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BIOC 4331 > Electron Transport Pathway > Flashcards

Electron Transport Pathway Flashcards

1
Q

Where do the electrons come from that enter the electron transport chain

A

Stored in NADH and FADH2 produced during glycolysis, acetyl-CoA formation, and the TCA cycle.

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2
Q

What parts of the ETC are exergonic? Endergonic?

A

The electrons are passed along in a series of exergonic redox reactions, their energy is used in the endergonic process of ATP formation in the process of oxidative phosphorylation

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3
Q

Which enzymes generate NADH and FADH2?

A

Enzymes that generate NADH and FADH2 are all Dehydrogenases

2 NADH:

Glyceraldehyde-3-phosphate Dehydrogenase

Pyruvate Dehydrogenase

Isocitrate Dehydrogenase

α-ketogluterate Dehydrogenase

Malate Dehydrogenase

2 FADH2:

Succinate Dehydrogenase

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4
Q

How many sets of ETC enzymes and ATP synthase molecules does a mitochondria in the liver have?

A

10,000

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5
Q

What physical property does the mitochondrial outer membrane have?

A

It is permiable to small molecules and ions

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6
Q

What physical properties does the mitochondrial inner membrane have?

A

It is impermiable to most small molecules and ions, including H+

Contains:

  • electron carrier complexes I-IV
  • ADP-ATP translocase
  • ATP synthase (F0F1)
  • Other membrane transporters
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7
Q

What physical properties does the mitochondrial matix have?

A

Contains:

  • pyruvate
  • TCA cycle enzymes
  • fatty acid β-oxidation enzymes
  • amino acid oxidation enzymes
  • DNA, ribosomes
  • Many other enzymes
  • ATP, ADP, Pi, Mg2+, Ca2+, K+
  • Many soluble metabolic intermediates
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8
Q

Enzyme complex I

Name

Mass

Number of Subunits

Prosthetic Group(s)

H+ pumped

A

Enzyme complex I

Name: NADH-ubiquinone oxidoreductase

Mass: 850 kDa

Number of Subunits: 43 (14 in bacteria)

Prosthetic Groups: FMN, Fe-S

accepts electrons from NADH, produces ubiquinone, transports 4 H+

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9
Q

Enzyme complex II

Name

Mass

Number of Subunits

Prosthetic Group(s)

H+ pumped

A

Enzyme complex II

Name: Succinate-ubiquinone reductase

Mass: 140 kDa

Number of Subunits: 4

Prosthetic Groups: FAD, Fe-S

accepts electrons from FADH2, produces ubiquinone also known as succinate dehydrogensae from the TCA cycle

Transfers 0 H+

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10
Q

Enzyme complex III

Name

Mass

Number of Subunits

Prosthetic Group(s)

H+ pumped

A

Enzyme complex III

Name: Ubiquinone: cytochrome c oxidoreductase

Mass: 250 kDa

Number of Subunits: 11

Prosthetic Groups: Henes, Fe-S

accepts electrons from reduced ubiquinone and passes them to cytochrome c , transports 4 H+

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11
Q

Enzyme complex IV

Name

Mass

Number of Subunits

Prosthetic Group(s)

H+ pumped

A

Enzyme complex IV

Name: Cytochrome oxidase

Mass: 160 kDa

Number of Subunits: 13 (3-4 in bacteria)

Prosthetic Groups: Heme, CuA, CuB

accepts electrons from cytochrome c and uses them to reduce O2, producing water , transports 2 H+

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12
Q

Cytochrome c

Mass

Number of Subunits

Prosthetic Group(s)

H+ pumped

A

Cytochrome c

Mass: 13 kDa

Number of Subunits: 1

Prosthetic Group: Heme

NOT A PUMP! A lipid-soluble intramembrane transporter

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13
Q

P side

A

Side of inner membrane facing intermembrane space between inner and outer mitochondrial membrane

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14
Q

N side

A

Matrix side of inner membrane

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15
Q

Which TCA cycle enzyme is embedded in the ETC? Where is it?

A

Succinate dehydrogenase, embedded in N side (matrix side) of complex II

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16
Q

Coenzyme Q is also called?

A

Ubiquinone

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17
Q

Complex I name and function

A
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18
Q

Which enzyme complexes transport H+?

A

Complex I, Complex III, Complex IV

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19
Q

How do electrons flow through electron transport?

A

Electrons flow:

I to III to IV

– or –

II to III to IV

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20
Q

Complex I detail

A
  • Passes electrons from NADH to CoQ.
  • Contains over 40 different polypeptide chains (7 are encoded by mitochondrial genes).
  • Contains one flavin mononucleotide (FMN) and 6-7 iron-sulfur clusters.
  • NADH binding site is on the matrix side
  • Non-covalently bound FMN accepts two electrons from NADH
  • Several iron-sulfur centers pass one electron at a time toward ubiquinone (CoQ) binding site
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21
Q

FMN structure

A
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22
Q

Which way do electrons flow from atom to atom as measured by standard reduction potential?

A
  • If a compound has a large positive Reduction Potential (E’° in volts),

it will accept electrons from compounds with lower R.P.

  • electrons flow from negative to positive
  • analagous to ∆G°’
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23
Q

How does reduction potential factor in to the ETC?

A

The more positive the standard potential, the greater the affinity for electrons.

To have sequential transfer of electrons, carriers must transfer electrons to carriers with higher standard potential

The further down the chain, the greater the RP

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24
Q

How are proton pumps powered by the ETC?

A

As electrons are passed through and between complexes, they move to positions of lower free energy. The energy released is used to pump protons, which in turn drive ATP synthesis.

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25
Q

Fe-S centers

A

Iron not associated with heme. Fe-S centers of iron-sulfur proteins may be as simple as (a), with a single Fe ion surrounded by the S atoms of four Cys residues or can associated with sulfurs from organic and inorganic sources. Associated with one electron transfers.

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26
Q

ubiquinone vs semiquinone vs ubiquinol

A

ubiquinone (Q) vs semiquinone (QH•) vs ubiquinol (QH2)

Q ,which is a lipid-soluble conjugated dicarbonyl, gets reduced to QH2 that can transport two electrons (with 2 H+, hence QH2) across the membrane

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27
Q

Complex II detail

A
  • Contains the citric acid cycle enzyme succinate dehydrogenase and three other subunits.
  • Accepts 2 electrons from succinate, passes them to CoQ.
  • No protons transported in this step, so less ATP can be made from FADH2 then from NADH.
  • Does so with covalently bound FAD.
28
Q

Why does reduced NADH provide more ATP generation capability than FADH2?

A

No protons transported by Complex II (succinate dehydrogenase), so less ATP can be made from FADH2 then from NADH. All ATP made from FADH2 comes from electrons transferred by CoQ.

29
Q

Complex III detail

A
  • Contains four redox cofactors: two b-hemes, one c-heme, and one [2Fe-2S] cluster.
  • Passes electrons from reduced CoQ to cytochrome c – both are mobile carriers.
  • One molecule of QH2 is oxidized to Q and two molecules of cytochrome c are reduced. Note that one 2 e- carrier donates one electron each to two 1 e- carriers.
30
Q

cytochromes have what prosthetic groups?

A

Each group consists of four, five-membered, nitrogen-containing rings in a cyclic structure called a porphyrin. The four nitrogen atoms are coordinated with a central iron ion as either Fe3+ or after accepting an electron, Fe2+

31
Q

Complex III detail

A

Dimer with 11 different subunits, but core is cytochrome b (green) with hemes bH and bL.

Also has Rieske iron-sulfur protein (purple).

32
Q

Cytochrome c detail

A
  • Cyt c is a soluble heme-containing protein in the intermembrane space
  • Heme iron can be either ferrous (Fe3+, oxidized) or ferric (Fe2+, reduced)
  • Cyt c carries a single electron from the cyt bc1 complex (complex III + Cyt c) to cytochrome oxidase (complex IV)
33
Q

cytochrome

A

Proteins with heme prosthetic group

covalently bound via thioether bonds.

Cytochromes (b, c1, c, a, a3) differ in:

  • protein structure
  • heme structure
  • absorption spectra
  • reduction potential
  • role in electron transport
34
Q

Complex IV detail

A

The terminal enzyme of the electron transport chain.

Mammalian enzyme has 13 subunits but bacteria only have 3 or 4.

Contains 2 heme groups and 2 copper ions

Four electrons are used to reduce one oxygen molecule into two water molecules

4 cytochrome c2+ + 8H+ + O2 —>4 cytochrome c3+ + 2H2O + 4H+

Four H+ are picked up from the matrix in this process

Somehow these 4 H+ are moved to the inter-membrane space (the mechanism is unknown)

35
Q

Overall reaction of ETC and ∆G°’

A

NADH + 1/2 O2 + H+ <-> NAD+ + H2O

36
Q

ATP yield from NADH

A

3 (2.5 revised) per NADH oxidised

37
Q

ATP yield from FADH2

A

2 (1.5 revised) ATP per FADH2 oxidised

38
Q

How many units of ATP or energy stored in reduced forms comes from glycolysis per glucose input?

A

2 ATP + 2 NADH

39
Q

How many units of ATP or energy stored in reduced forms comes from Ac-CoA synthesis per glucose input?

A

2 NADH

40
Q

How many units of ATP or energy stored in reduced forms comes from TCA cycle per glucose input?

A

6 NADH, 2 FADH2, 2 ATP

41
Q

How many NADH enter ETC? FADH2?

A
  • in electron transport, each NADH can yield 3 ATP so the 10 NADH yield 30 ATP (however, the 2 NADH from glycolysis are in the cytoplasm, and energy is required to get them into the mitochondrion, thereby reducing the ATP yield)
  • FADH2 yields 2 ATP, so 2 FADH2 yield 4 ATP
42
Q

Final ATP yield from glycolysis to ETC

A

•Final yield: 38 ATP. 4 from substrate level phosphorylation and 34 from oxidative phosphorylation

43
Q

What complex of the ETC does Rotenone inhibit?

A

Complex I

44
Q

What complex of the ETC does Antimycin inhibit?

A

Complex III

45
Q

What complex of the ETC does cyanide inhibit?

A
46
Q

How does ATP synthase generate ATP?

A

ATP synthase : translocates H+ out
(F1F0 ATPase) generates ATP

Synthase a complex structure in mitochondrial membrane has two major components : F1, F0

Protons flow through F0 complex of ATP synthase from intermembrane space to the matrix side, causing the F0 domain and central shaft γ to rotate.

This rotation leads to the conformational changes of all three αβ pairs in F1. The conformational change in one of the three pairs (one moves to T state, one in L and one in O) promotes ATP synthesis from ADP and Pi by the ‘binding change mechanism’.

47
Q

The Chemiosmotic Model

A
  • Proposed by P. Mitchell in 1961
  • put bacteria in acidic media, they can synthesize ATP even if electron transport is blocked
  • Electron transport establishes a proton gradient by pumping protons out of the inner mitochondrial membrane
  • This proton gradient is a form of potential energy that is used to drive ATP synthesis by ATP synthase: this electron diffusion is exergonic because entropy is increased. This energy is captured in the endergonic reaction: ADP + Pi –> ATP
48
Q

Which side of the inner membrane is positively charged?

A

P side (intermembrane space)

49
Q

Which side of the inner membrane is negatively charged?

A

N side (matrix)

50
Q

What are the three states of the F1 domain of ATP synthase complex?

A

L – binds ADP, Pi loosely (inactive)

T – binds ATP, ADP Pi tightly (active)

O – binds ATP loosely (inactive)

51
Q

How many protons must enter ATP synthase to drive the condensation of 1 ADP + Pi to ATP?

A

3 H+

52
Q

binding-change mechanism

A
53
Q

Thermogenin

A

Uncoupled Oxidative Phosphorylation

hormonally controlled uncoupling in brown fat
> no ATP synthesis, energy -> HEAT
uses uncoupling protein (UCP)

54
Q

Uncoupled Oxidative Phosphorylation

A

Uncouplers of oxidative phosphorylation in mitochondria inhibit the coupling between the electron transport and phosphorylation reactions and thus inhibit ATP synthesis without affecting the respiratory chain and ATP synthase (H(+)-ATPase). Miscellaneous compounds are known to be uncouplers, but weakly acidic uncouplers such as ionophores show very potent activities.

Ionophores (ex. the hindered phenol DNP (2,4-Dinitrophenol)) disrupt the proton gradient by carrying protons across a membrane through a protein channel called a thermogenin. This ionophore uncouples proton pumping from ATP synthesis because it carries protons across the inner mitochondrial membrane, depolarising the electrochemical gradient. Inhibits ATP synthase.

55
Q

What types of potential energy are used to make ATP?

A

Chemical potential energy (∆pH, matrix is alkaline) and electrical potential energy (∆ψ, matrix is negative), both of which contribute to the proton-motive force that drives protons across membrane

56
Q

How can NADH from glycolysis in the ______ provide the electrons for ATP synthesis if it occurs in the ________________?

A

How can NADH from glycolysis in the cytosol provide the electrons for ATP synthesis if it occurs in the mitochondrial matrix?

Transport of 2e- and H+ from the intermembrane space into the matrix using Malate-α-ketogluterate transporter, with removal of the oxidated species back to the intermembrane space for regeneration by the Glutamate-aspartate transporter.

57
Q

ionophore

A

An ionophore is a chemical species that reversibly binds ions. Many ionophores are lipid-soluble entities that transport ions across a cell membrane. Ionophore means “ion carrier” as these compounds catalyze ion transport across hydrophobic membranes such as liquid polymeric membranes (carrier-based ion selective electrodes) or lipid bilayers found in the living cells or synthetic vesicles (liposomes)

Some ionophores are synthesized by microorganisms to import ions into their cells. Synthetic ion carriers have also been prepared. Ionophores selective for cations and anions have found many applications in analysis.

The two broad classifications of ionophores synthesized by microorganisms are:

Carrier ionophores that bind to a particular ion and shield its charge from the surrounding environment. This makes it easier for the ion to pass through the hydrophobic interior of the lipid membrane. An example of a carrier ionophore is valinomycin, a molecule that transports a single potassium cation. Carrier ionophores may be proteins or other molecules.

Channel formers that introduce a hydrophilic pore into the membrane, allowing ions to pass through without coming into contact with the membrane’s hydrophobic interior. An example of a channel former is gramicidin A. Channel forming ionophores are usually large proteins.

58
Q

thermogenin

A

Thermogenin (called uncoupling protein by its discoverers and now known as uncoupling protein 1, or UCP1)[1] is an uncoupling protein found in the mitochondria of brown adipose tissue (BAT). It is used to generate heat by non-shivering thermogenesis, and makes a quantitatively important contribution to countering heat loss in neonates which would otherwise occur due to the high surface area-volume ratio.

59
Q

DNP

A

In living cells, DNP (2,4-dinitrophenol) acts as a proton ionophore, an agent that can shuttle protons (hydrogen cations) across biological membranes. It dissipates the proton gradient across mitochondria and chloroplast membranes, collapsing the proton motive force that the cell uses to produce most of its ATP chemical energy. Instead of producing ATP, the energy of the proton gradient is lost as heat.

DNP is often used in biochemistry research to help explore the bioenergetics of chemiosmotic and other membrane transport processes.

60
Q

Malate-α-ketogluterate transporter

A

Transports malate into the matrix from the intermembrane space and α-ketogluterate from the matrix to the intermembrane space

Malate in, α-ketogluterate out

61
Q

Glutamate-aspartate transporter

A

Transports glutamate into the matrix from the intermembrane space and aspartate from the matrix to the intermembrane space

glutamate in, aspartate out

62
Q

aspartate aminotransferase

A

reversibly aminates/deaminates aspartate to oxaloacetate by converting glutamate to α-ketogluterate

63
Q

malate dehydrogenase

A

Reversibly transfers 2 e- and 1 H+ from NADH + 1 H+ from solution to the ketone of oxaloacetate to form malate

64
Q

Describe the transfer of electron from reduced NADH from the cytosol to the mitochondrial matrix

A

2 e- + H+ from NADH and 1 H+ from cytosol are transferred to oxaloacetate by malate dehydrogenase, converting it to malate.

Malate is transported into the mitochondrial matrix by malate-α-ketogluterate transporter.

Oxaloacetate is regenerated in the matrix from malate by malate dehydrogenase, reducing NAD+ to NADH for use in the ETC.

Oxaloacetate is aminated to aspartate by aspartate aminotransferase.

Aspartate is transported out of the matrix to the innermembrane space by Glutamate-aspartate transporter.

Aspartate is deaminated by aspartate aminotransferase, regenerating oxaloacetate.

The amination/deaminations performed by aspartate aminotransferase use glutamine/α-ketogluterate, which must be transported out of (α-ketogluterate) and into (glutamine) of the matrix to balance the amino groups. Aspartate aminotransferase aminates oxaloacetate in the matrix and deaminates aspartate in the intermembrane space, the amines must be transferred out of the matrix to balance the concentration.

65
Q

How is glutamine and α-ketogluterate involved in the transfer of electrons obtained from glycolysis into the matrix for the ETC?

A

The amination/deaminations performed by aspartate aminotransferase use glutamine/α-ketogluterate, which must be transported out of (α-ketogluterate) and into (glutamine) of the matrix to balance the amino groups. Aspartate aminotransferase aminates oxaloacetate in the matrix and deaminates aspartate in the intermembrane space, the amines must be transferred out of the matrix to balance the concentration.

BIOC 4331 (19 decks)

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