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MCB2021F > Basic Metabolism > Flashcards

Basic Metabolism Flashcards

1
Q

What is a chemoautotroph?

A

Generates food from inorganic carbon sources with chemical energy

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2
Q

What is a chemoheterotroph?

A

Generates food from organic carbon sources with chemical energy

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3
Q

What is a photoautotroph?

A

Generates food from inorganic carbon sources using light energy from photosynthesis

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4
Q

What is a photoheterotroph?

A

Generates food from organic carbon sources using light energy from photosynthesis

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5
Q

What is catabolism?

A
  • The break-down/degradation of complex molecules
  • Energy-generating process (Generates energy that is used in anabolism)
  • Oxidative reaction
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6
Q

What is anabolism?

A
  • A synthetic process which produces complex molecules
  • An energy-requiring process (using energy generated in Catabolism)
  • A reductive reaction
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7
Q

Adenosine Triphosphate (ATP)

A
  • The energy currency of the cell
  • Energy is stored in energy-rich phosphoanhydride bonds of ATP
  • Links anabolism and catabolism
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8
Q

Difference between NADP/NADPH & NAD/NADH

A
  • NADP/NADPH are a direct source of reducing equivalents in the cell.
  • NAD/NADH are carriers of reducing equivalents from catabolism
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9
Q

3 mechanisms of regulation of metabolism

A

{Regulation achieved by regulation of enzymes}

  1. Allosteric regulation (Binding of molecules to site other than active site on enzyme)
  2. Covalent Modification of enzymes
  3. Expression of gene that codes for enzyme. Changing expression levels changes amount of enzyme that’s present
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10
Q

Types of thermodynamic systems

A
  1. Isolated systems
    - No exchange of energy or matter
    - Universe is isolated, biological systems aren’t
  2. Closed systems
    - Exchange of energy but not matter
  3. Open Systems
    - Exchange of energy & matter (Most biological systems)
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11
Q

1st Law of Thermodynamics

A

Conservation of energy

  • The total energy of an isolated system is conserved
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12
Q

What is the internal energy of a system?

A

The sum of the energy of the molecules in the system (Joules)

  • Changes in internal energy can only happen if energy enters or leaves systems in the form of heat or work
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13
Q

2nd Law of Thermodynamics

A

Systems tend to move from ordered states (low entropy) to disordered states (high entropy)

  • Entropy of Universe is unchanged for reversible processes and increases for irreversible processes.
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14
Q

What does Gibbs free energy tell us?

A

Whether a reaction will proceed spontaneously or not.

delta G < 0 - spontaneous (exergonic)

delta G > 0 - non-spontaneous (endergonic)

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15
Q

What are standard state reactions?

A

When the concentration of reactants and products are at 1M.

In biological systems standard state H+ conc isn’t equal to 1M (pH needs to be 7

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16
Q

What can make a reaction spontaneous?

A
  1. Negative delta G

2. If ratio of concentration of products is larger than reactants then delta G will become more positive (Le Chateliers)

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17
Q

What are high energy compounds?

A

Compounds with large negative free energies of hydrolysis (when bonds are broken lots of energy is released)

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18
Q

Principle of coupled reactions

A
  • Energy released from thermodynamically favorable reaction be used to drive another thermodynamically unfavorable reaction as long as overall delta G is negative
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19
Q

What are the 2 functions of Glycolysis?

A
  1. Catabolic Breakdown of glucose to pyruvate

2. Produces energy

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20
Q

Glycolysis Reaction 1

A
  • Hexokinase adds PO3 to glucose (forms glucose-6-P)
    a. increases glucose transport into cell (No longer recognised as glucose)
  • PO3 addition is energetically unfavourable, so coupled to ATP hydrolysis and also favoured by concentrations in cell
  • Hexokinase important site of regulation
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21
Q

Hexokinase regulation

A
  • Allosterically inhibited by glucose-6-phosphate (Negative feedback)
  • Liver contains glucokinase which is regulated by insulin and functions when blood glucose levels are high.
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22
Q

Glycolysis Reaction 2

A
  • Phosphohexose Isomerase transforms glucose-6-P (pyranose) to fructose-6-P (furanose)
  • Makes mol symmetrical in preparation of cleavage
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23
Q

Glycolysis Reaction 3

A
  • Phosphofructokinase adds PO3 (coupled to ATP hydrolysis because energetically unfavourable)
  • Enzyme is important site of regulation - it commits glucose to breakdown
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24
Q

Phosphofructokinase Regulation

A
  1. The energy requirements of the cell
    a. Allosterically inhibited by high [ATP]
    b. Inhibition is reversed by high [AMP]
  2. Flux through TCA cycle
    a. Allosterically inhibited by high [citrate]
  3. Hormones
    a. o Allosterically activated by fructose-2,6-bisphosphate
25
Q

Glycolysis Reaction 4

A
  • Fructose bisphosphate aldolase cleaves f-1,6-bp into glycerladehyde-3-P and dihydroxyacetone
  • delta G is positive, but conc own cells makes it slightly negative.
26
Q

Glycolysis Reaction 5

A
  • Conversion of Dihydroxyacetone to Glyceraldehyde-3-P
27
Q

Phase 1 of Glycolysis

A
  • First 5 reactions
  • starts with 1 mol Glucose
  • Ends with 2 mols Glycerladehyde-3-P
  • Net negative delta G
28
Q

Glycolysis Reaction 6

A
  • Glyceraldehyde-3-P oxidised to 1,3-Bisphosphoglycerate
  • Oxidation is exergonic, procedes via thirster intermediate (coupled rxn)
  • Energy used to reduce NAD+ and form PO3 bond
29
Q

Glycolysis Reaction 7

A
  • Substrate-level phosphorylation converts (2x) 1,3-bisphophoglycerate to (2x) 3-phosphoglycerate
  • “Pulls” previous reaction forward
  • Produces 2 mols ATP
30
Q

Glycolysis Reaction 8

A
  • PO3 moved from C3 to C2

- Generates a more reactive molecule

31
Q

Glycolysis Reaction 9

A

o Generates a mol that has a higher phosphoryl transfer potential – more readily donates PO3 to ADP
o Catalyzes Dehydration

  • Forms phosphoenolpyruvate from 2-phosphoglycerate
32
Q

Glycolysis Reaction 10

A
  • Forms pyruvate through substrate level phosphorylation
  • Coupled rxn with ATP formation
  • Important target for regulation
33
Q

Pyruvate Kinase Regulation

A
  1. Energy requirements of the cell:
    o Allosterically activated by AMP and inhibited by ATP
  2. Flux through glycolysis:
    o Allosterically activated by fructose 1,6-BP
  3. Covalent modification
    o Phosphorylation cascade (glucagon signaling)
    o Increases inhibition by ATP, increases Km
    o Pyruvate is fed into gluconeogenesis
34
Q

What is the fate of pyruvate after glycolysis?

A
  • In absence of O2, pyruvate is fermented

- In presence of O2, pyruvate enters TCA cycle

35
Q

Alcoholic Fermentation

A
  • Pyruvate decarboxylase converts pyruvate to acetaldehyde and CO2 is released
  • Alcohol dehydrogenase converts acetaldehyde to ethanol and oxidizes NADH
36
Q

Lactic Acid fermentation

A
  • Lactate dehydrogenase converts pyruvate to lactate and oxidizes NADH
  • Occurs in muscle tissue during vigorous exercise when O is limiting
37
Q

Pyruvate Decarboxylation

A
  • Pyruvate is converted into acetyl-CoA to allow it to enter the TCA cycle
  • Enzyme complex: pyruvate dehydrogenase complex (3 enzymes) and 5 co-enzymes
  • Happens in the Mitochondria
  • Decarboxylation – CO2 is released
  • NAD+ is reduced to NADH
38
Q

2 Functions of Acetyl-Coenzyme A

A
  1. Activation of acyl groups for transfer by nucleophilic attack
  2. Activation of alpha-hydrogen of acyl group for abstraction as proton (citrate synthetase reaction)
39
Q

Krebs cycle Reaction 1

A

What Happens?
[Oxidation of Acetyl-CoA]:
o Acetyl-CoA combined with oxaloacetate
o Enzyme forms Citrate with release of CoA carrier

Why?
o Oxidation of acetyl group to release CO2 requires cleavage of C(alpha)-C(Beta) bond
o Acetyl-CoA doesn’t have beta C, so condenses with oxaloacetate and then performs cleavage

  • Hydrolysis of the thioester bond (C-S Bond on CoA) drives the reaction forward and makes the overall reaction favorable
40
Q

Krebs cycle Reaction 2

A

What happens?
[Citrate converted from tertiary alcohol to secondary alcohol – by Isocitrate]
o Remove water from C3 – forms intermediate
o Add water back to C2

Why?
o Prepares 6C mol for oxidative decarboxylation (following steps)
o Citrate doesn’t readily undergo oxidative decarboxylation because it’s a tertiary alcohol

41
Q

Krebs cycle Reaction 3

A

What happens?
[∝-Ketoglutarate is formed]
o COOH removed, CO2 released, NAD+ converted to NADH
o Proceeds via high energy intermediate,

Why?
o Overall ∆Go’ is negative and pulls previous reaction forward.

42
Q

Krebs cycle Reaction 4

A

What happens?
[Succinyl-CoA formed]
o COO- lost as Co2
o NAD+ reduced to NADH

Why?
o Succinyl-CoA is high energy compound (due to high energy bond between C-S) used in subsequent steps

43
Q

Krebs cycle Reaction 5

A

What happens?
[Succinate formed through cleavage of C-S bond, CoA released]
o Substrate level phosphorylation – of GDP-> GTP

Why?
o Energy released from the cleavage of the thioester bond (C-S) is used to form GTP/ATP

44
Q

Krebs cycle Reaction 6

A

What happens?
o Oxidation of succinate to fumarate
o FAD picks up 2 H ions -> FADH2

Why?
o Oxidation of succinate is insufficient to form NADH, forms FADH2 instead

45
Q

Krebs cycle Reaction 7

A

What happens?
o Hydration of fumarate to L-Malate
o Stereospecific – only adds it to form L-Malate

46
Q

Krebs cycle Reaction 8

A

What happens?
o Reduction NAD+ to form NADH
o Oxidation of L-Malate -> Oxaloacetate

Overall reaction has positive ∆Go’ but is pulled forward in 2 ways:
o Negative ∆Go’ of the 1st reaction of the cycle
o Utilisation of NADH in electron transport chain

47
Q

Regulation of Krebs Cycle

A
  • Regulated by energy status of cell
    o ADP/ATP ratio
    o NAD+/NADH ratio
  • Regulated by pathway intermediates
    o Succinyl-CoA
    o Citrate
  • Regulation by Ca2+ second messenger in signaling cascades
48
Q

What does pyruvate carboxylase do?

A
  • Converts pyruvate to oxaloacetate

- Is activated when acetyl-CoA exceeds oxaloacetate levels

49
Q

Regulation of the pyruvate dehydrogenase complex

A
  • Commits Acetyl-CoA into the cycle
  • Allosteric inhibition
    o Acetyl-CoA (product)
    o NADH
    o ATP
  • Covalent modification:
    o Inhibited by phosphorylation
    o Kinase activated by acetyl-CoA and NADH
    o Phosphatase activated by Ca2+
50
Q

What is reduction potential?

A

It quantitates the tendency of chemical species to be oxidised or reduced

51
Q

ETC Complex I

A
  • Accepts electrons from NADH
  • e- then passed through series of redox centres (redox reactions occur in these centres) and then transferred to co-enzyme Q which is reduced to ubiquinol (picks up 2H+)
  • Ubiquinone is membrane soluble and carries electrons to complex III.
  • Energy released from electron movement is used to drive transfer of 2H+ across the membrane.
52
Q

ETC Complex II

A
  • Complex is Succinate dehydrogenase (enzyme that reduces FAD-> FADH2 and transforms succinate to fumarate)
  • In TCA cycle
  • e- passed through redox centres and then transferred to co-enzyme Q which is reduced to ubiquinol (picks up 2H+)
  • Ubiquinone is membrane soluble and carries e- to complex III
  • Does NOT pump H+ ions across the membrane because not enough energy is produced.
53
Q

ETC Complex III

A
  • Accepts e- from ubiquinol
  • Protons from ubiqionol are released into the inter membrane space

1st CYCLE:

  • 1 e- is transferred to a bound ubiquinone (semiquinone radical ion)
  • 2nd electron is transferred to cytochrome C (can only carry 1 e-) through a series of redox centres
  • Accepts electrons from ubiquinol
  • Protons from ubiquinol are released into the intermembrane space (contributes to gradient)

2nd CYCLE:

  • 1 electron is transferred to semiquinone to form ubiquinol (recycle electrons) and 2H+ picked up from matrix
  • One electron is transferred to cytochrome c
54
Q

ETC Complex IV

A
  • Is Cytochrome C Oxidase
  • Accepts electrons from cytochrome c
  • Electrons are transferred via heme centre and copper atoms to oxygen
  • Electron transfer drives the transfer of protons into the intermembrane space
55
Q

What is chemiosmotic coupling?

A
  • Pumping of protons across the membrane creates a concentration and electrical gradient, which is used to generate ATP (Peter Mitchells theory)
56
Q

What is the total ATP produced through 1 cycle of oxidative phosphorylation?

A

Glycolysis:

  • 2 ATP Molecules directly produced
  • Each NADH produces either 1.5 - 2.5 ATP in the ETC depending on transport molecule
  • 2 NADH = 3-5 ATP (from Oxidative Phosphorylation)

Krebs cycle:

  • 2 ATP Molecules directly produced
  • Each NADH produces either 2.5 ATP in the ETC
  • 8 NADH (2 from Pyruvate Decarboxylation, 6 from TCA) = 20 ATP
  • 2 FADH2 (Produce 1.5 ATP) = 3 ATP
  • Subtotal = 23 ATP (From Oxidative Phosphorylation)

Total = 30-32 ATP Molecules

57
Q

Structure of ATP Synthetase

A
  • F0 (stalk) – spans the membrane and contains proton channel
  • F1 (knob) – contains the catalytic domains
  • Rotating molecular motor – protons moving through channel drives rotation of F1 and ATP synthesis
58
Q

Mechanism of ATP Synthetase

A
  • Beta subunits of the F1 domain exist in 3 conformations:
    o Open: low affinity for ligands; inactive
    o Loose: increased infinity for ligands – trapped in the subunit; inactive
    o Tight: high affinity for ligand; active
  • Proton movement drives the conformational changes in the beta subunits
59
Q

What can disrupt electron transport and ATP synthesis?

A
  • Inhibitors of the ETC reduce proton gradient formation
  • Inhibitors of ATP synthase prevents ATP synthesis
  • Uncouplers dissipate the gradient without forming ATP (energy lost as heat)
  • Thermogenin is an endogenous uncoupler

MCB2021F (5 decks)

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