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BIOC2005 CH > 9. Respiratory Chains and ATP synthesis > Flashcards

9. Respiratory Chains and ATP synthesis Flashcards

1
Q

What is the average energy requirement of a person?

A

100W (standard electric lightbulb), required to keep the body running

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2
Q

How does the amount of mitochondria vary between cells?

A

Muscle/Brain cells have lots, RBCs have none

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3
Q

How may the shape of mitochondria vary?

A

May form reticular networks or be sausage shaped

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4
Q

What is the name of the inner/outer bits of the mitochondria? What does each contain?

A

Matrix (inner cytoplasm): contains metabolic enzymes (CAC, AA metab. urea synthesis)

Inner membrane: contains respiratory chain machinery, ATP synthase, highly invaginated

Outer membrane: dunno

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5
Q

Where does the energy for ATP synthesis come from?

A

Stuff we eat: sugars metabolised to pyruvate, pyruvate oxidised, FA oxidised

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6
Q

What is the name of the pathway that oxidises sugars to pyruvate?

A

Glycolysis

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7
Q

What is the name of the cycle that oxidises pyruvate to CO2?

A

Citric acid cycle/TCA cycle/Krebs cycle in the mitochondrial matrix

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8
Q

Where does FA oxidation occur?

A

Mitochondrial matrix

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9
Q

How is pyruvate transported into the mitochondrial matrix?

A

OMM has pores to allow pyruvate through, then IMM has pyruvate transporter which allows pyruvate to meet with the TCA enzymes present in the Mitochondrial matrix

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10
Q

Where does glycolysis occur?

A

in the cytoplasm, release pyruvate and NADH which are needed in the mitochondrial matrix

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11
Q

After pyruvate is imported into the mitochondria matrix, what occurs?

A
  1. Acetyl group of pyruvate is attached to CoA to form Acetyl CoA (ACA), NADH is produced
  2. ACA enters TCA cycle where it is oxidised to CO2 producing 3 more NADH’s

1 Pyruvate –> ACA –> Citrate –> Isocitrate -(NADH OUT)-> alpha-ketoglutarate -(NADH OUT)-> succinate –> fumarate –> malate -(NADH OUT)-> OAA –> Citrate

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12
Q

How is cytosolic NADH imported into the matrix?

A

The IMM is impermeable to NADH so a malate-aspartate substrate shuttle is used

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13
Q

Describe the process of the malate-aspartate substrate shuttle

A
  1. NADH produced in glycolysis converts cytoplasmic OAA into malate
  2. Malate transported into matrix by anti porter (malate in, alpha keto glutarate out)
  3. Malate oxidised by malate dehydrogenase (TCA enzyme) which regenerates NADH and produces OAA
  4. OAA reacts with glutamate to regenerate alpha-keto-glutarate and aspartate
  5. Aspartate then leaves matrix through second anti porter which simultaneously allows glutamate in
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14
Q

Why is NADH needed for the ETC?

A

It is electron rich, so is the electron donor

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15
Q

How many NAHD, FADH2 and ATP does one molecule of glucose produce?

A

1 glucose = 2 pyruvate

Glycolysis: 2 NADH, 2 ATP

Pyruvate Oxidation: 2 NADH

TCA: 6 NADH, 2 FADH2, 2ATP/GTP

Total: 10 NADH, 2 FADH2, 4 ATP from oxidation of one glucose molecule

Total ATP: 34 ATPs

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16
Q

How do mitochondria make ATP?

A

Electron rich products of glycolysis/PO/TCA (NADH, FADH2) are used as electron donors to pass along ETC, pump protons and reduce O2 to H2O. Proton motive force generated is used to drive ATP synthase

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17
Q

What are the 6 key features of chemiosmotic coupling?

A
  1. ETC and ATP synthase embedded in same membrane (IMM)
  2. IMM is proton impermeable
  3. ETC has reaction sites in contact with either side of IMM
  4. Electron transfer results in proton uptake at one side and proton release at the other (pumping)
  5. Reactions result in pH and charge difference across the IMM
  6. Protons can pass back across the IMM through ATP synthase, providing energy for ATP synthesis
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18
Q

What is a vectorial redox loop?

A

A system involving alternating electron transfer components and components which change pkAs and cause proton uptake

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19
Q

What is another name for coenzyme Q?

A

Ubiquinone (YOO-BICK-WEEN-OWN)

Alternative pronunciation: Ubby-queenie-neenie-oonie-eenie

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20
Q

What is the role of ubiquinone? How does it carry out it’s function (2)?

A

A hydrogen atom carrier

  1. Benzene ring of ubiquinone takes up 2e- and causes the pKa’s on it’s two oxygens to change from low to high. This causes proton uptake. Occurs at the quinone reduction site
  2. Ubiquinol then diffuses across the membrane and reaches the quinoa oxidation site where oxidation occurs and protons are released to IMS
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21
Q

Describe the 4 respiratory chain components

A

Complex I: NADH:Ubiquinone oxidoreductase - oxidases NADH, 45 subunits

Complex II: Succinate:ubiquinone oxidoreductase - oxidises succinate, 4 subunits

Complex III: ubiquinol:cytochrome c oxidoreductase - passes electrons via Cyt C to IV, 11 subunits

Complex IV: Cytochrome C oxidase - converts O2 –> H2O, 13 subunits

Complex V: ATP synthase, 12 subunits

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22
Q

What are the prosthetic groups of each complex?

A

I: FMN, 8 Fe-S

II: FAD, 3 Fe-S, heme B

III: Fe-S, 2 heme B, heme C

IV: CuA, CuB, 2 heme A

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23
Q

How were the ETC complexes discovered (4)?

A
  1. Cell was first lysed, the mitochondria treated with digitonin to rupture them
  2. Outer membrane fragments were discarded, leaving the inner membrane fragments
  3. IMM fragments were solubilised with detergent then separated using ion exchange chromatography
  4. Each complex was separated into a different test tube where in vitro reactions were carried out to find the reactions which the complexes catalysed
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24
Q

What experiment was conducted to determine the rotation of ATP synthase?

A

His-tagged head group of ATP synthase and stuck to a glass slide. Attached actin filament w’ fluorescent molecules to rotary c ring. Watched actin filament rotate in real time.

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25
Q

How much ATP is there present in the body at any one time? How much ATP is made by the body each day?

A

3-4g in body

65kg made per day

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26
Q

What is ATP made up of?

A

Adenine, Ribose, Phosphate groups

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27
Q

What are the subunits of ATP synthase?

A

Split into two main groups F0 and F1. F1 particle is the head and stalk region, and F0 is a pore

c ring - a pore made up of identical c subunits - rotates, drive by proton motive force

b stator - holds the head stationary

a - binds b stator to c ring, helps protons bind to c ring

epsilon - binds lambda stalk to c ring

lambda stalk - confers rotary action from c ring to head groups

alpha/beta - head groups bind ADP/ATP/Pi

delta - Links F0 and F1

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28
Q

How does the c ring of ATP synthase rotate?

A

Each c subunit contains aspartate and two half channels.

H+ from cytosol diffuses via half channel to asp on C ring subunit c1, neutralising it. Subunit can now move to interface membrane allowing ring to rotate. c9 interfaces with matrix and half channel allows H+ to diffuse into the matrix.

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29
Q

What is the H+/Stoichiometry of ATP synthase? How does it vary with species?

A

One complete rotation of c ring produces 3 ATPs

Yeast has 10 c subunits in ring –> 3.33 protons/ATP

Humans have 8 c subunits in ring so –> 2.67 protons/ATP

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30
Q

What is the correlation between no. of subunits in C ring and strength of energy source?

A

Weaker energy sources require more subunits

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31
Q

How is the ATP transferred into the cytoplasm?

A

Strict exchange process - ATP exported and ADP/Pi brought back in - costs one proton from the proton motive force

Phosphate translocase symporter moves H2PO4- and H+ into matrix from IMS.

Adenine nucleotide translocase anti porter takes ATP4- out of cell and imports ADP3-

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32
Q

What are the four types of Fe-S cluster?

A

2Fe-2S, 2Fe-2S Rieske, 3Fe-4S and 4Fe-4S

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33
Q

What are Fe-S clusters? How doe they vary?

A

Prosthetic groups which accept/donate 1 electron along ETC. The different types can vary in the amount of iron/sulphur which gives them different properties. Wildly varying redox potentials.

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34
Q

What is the role of the haem cofactor? What are the different types of haem cofactor in humans? How do they vary?

A

One electron donor/acceptor

A: high potential, h’phobic tail
B: quite low potential
C: quite high potential, covalently linked to protein

Present in bacteria: D, O

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35
Q

What haem group does cytochrome c contain?

A

Covalently linked Haem C group, transfers electrons from complex III to complex IV

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36
Q

What are the two main types of flavin cofactor? What is their role?

A

FMN (flavin mononucleotide) and FAD (flavin adenine dinucleotide)

Accept 2H (2e- + 2H+) but may give up e- one at a time

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37
Q

Where are the FMN and FAD cofactors present?

A

FMN is found in complex I

FAD is found in complex II (& other dehydrogenases)

FMN and FAD both have quite low potentials

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38
Q

What is the reduce potential so oft mentioned in these slides?

A

A measure of the tendency of a chemical species to acquire electrons. High potential means higher affinity for electrons.

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39
Q

Describe the structure of complex I

A

NADH:ubiquinone oxidoreductase

  • 45 subunits (7 encoded by mtDNA)
  • huge I shaped structure - one arm in membrane, other arm projects into matrix
  • hydrophobic proteins in membrane arm (hydrophilic inside), 4 H+ pumping subunits
  • metal centres (8Fe-S) in hydrophilic matrix arm
  • long alpha helix runs along h’phobic arm back toward hydrophilic arm
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40
Q

How does complex I pump protons across the membrane?

A
  1. Ubiquinone enters hydrophilic arm
  2. NADH reduces FMN present in hydrophilic arm
  3. Electron potential carried to ubiquinone to reduce it to ubiquinol
  4. Ubiquinol then causes a conformational change of the hydrophobic arm which causes protons to be bound at one side and pushed out the other
41
Q

What is the difference between bacterial and mammalian complex I?

A

Bacterial has same core proteins but human has loads of extra proteins around the outside which we don’t know what they do

42
Q

What is the structure of complex II?

A

Succinate Dehydrogenase - not involved in proton translocation

Small chain of ETC components: FAD, 3 Fe-S clusters, Haem B (structural - glue)

43
Q

What is the overall reaction of complex I?

A

NADH2 + ubiquinone + 4H+ matrix –> NAD + ubiquinol + 4H+ cytosol

44
Q

How is succinate oxidised in complex II?

A

Succinate oxidised to fumarate by FAD, electrons passed down through Fe-S clusters to reduce ubiquinone to ubiquinol

45
Q

What is the overall reaction of complex II?

A

Succinate + Ubiquinone –> Fumarate + Ubiquinol

46
Q

What is the structure of complex III?

A

Ubiquinol:cytochrome C oxidoreductase OR Coenzyme Q

3-11 subunits. 3 subunits with prosthetic groups:

  • cytochrome b subunit - 2 Heme B
  • cytochrome c subunit - 1 Heme C
  • Iron sulphur subunit - 1 2Fe-2S Rieske cluster
47
Q

How is the electron and proton transfer coupled in complex III?

A

The Q Cycle (It’s James Bond’s bicycle)

  1. Ubiquinol is oxidised releasing 2H+ into the cytosol
  2. one electron passes to Cytochrome C through the FeS cluster
  3. The other electron is transferred across membrane to ubiquinone reduction site
  4. A second ubiquinol is oxidised in the same way (2 electrons are now in the quinone reduction site (Qi))
  5. A ubiquinone is then reduced in the Qi site and two protons are taken up from the matrix
48
Q

What is the overall reaction of complex III?

A

Ubiquinol + 2cyt c3+ + 2H+ matrix –> ubiquinone + 2cyt c2+ + 4H+ cytosol

49
Q

What occurs in the CcO reaction (complex IV)?

A
  1. 4 electrons are transferred from Cyt C
  2. Electrons are passed one at a time through CuA and Haem a (metal containing centres) to the binuclear centre (BNC - haem a3/Cub)
  3. Oxygen also binds to the BNC and the 4 electrons reduce it to water (with four protons from mitochondrial matrix)
  4. The reduction of O2 to 2H2O also causes the pumping of 4H+ from the matrix into the IMS
  5. This creates a pH and charge gradient which generates the PMF
50
Q

What is the overall reaction of complex IV?

A

4 cyt c2+ + O2 + 8H+in –> 4 cyt c3+ + 2 H2O + 4H+out

51
Q

How many additional subunits of mammalian CcO are there compared to bacteria CcO?

A

10 additional subunits, not sure what they do but not involved in electron/proton transfer reactions, probs assembly, structure, control

52
Q

What metal centres do all CcO’s contain?

A

Binuclear copper site CuA - like an Fe-S cluster but with Cu instead of Fe

Haem a - 6 coordinate bis-HIS-ligated heme A

Haem a3/CuB binuclear centre - 5 coordinate hem A and a HIS-coordinated copper

53
Q

What is the role of the three subunits in CcO?

A

I: contains the BNC, Haem a (& Mg(II) in mammals)

II: contains CuA - docking site for Cyt C

III: no cofactors but is where oxygen enters (then binds to CuB in I)

54
Q

What is the electron transfer route from Cyt C in CcO?

A

Cyt C –> CuA –> Haem a –> BNC –> O2

55
Q

How do protons enter CcO/complex IV?

A

Through subunit I

56
Q

Describe the binuclear centre of complex IV

A

Haem a3 and CuB are kinda flat against each other, the Cu of CuB is coordinated with 3 His ligands and the Fe of Haem is coordinated with one His ligand. The distance between the metal ions is 5 angstroms.

57
Q

Describe the overall proton stoichiometries of each complex of the ETC

A

I: 4H+ pumped into IMS
II: nada
III: 4H+ pumped into IMS
IV: 2H+ pumped into IMS per each water molecule generated
V: 8/10H+ travels form IMS to matrix generating 3ish ATP

58
Q

What may be an alternative fate of cytosolic NADH? Where does this occur in the body?

A

Glycerol 3 Phosphate Dehydrogenase!

Rather than transporting NADH into mitochondria G3PDH uses it to directly donate electrons into ubiquinone pool.

NADH reduces dihydroxyacetone phosphate which is then reoxidised by G3PDH and FAD to produce FADH2 (which can donate electrons into ubiquinone pool)

This process occurs in the brain

59
Q

What are the pros and cons of using G3PDH to oxidise NADH and produce FADH2?

A

Pros: Quicker than using complex I
Cons: less energy efficient

60
Q

What do most extra respiratory chain components do? Give an example of two

A

Feed directly into ubiquinone pool

Dihydroorotate dehydrogenase (DHO->O)- has FMN, DNA->RNA metabolism

Choline Dehydrogenase (Ch->betaine-aldehyde)- cholesterol biosynthetic pathway

61
Q

What further components of the ETC are present in yeast/algae/higher plants?

A
  • Extra & simpler NADH-ubiquinone oxidoreductases (NDH-2) on either face of IMM
  • Ubiquinol oxidase on matrix side of IMM

Neither of these are coupled to proton pumping

62
Q

What does NDH-2 do?

A

NADH->NAD

63
Q

Describe the structure of the NDH-2 and ubiquinol oxidase

A

NDH-2: single polypeptide, attach to membrane via h’phobic patch, contain FAD that directly reduces ubiquinone

UO: single polypeptide, attach to membrane via h’phobic patch, non-haem di-iron carboxylate active site that oxidises ubiquinol & reduces O2

64
Q

In what situation may a plant be trying to get metabolic flux (rate of molecular turnover) as fast as possible (not limited by ATP synthesis)?

A

Seed Germination, the focus here is not on getting maximum energy from food sources (as have enough) it is just growing super fast

65
Q

Give an example of a type of plant which may uncouple the respiratory chain

A

The type of plant which heats up a spike - in order to generate smells or suchlike e.g. Devils Tongue.

Throws energy away as heat by uncoupling ETC burning up all the starch

66
Q

Which protozoan pathogen relies only on ubiquinol oxidase?

A

Trypanosoma brucei (sleeping sickness) utilises G3PDH and ubiquinol oxidase to generate metabolic flux (without proton motive force). They focus on generating products to enable growth.

67
Q

HOW DOES TRYPANOSOME BRUCEI CREATE A PMF?

A

Sorry Caps Lock

ATP is used to generate a proton gradient. ATP synthase used in reverse, hydrolyses ATP to push protons out.

68
Q

Why does a PMF need to be generated in cells not using the PMF to generate energy?

A

The proton gradient can be used to drive flagella

69
Q

How did mitochondria originate?

A

Initially cell only undertook glycolysis. Bacteria invaded cell and become mitochondria :)

70
Q

What the evidence of the bacterial origin of mitochondria?

A

Mitochondria look like bacteria, have bacterial ribosomes and homologues of all major reparatory components can be found in bacteria. Also DNA repair system of mtDNA is different to regular DNA

71
Q

Why does the mtDNA have more mutations than regular DNA?

A

Only has mitochondrial repair system, and near to ETC which can cause many short circuits (free radicals, electrons, dangerous place!)

72
Q

How many proteins does mtDNA code for?

A

13 proteins w/ different tRNAs with different nuclear code! wuttttt

73
Q

How do oxidases vary between bacteria and eukaryotes?

A

bovine - haem a and haem a3
e. coli - haem b and haem o3 (no CuA)

Different haem groups
Copper binds elsewhere
Different number of haem groups
Different number of copper bound

74
Q

Give some alternative anaerobic oxidants (in order from strongest to weakest)

A

O2, NO3-(–>NO2-), Fumarate, SO42-(–>H2S)

75
Q

Give some alternative reductants in order from strongest to weakest

A

H2, H2S, NO3-

76
Q

What is menaquinone?

A

Similar to ubiquinone but with a lower redox potential

77
Q

Give some examples of bacterial electron sources and sinks

A

Look on slide 20 PR4

78
Q

What do the wide variety of donors and acceptors allow bacteria to do?

A

Adapt easily to different environments e.g. repairing aerobically or anaerobically

79
Q

How does the Paracoccus denitrificans ETC vary depending on whether its present in aerobic or anaerobic conditions?

A

In aerobic conditions pretty similar to our ETC but in anaerobic complex III is skipped and Nitrate reductase (NO3- –> NO2-) is used instead of complex IV.

Both complex I and nitrate reductase can generate a PMF (6H+)

80
Q

What may nitrate be used as?

A

A terminal electron acceptor, like O2 in human ETC

81
Q

What may nitrate (NO3-) be reduced to?

A

NO2- = 2 e- 2H+
NO
N2O
N2 gas - with 8 electrons and 8 protons

82
Q

Which bacteria can reduce nitrate to nitrogen?

A

Paracoccus and Pseudomonas

83
Q

Describe the process of denitrification

A

Nitrate is reduced to Nitrogen gas - carefully regulated as some products are toxic

84
Q

What subunits do N2O reductase and NO reductase have homology with? What does this suggest?

A

Subunits II and I of cytochrome c oxidase

Suggests that CcO evolved from pre-existing enzymes for nitrogen metabolism after oxygenic photosynthesis had increase oxygen levels of planet

85
Q

What is important in sulphate reduction?

A

That it is kept strictly anaerobic

86
Q

What happens if oxygen is present in sulphate reduction?

A

Interferes with enzymes making radical species which damage the protein

87
Q

Describe the process of sulphate reduction

A

Sulphate SO4 2- is reduced to Sulphide S2- with the addition of 8 electrons and 10 protons

Most commonly used reductants for this: acetate, lactate, malate, pyruvate (these are abundant in anaerobic environments)

88
Q

Give the equation for the reduction of sulphate using acetate

A

acetate + SO4 2- + 3H+ –> 2CO2 + H2S + 2H2O

89
Q

You can use S compounds as acceptors or donors

A

you can :)

90
Q

What may CO2 act as?

A

Act as electron acceptor but not electron donor as it is the most oxidised variant of carbon

Microbes often use it as terminal electron acceptor

91
Q

What are the most common group of bacteria that take advantage of bicarbonate carbon?

A

the METHANOGENS

92
Q

What does CO2 reduction require?

A

Something with a low reduction potential (as CO2 has a lower reduction potential)

93
Q

What do hydrogenases do?

A

Oxidise molecular hydrogen or reduce protons to hydrogen

94
Q

What two types of active site are present in hydrogenases?What does electron transfer to/from the active site involve?

A

Ni-Fe and Fe-Fe

Fe-S clusters

95
Q

How are the metals of the active sites attached to proteins?

A

Ligated by cysteines with CO and cyanide ligands attached

96
Q

How may ferrous iron be used as an energy source?

A

Usually ferrous iron has a high redox potential so is a poor electron donator, but at low pH the potential of O2–>H2O is high enough that Ferrous iron oxidation by O2 provides an energy source.

97
Q

Describe the ETC of Acidithiobacillus ferrooxidans

A

Rusticyanin oxidises Fe(II) to Fe(III), passes electrons to Cyt C which then pass electrons to aa3 type oxidase. aa3 uses electrons to reduce O2 to H2O and pump 4 protons into the periplasm. The PMF is used to power ATP synthase to make ATP. NADH2 is formed by reversed complex I using a proton traversing down the proton gradient into the cytoplasm.

98
Q

Describe the Sodium-motive circuit. Where may this be used? Which bacteria use this circuit?

A

Similar to proton motive circuit but uses Na+ instead of H+

Bacteria which live in high salinity conditions e.g. Vibrio alginolyticus (seafood poisoning)

99
Q

Na-NQR is unrelated to complex I or to NDH-2

A

Yep

BIOC2005 CH (13 decks)

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