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Biochem > Ch. 10: Carbohydrate Metabolism II: Aerobic Respiration > Flashcards

Ch. 10: Carbohydrate Metabolism II: Aerobic Respiration Flashcards

1
Q

what are 2 other names for the citric acid cycle?

A
  1. Krebs cycle
  2. tricarboxylic acid (TCA) cycle
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2
Q

in what part of the cell does the TCA cycle occur?

A

the mitochondria

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3
Q

main func: TCA cycle

A

the oxidation of acetyl-CoA to CO2 and H2O

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4
Q

added func: TCA cycle

A

produces the high-energy electron-carrying molecules NADH and FADH2

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5
Q

from what 3 things can acetyl-CoA be obtained?

A

from the metabolism of carbohydrates, fatty acids, and amino acids

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6
Q

summary from Ch. 9 (2_: what happens to the product of glycolysis, pyruvate, after it enters the mitochondrion via active transport

A
  1. it is oxidized and decarboxylated
  2. these rxns are catalyzed by a multienzyme complex (pyruvate dehydrogenase complex), located in the mitochondrial matrix
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7
Q

what 5 enzymes make up the pyruvate dehydrogenase complex?

what do the first 3 work together to do? what do the last 2 do?

A
  1. pyruvate dehydrogenase (PDH)
  2. dihydrolipoyl transacetylase
  3. dehydrolipoyl dehydrogenase
  4. pyruvate dehydrogenase kinase
  5. pyruvate dehydrogenase phosphatase

1-3: work together to convert pyruvate to acetyl-CoA

4-5: regulate the actions of PDH

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8
Q

is the conversion of pyruvate to acetyl-CoA endergonic or exergonic? + image of deltaGknot’

A

exergonic

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9
Q

diagram: overall reaction of pyruvate dehydrogenase complex

A
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10
Q

what inhibits the pyruvate dehydrogenase complex?

A

an accumulation of acetyl-CoA and NADH that can occur if the electron transport chain

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11
Q

why is coenzyme A (CoA) sometimes written as CoA-SH?

A

because CoA is a thiol, containing an -SH group

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12
Q

how does acetyl-CoA form?

A

via covalent attachment of the acetyl group to the -SH group, resulting in the formation of a thioester, which contains sulfur instead of the typical oxygen ester -OR

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13
Q

why is the formation of a thioester during the formation of acetyl-CoA rather than typical ester worth noting?

A

because of the high-energy properties of thioesters

when a thioester undergoes a reaction such as hydrolysis, a significant amount of energy will be released, which can be enough to drive other reactions forward, like the TCA cycle

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14
Q

diagram: mechanism of pyruvate dehydrogenase complex

A
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15
Q

what are 3 pathologies that are associated with a decrease in glucose metabolism and oxidative phosphorylation in the brain?

A
  1. Alzheimer’s disease
  2. Huntington’s disease
  3. alcoholism
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16
Q

decreased amounts of acetyl-CoA, leads to concerns of production of what 2 things?

A
  1. energy
  2. acetylcholine
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17
Q

sequential order of pyruvate dehydrogenase complex enzymes needed to catalyze acetyl-CoA formation

A
  1. Pyruvate dehydrogenase (PDH)
  2. Dihydrolipoyl transacetylase
  3. Dihydrolipoyl dehydrogenase
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18
Q

func: pyruvate dehydrogenase

A

pyruvate is oxidized, yielding CO2, while the remaining 2-C molecule binds covalently to thiamine pyrophosphate (vitamin B1, TPP)

Mg2+ is also required

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19
Q

defn + aka + relationship to PDH: thiamine pyrophosphate (TPP)

A

vitamin B1

a coenzyme held by noncovalent interactions to PDH

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20
Q

3 steps before + func + product: dihydrolipoyl transacetylase

A
  1. the 2C molecule bonded to TPP is oxidized and transferred to lipoic acid (a coenzyme that is covalently bonded to the enzyme)
  2. lipoic acid’s disulfide group acts as an oxidizing agent, creating the acetyl group
  3. the acetyl group is not bonded to lipoic acid via thioester linkage

func: dihydrolipoyl transacetylase catalyzes the CoA-SH interaction with the newly formed thioester link, causing transfer of an acetyl group to form acetyl-CoA

other product: lipoic acid is left in its reduced form

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21
Q

func: dihydrolipoyl dehydrogenase

A
  1. flavin adenine dinucleotide (FAD) is used as a coenzyme in order to reoxidize lipoic acid, allowing lipoic acid to facilitate acetyl-CoA formation in future reactions
  2. as lipoic acid is reoxidized, FAD is reduced to FADH2
  3. in subsequent reactions this FADH2 is reoxidized to FAD, while NAD+ is reduced to NADH
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22
Q

the ultimate production of acetyl-CoA allows what 4 pathways to culminate in the final common pathway of the TCA cycle?

A
  1. fatty acid oxidation (Beta-oxidation)
  2. amino acid catabolism
  3. ketones
  4. alcohol
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23
Q

process/steps (4) + diagram: fatty acid oxidation (beta-oxidation)

A
  1. in the cytosol, a process called activation causes a thioester bond to form between carboxyl groups of fatty acids and CoA-SH
  2. because this activated fatty acyl-CoA cannot cross the inner mitochondrial membrane, the fatty acyl group is transferred to carnitine via a transesterification reaction
  3. once acyl-carnitine crosses the inner membrane, it transfers the fatty acyl group to a mitochondrial CoA-SH via another transesterification reaction
  4. once acyl-CoA is formed in the matrix, beta-oxidation can occur, which removes 2-C fragments from the carboxyl end
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24
Q

char + func in beta-oxidation: carnitine

A

char: a molecule that can cross the inner mitochondrial membrane with a fatty acyl group in tow

func: to carry the acyl group from a cytosolic CoA-SH to a mitochondrial CoA-SH

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25
Q

process (4): amino acid catabolism

A
  1. certain amino acids can be used to form acetyl-CoA
  2. these amino acids must lose their amino group via transamination
  3. their carbon skeletons can then form ketone bodies (so the amino acids are ketogenic)
  4. ketone bodies can be converted to acetyl-CoA
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26
Q

acetyl-CoA is typically used to produce ketones when the pyruvate dehydrogenase complex is inhibited, can the reverse reaction also happen?

A

yes

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27
Q

process (3): alcohol dehydrogenase and acetaldehyde dehydrogenase

A
  1. when alcohol is consumed in moderate amounts, these enzymes convert it to acetyl-CoA
  2. this reaction is accompanied by NADH buildup, inhibiting the Krebs cycle
  3. thus, the acetyl-CoA formed through this process is used mostly to synthesize fatty acids
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28
Q

where does the TCA cycle take place?

A

in the mitochondrial matrix

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29
Q

what does the TCA cycle begin with?

A

the coupling of a molecule of acetyl-CoA to a molecule of oxaloacetate

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30
Q

is oxygen required for the TCA cycle?

A

Not directly required, but the pathway will not occur anaerobically

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31
Q

why will the TCA cycle not occur anaerobically?

A

NADH and FADH2 will accumulate if oxygen is not available for the ETC and will inhibit the cycle

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32
Q

diagram: citric acid cycle

A
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33
Q

TCA cycle step 1: citrate formation (2 + char + eqn)

A
  1. acetyl-CoA and oxaloacetate undergo a condensation reaction to form citryl-CoA, an intermediate
  2. then, the hydrolysis of citryl-CoA yields citrate and CoA-SH (this rxn is catalyzed by citrate synthase)

char: part (2) energetically favors the formation of citrate and helps the cycle revolve forward

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34
Q

defn: synthases

A

enzymes that form new covalent bonds without needing significant energy

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35
Q

TCA step 2: citrate isomerized to isocitrate (4 + char + what is this necessary for + diagram)

A
  1. achiral citrate is isomerized to one of 4 possible isomers of isocitrate
  2. first, citrate binds at 3 points to the enzyme aconitase
  3. then water is lost from citrate, yielding cis-aconitate
  4. water is added back to form isocitrate

char: this results in a switching of a hydrogen and a hydroxyl group

necessary to: facilitate the subsequent oxidative decarboxylation

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36
Q

char: aconitase

A

an enzyme that is a metalloprotein that requires Fe2+

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37
Q

TCA cycle step 3: alpha-ketoglutarate and CO2 formation (2 + diagram)

A
  1. isocitrate is first oxidized to oxalosuccinate by isocitrate dehydrogenase
  2. then oxalosuccinate is decarboxylated to produce alpha-ketoglutarate and CO2
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38
Q

why is step 3 of the TCA cycle (alpha-ketoglutarate and CO2 formation) so important? (3)

A
  1. isocitrate dehydrogenase is the rate-limiting enzyme of the TCA cycle
  2. the first 2 C’s from the cycle is lost here
  3. this is also the first NADH produced from intermediates in the cycle
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39
Q

TCA cycle step 4: succinyl-CoA and CO2 formation (4 char + diagram)

A
  1. these reactions are carried out by the alpha-ketoglutarate dehydrogenase complex (similar in mechanism, cofactors, and coenzymes to the pyruvate dehydrogenase complex)
  2. in the formation of succinyl-CoA, alpha-ketoglutarate and CoA come together and produce a molecule of CO2
  3. this CO2 represents the second and last C lost from the cycle
  4. reducing NAD+ produces another NADH
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40
Q

defn + func + what to look out for: dehydrogenases

A

defn: a subtype of oxidoreductases (enzymes that catalyze a redox reaction)

func: transfer a hydride ion (H-) to an electron acceptor, usually NAD+ or FAD

what to look out for: whenever you see dehydrogenase in aerobic metabolism, lookout for a high-energy electron carrier being formed

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41
Q

TCA cycle step 5: succinate formation (5 char + diagram)

A
  1. hydrolysis of the thioester bond on succinyl-CoA yields succinate and CoA-SH and is coupled to the phosphorylation of GDP to GTP
  2. this rxn is catalyzed by succinyl-CoA synthetase
  3. recall: the hydrolysis of thioester bonds is accompanied by a significant release of energy
  4. thus, phosphorylation of GDP to GTP is driven by the energy released by thioester hydrolysis
  5. once GTP is formed, an enzyme called nucleosidediphosphate kinase catalyzes phosphate transfer from GTP to ADP, producing ATP
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42
Q

func: synthetases

A

create new covalent bonds with energy input

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43
Q

what is unique about step 5 of the TCA cycle: succinate formation?

A

it is the only time in the entire TCA cycle in which ATP is produced directly

ATP production occurs predominantly within the electron transport chain

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44
Q

step 6 TCA cycle: fumarate formation (3)

A
  1. succinate undergoes oxidation to yield fumarate (this is catalyzed by succinate dehydrogenase)
  2. as succinate is oxidized to fumarate, FAD is reduced to FADH2
  3. each molecule of FADH2 then passes the electrons it carries to the electron transport chain, which eventually leads to the production of 1.5 ATP
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45
Q

amount of ATP produced by FADH2 vs. by NADH

A

FADH2 –> 1.5 ATP

NADH –> 2.5 ATP

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46
Q

why is FAD the electron acceptor in step 6 fumarate formation of the TCA cycle?

A

the reducing power of succinate is not great enough to reduce NAD+

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47
Q

what is unique about step 6 of the TCA cycle?

A

it is the only step of the citric acid cycle that doesn’t take place in the mitochondrial matrix, but instead occurs in the inner membrane

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48
Q

why is succinate dehydrogenase considered a flavoprotein? + char

A

because it is covalently bonded to FAD, the electron acceptor in this reaction

this enzyme is an integral protein on the inner mitochondrial membrane

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49
Q

mnemonic: substrates of the citric acid cycle

A

Please Can I Keep Selling Seashells For Money, Officer?

Pyruvate
Citrate
Isocitrate
alpha-Ketoglutarate
Succinyl-CoA
Succinate
Fumarate
Malate
Oxaloacetate

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50
Q

step 7 TCA cycle: malate formation

A

the enzyme fumarase catalyzes the hydrolysis of the alkene bond in fumarate, giving rise to malate

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51
Q

does L-malate or D-malate form in step 7 of the TCA cycle?

A

L-malate only

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52
Q

step 8 TCA cycle: oxaloacetate formed anew

A
  1. the enzyme malate dehydrogenase catalyzes the oxidation of malate to oxaloacetate
  2. a third and final molecule of NAD+ is reduced to NADH
  3. the newly formed oxaloacetate is ready to take part in another turn of the citric acid cycle and we’ve gained all of the high energy electron carriers possible
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53
Q

diagram: step 5-8 TCA cycle

A
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54
Q

what is the net yield from the previous processes starting with pyruvate dehydrogenase complex?

A

PDH Complex: (products: one acetyl-CoA, one NADH)

Pyruvate + CoA-SH + NAD+ –> acetyl-CoA + NADH + CO2 + H+

Citric Acid Cycle: (steps 3, 4, 8 each produce one NADH; step 6 one FADH2; step 5 one GTP, which can be converted to ATP; 2 C’s leave the cycle as CO2; each NADH can be converted to 2.5 ATP, each FADH2 yields 2.5 ATP)

Acetyl-CoA + 3 NAD+ + FAD + GDP + Pi + 2 H2O –> 2 CO2 + CoA-SH + 3 NADH + 3 H+ + FADH2 + GTP

ATP Production:
- 4 NADH –> 10 ATP (2.5 ATP per NADH)
- 1 FADH2 –> 1.5 ATP (1.5 ATP per FADH2)
- 1 GTP –> 1 ATP

Total: 12.5 ATP per pyruvate = 25 ATP per glucose

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55
Q

how many ATP and NADH does glycolysis yield?

A

yields 2 ATP and 2 NADH, providing another 7 molecules of ATP

56
Q

what is the net yield of ATP for one glucose molecule from glycolysis through oxidative phosphorylation?

A

30 - 32 ATP

57
Q

why is there a range of ATP yield from one molecule of glucose?

A

the efficiency of glycolysis varies slightly from cell to cell

58
Q

what is the recurring theme about what inhibits energy production processes?

A

energy products inhibit energy production processes

59
Q

summary + ultimate effect + process (4): pyruvate dehydrogenase complex regulation

A

sum: phosphorylation of PDH facilitated by pyruvate dehydrogenase kinase

ultimate effect: regulates the TCA cycle upstream of its actual starting point

  1. whenever levels of ATP rise, phosphorylating PDH inhibits acetyl-CoA production
  2. conversely, the PDH complex is reactivated by the enzyme pyruvate dehydrogenase phosphatase in response to high levels of ADP
  3. by removing a phosphate from PDH, pyruvate dehydrogenase phosphatase is able to reactivate acetyl-CoA production
  4. Acetyl-CoA also has a negative feedback effect on its own production
60
Q

what happens to Acetyl-CoA production when using alternative fuel sources such as fats?

A

the acetyl-CoA production is sufficient to make it redundant to continue producing acetyl-CoA from carbohydrate metabolism (this is part of why eating a high-fat meal fills you up so quickly)

61
Q

how do ATP and NADH inhibit PDH?

A

as markers of the cell being satisfied energetically

62
Q

what are the 3 essential checkpoints that regulate the TCA cycle from within? what 2 things regulate THOSE?

A
  1. citrate synthase
  2. isocitrate dehydrogenase
  3. alpha-ketoglutarate dehydrogenase complex

regulated by: 1. allosteric activators and 2. inhibitors

63
Q

diagram: checkpoints and regulation of the TCA cycle

A
64
Q

what 4 things inhibit citrate synthase and why/how?

A
  1. ATP and 2. NADH function as allosteric inhibitors of citrate synthase

this makes sense because both are products (indirect and direct, respectively) of the enzyme

  1. citrate and 4. succinyl-CoA allosterically inhibit citrate synthase directly
65
Q

what 2 things inhibit isocitrate dehydrogenase? what 2 things activate it?

what is this enzyme’s func?

A

func: this enzyme catalyzes the TCA cycle

inhibited by: 1. ATP and 2. nADH

allosterically activated by: 1. ADP and 2. NAD+ and enhance its affinity for substrates

66
Q

what 3 things inhibit the alpha-ketoglutarate dehydrogenase complex? what 2 things stimulate it?

A

inhibited by: the reaction products 1. succinyl-CoA and 2. NADH

also 3. ATP (also slows the rate of the cycle when the cell has high levels of ATP)

stimulated by: ADP and calcium ions

67
Q

how do high levels of ATP and NADH affect the TCA cycle?

how do high levels of ADP and NAD+ affect the TCA cycle?

why does this make sense?

A

ATP and NADH –> inhibit TCA cycle

ADP and NAD+ –> promote TCA cycle

rationale: 1. when energy is being consumed in large amounts, more and more ATP is converted to ADP and NADH is converted to NAD+

  1. thus, it is the ATP/ADP ratio and NADH/NAD+ ratio that help determine whether the TCA cycle will be inhibited or activated
  2. during a metabolically active state, ADP and NAD+ levels should rise as ATP and NADH levels decline, thus inducing activation at the previous checkpoints described above, replacing the energy used up by active tissues
68
Q

what is the final common pathway that utilizes the harvested electrons from different fuels in the body?

A

the electron transport chain

69
Q

what is it that is generated by the ETC that ultimately produces ATP? what is NOT?

A

NOT: the flow of electrons

IS: the proton gradient it generates

70
Q

why is the aerobic metabolism the most efficient way of generating energy in living systems?

A

the mitochondrion

the aerobic components of respiration are executed in mitochondria, while anaerobic processes such as glycolysis and fermentation occur in the cytosol

71
Q

where are the assemblies needed to complete oxidative phosphorylation housed?

A

adjacent to the matrix in the inner membrane of the mitochondria

72
Q

func + defn: cristae

A

folds that the inner mitochondrial membrane is assembled into

func: maximize the surface area

73
Q

what is the inner mitochondrial membrane essential for?

A

generating ATP using the proton-motive force

74
Q

defn: proton-motive force

A

an electrochemical proton gradient generated by the complexes of the electron transport chain

75
Q

what is the final step in aerobic respiration?

A

it is actually 2 steps

  1. electron transport along the inner mitochondrial membrane and 2. the generation of ATP via ADP phosphorylation

the two processes are separate entities, but very much coupled

76
Q

process (5): final step of aerobic respiration (1. electron transport along the inner mitochondrial membrane and 2. the generation of ATP via ADP phosphorylation)

A
  1. the electron-rich molecules NADH and FADH2 are formed as byproducts at earlier steps in respiration
  2. they transfer their electrons to carrier proteins located along the inner mitochondrial membrane
  3. finally, these electrons are given to oxygen in the form of hydride ions (H-) and water is formed
  4. while this is happening, energy released from transporting electrons facilitates proton transport at 3 specific locations in the chain
  5. protons are moved from the mitochondrial matrix into the intermembrane space of the mitochondria, thereby creating a greater concentration gradient of hydrogen ions that can be used to drive ATP production
77
Q

is the formation of ATP endergonic or exergonic? what about electron transport?

A

ATP formation is endergonic

electron transport is exergonic

78
Q

given that ATP formation is endergonic and electron transport is exergonic, what impact is had by coupling these reactions?

A

the energy yielded by one reaction can fuel the other

79
Q

what must be true in order for energy to be harnessed via electron transport reactions?

A

the proteins along the inner membrane must transfer the electrons donated by NADH and FADH2 in a specific order and direction

80
Q

what is the physical property that determines the direction of electron flow?

A

reduction potential

81
Q

if you pair two molecules with different reduction potentials, which is oxidized and which is reduced?

A

the molecule with the HIGHER potential will be reduced

the molecule with the LOWER potential will be oxidized

82
Q

how can we think of the ETC in terms of oxidation and reduction?

A

it is nothing more than a series of oxidations and reductions that occur via the same mechanism

83
Q

is NADH a good or bad electron donor?

A

good

84
Q

what makes oxygen a great final acceptor in the electron transport chain?

A

its high reduction potential

85
Q

diagram: respiratory complexes on the inner mitochondrial membrane

A

note: steps 1 and 2 of complex III are drawn as the two separate steps here for clarity; however the same CoQH2-cytochrome c oxidoreductase complex is used for both steps

86
Q

what are the 4 complexes of the electron transport chain?

A
  1. Complex I = NADH-CoQ oxidoreductase
  2. Complex II = Succinate-CoQ oxidoreductase
  3. Complex III = CoQH2-cytochrome c oxidoreductase
  4. Complex IV = cytochrome c oxidase
87
Q

struct + main func + char: complex I (NADH-CoQ oxidoreductase

A

main func: the transfer of electrons from NADH to coenzyme Q (CoQ) is catalyzed here

struct: has over 20 subunits

one of 3 sites where proton pumping occurs, as 4 protons are moved to the intermembrane space

88
Q

what are the 2 highlighted subunits of complex I?

A
  1. a protein that has an iron-sulfur cluster
  2. a flavoprotein that oxidizes NADH
89
Q

what coenzyme does the flavoprotein have bonded to it? how is it bonded to it?

A

flavin mononucleotide (FMN)

covalently bonded

90
Q

what is FMN similar to in structure?

A

FAD (flavin adenine dinucleotide)

91
Q

process: complex I reactions + equations

A
  1. NADH transfers its electrons over to FMN, thus become oxidized to NAD+ as FMN is reduced to FMNH2
  2. the flavoprotein becomes reoxidized while the iron-sulfur subunit is reduced
  3. finally, the reduced iron-sulfur subunit donates the electrons it receive from FMNH2 to coenzyme Q (aka ubiquinone)
  4. Coenzyme Q becomes CoQH2
92
Q

what is the net effect of complex I? (words + equation)

A

passing high-energy electrons from NADH to CoQ to form CoQH2

93
Q

main func + where does it receive electrons from + char: complex II (succinate-CoQ oxidoreductase)

A

main func: complex II transfers electrons to coenzyme Q

receives electrons from: succinate (a TCA cycle intermediate)

char: no hydrogen pumping occurs here to contribute to the proton gradient

94
Q

process (4) + equations: complex II reactions

A
  1. succinate is oxidized to fumarate upon interacting with FAD which is covalently bonded to complex II
  2. once succinate is oxidized, it is converted to FADH2
  3. after this, FADH2 gets reoxidized to FAD as it reduces an iron-sulfur protein
  4. the final step reoxidizes the iron-sulfur protein as coenzyme Q is reduced
95
Q

why does it make sense that succinate dehydrogenase is a part of complex II?

A

succinate dehydrogenase is responsible for oxidizing succinate to fumarate in the TCA cycle

96
Q

what is the net effect of complex II (words + eqn)?

A

passing high-energy electrons from succinate to CoQ to form CoQH2

97
Q

how can ubiquinone be created from its corresponding phenol?

A

by oxidation and represents an example of a quinone (2,5-cyclohexadiene-1,4-diones)

98
Q

aka + main func: complex III (CoQH2-cytochrome c oxidoreductase)

A

aka: cytochrome reductase

func: facilitates the transfer of electrons from coenzyme Q to cytochrome c in a few steps

99
Q

defn: cytochromes

A

proteins with heme groups in which iron is reduced to Fe2+ and reoxidized to Fe3+

100
Q

process (6) + diagram: complex III reactions

A

overall: involves the oxidation and reduction of cytochromes

  1. in the transfer of electrons from iron, only one electron is transferred per reaction, but because coenzyme Q has two electrons to transfer, 2 cytochrome c molecules will be needed
  2. complex III’s main contribution to the proton-motive force is via the Q cycle
  3. in the Q cycle, two electrons are shuttled from a molecule of ubiquinol (CoQH2) near the intermembrane space to a molecule of ubiquinone (CoQ) near the mitochondrial matrix
  4. another two electrons are attached to heme moieties, reducing two molecules of cytochrome c
  5. a carrier containing iron and sulfur assists this process
  6. in shuttling these electrons, 4 protons are displaced to the intermembrane space; therefore the Q cycle continues to increase the gradient of the proton-motive force across the inner mitochondrial membrane
101
Q

are coenzyme Q and cytochrome c part of the complexes of the ETC?

A

no

however, because both are able to move freely in the inner mitochondrial membrane, this degree of mobility allows these carriers to transfer electrons by physically interacting with the next component of the transport chain

102
Q

explain how cyanide is an inhibitor of cytochrome subunits a and a3

A

the cyanide anion is able to attach to the iron group and prevent the transfer of electrons

thus, tissues that rely heavily on aerobic respiration such as the heart and CNS can be greatly impacted

103
Q

func + components: complex IV (cytochrome c oxidase)

A

func: facilitates the culminating step of the electron transport chain: transfer of electrons from cytochrome c to oxygen, the final electron acceptor

components: includes subunits of cytochrome a, cytochrome a3, and Cu2+ ions

104
Q

what do cytochrome a and cytochrome a3 make up together?

A

cytochrome oxidase

105
Q

process + char + equations: complex IV reactions

A
  1. through a series of redox reactions, cytochrome oxidase gets oxidized as oxygen, becomes reduced, and forms water
  2. this is the final location on the transport chain where proton pumping occurs, as two protons are moved across the membrane
106
Q

what 2 things happen simultaneously as [H+] increases in the intermembrane space?

A
  1. pH drops in the intermembrane space
  2. matrix increases due to proton pumping
107
Q

what impact do these two changes (1. pH drops in the intermembrane space
2. matrix increases due to proton pumping) contribute to?

A

an electrochemical gradient (a gradient that has both chemical and electrostatic properties)

108
Q

why is the electrochemical gradient across the inner mitochondrial membrane called the proton-motive force?

A

because it is basesd on protons

109
Q

func: electrochemical gradient

A

stores energy

110
Q

func: ATP synthase

A

harness the energy of the electrochemical gradient to form ATP from ADP and an inorganic phosphate

111
Q

what is the variable efficiency of aerobic respiration (producing a range of 30-32 net ATP yield per glucose) caused by?

A

by the fact that cytosolic NADH formed through glycolysis cannot directly cross into the mitochondrial matrix

112
Q

how is cytosolic NADH transported since it cannot directly contribute its electrons to the transport chain?

A

it must find alternate means of transportation (shuttle mechanisms)

113
Q

func: shuttle mechanism

A

transfers the high-energy electrons of NADH to a carrier that can cross the inner mitochondrial membrane

114
Q

how much ATP is produced with the shuttle mechanisms?

A

depending on which of the two shuttle mechanisms NADH participates in, either 1.5 or 2.5 ATP

115
Q

what are the 2 shuttle mechanisms?

A
  1. glycerol 3-phosphate shuttle
  2. malate-aspartate shuttle
116
Q

process (4) + diagram: glycerol 3-phosphate shuttle

A
  1. the cytosol contains one isoform of glycerol-3-phosphate dehydrogenase, which oxidizes cytosolic NADH to NAD+ while forming glycerol 3-phosphate from dihydroxyacetone phosphate (DHAP)
  2. on the outer face of the inner mitochondrial membrane, there exists another isoform of glycerol-3-phosphate dehydrogenase that is FAD-dependent
  3. this mitochondrial FAD is the oxidizing agent, and ends up being reduced to FADH2
  4. once reduced, FADH2 proceeds to transfer its electrons to the ETC via complex II, thus generating 1.5 ATP for every molecule of cytosolic NADH that participates in this pathway
117
Q

process (6) + diagram: malate-aspartate shuttle

A
  1. cytosolic oxaloacetate, which cannot pass through the inner mitochondrial membrane, is reduced to malate which can (this is accomplished by cytosolic malate dehydrogenase)
  2. accompanying this reduction is the oxidation of cytosolic NADH to NAD+
  3. once malate crosses into the matrix, mitochondrial malate dehydrogenase reverses the reaction to form mitochondrial NADH
  4. now that NADH is in the matrix, it can pass along its electrons to the ETC via complex I and generate 2.5 ATP per molecule of NADH
  5. recycling the malate requires oxidation to oxaloacetate, which can be transaminated to form aspartate
  6. aspartate crosses into the cytosol and can be reconverted to oxaloacetate to restart the cycle
118
Q

what is the payout site of aerobic respiration?

A

ATP synthesis

119
Q

where does the link between electron transport and ATP synthesis start with?

A

a protein complex called ATP synthase which spans the entire mitochondrial membrane and protrudes into the matrix

120
Q

what is the significance of the fact that a small fraction of polypeptides that are necessary for oxidative phosphorylation are encoded by mitochondrial DNA?

A

mitochondrial DNA has a mutation rate nearly ten times higher than that of nuclear DNA

121
Q

how does the proton-motive force interact with ATP synthase?

A

it interacts with the portion of the ATP synthase that spans the membrane (the F0 portion)

122
Q

func: F0

A

functions as an ion channel, so protons travel through F0 along their gradient back into the matrix

123
Q

defn: chemiosmotic coupling

A

happens at the same time as F0’s function

allows the chemical energy of the gradient to be harnessed as a means of phosphorylating ADP, thus forming ATP

in other words, the ETC generates a high concentration of protons in the intermembrane space; the protons then flow through the F0 channel of ATP synthase back into the matrix

124
Q

what happens to F1 portion (the other portion of ATP synthase) at the same time as chemiosmotic coupling and the F0 functionality?

A

F1 portion utilizes the energy released from this electrochemical gradient to phosphorylate ADP to ATP

125
Q

diagram + summary: ATP synthase reaction

A

ATP synthase generates ATP from ADP and inorganic phosphate by allowing high-energy protons to move down the concentration gradient created by the ETC

126
Q

char: chemiosmotic coupling

A
  1. describes a direct relationship between the proton gradient and ATP synthesis
  2. it is the predominant mechanism accepted in the scientific community when describing oxidative phosphorylation
127
Q

char + process: conformational coupling

A

char: 1. suggests that the relationship between the proton gradient and ATP synthesis is indirect

defn: 1. ATP is released by the synthase as a result of conformational change caused by the gradient
2. the F1 portion of ATP synthase is reminiscent of a turbine spinning within a stationary compartment to facilitate the harnessing of gradient energy for chemical bonding

128
Q

how much energy was required to generate ATP? and why does this make sense?

A
  1. when the proton-motive force is dissipated through the F0 portion of ATP synthase, the free energy change of the reaction is (see picture), a highly exergonic reaction
  2. this makes sense because phosphorylating ADP to form ATP is an endergonic process. so by coupling these reactions, the energy harnessed from one reaction can drive another
129
Q

defn: uncouplers

A

compounds that prevent ATP synthesis without affecting the ETC, thus greatly decreasing the efficiency of the ETC/oxidative phosphorylation pathway

130
Q

when ADP builds up and ATP synthesis decreases, how does the body respond to this perceived lack of energy?

A

by increasing O2 consumption and NADH oxidation

the energy produced from the transport of electrons is released as heat

131
Q

why isnt it surprising that the rates of oxidative phosphorylation and the TCA cycle are closely coordinated?

A

because the TCA cycle provides the electron-rich molecules that feed into the ETC

131
Q

what are the 2 key regulators of oxidative phosphorylation?

A
  1. O2
    2 .ADP
132
Q

what happens if O2 is limited in oxidative phosphorylation? (3)

A
  1. the rate of ox phos decreases
  2. the concentrations of NADH and FADH2 increase
  3. the accumulation of NADH inhibits the TCA cycle
133
Q

defn: respiratory control

A

the coordinated regulation of the TCA cycle and oxidative phosphorylation

134
Q

in the presence of adequate O2, what is the rate of ox phos dependent on?

A

the availability of ADP

135
Q

how are the concentrations of ADP and ATP related? (sum + 3)

A

sum: they are reciprocally related

  1. an accumulation of ADP is accompanied by a decrease in ATP and the amount of energy available to the cell (so ADP accumulation signals the need for ATP synthesis)
  2. ADP allosterically activates isocitrate dehydrogenase, thus increasing the rate of the TCA cycle and the production of NADH and FADH2
  3. the elevated levels of these reduced coenzymes, in turn, increase the rate of electron transport and ATP synthesis

Biochem (12 decks)

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