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Biochemistry > Oxidative Phosphorylation I & II > Flashcards

Oxidative Phosphorylation I & II Flashcards

1
Q

Describe the ultrastructure of a mitochondria.

A

• Have 2 membrane systems
– Outer membrane (permeable due to presence of porin aka VDAC)
– Inner membrane – (impermeable, has metabolite
transporters, folded into series of cristae)
• Two compartments
– Intermembrane space
– Matrix (site of TCA cycle and fatty acid oxidation)
• Oxidative phosphorylation – inner membrane

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2
Q

Describe the mitochondria genome.

A

• Mitochondria semi autonomous organelles
• Endosymbiotic relationship with host cell
• Free living organism engulfed by another cell
• Genome ranges in size between species
• Sequence data shows all mito. derived from R.
prowazekii due to a single endosymbiotic event
• Have their own DNA, make proteins and RNAs
• Human mito DNA has 16, 569 bp and encodes
13 respiratory chain proteins, rRNAs, tRNAs

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3
Q

What is the overview of oxidative phosphorylation?

A
  • TCA cycle generates NADH and FADH2
  • In oxphos these high energy electrons flow through 4 protein complexes called the electron transfer chain (ETC)
  • Electrons reduce molecular O2 to water
  • Three of the complexes pump protons from matrix to intermembrane space
  • Protons return to matrix by flowing through another complex called ATP synthase powering the synthesis of ATP
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4
Q

What are the components of the electron transport chain?

A

• Electrons transferred from NADH to O2 via three large protein complexes
– NADH Q oxido reductase
– Q cytochrome c oxidoreductase
– Cytochrome c oxidase
• Electron flow exergonic
• Powers flow of protons across inner membrane
• Fourth complex is succinate Q reductase
• Has succinate dehydrogenase which FADH2 generates in TCA cycle
• Electrons from FADH2 enters through Q cytochrome c oxidoreductase
• Succinate Q reductase does not pump protons

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5
Q

List and describe the electron carriers.

A
  • Coenzyme Q aka ubiquinone
    * Transfers electrons from NADH Q oxidoreductase and the Succinate Q reductase to Q cytochrome c oxidoreductase
    * Coenzyme Q has long tail made of 5 – C isoprene units which makes it hydrophobic
    * Most common is CoQ 10
  • Cytochrome c
    * Shuttles electrons from Q cytochrome c oxidoreductase to cytochrome c oxidase
    * Final component of the chain
    * Catalyzes reduction of O2
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6
Q

List iron sulfur clusters?

A
  • Single iron ion tetrahedrally coordinated to SH groups of four Cys residues of the protein
  • Two iron ions, two inorganic sulfides and four Cys residues (2Fe-2S)
  • Four iron ions, two inorganic sulfides and four Cys residues (4Fe-4S)
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7
Q

What is Friedreich’s Ataxia?

A
  • Mutations in the protein Frataxin
  • Loss of function of
  • Small mitochondrial protein crucial for the synthesis of Fe-S clusters
  • Affects the CNS and PNS as well as heart and skeletal system
  • Most common mutation is trinucleotide expansion in Frataxin gene
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8
Q

Describe complex I

A
  • First point of entry of electrons from NADH
  • Complex I aka NADH dehydrogenase aka NADH-Q oxidoreductase
  • Large protein (>900 kDa, with 46 polypeptide chains)
  • Encoded by nuclear and mitochondrial genes
  • L shaped with a horizontal arm lying in the inner membrane and vertical arm that projects into matrix
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9
Q

Describe what happens in complex II

A
  • FADH2 enters the ETC through Succinate-Q reductase complex (Complex II)
  • FADH2 does not leave the complex
  • Its electrons transferred to FeS and then to Q to form QH2
  • Does not pump protons
  • Consequently less ATP synthesized from oxidation of FADH2
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10
Q

Describe what happens in complex III

A
  • Electrons from QH2 are passed on to cytochrome c by cytochrome c reductase aka Complex III
  • Flow of electrons through this complex leads to transport of 2 protons to cytoplasmic side
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11
Q

Describe Cytochrome C Oxidase

A

• Last complex aka Complex IV
• Cyt c oxidase catalyzes transfer of electrons
from reduced Cyt c to molecular oxygen, the final acceptor
• Makes these reactions aerobic
• Makes humans “breathe”
• Four electrons funneled to oxygen to reduce it to water
• Concomitantly protons are pumped from matrix to cytoplasmic side of inner membrane

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12
Q

Describe free radicals

A
  • Complete reduction of oxygen forms water
  • Partial reduction forms dangerous species
  • Transfer of a single electron to oxygen forms superoxide anion
  • Transfer of 2 electrons to oxygen forms hydrogen peroxide
  • Hydroxyl radical formed from both
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13
Q

Name two antioxidants

A

Superoxide dismutase (SOD)

Catalase

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14
Q

Describe the Chemiosmotic Hypothesis

A
  • ETC accompanied by transport of protons from matrix to cytoplasmic side of inner membrane
  • Generates a pH gradient and membrane potential
  • Constitutes a proton motive force
  • Used to drive ATP synthesis
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15
Q

Give the Evidence for the Chemiosmotic Hypothesis

A
  • Synthetic phospholipid vesicles made
  • Purified ATP synthase and bacteriorhodopsin reconstituted into the vesicles
  • Incubated with ADP + Pi
  • Exposed to light
  • ATP generated
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16
Q

Describe the structure of ATP Synthase

A

• Aka Complex V
• Embedded in inner membrane
• Ball and stick structure
• F0 subunit is stick – embedded in membrane
• Has a proton channel
• F1 subunit is ball, protrudes into matrix side
• Contains catalytic domains
• F1 subunit made of 5 types of polypeptide chains with
different stoichiometries
• Alpha3, Beta3, gamma, delta and epsilon
• Alpha and beta arranged alternately in a hexameric ring
• Both bind nucleotides but only the beta are catalytically active
• Above the alpha and beta is a stalk made of gamma and epsilon proteins
• The gamma subunit has a long helical coil that extends into the center of the alpha3 and beta3 hexamer
• The gamma subunit breaks the symmetry of the 3 beta
subunits making each one distinct
• F0 has a proton channel made of 8-14 c
subunits embedded in membrane
• F0 and F1 connected in 2 ways:
– 1. central gamma and epsilon stalk
– 2. Exterior column – 1 a su, 2 b su, and delta su

17
Q

Explain what ATP synthase does

A

• ATP synthase molecules associate with each
other to form dimers
• Dimers come together to form oligomers
• Stabilizes the individual molecules to rotational forces required for catalysis
• Maintains curvature in inner membrane
• Cristae allow the proton gradient to be in close proximity to the ATP synthase

18
Q

What is the Role of a proton gradient?

A

• ATP synthase when incubated with ADP and Pi
formed ATP in absence of a proton gradient

• Release the ATP from the synthase

19
Q

What happens at the ATP synthase nucleotide binding sites?

A
  • The 3 beta su comprise active site of ATP synthase
  • The gamma su passes through center, creating asymmetry
  • The proton motive force causes the 3 su to sequentially change conformation
  • Conformational change alters function
  • Rotation of the Gamma su switches these forms
20
Q

What are the three steps in ATP synthesis?

A

– 1. Binding of ADP and Pi (L conformation)
– 2. ATP synthesis (T conformation)
– 3. Release of ATP (O conformation)

21
Q

What are Progressive alterations of the forms of the 3 active sites?

A

SU 1 – L T O L T O
SU 2 – O L T O L T
SU 3 – T O L T O L

22
Q

Describe the Proton conducting unit of ATP synthase

A
  • The c subunit made of 2 alpha helices that span membrane
  • An aspartic acid residue lies in the center of the membrane
  • The a subunit has 2 half channels
  • Allows proton to enter and pass partway but not completely
23
Q

Describe the Mechanism of action of ATP-ADP translocase

A
  • ATP and ADP not permeable across mito membrane
  • Need a carrier
  • ATP-ADP translocase
  • Flow of ATP and ADP coupled, i.e., ADP enters matrix only if ATP leaves
24
Q

Describe the Regulation of Cellular Respiration

A

• Levels of ATP regulate respiration
• Electrons flow through ETC only when ADP
phosphorylated to ATP
• Regulation by ADP levels called respiratory
control

25
Q

How is ATP synthase regulated?

A

• Inhibitory factor I – inhibits hydrolytic activity of ATP synthase
• Prevents the reverse reaction, i.e., ATP breakdown
• In ischemia or oxygen deprivation
• In cancers – facilitates the switch from aerobic
to anaerobic respiration (Warburg effect)

26
Q

Describe Uncoupling and Heat Generation

A

• Some organisms can uncouple oxphos from ATP synthesis
• Used to generate heat and maintain body temperature
(hibernating animals)
• Happens in brown adipose tissue
• Rich in mitochondria
• Reddish brown due to cytochromes and hemoglobin
• Inner mitochondrial membrane contains uncoupling protein
(UCP 1) aka thermogenin.
• Transfers protons from cytoplasm to matrix side
• Energy converted to heat instead of ATP
• UCP 2 and UCP-3 also uncouple oxphos from ATP synthesis
• Play role in energy homeostasis

27
Q

How is Ox Phos inhibited?

A

• Inhibition of ETC
• Inhibition of ATP synthase – oligomycin
(antibiotic and antifungal agent) inhibits influx
of proteins into ATP synthase by binding to c
su
• Uncoupling electron transport from ATP
synthesis – by 2, 4 – dinitrophenol. Dissipates
the proton gradient
• Inhibition of ATP export – atractyloside and
bongkrekic acid inhibit ATP-ADP translocase

28
Q

List the inhibitors of the electron transport chain.

A

rotenone and amytal blocks NADH-Q to QH2

antimycin A blocks Q-cytochrome c to cytochrome c

CN-, N3-, CO blocks cytochrome c to O2

Biochemistry (13 decks)

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