP (4 total ATP)
2 NADH
2 pyruvate

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18
Q

What is the purpose of the preparatory stage of glycolysis?

A

the generation of two more energetic molecules (G3P) from a single molecule of glucose

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19
Q

Which reactions in glycolysis are coupled to ATP hydrolysis?

A
  1. Glucose + ATP —-> glucose 6-P + ADP via hexokinase and Mg2+
  2. Fru-6-P + ATP —-> Fru-1,6-bisP + ADP via phosphofructokinase (PFK-1)
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20
Q

How does coupling to ATP breakdown affect deltaG?

A

can allow a reaction that would normally not proceed in the forward direction (+deltaGo) garner a -deltaGo and proceed favorably in the forward direction

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21
Q

overview of glycolysis preparatory stage

A

Step 1-Step 5; 2 ATP are consumed in these steps, generating 2 G3P for the payoff stage

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22
Q

overview of glycolysis payoff stage

A

Step 6-Step 10; 4 ATP, 2 NADH, and 2 pyruvate are produced in these steps; remember that 2 net ATP produced because of consumption in prep stage

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23
Q

Which reactions in glycolysis yield NADH?

A

G3P + P + NAD+ <—-> 1,3-Biphosphoglycerate + NADH; this is the only redox reaction in glycolysis, and the energy of oxidation preserved in phosphate bond and NADH

This occurs twice/glucose (2 G3P generated in prep stage)

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24
Q

Where is the energy of oxidation from the dehydrogenase reaction of glycolysis preserved?

A
  1. Phosphate bond
  2. NADH
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25
Q

What is unique about the dehydrogenase reaction in glycolysis?

A

it is the only redox (oxidation) reaction in glycolysis; is also coupled to the reduction of NAD+

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26
Q

dehydrogenation

A

common redox reaction in which a C-H or C-C bond is oxidized and a cofactor such as NAD+ is reduced (or vice versa)

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27
Q

Do all oxidations involve O2?

A

No, in dehydrogenation, O comes from H2O or a phosphate in dehydrogenase rather than from O2

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28
Q

Which reactions in glycolysis yield ATP (payoff steps)?

A

Both of these occur twice, as glucose has split into two G3P:
1. 1,3-Bisphosphoglycerate + ADP <—-> 3-Phosphoglycerate + ATP via a kinase; first payoff, coupled to substrate level phosphorylation
2. Phosphoenolpyruvate + ADP <—-> Pyruvate + ATP; second payoff

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29
Q

What are inhibitory factors of PFK-1?

A

high energy molecules such as ATP, fatty acids

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30
Q

What are stimulatory factors of PFK-1?

A

low energy molecules such as AMP, ADP

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31
Q

When defines a point of regulation (i.e., when is enzyme regulation necessary)?

A

any irreversible step such as those which involve a large -deltaG or are very far from Keq are points of regulation; enzymes are highly regulated at these points

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32
Q

After glycolysis, what happens to pyruvate?

A
  1. Under aerobic conditions, aerobic respiration involving Acetyl-CoA occurs
  2. Under anaerobic conditions, fermentation occurs
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33
Q

Pasteur effect

A

yeast glucose consumption is much greater under anaerobic conditions than aerobic conditions; that is, only 2 ATP/glucose under anaerobic conditions, but 30 ATP/glucose under aerobic conditions

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34
Q

What is the primary purpose of fermentations (aside from ATP production)?

A

ways to anaerobically regenerate NAD+ from NADH to maintain glycolysis

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35
Q

2 types of fermentation

A
  1. Pyruvate to lactate via lactate dehydrogenase (“Athletes and Alligators”)
  2. Pyruvate to ethanol via pyruvate decarboxylase and alcohol DH (yeast)
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36
Q

lactate dehydrogenase fermentation

A

pyruvate + NADH —-> lactate + NAD+ via lactate dehydrogenase enzyme; used in “Athletes and Alligators”

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37
Q

ethanol fermentation

A

2 step reaction; Step 1 catalyzed by pyruvate decarboxylase, Step 2 carried out by alcohol dehydrogenase (in this step NAD+ is regenerated); CO2 byproduct of first step

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38
Q

What is the unique byproduct of ethanol fermentation?

A

CO2

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39
Q

How does the energy density of ethanol compare to that of glucose?

A

ethanol has much greater energy density (7.1kcal/g) despite glucose having more usable bonds; this is because glucose has a higher percentage of oxidized bonds

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40
Q

Where does glycolysis occur?

A

cytoplasm

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41
Q

Where does pyruvate oxidation occur?

A

mitochondrial matrix

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42
Q

Where does the Citric Acid Cycle occur?

A

mitochondrial matrix

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43
Q

Where does fatty acid oxidation occur?

A

mitochondrial matrix

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44
Q

Where does ATP synthesis via ATP synthase occur?

A

inner membrane of mitochondria

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45
Q

pyruvate oxidation

A

pyruvate + CoASH + NAD+ —-> acetyl-CoA + CO2 + NADH via the pyruvate dehydrogenase complex; energy of oxidation preserved in NADH and thiolester bond of acetyl-CoA

This step is a preparatory one that is required for entry into the Citric Acid Cycle

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46
Q

yield of pyruvate oxidation

A

NADH, CO2, acetyl-CoA per pyruvate
2 NADH, 2 CO2, 2 acetyl-CoA per glucose

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47
Q

Where is energy of pyruvate oxidation preserved?

A
  1. NADH
  2. thiolester bond of acetyl-CoA
48
Q

pyruvate dehydrogenase complex

A

huge regulated enzyme complex with 3 subunits (E1, E2, E3); inhibited by high energy molecules (NADH, ATP, acetyl-CoA) and stimulated by low energy molecules (NAD+, AMP, CoA); TPP and lipoate along with NAD+ and FAD are key cofactors

49
Q

What are the key cofactors of pyruvate dehydrogenase complex?

A
  1. thiamine (TPP)
  2. lipoic acid
50
Q

What occurs at E1 in pyruvate DH?

A

decarboxylation; TPP anion attacks pyruvate; CO2 byproduct

51
Q

What occurs at E2 in pyruvate DH?

A

oxidation; acetyl-CoA product from step 2
1. TPP-pyruvate complex from E1 attacks oxidized lipoic acid
2. CoASH attacks intermediate (lipoic acid is in acylated form), releasing acetyl-CoA and resulting in reduced form lipoic acid

52
Q

What does the “long arm” of oxidized lipoic acid do?

A

on E2, this long arm facilitates shuttling of substrate

53
Q

What occurs at E3 in pyruvate DH?

A

shuttling electrons to NAD+ (carrier), enabling PDH to go another round
1. Reduced form lipoic acid converted to oxidized form, FAD becomes FADH2
2. FADH2 donates its electrons to NAD+, forming FAD and NADH

54
Q

overview of citric acid cycle

A

Per one molecule of acetyl-CoA (remember there are 2 acetyl-CoA/glucose molecule):
Input:
Acetate of Acetyl-CoA (2 C and 4 reduced bonds)

Output:
3 NADH, FADH2, 2 CO2, and a GTP

55
Q

What drives the first step of the citric acid cycle (oxaloacetate to citrate)?

A

large -deltaG of hydrolysis of high-energy (CoA-linked) form of acetate; i.e., “cash in” some of saved energy in PDH reaction

56
Q

progressive oxidation

A

idea of molecules starting in an energy rich, reduced state, and being oxidized through a series of steps until they are energy poor and fully oxidized; dehydrogenases catalyze progressive oxidations in clockwise direction of citric acid cycle

57
Q

How many dehydrogenases are in the Citric Acid Cycle?

A

4

58
Q

How many reduced cofactors are in the Citric Acid Cycle?

A

4

59
Q

alpha-ketoglutarate dehydrogenase complex

A

analogous to PDH; similar E1 and E2, identical E3, energy of oxidation conserved in thiolester bond of Succinyl-CoA and NADH, both thiamine and lipoate are cofactors

60
Q

Which reactions in the citric acid cycle yield FADH2?

A

desaturation (oxidation) reaction that converts succinate (7 oxidizable bonds) to fumarate (6 oxidazable bonds); FAD serves as an e- acceptor in this reaction, yielding FADH2

61
Q

Why is the fumarase reaction of the citric acid cycle unique?

A

it is a hydration reaction; simply prepares substrate for final oxidation

62
Q

How many CO2 molecules are produced per glucose in pyruvate oxidation?

A

2 CO2; one from each pyruvate

63
Q

How many CO2 molecules are produced per glucose in the citric acid cycle?

A

4 CO2; 2 CO2 per acetyl-CoA, 2 acetyl-CoA from 2 pyruvates

64
Q

What is unique about oxaloacetate concentration in the final step of the citric acid cycle (malate to oxaloacetate)?

A

concentrations must be kept extremely low due to the fact that deltaGo is very large and positive; deltaG must be very large and negative, and this low concentration allows for that

65
Q

Warburg effect

A

normal cells produce lactate only when anaerobic, whereas cancer cells produce lactate under both anaerobic and aerobic conditions

66
Q

triacylglycerols vs carbs (energy)

A

with hydration, triacylgycerols have ~6.75x more energy per gram of fat relative to carbohydrate

67
Q

3 steps of fatty acid oxidation

A
  1. Activation - fatty acid joined to CoA
  2. Transport - across inner mitochondrial membrane into matrix
  3. Beta-oxidation - conversion of fatty acid into acetyl-CoA units in mitochondrial matrix
68
Q

How are fatty acids activated?

A

acyl-CoA synthetases react with ATP and CoASH to form fatty acyl-CoA

69
Q

Where does fatty acid activation occur?

A

cytosol of mitochondria; from here, must be transported into the cell

70
Q

What is the role of carnitine acyltransferase I?

A

synthesize fatty acyl-CoA-carnitine complex so it can enter the mitochondrial matrix

71
Q

What is the role of carnitine in fatty acid synthesis?

A

forms a complex with fatty acyl-CoA, allowing it to be transported across the mitochondrial membrane into the matrix

72
Q

What did the Knoop experiment conclude?

A

that fatty acid oxidation is a step-wise breakdown by 2C units and that oxidation occurs at the beta carbon

73
Q

How many acetyl-CoAs are formed from beta-oxidation?

A

n+1 acetyl-CoAs formed from n beta-oxidations; e.g., C8 undergoes 3 beta-oxidations, so 4 acetyl-CoAs formed

74
Q

yield of beta-oxidation

A

A single beta-oxidation yields:
2 acetyl-CoA, 1 FADH2, 1 NADH

These 2 acetyl-CoA can go through citric acid cycle to yield an additional 6 NADH, 2 FADH2, and 2 GTP

75
Q

How many beta-oxidations will a fatty acid undergo?

A

a Cn fatty acid will undergo (n/2)-1 beta-oxidations; e.g., C16 fatty acid will undergo 7 beta-oxidations

76
Q

Why do we subtract 2 ATP from the net yield of beta-oxidation?

A

the activation of palmitate in fatty acid activation requires the breakage of 2 high energy P bonds

77
Q

Can fatty acids be inhibitory?

A

Yes, in animals, fatty acids can inhibit PDH in pyruvate oxidation

78
Q

What is the purpose of the urea cycle?

A

using amino acids for fuel generates toxic NH4+, so we use the urea cycle to eliminate NH4+ in urine as urea

79
Q

detoxification by glutamine synthetase

A

Glutamate + NH3 + ATP —-> Glutamine + ADP; resulting glutamine delivered to liver, where it can go through urea cycle

80
Q

aminotransferase reactions

A

transaminations (swapping amino groups); these reactions always involve glutamate and alpha-ketoglutarate

81
Q

How is aspartate generated for the urea cycle?

A

glutamate reacts with aspartate aminotransferase to form aspartate

82
Q

How is citrulline formed in the urea cycle?

A

Carbamoyl Phosphate + Ornithine

83
Q

What enzyme releases urea?

A

arginase

84
Q

glutamine and glutmate urea cycle reaction

A

Glutamine —-> Glutamate + NH4+ via glutaminase; provides the “first” N for the urea cycle

85
Q

How does NH4+ enter the urea cycle (2 ways)?

A
  1. Glutamine acted on by glutaminase to form glutamate + NH4+. This ammonia reacts with ATP (carbamoyl phosphate synthetase I enzyme) to form carbomoyl phosphate. Carbamoyl phosphate reacts with ornithine to form citrulline
  2. ATP is used to energize citrulline, allowing it to react with aspartate to form argininosuccinate
86
Q

ketogenic amino acids

A

amino acids whose carbons end up in acetate (acetyl-CoA or acetoacetyl-CoA)

87
Q

glucogenic amino acids

A

amino acids whose carbons end up within citric acid cycle intermediates

88
Q

reduction potential (E)

A

affinity for electrons; i.e., tendency to become reduced or oxidized

89
Q

Eo

A

standard reduction potential; more positive Eo in a half-reaction is the reaction that proceeds in the forward direction (i.e., is reduced)

90
Q

path of NADH e- in the electon transport chain

A
  1. Complex I
  2. Ubiquinone
  3. Complex III
  4. cyt C
  5. Complex IV
  6. O2
91
Q

path of succinate/FADH2 e- in the electron transport chain

A
  1. Complex II
  2. Ubiquinone
  3. Complex III
  4. cyt C
  5. Complex IV
  6. O2
92
Q

What electrons enter the ETC at complex I?

A

electrons from NADH

93
Q

What electrons enter the ETC at complex II?

A

electrons from succinate/FADH2

94
Q

Which molecules are oxidized at complex I in the ETC?

A

NADH

95
Q

Which molecules are oxidized at complex II in the ETC?

A

succinate (FADH2 cofactor)

96
Q

Which molecules are oxidized at complex III in the ETC?

A

ubiquinol (QH2)

97
Q

Which molecules are oxidized at complex IV in the ETC?

A

cytochrome c

98
Q

Which molecules are reduced at complex I in the ETC?

A

ubiquinone (Q)

99
Q

Which molecules are reduced at complex II in the ETC?

A

ubiquinone (Q)

100
Q

Which molecules are reduced at complex III in the ETC?

A

cytochrome C

101
Q

Which molecules are reduced at complex IV in the ETC?

A

O2

102
Q

How many protons are pumped at complex I in the ETC?

A

4 (per NADH, which carries 2 e-)

103
Q

How many protons are pumped at complex II in the ETC?

A

none, only increases pool of ubiquinol by reducing ubiquinone via succinate dehydrogenase

104
Q

How does ubiquinol arise in the ETC?

A

Complexes I and II reduce ubiquinone, forming ubiquinol

105
Q

How many protons are pumped at complex III in the ETC?

A

4 (per 2 e-)

106
Q

How many protons are pumped at complex IV in the ETC?

A

2 per 2e-, 4 per O2

107
Q

cytochrome c

A

protein that shuttles electrons between complexes III and IV in the ETC

108
Q

What is the significance of the reaction at complex IV in the ETC?

A

the reduction of O2 to H2O accounts for greater than 99% of the O2 we use

109
Q

How do we defend against reactive oxygen from ETC?

A

glutathione peroxidase enzyme reduced peroxide into water

110
Q

electron transport coupling

A

oxidation/electron transport are coupled to proton pumping; NADH/succinate/FADH2/QH2/cyt c will only be oxidized if proton (H+) pumping can also occur

111
Q

ATP synthesis coupling

A

ATP production is coupled to H+ flow through ATP synthase; protons will not flow through ATP synthase unless the substrates (ADP + P) are present

112
Q

What would happen if the proton gradient were built up to equilibrium (e.g., when ATP synthase not operating to dissipate H+ gradient)?

A

there would be no further net oxidations, e- transport or H+ pumping

113
Q

uncouplers

A

reduce or prevent ATP synthesis, but speed up e- transport

114
Q

DNP and weight loss

A

if you ingested a non-toxic dose of DNP and did not change your eating habits, you would lose weight because glycolysis and lipid catabolism would increase to “keep up” following disruption of ATP synthesis

115
Q

How do uncouplers (e.g., DNP) affect O2 consumption?

A

O2 consumption increases, as the electron transport chain increases; more O2 consumed and converted to H2O at complex IV

116
Q

Is ubiquinone membrane soluble?

A

Yes, ubiquinone is membrane soluble

Biochemistry 501 (4 decks)

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