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1) Biochemistry I > Metabolism and Bioenergetics > Flashcards

Metabolism and Bioenergetics Flashcards

1
Q

Define metabolism.

A

All the reactions in a living cell, pathways are all interconnected and allow for compounds to come in and out

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2
Q

Why is metabolism essential?

A

For energy production

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3
Q

Define intermediary metabolism.

A

Reactions that involve the interconversion of small molecules (less than 1000Da)

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4
Q

Define catabolism.

A

Breakdown -> generates E (convergent)

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5
Q

Define anabolism.

A

Use small components as building blocks -> uses energy (divergent)

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6
Q

Name the 3 laws of thermodynamics.

A

1) Energy cannot be created or destroyed, only transformed (E = mc^2)
2) Universe has a tendency to increase disorder
3) As T approaches absolute 0, atomic motion ceases

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7
Q

How many oC = K?

A

25oC = 298K

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8
Q

Define exergonic reactions.

A

-x kJ/mol is released
spontaneous
- delta G

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9
Q

Define endogenic reactions.

A

x kJ/mol is released
not spontaneous
+ delta G

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10
Q

What does delta G = 0 mean?

A

Reaction is at equilibrium, rate of substrate to product = rate of product to substrate

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11
Q

Name an example of an exergonic reaction

A

Oxidation of glucose

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12
Q

What is the oxidation of glucose reaction formula?

A

C6H12O6 + 6O2 -> 6 CO2 + 6 H2O

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13
Q

How does the oxidation of glucose work?

A

High energy electrons come from photosynthesis, oxygen is required to pick up low energy electrons at the end of the cycle and make H2O

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14
Q

Define delta G ++

A

Energy of activation (double dagger)

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15
Q

Since we can’t measure delta G and delta H directly, what do we do?

A

Compare under standard conditions

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16
Q

Define delta G^o

A

Standard free energy change (298 K, 1 atm, solution of 1 M)

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17
Q

Define delta G^o’

A

Biochemical free energy change (298 K, 1 atm, solution of 1 M, pH = 7.0)

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18
Q

Why is measuring delta G^o’ difficult?

A

Because monitoring delta S is difficult

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19
Q

Why do we need to know keq?

A

To know the processes in the cell, you need to understand all the interconnected reactions in a cell

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20
Q

What is the equation for keq?

A

keq = ((C)(D))/((A)(B))

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21
Q

What is the equation for delta G^o’?

A

G^o’ = -RT ln(keq)

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22
Q

What does a small keq mean? Large?

A

Small: delta G^o’ is positive and large (not spontaneous)
Large: delta G^o’ is negative and large (spontaneous)

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23
Q

How would you find keq experimentally?

A

Add 20 mol of reactant, at various times take measurements of reactant and product, at some point, there will be no more change -> equilibrium -> find keq

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24
Q

What is important to know about delta G^o’?

A

STANDARD FREE ENERGY IS AT 1 MOLAR

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25
Q

Name 2 ways we can drive unfavourable reactions.

A

1) Coupling reactions

2) Changing the position of the equilibrium

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26
Q

Do coupling reactions consume energy?

A

Yes

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27
Q

How do you find the overall keq when coupling reactions?

A

keqs are MULTIPLIED, not added

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28
Q

How does the delta G for ATP hydrolysis when the concentrations of ATP and ADP in the cell are taken into consideration compare to the delta G^o’ if its in a cell?

A
  • delta G increases when you factor in the concentration of a cell compared to delta G^o’
  • Delta G^o’ =-30.5kJ/mol
  • Delta G = -50 to -65 kj/mol
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29
Q

What is the primary source of energy to get work done?

A

ATP

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30
Q

Which compounds are high energy compounds?

A

Compounds with a delta G^o’ of hydrolysis > -25 kJ/mol = high energy

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31
Q

Name 4 reasons why phosphoanhydride bonds are high energy.

A

1) At pH 7, ATP carries 4 negative charges (hydrolysis releases electrostatic stress)
2) Resonance delocalization of PO4^2- (following hydrolysis, ionization increases randomness)
3) ADP and HPO4^2- ionizes releasing a proton (increase delta S)
4) ATP hydrolysis increase the solvation of ADP and pi

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32
Q

How do the number of water molecules needed to solvate ATP compare to inorganic phosphate and ADP?

A

number of H2O molecules needed to solvate ATP is less than inorganic phosphate and ADP, increase delta S

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33
Q

What else do these physiochemical properties of phosphohydride bonds account for?

A

Energy released by hydrolysis of ADP to AMP or compounds such as G-6-P

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34
Q

How can energy be stored?

A

In the form of reducing electron carriers (NADH, NADPH, FADH2)

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35
Q

How are electrons transported?

A

As a hydride

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36
Q

Define a hydride.

A

A proton with two electrons (negatively charged)

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37
Q

Describe the 2 half cell reactions and the overall reaction.

A

Ared -> A ox + ne-
Box + ne- -> B red
—> A red + Box Bred + Aox

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38
Q

What does the equilibrium point for a red-ox reaction depend on?

A

On the relative affinity of Aox and Box for electrons

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39
Q

How can the flow of electrons be measured?

A

Measured by a voltmeter

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40
Q

Define reduction potential.

A

Tendency of a compound to ACQUIRE electrons, and thereby be reduced
The more positive the V, the better the oxidizing agent (gains electrons)
The more negative the V, the better the reducing agent (loses electrons)

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41
Q

What is delta E^o’?

A

Reduction potential tendency (1M, 1 atm, 25oC, at pH=7)

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42
Q

What is one of the half reactions in a biological system? What is E^o’

A

2 H+ + 2e- H2

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43
Q

What does a negative delta E^o’ mean? Positive?

A

Positive: tendency to gain electrons (the more oxidizing potential)
Negative: tendency to give up electrons (the more reducing potential)

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44
Q

Describe the equation involving delta G^o’ and delta E^o’. What is n? What is F?

A

delta G^o’ = -nF delta E^o’
n = nb of electrons transferred
F = Faraday’s constant (96.5 kJ/Vmol)

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45
Q

How do you calculate delta E^o’?

A

delta E^o’ = E^o’ (e- acceptor) - E^o’ (e- donor)

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46
Q

e- acceptor always has a ____ potential.

A

lower

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47
Q

What happens when you increase reducing potential?

A

Increase negative volts

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48
Q

Define reduction and oxidation.

A

Reduction: gain of electrons
Oxidation: loss of electrons

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49
Q

Name 2 things that decrease down the electron transport chain cascade.

A
  • Electron energy decreases

- Reducing potential decreases

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50
Q

What is the oldest pathway?

A

Glycolysis

51
Q

Define glycolysis.

A

the breakdown of glucose by enzymes, releasing energy and pyruvic acid.

52
Q

Is glycolysis aerobic?

A

It is anaerobic

53
Q

Where does glycolysis occur? Where does extra extraction occur?

A
  • Occurs in cytosolic compartment

- Extra extraction in the mitochondria

54
Q

What % of energy is captured without oxidative phophorylation?

A

5%

55
Q

Name the 2 phases of glycolysis.

A

1) Preparatory phase

2) Payoff phase

56
Q

Why does glycolysis need a preparatory phase?

A

You need to do something to make it unstable to activate glucose molecule -> break bonds

57
Q

What is the overall reaction for glycolysis?

A

Glucose + 2 ADP + 2 NAD+ + 2 Pi -> 2 pyruvate + 2 ATP + 2 NADH + 2 H2O

58
Q

How many molecules of ATP and NADH does one glucose molecule generate?

A

2 ATP + 2 NADH

59
Q

What happens if you deplete NAD+?

A

Glycolysis stops

60
Q

What does the preparatory phase require?

A

Requires 2 ATP

61
Q

What is glucose catabolyzed to during the preparatory phase?

A

Glyceraldehyde-3-phosphate and dihydroxyacetone phosphate

62
Q

Why is the final compound in the preparatory phase unstable?

A

2 negatively charged phosphates = repulsive forces

63
Q

Describe the enzymatic steps of the preparatory phase.

A

1) Hexokinase
2) Phosphohexoisomerase
3) Phospho-fructosekinase-1
4) Aldolase
5) Triose phosphate isomerase

64
Q

What does the payoff phase require? What does it produce?

A

Requires high energy intermediates

Produces ATP and NADH

65
Q

What enters the payoff phase?

A

2 glyceraldehyde-3-phosphate molecules

66
Q

What does the payoff phase generate?

A

Converts to 2 pyruvates which generate 4 ATP and 2 NADH/glucose units

67
Q

What is the net production of the payoff phase?

A

2 ATP

68
Q

Describe the enzymatic steps of the payoff phase.

A

6) Glyceraldehyde-3
7) Phospho-glycerate kinase
8) Phospho-glycerate mutase
9) Enolase
10) Pyruvate kinase

69
Q

Describe substrate level phosphorylation. When does it occur?

A

Phospho-glycerate kinase moves phosphate from ADP to make molecules of ATP, occurs when you have high energy phosphate

70
Q

Where is 90% of the energy trapped?

A

Trapped in the 2 molecules of pyruvate

71
Q

What is a characteristic of C=C and phosphoesther?

A

Very high energy

72
Q

Define a pathway

A

Product of first reaction is the substrate of the second reaction

73
Q

What is glucose normally in the blood?

A

4-5 mM

74
Q

Why does high levels of glucose relate to vision problems?

A

Modification of some proteins = problems with vision (lens proteins don’t turn over fast)

75
Q

What is the role of glycogen?

A

Reservoir for fight/flight under anaerobic conditions

76
Q

What inhibits hexokinase? What kind of inhibition is it?

A

High levels of G-6-P (competitive)

77
Q

What does hexokinase do?

A

Uses ATP to generate G-6-P

78
Q

Is adding a phosphate to glucose favourable?

A

Not spontaneous

Coupling with ATP -> both favourable

79
Q

Is isomerization : conversion of G-6-P to F-6-P favourable?

A

Not spontaneous, so we change the position of the equilibrium

80
Q

Is making fructose 1,6-biphosphate favourable?

A

Not spontaneous

Coupled with hydrolysis of ATP

81
Q

Define allosteric enzyme.

A

Provide subtle regulations to control and meet cells metabolic processes

82
Q

Explain PFK-1 versus the reaction velocity.

A

Low ATP: reaction rates are faster

High ATP: reaction rates are slower

83
Q

What happens when ATP levels drop?

A

ADP increases, which will bind to enzyme

84
Q

Where is citrate found? What does it do?

A

From TCA cycle - found in matrix of mitochondria

Will inhibit PFK-1

85
Q

Name 2 allosteric compounds (inhibitors and activators of PFK-1).

A

1) ATP and citrate are allosteric inhibitors of PFK-1

2) ADP and AMP, F-2, 6-P are allosteric activators of PFK-1

86
Q

Is aldol cleavage favourable?

A

No

Driving reaction by changing position of equilibrium

87
Q

Is the conversion of glyceraldehyde-3-phosphate to 1,3-biphosphoglycerate favourable?

A

Delta G^’o is not favourable

BUT Delta G IS (temperature in red blood cells, all that matters)

88
Q

Is substrate level phosphorylation favourable?

A

It is favourable, delta G is negative

89
Q

Compare delta G and delta G^’o for the glycolysis reaction.

A

Delta G^’o: -130.9 kJ/mol

Delta G: -103.8 kJ (stays flat - reaction equally favourable forward and reverse)

90
Q

How are the 4 points of allosteric effects and inhibition regulation in glycolysis?

A

1) Hexokinase
2) Phosphofructokinase
3) Glyceraldehyde-3-phosphate dehydrogenase
4) Pyruvate kinase

91
Q

Under anaerobic conditions, 2 pyruvates retain what % of energy in glucose?

A

90%

92
Q

What kind of energy does catabolism release?

A

Some as ATP and reduced electron carriers (NADH)

93
Q

ATP and NADH generated from catabolism are used for what?

A

As energy to power anabolic reactions

94
Q

Describe Gibbs free energy equation? What is the unit of T?

A

G = H - TS

T is in Kelvin

95
Q

In the oxidation of glucose, what is BEING reduced and what is being oxidized?

A

Oxidized: C6H12O6 -> 6 CO2 (losing electrons)
Reduced:
6O2 -> 6H2O (gaining electrons)

96
Q

What does glucose in the presence of oxygen need in order to oxidize?

A

Needs energy of activation

97
Q

Does delta G provide information on the reaction rates?

A

NO

98
Q

In what form are chemical reactions written in?

A

They are all written in the REDUCING form, so you need to flip them around

99
Q

Which glycolysis steps need to be coupled in order to drive unfavourable steps?

A
  • Phosphorylation of glucose by hexokinase (driven by ATP hydrolysis)
  • F-6-P to F-1,6-P (driven by ATP hydrolysis)
  • Isomerization of DHAP to G-3-P by triosephosphate isomerase (coupled to other Rx which have a large negative delta G^o’)
100
Q

What kind of agent would the electron acceptor be? Electron donor?

A

Electron acceptor: oxidizing

Electron donor: reducing

101
Q

Why is oxygen a very good electron acceptor?

A

It has a high delta E^o’

102
Q

What is Faraday constant?

A

96.5 kJ/Vmol

103
Q

How many ATP molecules and NADH molecules are produced per glucose unit entering glycolysis? What is the NET production?

A
  • 4 ATP and 2 NADH

- Net: 2 ATP

104
Q

What are glucose levels regulated by?

A

Insulin and glucagon

105
Q

How is glucose taken into the cell? How is it trapped in cytosol?

A
  • Taken in by transporters

- Trapped in cytosol by phosphorylation

106
Q

What enzyme is a major point for the regulation of glycolysis?

A

Phosphofructokinase-1

107
Q

What happens to glycolysis when levels of of ATP are high?

A

Mechanisms inhibit glycolysis

108
Q

What happens to Fructose-6-Phosphate when ATP levels are high? Low?

A

High ATP: low F-6-P

Low ATP: high F-6-P

109
Q

Which steps in glycolysis are driven by changing the equilibrium?

A
  • Aldol cleavage of F-1,6-P into G-3-P and DHAP (driven by rapid removal of G-3-P)
  • Conversion of G-6-P to F-6-P
110
Q

Which reaction in the glycolytic pathway is readily reversible?

A

Aldolase and triose phosphate isomerase catalyzed reactions

111
Q

Which step in glycolysis has a postive delta G^o’ but a negative delta G?

A

Conversion of G-3-P to 1,3-biphosphoglycerate (at 37oC using steady state concentration in red blood cell)

112
Q

What is the first step in recovery of energy from glycolysis? What does it produce? What is it catalyzed by?

A
  • Conversion of G-3-P to G-1,3-P
  • Produces 2 NADH/glucose
  • Catalyzed by glyceraldehyde-3-phosphate dehydrogenase
113
Q

How does G-3-P get converted to G-1,3-P?

A

1) Aldehyde group of G-3-P reacts with an active sulhydryl group (cysteine) on enzyme
2) Formation of covalent intermediate + transfer of a hydride group to NAD+ to form NADH
3) NADH is released from the enzyme and Pi attach the thiol acyl bond release G-1,3-P

114
Q

What are the inhibitors for hexokinase?

A

ATP and G-6-P

115
Q

What regulates the levels of glyceraldehyde-3-phosphate dehydrogenase?

A

NAD+

116
Q

What inhibits pyruvate kinase? What activates it?

A

Inhibitors: acetyl-CoA and ATP
Activators: fructose-1,6-biphosphate and AMP

117
Q

Define reducing potential.

A

The likelihood of reducing something else

118
Q

What are the three possible fates of pyruvate after glycolysis?

A

1) Alcohol fermentation (anaerobic)
2) Homolactic acid fermentation (anaerobic)
3) TCA cycle (aerobic)

119
Q

Define fermentation.

A

The process of generating NAD+ from NADH is termed fermentation
NADH + H+ -> NAD+

120
Q

What does alcohol fermentation produce?

A

CO2 + Ethanol

121
Q

What is produced in homolactic acid fermentation?

A

Lactic acid

122
Q

What is produced in the TCA cycle?

A

CO2 + H2O

123
Q

What is used in the TCA cycle?

A

NAD+ -> NADH + H+

1) Biochemistry I (12 decks)

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