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Chemistry > Metabolism Exam > Flashcards

Metabolism Exam Flashcards

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1
Q

What activates the apoptosome?

A

The Mito releasing Cyto-C

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2
Q

What is oxidative phosphorolation?

A

The coupled reactions in the Mito that generate ATP. Specifically the oxidation of NADH/the reduction of H+ to water and the phosphorylation of ADP to ATP.

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3
Q

What is Beta-oxidation?

A

The catabolic metabolic process that breaks down fatty acids to generate acetyl-CoA,FADH2 and NADH in the cytosol of prokaryotes and the Mito matrix in eukaryotes.
It gives 17ATP per 2 C-units cleaved.

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4
Q

How many Mito’s per cell?

A

cells can contain 800-2500 Mitos except red blood cells which have none.

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5
Q

What is different about the inner Mito membrane compared to other membranes?

A

The inner Mito membrane is 50-70% protein rather than lipids, this is all proteins for the ETC.

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6
Q

What is HPLC and how does it work?

A

HPLC=High Performance Liquid Chromatography.
A machine uses columns filled with silica beads held place in petrol (C9H10) this is the stationary phase and provides a hydrophobic porous film that catches hydrophobic residues and reduces flow.
The mobile phase is when a liquid is flowed through the column as high pressure.
The absorption is measured in the mobile phase and the resting phase.

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7
Q

What would you use to test the O2 concentration of a system during respiration, potentially in the presence of inhibitors?

A

Oxygen electrode chambers (Clark electrode), they give you the curvy graph that shows O2 change in the liquid when Mito or inhibitors are present.

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8
Q

Describe Complex I.

A

Boot shaped with H+ in the toe and CoQ interaction in the heel. The foot contains hydrophilic channels that are connected by HL alpha-helixes that controls the opening and closing of the channels.
There are a total of 9 [Fe-S].
Takes 2e- from NADH to pump out 4H+ before passing e- to CoQ which also pumps 4H+.
NADH reduces FMN first to pass e- one at a time to the [Fe-S]
The energy to pump H+ comes from the large deltaG between NADH and CoQ.

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9
Q

What is the side reaction CoQ does with O2?

A

O2 can react with CoQ and steal an e- to become superoxide O2*- about 3% of the O2 we breath does this which is a big loss of e- from the ETC

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10
Q

What is the most damaging result of free radicals in cells?

A

Protein hydroperoxide is the formation of

PrOOH which can form DNA-Protein conjugates or Protein-Lipid conjugates which can cause lysis.

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11
Q

What is SOD?

A

Superoxide Dismutase is the fastest known enzyme and the only enzyme know to react directly with free radicals. It generates H2O2 which gets broken down by Glutathione Peroxidase into H2O or O2.

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12
Q

Describe complex II

A

Aka: Succinate-CoQ reductase, oxidises succinate and reduces CoQ to CoQH2
Is assembled in the cytosol from the nucleus genome and transported to the inner Mito membrane.
The energy difference between succinate and CoQ is insufficient to pump H+.
Has 4subunits each containing 2 [Fe-S],the three types of [Fe-S]: 4Fe-4S, 3Fe-4S and 2Fe-2S.
The reaction pathway is succinate to FADH2 to 2Fe2+ to UQH2
The Net reaction is Succinate + CoQ = Fumarate + CoQH2

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13
Q

What are adipocytes?

A

Specialised fat cells with very little water and small nuclei that DO NOT burn fat. They break down glycerides to FFAs which then get trasported by Albumin.

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14
Q

What are the preparatory steps in beta oxidation?

A
  1. Trasport of FFAs to the cytoplasm by albium.
  2. Use Fatty-acetyl-CoA synthatase to convert FFA to Fatty-acetyl-CoA.
  3. Convert Fatty-acetyl-CoA to Acyl-carnitine.
  4. Transport it into the Mito using Carnitine translocase.
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15
Q

What oxidation states is [Fe-S] cycling?

A

Fe3+ and Fe2+

Remember each [Fe-S] can only move 1e- at a time.

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16
Q

What are some inhibitors of the ETC?

A 
Complex I: Rotenone
Complex III: Antimycin
Complex IV: Cyanide and CO
ATP synthase: Oligomycin
Uncoupling agent just uncouples the H+ gradient preventing ATP synthesis.
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17
Q

What are NADH and FADH2 used for in the Mito and where do they come from?

A

FADH2 and NADH are produced in the TCA cycle (3NADH and 1 FADH2) and a little NADH comes from glycolysis and pyruvate metabolism.

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18
Q

How does FADH2 add e- to the UQ pool?

A

It can’t react directly so it uses the trasport enzyme Electron Transferase Flavoprotein ETF. ETF shuttles 2e- to an enzyme bound on the membrane that feeds the UQ pool. The membrane bound enzyme is ETF-ubiquinone oxidoreductase ETF:UQ. It transfers e- to the UQ pool doing the same job as Complex II

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19
Q

How do Peroxosomes produce peroxide?

A

Peroxisomes do beta-oxidation on long chain fatty acids (+22C long) because the peroxisome has no ETC it can’t do anything with the by products such as FADH2 so it gets oxidised to FAD and reduces O2 to H2O2.

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20
Q

What is the key control step of TAG synthesis?

A

A carboxylase reacting to turn acetyl-CoA into Malonyl-CoA. This is inhibited by glucagon and FFAs.
Insulin promotes the carboxylase activity.

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21
Q

What is glucagon and what does it do?

A

Glucagon is a peptide hormone produced by the alpha-cells of the pancreas. It promotes glycogenolysis and formation of FFAs from stored fat in adepocytes. Adrenalin has the same metabolic control.

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22
Q

What happens when excess glucose enters the TCA cycle?

A

Excess citrate is shunted into the cytosol to be converted to acetyl-CoA for fatty acid synthesis.

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23
Q

What is unique about the [Fe-S] in the Rieske protein? And why does it matter?

A

It is unique because the Fe is coordinated by two histidines rather than two cysteines which lowers its reduction potential to help the reaction progress.

24
Q

What is different about complex IV from complexes I and III?

A

Complex IV has no moving parts as everything is moved through the complex with electrostatics.

25
Q

What is Complex IV also know as?

A

Cyto-C Oxidase.

26
Q

How many H+ does complex IV use?

A

8H+

4 are pumped across the membrane and the other 4 react with O2 to give 2 H2O

27
Q

What is the official for ATPsynthase?

A

F1-F0 ATPase.

28
Q

What is the Mitchell hypothesis?

A

That a H+ concentration gradient powered ATPase mechanically. This later won Peter Mitchell the Nobel prize.

29
Q

What is the F0 domain of ATPase?

What is the F1 domain of ATPase?

A

The F0 domain is the three very hydrophobic subunits bound in the membrane that form the transmembrane H+ pore channel.

The F1 domain is the moving catalytic head containing the gamma,beta and alpha subunits and the active sites.

30
Q

What are the three states that the ATPase reaction centres can be in?

A

Loose state: allows ADP + Pi to bind

Tight state: causes an equilibrium shift to ATP formation.

The transition here is what requires energy

Open state: does not bind ATP or ADP so the ATP is ejected without hydrolysis.

31
Q

In ATPase what are C-peptides?

A

The C-peptides are the hydrophobic subunits that rotate the bottom of the gamma subunit.

32
Q

How does the C-peptide barrel work?

A

There is a Aspartate- on the C-peptide that is electrostaticly locked in place by Arginine+. When a H+ enters it binds to the Aspartate- and neutralises the charge letting the barrel rotate around to the next aspartate- which becomes locked until the next H+ enters.

33
Q

How fast does ATPase rotate?

A

350 rotations per second @ 37degrees Celsius
Or
21,000RPM

34
Q

In liver Mito what is the difference across the membrane?

A

0.168V and 0.75pH difference across the 8nm membrane.

35
Q

How does NADH get into the Mito?

A

It is first transformed into malate and passed into the membrane using the malate-alpha-ketoglutarate transporter.

In: Malate and glutamate

Out: alpha-ketoglutarate and aspartate

36
Q

What is the 4th enzyme to feed into the UQ pool?

A

Mito glycerol-3-phosphate dehydrogenase. It reacts with glycerol-3-phosphate to feed reducing power into FAD to FADH2 to UQH2.

37
Q

If the Mito membrane is impervious to charge particle how does ATP leave?

A

ATP/ADP translocase swaps the two around for the energy of 1H+. This means the exportation of 1ATP = 4H+

38
Q

What happens when the H+ Gradient becomes uncoupled?

A

The H+ flow into the matrix and the energy is lost as heat.

39
Q

What regulates UCP (uncoupling protein)?

A

UCP is up regulated by high [FFA] and down regulated by high [ADP].
Noreadrenalin is the signal hormone that triggers [FFA] to increase.

40
Q

What do the light and dark reactions produce?

A

Light reaction: 2H+, 3ATP, O2 and 2NADPH

Dark reactions: 3-phosphoglycerate, 3H2O, 9ADP, 8Pi, 6NADP+

41
Q

What is the OEC?

A

The Oxygen evolving centre, it requires 4H2O to be oxidised photochemically in a light flash event to produce 2O2. Each light flash moves 1e- and 1H+ so it requires 4 light flashes. These correspond with the oxidation states of Mn(II,III,IV,V)

42
Q

Scavenging systems in plants mop up radicals but what are some of them called?

A

Carotenoids and ascorbate

43
Q

Purple bacteria are a strange mid way between plants and Mito in their ETC, but how?

A

Because purple bacteria use photosystems like a plant but cycle e- using cyto-c like in Mito.

44
Q

What is the process that carotenoids use to deal with radicals?

A

NPQ=Non-Photochemical Quenching

It releases the energy as heat but some carotenoids can release as fluorescence.

45
Q

What are the three phases of the CB-cycle?

A
  1. Carboxylation
  2. Reduction
  3. Regeneration
46
Q

What are Fd and FNR for?

A

Fd= Ferredoxin which is the terminal e- acceptor in chloroplast ETC.

FNR= Ferredoxin-NADP+ reductase

Together Ferredoxin passes e- to Ferredoxin-NADP+ reductase which reduces NADP+ to NADPH

47
Q

What is the first product in the CB cycle for C4 plants?

A

The 4 C compound, oxaloacetic acid.

48
Q

CAM plants separate their metabolism temporally but what does CAM mean?

A

Crassulaccan Acid Metabolism.

49
Q

What is the first product of C fixation in CAM plants?

A

The 4 C malic acid which is produced at night and stored to be used as CO2 during the day.

50
Q

Of C3 and C4 plants which is more effective?

A

C4 plants are more effective at lower intercellular [CO2] but C3 plants can produce more sugars at high [CO2] than C4 plants can.

51
Q

How do stomata operate?

A

They have chloroplasts and light receptors but they close using osmotic pressure.

52
Q

What happens when RuBisCo fixes O2?

A

Photorespiration happens, this will happen with ~25% of the reactions catalysed.

53
Q

What is the point of photorespiration?

A

To regenerate ribulose-1,5-bisphosphate or to generate 3-phosphglycerate which can be used in the CB-cycle.
The first product of photorespiration is glycine which is important in AA generation and nitrogen fixation.

54
Q

What is used up in the regenerative phase of the CB-cycle?

A

2NADPH and 3ATP

55
Q

What is restored in the regeneration cycle?

A

3-phosphogycerate and glutamate

56
Q

What shape are C-peptides?

A

They are two alpha-helixes connected by four residue polar loops. They are arranged n a banana shaped antiparallel coiled coil.

Chemistry (6 decks)

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