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Introduction to Biochemistry > Metabolism > Flashcards

Metabolism Flashcards

Lectures 21-26 (Declan Doyle)

1
Q

What is the meaning of catabolic?

A

A reaction that releases energy.

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2
Q

What is the meaning of anabolic?

A

A reaction that uses energy.

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3
Q

What are the two functions of the oxidative catabolism of glucose?

A
  • Production of ATP
  • Production of intermediates from glycolysis and TCA cycle (for other metabolic pathways)
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4
Q

What is the equation for Gibbs free energy?

A

Enthalpy - temperature x entropy (ΔH-TΔS)

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5
Q

What is ΔG∘’?

A

Gibbs free energy at pH 7, also known as gibbs free energy during reactions.

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6
Q

What is ΔG∘?

A

Gibbs free energy at pH 0.

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7
Q

What does a negative ΔG∘ tell you about a reaction?

A

Reaction is exergonic meaning free energy is released during it.

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8
Q

What does a positive ΔG∘ tell you about a reaction?

A

The reaction is endergonic and free energy is absorbed during it.

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9
Q

What is Kc?

A

An equilibrium constant, otherwise known as the ratio of concentration of products to reactants.

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10
Q

What does a small Kc tell you about a reaction?

A

It lies to the left, meaning the reactants are much smaller than the products.

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11
Q

What is the Van’t Hoff Isotherm equation?

A

ΔG = ΔG∘’ + R(Gas constant)T InQ

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12
Q

What is the Van’t Hoff Isotherm used for?

A

It can be used to predict if a reaction is spontaneous or not.

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13
Q

What are the two things the ΔG is dependant on?

A

Constant term: Value depends only on if reaction happens or not.
Variable term: Dependent on concentrations of reactants and products.

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14
Q

What is the importance of ΔG being additive?

A

Throughout a metabolic pathway, ΔG of any one reaction can be positive and the pathway can still occur as long as the overall ΔG is negative.

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15
Q

Why are metabolic pathways irreversible?

A

They are highly exergonic so the reverse would be highly endergonic which doesnt work.

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16
Q

What is feedback inhibition and how does it prevent metabolic pathways?

A

It is when the product of a pathway stops the pathway occurring again by switching on/off the gene for the first enzyme, so not too much product is made.

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17
Q

Why is glycolysis irreversible?

A

It has a large positive ΔG.

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18
Q

What is the first main step of glycolysis?

A

D glucose → Glucose 6 Phosphate (via Hexokinase reaction that requires ATP)

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19
Q

What is the second main step of glycolysis?

A

Fructose 6 phosphate → Fructose 1,6 Biphosphate (via phosphofructokinase that requires ATP)

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20
Q

What s the third main step of glycolysis?

A

PEP → Pyruvate (Via pyruvate kinase that requires ATP)

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21
Q

What is a cofactor?

A

A non protein component of an enzyme.

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22
Q

What is a coenzyme?

A

An organic cofactor.

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23
Q

What is oxidation?

A

A loss of electrons/hydrogen. Results in many C-O bonds and lower potential energy.

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24
Q

What is reduction?

A

Gain of electrons and hydrogen. Results in many C-H bonds and higher potential energy.

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25
Q

Are phosphorylation reactions ender or exogonic?

A

They are endergonic. They are also irreversible because to take the phosphate and add it to ADP is highly endergonic.

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26
Q

What are the 3 reasons the kJ/mol from glucose isn’t simply released as heat?

A
  1. Biological systems do not utilise heat as a source of energy.
  2. No single energy requires that much energy to be released.
  3. The activation energy needs to be overcome and enzymes only act on small changes
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27
Q

How is glucose energy released?

A

Glucose is catabolised in small steps and energy is released in usable bouts of ATP. These are 30kJ/mol.

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28
Q

What is ATP coenzyme used for?

A

Phosphate transfer.

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29
Q

What is NAD+/NADH used for?

A

Oxidation/reduction

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30
Q

What is the use of glycerol?

A

Readily metabolised into an intermediate glycolysis. Either converted into pyruvic acid or used in gluconeogenesis.

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31
Q

What is the first of ten steps of glycolysis?

A

Facilitated diffusion via transport proteins, moving from a high to low concentration of glucose.
- Needs no energy

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32
Q

What is the second of ten steps of glycolysis? Is this reversible?

A

G6P → F6P via phosphoglucose isomerase.
- Done because it needs to phosphorylate a hydroxyl group so that after lysis both 3 carbons are phosphorylated.
- Reversible.

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33
Q

What is the third of ten steps of glycolysis? Is this reversible?

A

F6P → F-1,6-Biphosphate via phosphofructokinase.
- Two phosphate groups added.
- Irreversible

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34
Q

What is the fourth of ten steps of glycolysis? Is this reversible?

A

F-1,6-BP → DHAP and GAP via aldolase.
- Reversible.

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35
Q

What is the fifth of ten steps of glycolysis? Is this reversible?

A

DHAP → GAP via triose phosphate isomerase.
- Reversible

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36
Q

What is the sixth of the ten steps of glycolysis? Is this reversible?

A

Gap ↔ 1,3BP via GAP hydrogenase.
- Uses NAD⁺ or NADH + H⁺
- Reversible
- Oxidation step, converting an aldehyde to a carboxylic acid.

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37
Q

What is the seventh of the ten steps of glycolysis? Is this reversible?

A

1,3BP ↔ 3 phosphoglycerate via phosphoglycerate kinase.
- Uses ADP or ATP as it is reversible.
- Acid from phosphate leads to greater negative ΔG.

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38
Q

What is the eighth of the ten steps of glycolysis? Is this reversible?

A

3P (Phosphoglycerate) ↔ 2P via phosphoglycerate mutase.
- Reversible.
- Not exergonic enough to produce ATP.

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39
Q

How is 2P transformed into PEP in Glycolysis?

2P = 2 phosphoglycerate
PEP = Phosphoenol Pyruvate

A

2 Phosphoglycerate ↔ Phosphoenol pyruvate via enolase.
- Reversible, H₂O produced when forward.
- Highly exergonic.

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40
Q

Why is the ninth step of glycolysis so exergonic?

A

The phosphoryl group traps the molecule in an unstable enol (alkaline with hydroxyl group) form.
- Enol converts into more stable ketone (pyruvate)

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41
Q

What is the tenth of the ten steps of glycolysis? Is this reversible?

A

Phosphoenol pyruvate → pyruvate via pyruvate kinase.
- Produces ATP
- Irreversible

42
Q

What are the two types of coenzymes?

A

Apoenzyme: Becomes active by binding of coenzymes to enzyme
Holoenzyme: Formed when associated cofactor binds to enzymes active site.

43
Q

What happens to pyruvate in aerobic conditions?

A

Enters the mitochondria via the porins and MPC, to be consumed in the TCA cycle.
There is enough NAD+ for this because of the electron transport chain.

44
Q

What happens to pyruvate in anaerobic conditions?

A
  • No NAD+ :(
  • Converted into stuff like lactate. All of it has to be converted for ATP synthesis to continue.
45
Q

Where does glycolysis take place in prokaryotic and eukaryotic cells?

A

Both in the cytoplasm.

46
Q

Where does the TCA cycle take place in prokaryotic and eukaryotic cells?

A

Prokaryotic: Cytoplasm
Eukaryotic: Mitochondria

47
Q

Where does ETC take place in prokaryotic and eukaryotic cells?

A

Prokaryotic: Cell membrane
Eukaryotic: Mitochondrial membrane

48
Q

Why do eukaryotes separate glycolysis and TCA but prokaryotes don’t?

A

Eukaryotes are huge compared to prokaryotes and therefore don’t rely on diffusion so they are compartmentalised. One TCA enzyme is an integral membrane protein so cell has to select 1 membrane (close between TCA and ETC)

49
Q

How is pyruvate transported in the mitochondria?

A
  • MPC (Mitochondrial pyruvate carrier)
    Enters through pores, through intermembrane space, into outer then inner membrane and then through MPC.
50
Q

How is NADH transported in the mitochondria?

A

No specific transporter needed, porins allow NADH access to the inter mitochondrial space.

51
Q

Describe the link reaction.

A

Pyruvate → Acetyl CoA. Uses enzyme pyruvate dehydrogenase complex, which produces NADH and CO2 out of NAD+ and CoA-SH.

52
Q

What is CoA?

A

A coenzyme. It carries acetyl to active sites.
- It is a thiol (Have SH) and can react with carboxylic acid to form thioesters.
- Used in synthesis of fatty acids when there is excess glucose
- Contains unit of ADP

53
Q

What evidence is there for mitochondria being derived from symbiotic bacteria?

A
  • Bacillus rod shape
  • Both replicate via fission
  • Both contain circular DNA plasmids
  • Mitochondrial ribosomes are more similar to bacterial ribosomes than ours, same with their membrane proteins.
54
Q

What is a prosthetic group?

A

A tightly bound non polypeptide unit required for enzyme activity.

55
Q

What is the point of an enzyme complex?

A

Speeds up reactions because the products of a reaction can continue to the next one without having to go through diffusion. Also prevents other unfavourable reactions.

56
Q

How is Citrate produced in the TCA cycle?

1st Step

A

Oxaloacetate and Acetyl → Citrate via citrate synthase.
- Produces CoA-SH.
- Irreversible due to very negative ΔG’∘.

57
Q

How is Citrate transformed into Isocitrate in the TCA cycle?

2nd step

A

Citrate →Cis-Aconitate → Isocitrate via aconitase.
Citrate: Tertiary alcohol due to HO-C
Isocitrate: Secondary alcohol due to HO-CH
- Irreversible

58
Q

What is the 3rd step in the TCA cycle?

A

Isocitrate →(+ NADH and H+) Oxalosuccinate → α-Ketoglutarate (+ Co2).
- Both reactions via isocitrate dehydrogenase
- 1 of 4 oxidative decarboxylation reactions

59
Q

How is α-ketoglutarate transformed into Succinyl CoA in the TCA cycle?

Step 6

A

α- Ketoglutarate (5C) → Succinyl CoA (5C).
- Via α- Ketoglutarate dehydrogenase
- Produces Co2, NADH and H+.
- 2 of 4 oxidative decarboxylation reactions

60
Q

What is the 5th step in the TCA cycle?

A

Succinyl CoA → Succinate via succinyl CoA-synthetase.
- Reversible, when forward produces GTP and CoA-SH.
- Energy from GTP released from hydrolysis of a thioester bond, providing energy for substrate level phosphorylation.

61
Q

What is the 6th step in the TCA cycle?

A

Succinate → Fumarate via succinate dehydrogenase.
- Reversible, when forward produces FADH₂
- Only enzyme of TCA in the inner mitochondrial membrane
- 3rd of 4 oxidative decarboxylation reactions

62
Q

What is the 7th step in the TCA cycle?

A

Fumarate → L-Malate via fumarase.
- Reversible, when forward produces H₂O
- Catalyses a trans addition of a hydrogen atom and hydroxyl group

63
Q

What is the 8th step of the TCA cycle?

A

L-Malate → Oxaloacetate via malate dehydrogenase.
- Reversible, when forward produces NADH and H+
- 4th of 4 oxidative decarboxylation reactions.

64
Q

What restarts the TCA cycle?

A

Step 1 is incredibly exergonic so oxaloacetate used up immediately again.

65
Q

What is the net gain of ATP from glycolysis?

A

8 ATPs. Comes from:
- 2 ATPs used to prime glycolysis,
- 4 ATPS produced from substrate level phosphorylation
- 2 NADH produced ( = 3 ATP each)

66
Q

How much energy is produced from the catabolism of pyruvate?

A
  • 4 NADHs (1 from Acetyl CoA production, 3 from TCA cycle)
  • 1 FADH₂ from TCA
  • 1 GTP/ATP from TCA
67
Q

How much energy is produced from the complete oxidation of glucose?

A
  • 8 ATP (Glycolysis)
  • 30 ATP (15 x 2, TCA cycle)
68
Q

Why doesn’t NADH have a transporter into the mitochondria?

A

It would move with the concentration gradient out of the mitochondria which is not wanted.

69
Q

How does NADH get into the matrix?

A

A Malate Aspartate Shuttle or the Glycerol-Phosphate Shuttle.

70
Q

How does the MAS transfer NADH?

MAS = Malate Aspartate Shuffle

A
  • Two specific inner mitochondrial transporters
  • Electrons and proteins from cytoplasmic NADH transferred to NAD+ in mitochondrial matrix.
  • NADH made here results in 3 ATP
71
Q

Where are MAS found? Why?

A

Low energy requirement tissue like the liver.
- Because if too much NAD+ was produced in the tissue the shuttle would reverse itself.

72
Q

How does the Glycerol-Phosphate Shuttle transfer NADH?

A
  1. Transfers electrons from NADH to Dihydroxyacetone Phosphate creating Glycerol 3 Phosphate.
  2. Transfers electrons from G3P into mitochondrial ETC.
    - 2 types of glycerol 3 phosphate dehydrogenases: Cytoplasmic (1st step) and mitochondrial (2nd step)
73
Q

What stops the GPS from reversing?

A

One less ATP as it decouples matrix NADH from cytoplasmic NADH.

74
Q

How much ATP does the GPS produce?

A

2, because the cycle of oxidation/reduction produced FADH₂.

75
Q

Where is the GPS found?

A

Metabolically high active tissue such as neurons.

76
Q

What is the difference between the permeability of the inner and outer mitochondrial membrane?

A

The inner is highly impermeable and requires specific transporters. The outside doesn’t.

77
Q

Where is FADH₂ produced?

A

Inner membrane.
- From the reaction of Succinate → Fumarate via succinate dehydrogenase.

78
Q

Are oxidation reactions exer or endergonic?

A

Exergonic, due to very large negative ΔG∘ (-220kj/mol for NADH and -150kj/mol for FADH₂)
- Therefore spontaneous

79
Q

What is the basic function of the ETC?

A
  • NADH and FADH₂ pass their electrons to transmembrane protein complexes in the inner membrane
  • Carrier affinity for electrons slowly increases
  • Eventually electrons passed to oxygen to produce water.
80
Q

How is ATP generated from the energy of coenzymes?

A
  • Indirectly
  • Energy is coupled to proton transport from matrix to intermembranous space
  • Generates an electrochemical gradient across the inner membrane that produces ATP
81
Q

What are the two parts of the electrochemical gradient?

A
  1. Chemical gradient: Difference in solute concentration across a membrane
  2. Electrical gradient: Difference in charge across a membrane
82
Q

Why are electrons transferred from NADH to oxygen in stages? How does it do this?

A

It is too much to be released all at once.
- Electrons are transferred between acceptors, releasing energy at each stage.
- Proton gradient formed generates ATP.

83
Q

Why must electrons be moved in a H+ pump?

A

It provides energy that destabilises the proton in the negative binding site at the top of the pump. The proton is pretty cushty so it needs some help in moving.

84
Q

What are the main parts of a H+ pump?

A

A rotor part in the IMS and a non moving head part where ATP is hydrolysed in the matrix. This non moving part is a heterohexamer made of 3α and 3β subunits.

85
Q

How many H+ are needed for a pump to produce an ATP?

A

3

86
Q

How does the movement of electrons in a H+ pump cause movement of protons?

A

The electron transfer drives the H+ affinity to decrease, alongside the opening of the gates and the conformational change required to release the proton.

87
Q

What are α subunits in H+ pumps used for?

A

Can bind ATP, but do not participate in catalysis.

88
Q

What are the 3 types of β subunits in the H+ pump, and what do they do?

A

L = Loose state, binds to ATP and Pi tightly.
T = Tight state, favours ATP binding + formation.
O = Open state favours ADP binding + disassociation of ATP.

89
Q

How does rotation drive ATP synthesis?

A

Causes confirmational changes in the head groups subunits of the stator, driving ATP synthesis from ADP and Pi.
- Unbinding requires energy

90
Q

What is the name and function of NADH oxidation Complex I?

A

It is called NADH Q Reductase.
- Oxidises NADH by transferring 2 electrons to mobile carrier ubiquinone and 4 protons across the inner mitochondrial membrane

91
Q

Where does reduced ubiquinone(QH₂) travel to?

Reduced ubiquinone is called ubiquinol, or QH₂.

A

Through the mitochondrial membrane, where QH₂ delivers its electrons to complex III.

92
Q

What is the name and function of NADH oxidation Complex III?

A

Q cytochrome- c oxidoreductase.
- Transfers two electrons (from QH₂) between two mobile electron carriers o soluble cytochrome-c in IM.

93
Q

How many protons are transferred by complex III? Where to?

A

1 transferred to cytochrome-c with two protons.
- 2nd is stored internally and then moved to second cytochrome-c, resulting in 2 more being transferred from the matrix to IMS.
4 in total transferred.

94
Q

What is the name and function of NADH oxidation Complex IV?

A

It is called Cytochrome oxidase.
- Transfers 2 electrons from cytochrome-c proteins to mitochondrial matrix.
- Accompanied by 2H+ to IM space and reduction of oxygen in the matrix to produce H20.

95
Q

How many protons are transferred from all complexes from one NADH?

A
    • 4 from complex I
    • 4 from complex III
    • 2 from complex IV
      All go to the IM space.
96
Q

Where does the oxidation of FADH₂ take place? What enzyme is used?

A

Complex II, III and IV.
- Succinate dehydrogenase

97
Q

How much ATP and H+ does one FADH₂ produce?

A

2 ATP.
6 protons (4 from Complex III and 2 from Complex IV) into the IMS.

98
Q

Is ATP stored?

A

No. It has to be made on demand. Specific transporters are required to make ATP on command. These only work if ADP is on the other side.

99
Q

How are ATP transporters driven?

A
  • Voltage gradient
    -4 charge on ATP means it prefers to move out, but -3 charge on ADP moves it into the matrix.
100
Q

What happens if there is no ADP?

A

H+ cannot return to the matrix.
- Proton gradient will be matched by NADH oxidation.
- Electron transport will stop and so will ATP.

Introduction to Biochemistry (5 decks)

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