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Biochemistry II > Chapter 19 > Flashcards

Chapter 19 Flashcards

1
Q

Convergence at oxidative phosphorylation

A

All of the steps in the degradation of carbohydrates, fats and amino acids converge at oxidative phosphorylation

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2
Q

Oxidative Phosphorylation Implications

A

The energy of oxidation indirectly drives the synthesis of ATP

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3
Q

Photosynthetic Organism energy capture

A

Capture energy of sunlight and harness it to make ATO in photophorsphorylation

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4
Q

Oxidative Phosphorylation Definition

A

Reduction of O2 to H2O

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5
Q

Photophosphorylation Definition

A

Oxidation of H2O to O2

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6
Q

Similarities between oxidative phosphorylation and photophosphorylation

A
  1. Electron flow through a chain of membrane-bound carriers
  2. Free energy of exergonic “downhill” electron flow is coupled to transport of protons “uphill” across a proton-impermeable membrane
  3. Transmembrane flow of protons down their concentration gradient through specific protein channels provides free-energy to drive ATP synthesis
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7
Q

Oxidative phosphorylation in mitochondria

A
  • Outer membrane permeability

- Inner membrane permeability

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8
Q

Outer mitochondrial membrane permeability

A

Permeable to small molecules (

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9
Q

Inner mitochondrial membrane permeability

A

Contains membrane-bound carriers of electrons as well as ATP synthase to make ATP and transporters including translocases which transport ATP out of the mitochondria

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10
Q

Electron acceptors for oxidations

A
  • Nicotinamide nulceotide-linked dehydrogenases

- Flavoproteins

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11
Q

Nicotinamide nucleotide-linked dehydrogenases

A

Enzymes that pass electrons during the oxidation of a substrate to FMN or FAD

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12
Q

FMN and FAD electron acceptors

A
  • Each can accept one (semiquinone) or two electrons (FMNH2/FADH2)
  • Two electrons are tightly bound, sometimes covalently
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13
Q

Membrane-bound carriers

A
  • Ubiquinone/Coenzyme Q
  • Cytochromes
  • Iron-sulfur proteins
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14
Q

Ubiquinone/Coenzyme Q General Information

A

Lipid-soluble benzoquinone head group with long isoprenoid lipid chain tail

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15
Q

Cytochromes General Information

A

Proteins with an iron-containing heme prosthetic group

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16
Q

Iron-sulfur proteins General Information

A

Proteins containing iron associated with inorganic sulfur atoms or the sulfur atoms of Cys or both

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17
Q

Uboquinone/Coenzyme Q

A
  • Lipid soluble benzoquinone with a long isoprenoid tail
  • Allows free diffusion within the lipid bilayer of the inner mitochondrial membrane
  • Can accept one electron and one proton to form a semiquinone
  • Can accept electrons and two protons to form a ubiquinol
  • Only accepts one at a time!
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18
Q

Cytochromes

A
  • Inner mitochondrial membrane bound (except cytochrome c)
  • Have associated or covalently bonded iron-containing heme prosthetic groups
  • Fe3+ in the heme can directly accept an electron forming Fe2+
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19
Q

Iron-sulfur proteins

A
  • Contain iron-sulfur centers
  • Irons are present as Fe3+, Fe2+ or sometimes there are multiple irons with different charges
  • All centers participate in one electron transfers, oxidizing or reducing
  • Has 1, 2 or 4 irons
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20
Q

Iron-sulfur centers

A

One or more irons are coordinated to the sulfur residues and possible inorganic sulfur atoms

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21
Q

Four isolatable multi enzyme complexes in electron transport

A

-Each can be physically separated and individually catalyze electron transfer through a portion of the chain

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22
Q

Complex 1 Name and Prosthetic Groups

A
  • NADH Dehydrogenase

- Prosthetic Groups: FMN, Fe-S

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23
Q

Complex 2 Name and Prosthetic Groups

A
  • Succinate Dehydrogenase

- Prosthetic Groups: FAD, Fe-S

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24
Q

Complex 3 Name and Prosthetic Groups

A
  • Ubiquinone cytochrome c oxidoreductase

- Prosthetic Groups: Heme, Fe-S

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25
Q

Cytochrome C Name and Prosthetic Groups

A
  • Not part of a complex

- Prosthetic Groups: Heme

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26
Q

Complex 4 Name and Prosthetic Groups

A
  • Cytochrome Oxidase

- Prosthetic Groups: Heme, CuA, CuB

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27
Q

NADH’s path through the electron transport chain

A

Complex 1 -> Coenzyme Q -> Complex 3 -> Cytochrome C -> Complex 4 -> H2O

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28
Q

FADH2 (succinate)’s path through the electron transport chain

A

Complex 2 -> Coenzyme Q -> Complex 3 -> Cytochrome C -> Complex 4 -> H2O

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29
Q

Complex 1

A
  • NADH to Ubiquinone

- The energy from electron transfer drives the proton pump

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30
Q

Complex 1 Catalysis

A
  1. Exergonic transfer of a hydride ion from NADH and a proton from the matrix to ubiquinone
  2. Endergonic transfer of four protons from the matrix to the inter membrane space
31
Q

Complex 2

A
  • Succinate to Ubiquinone
  • Catalyze oxidation of succinate to fumarate passing electrons to the covalently bonded FAD
  • Heme b site may prevent leaking of O2
32
Q

Movement of electrons from Complex 2 from FAD

A

-Electrons are then passed through the three 2Fe-2S centers to ubiquinone

33
Q

Flavoproteins to Ubiquinone

A
  • Glycerol 3-phosphate dehydrogenase

- Acyl-CoA dehydrogenase

34
Q

Glycerol 3-phosphate dehydrogenase

A

-Bypasses complexes 1 and 2 and passes electrons directly from FADH2 to ubiquinone

35
Q

Acyl-CoA dehydrogenase

A

-Passes electrons to electron transferring flavoprotein then to EFT: ubiquinone oxidoreductase then finally to ubiquinone

36
Q

Complex 3

A
  • Ubiquinone to Cytochrome c
  • couples the transfer of electrons from ubiquinol to chyotchrome c with transport of four protons from the matrix to the intermembrane space
37
Q

Electron transfer in complex 3

A

electron transfer occurs from ubiquinone through a 2Fe-2S center and 3 different cytochromes (2 b type and 1 c type) finally to cytochrome c

38
Q

Complex 4

A
  • cytochrome c to O2
  • couples the transfer of 4 electrons from cytochrome c to molecular oxygen reducing it to H2O with th epumping of 4 protons from the matrix to the intermembrane space
39
Q

Electron transfer in complex 4

A

electrons are transferred from cytochrome c -> binuclear copper center -> coordinated to 2 -SH of Cys -> CuA -> heme a -> heme a3 -> CuB -> O2

40
Q

Electron transfer energy conservation

A
  • Energy is conserved in the gradient
  • The standard free energy is very favorable thermodynamically
  • The actual free energy is even more thermodynamically favorable as the NAD/NADH is below unity
41
Q

Proton transfer by complexes

A

4 by Complex 1
4 by Complex 3
2 by Complex 4

42
Q

Proton Motive Force

A

Energy stored in the gradient

43
Q

Chemical Potential Energy

A

Difference in concentration in two regions separated by a membrane

44
Q

Electrical Potential Enrergy

A

Difference in charge across a membrane

45
Q

pH difference across the proton gradient

A

0.75

46
Q

Free energy for pumping protons outward

A
  • found using pH
  • 20 kJ/mol
  • pumping 10 moles of protons would give 200 kJ/mol
  • 200 kJ/mol of the 220 released by the oxidation of a moles of NADH is conserved in the proton gradient
  • about a 10% loss
47
Q

ATP synthesis thermodynamics

A
  • electron transfer of a mole of electron pair from NADH results in about 200 kJ/mol of free-energy
  • there is more than enough free energy from this transfer of electrons to synthesize a mole of ATP
48
Q

Chemiosmotic model

A

-electrochemical energy due to the difference in proton concentratio/change across the membrane drives the synthesis of ATP as protons flow back into the matrix through a proton pore in the protein ATP synthase

49
Q

Chemiosmotic

A

describes the enzymatic reactions that involve coupling a chemical reaction and a transport process

50
Q

Isolated mitochondria

A
  • with ADP, Pi, and substrate in solution
  • causes;
    1. substrate oxidation
    2. O2 comsumption
    3. ATP synthesis
51
Q

Inhibition of electron transport

A

ultimately leads to O2 blocking ATP synthesis

52
Q

Inhibition of ATP synthesis

A
  • blocks electron transfer in intact mitochondria

- 2,4-dinitrophenol

53
Q

2,4-dinitrophenyol

A
  • carries protons across the membrane, dissipating the proton gradient and uncoupling the two processes
  • allows electron transport without ATP synthesis
54
Q

FoF1 ATPase/ATP synthase

A

-found on the inner mitochondrial membran in animal cells

55
Q

ATP synthase structure

A
  • FoF1 has two distinct associated components

- F1 and Fo

56
Q

F1 Structure

A

-a peripheral membrane protein containing the active site for ATP hydrolysis/synthesis
-3 α and 3 β alternating subunits arranged like segments of an orange
-3 additional subunits γ (central shaft), δ,
& ε
-ATP/ADP binds on the β subunit.

57
Q

Fo Structure

A

-an integral membrane protein containing the proton pore
-Fo is composed of three distinct
subunits in the proportion ab2c10-12.
-Subunit c is composed of 2
transmembrane helices and
associated to form a cylindrical pore.

58
Q

F1 stabilization

A
  • has a higher affinity for ATP over ADP
  • 40 kJ more binding energy for ATP
  • the binding energy of the product, ATP, on the enzyme surface lowers the activation energy facilitating formation of the product
59
Q

Release of ATP

A

the release of ATP from ATP synthase is a major energy barrier rather than the formation of ATP

60
Q

ATP synthase substrate/product binding

A
  • the conformations of the 3 β are different
  • when crystallized with ADP each of the subunits are different
  • one with ATP
  • one with ADP
  • one empty
61
Q

ATP synthase conformational changes

A

-γ moves causing a conformational change to force ATP out of the active site

62
Q

Car analogy

A

-ATP synthase is like putting a car on the top of a hill and pushing it down and having it produce gas

63
Q

ATP synthase mechanism

A
  • rotational catalysis
  • protons passing through the Fo subunit cause the cylinder of c subunits and the γ subunit of F1 to rotate
  • rotation causes each of the β subunits to interact differently, changing their conformation making ATP dislocate
64
Q

Stoichiometry of O2 consumption and ATP synthesis

A
  • 10 electrons are pumped out per NADH
  • 6 electrons are pumped out per FADH2
  • it takes the passage of 4 electrons to generate one ATP
65
Q

P/O ratios

A 
NADH = 10/4 =2.5 ATP
FADH2 = 6/4 = 1.5 ATP
66
Q

Adenine nucleotide translocase

A
  • an antiporter
  • moves 1 ADP into the matrix and 1 ATP into the intermembrane space
  • driven by proton motive force; drives 4 (-) out and 3 (-) into the matrix
  • effectively uses/cancels out one proton of the gradient
67
Q

Cytosolic to mitochondrial NADH for oxidation

A
  • NADH dehydrogenase only accepts electrons from NADH in the mitochondria
  • special shuttle systems using transporter proteins allow indirect conversion of cytosolic NADH into mitochondrial NADH
68
Q

Shuttle systems

A
  • Malate-aspartate shuttle

- Glycerol 3-phosphate shuttle

69
Q

Malate-aspartate shuttle

A
  • electrons from NADH are passed into the matrix as malate using the malate-α-ketoglutarate transporter
  • malate is converted to aspartate and transported out of the matrix with the glutmate-aspartate transporter
70
Q

Glycerol 3-phosphate shuttle

A
  • cytosolic glycerol 3-phosphate dehydrogenase uses NADH to pass electrons to glycerol 3-phosphate
  • mitochondrial glycerol 3-phosphate dehydrogenase uses FAD to pass electrons from glycerol 3-phosphate to ubiquinone
  • only produces 6 e- moved
  • skip complex 1 and complex 2
71
Q

Why have the glycerol 3-phosphate shuttle?

A
  • primarily used in the brain and skeletal muscle
  • used to rapidly regenerate NAD+ so that glucose can be oxidized to provide more energy
  • malate-aspartate shuttle primarily functions in the liver, kidney and heart
  • KINETICS
72
Q

Complete oxidation of glucose

A
  • yields 30 ATP using the glycerol 3-phosphate shuttle

- yields 32 using the malate-aspartate shuttle

73
Q

Oxidative phorphorylation regulation

A
  • regulated by cellular needs
  • O2 consumption inhibited by the avaliability of ADP as substrate
  • mass action ratio is high ATP-ADP is almost fully phosphorylated
  • mass action ratio only slightly fluctuates even during extreme energy demand
  • ATP is formed only as fast as it is used

Biochemistry II (8 decks)

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