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Biochemistry > Bioenergetics L9, 11, 12 > Flashcards

Bioenergetics L9, 11, 12 Flashcards

1
Q

what are some of the key characteristics of living matter

A

Structurally complicated/Highly organised
Extracts, transforms and uses energy from the environment
Capacity for self replication (reproduce) and self assembly

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2
Q

what is bioenergetics

A

describes how living systems capture, transform and use energy to perform work and stay alive

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3
Q

what are examples of biological work

A

synthetic
mechanical
concentration (active inward transport of molecules)
electrical work (active outward transport of ions)
heat
bioluminescent

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4
Q

what is hydrocarbon combustion

A

CH4 +2O2 –> 2H2O + CO2 +energy (usually heat)

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5
Q

how can energy be produced from carbohydrate and lipids

A

C6H12H6 + O2 —> 6CO2 +6H2O + energy

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6
Q

how do biochemists measure energy involved in metabolism

A

mostly use equilibrium thermodynamics

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7
Q

what is a system

A

matter within a defined region of space

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8
Q

what is an open system

A

energy an matter can move in and out system

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9
Q

what is a closed system

A

only energy can leave system

matter cannot leave system

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10
Q

what is an isolated system

A

neither energy or matter can leave the system

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11
Q

what is the concept of equilibrium thermodynamics

A

Study of heat exchange that occurs in a reaction that is closed system as reaction reaching equilibrium

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12
Q

what do biochemists mean by energy

A

usually the chemical energy that is exchanged in reactions

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13
Q

what happens in a steam engine in equilibrium thermodynamics

A

steam /heat converted to kinetic energy

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14
Q

what happens in a internal combustion engine

A

petrol, diesel etc chemical energy converted to kinetic energy

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15
Q

what is the biological piston engine - muscle fibre contraction

A

Biological engine
Muscle fibers made of thick and thin filaments, when contract they slide into each other
Thick – myosin act like ores (rowing a boat) , in cyclic fashion wind themselves in into thin filament
Convert chemical energy (ATP) to kinetic – muscle contraction

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16
Q

what is the first law of thermodynamics

A

Energy within a system is conserved, it can be changed from one form to another , but it cannot be created or destroyed
initial=end

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17
Q

what is the reaction equation that relates to the first law of thermodynamics

A 
ΔE = Q – W
ΔE = change in the ‘internal energy’ 
Q = heat added to cylinder
W = work done by piston
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18
Q

what is the equation that shows if a reaction occurs in well insulated container and no heat exchange

A

ΔE = Q – W

Q=0,
ΔE = E – W

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19
Q

if the piston is prevented from moving, there is no work done what is the equation

A

ΔE = Q – W

W=0
ΔE = Q

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20
Q

what is a bomb calorimeter function

A

most direct way of measuring the energy content of metabolites and food stuffs

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21
Q

what happens to the energy made from bomb calorimeter

A

energy produced by combusting or oxidizing a substrate can be measured as a change in internal energy, ΔE

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22
Q

what is the ΔE in an exothermic reaction

A

negative

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23
Q

how are metabolites energy content measured

A

Crucible add in substance want to measure
Placed in the steel bomb and sealed
Filled with pure oxygen 1 atm pressure ignited – fully combustion
Release of energy in form of heat
Heat exchanged to the water surrounding the steel bomb and the temperature change is measured by the thermometer
no energy added so ΔE= Q

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24
Q

what are the temperature differences between system and surrounding in living

A

living systems temperature differences between system and surroundings are small (10-20°C)

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25
Q

what is the enthalpy of a system

A

measure of the heat change during a reaction at constant pressure and volume

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26
Q

how are enthalpy changes found

A 
ΔE = ΔH – PΔV
(E = internal energy, P = Pressure, V = volume)
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27
Q

what assumptions are made when calculating enthalphy

A 
constant pressure (atmospheric)
volume changes are negligible
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28
Q

what does ΔH ^O or ΔH^-O- mean

A

enthalpy changes under standard conditions

molar quantities, atmospheric pressure and 25OC (298K

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29
Q

what does a bomb calorimeter help us calculate

A

the energy produced in reactions

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30
Q

how is efficiency measured

A

energy out / energy in x 100

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31
Q

how does lactate form in sprinters

A

use fast muscle fibres to convert glucose to lactate

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32
Q

what forms from marathon runners

A

slow muscles to convert glucose and fat to carbon dioxide and water

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33
Q

what does the heart muscle convert

A

fatty acids to carbon dioxide and water

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34
Q

how efficient is the conversion of glucose to lactate

A

ΔH = - 50 kJmol-1 is only 1.8% efficient

Not all 50kJmol-1 used for cellular processes and metabolism

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35
Q

what does entropy mean

A

useless energy

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36
Q

what is free energy

A

energy available to drive biochemical reaction

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37
Q

what is the Gibbs-Helmholtz equation

A

ΔG° = ΔH° - TΔS°

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38
Q

what is ΔG° in the Gibbs-Helmholtz equation

A

Gibbs or free energy

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39
Q

what is ΔH° in the Gibbs-Helmholtz equation

A

Change in enthalpy

40
Q

what is -T in Gibbs-Helmholtz equation

A

Absolute temperature (K)

41
Q

what is ΔS° in the Gibbs-Helmholtz equation

A

Change in entropy

42
Q

what does the Gibbs-Helmholtz equation relate to

A

Constant Pressure and Temperature

43
Q

what is the concept of free energy and entropy

A

Water in reservoir has capacity to do useful work that drives turbines and make electricity (free energy)
Water downstream lost capacity to make energy
(entropy)

44
Q

what is the second law of thermodynamics

A

free energy must be negative

entropy must be positive

45
Q

what is the reaction if ΔG <0

A

reactants convert into products (forward reaction)

46
Q

what is the reaction if ΔG >0

A

reverse reaction is favoured

47
Q

what is the reaction if ΔG = 0

A

equilibrium

48
Q

can biochemical pathways in metabolic pathways be reversed

A

thought of as irreversible as require energy to reverse

49
Q

what is the probability of second law of thermodynamics

A

when energy under pressure / heated
If remove ‘barrier’ energy will disperse itself within system/environment till reach thermal equilibrium
Telling us what is more probable
All go from less probable to a more probable reaction –drive biochemical reaction
Require energy to reverse a reaction

50
Q

which reaction is favoured

A

reaction with the higher entropy is more probable

51
Q

where are free energy changes

A

Free energy changes are most easily obtained from studies of a reaction approaching equilibrium

52
Q 
what is the Gibbs free energy equation
equilibrium constant (Keq)
A

ΔG° = - R.T. ln Keq

53
Q

what does ΔG° mean in the Gibbs free energy equation

A

standard free energy change

54
Q

what does R mean in the Gibbs free energy equation

A

gas constant (8.31 joule mol-1 K-1)

55
Q

what does T mean in the Gibbs free energy equation

A

absolute temperature

56
Q

what does ln mean in the Gibbs free energy equation

A

natural log

57
Q

how can equilibrium constants be measured in biochemistry

A 
often easy to measure equilibrium constants
Lactic acid (‘lactate’) and pyruvic acid (‘pyruvate’) are readily interconverted in the liver
58
Q

what is ΔG’

A

actual energy change

59
Q

what is ΔG°’

A

standard energy change

60
Q

what is most of a cells free energy used for

A

to synthesize proteins by creating peptide bonds

61
Q

what are the energetics of peptide bond formation and protein synthesis

A

polyribosomes synthesise peptide bonds very efficiently - translation
reaction must be ‘driven’ by hydrolysis of ATP & GTP
free energy changes associated with ATP/GTP hydrolysis are more than enough to compensate for the unfavourable free energy changes associated with peptide bond formation

62
Q

what is energy coupling

A

Overall ΔG° must be negative
Free Energy must decrease and entropy must increase
In theory 3 molecules of ATP/GTP are used for every peptide bond produced

63
Q

what requires energy in animals

A
  • creating cellular infrastructure
  • synthesis of amino acids
  • active transport of nutrients
  • ‘wasteful’ or ‘futile’ cycle of protein turnover
64
Q

what are high energy phosphate bonds

A

Not energy in the bonds themselves – not the energy when break bonds
Difficult to break bonds and release energy
Big change in free energy from the initial state to final state

65
Q

what are phosphate group transfers and ATP

A

ATP reactant, makes large changes in free energy
Less probable to more probable
Negative oxygen repel – unstable, wants to move and make it more stable – electrostatic repulsion
Release of this charge by remove water
Resonance stabilisation – become more stable
Really unstable to more stable state – driving hydrolysis of ATP – get such large changes in energy (high energy phosphate bonds)

66
Q

what are the origins of high energy phosphate bonds

A
  1. Relief of charge/charge repulsion between phosphates

2. Increased possibilities for resonance and delocalisation of electrons

67
Q

what is the energy charge or a cell

A

ratio of ATP relative to ADP and AMP

68
Q

how is ATP recharged

A

other coupling reactions

69
Q

how is ATP re-synthesised

A

need to put in energy 30kJmol-1
Result of it being positive it must couple to something with a high negativity (phosphoenol pyruvate) uses pyruvate kinase, -52kJmol-1
Decrease in free energy as -22kJmol-1

70
Q

what is the oxidation of carbohydrates and lipids

A

Glycolysis produces acetyl co-enzyme A, enters the Krebs cycle, produces CO2 and active hydrogens (NADH and FADH2)

71
Q

what are the compounds used to produce more ATP

A

active hydrogen in NADH and FADH2

72
Q

how is NAH reduced

A

In NAD has nicotine amide ring, substrate hydrolysed it releases a hydrogen and two electrons

73
Q

what reaction occurs in transfer of hydrogen

A

electrons is redox

74
Q

what happens in reduced coenzymes and electron transport

A

Co enzymes produce ATP and NADH
High energy electrons – inactive hydrogen
NADPH has extra phosphate – stimulated by light
Active hydrogens transfer electrons to electron transport chain, produce further ATP

75
Q

how are redox couple written

A

oxidised ‘half couple ‘on the left

76
Q

how are standard reduction potentials generated

A

Reference cell (hydrogen ion [1M] equilibrated with hydrogen gas) is 0 volts
Reference cell connected to an electrode via a voltmeter
Electrode in a half cell pH7, with [1M] redox couple were interested in
Salt bridge connects the two half cells – electrons to flow, will transfer from the lowest standard electrode potential

77
Q

what happens to the electrons in the redox couples in half cells

A

redox couples in solution always get spontaneous transfer of electron, depends which direction the electron is going to go depending on the affinity for a redox couple to accept an electron

78
Q

how are standard redox potentials displayed

A 
redox couples in league tables
oxidised couple on LHS
\+ at top
E=0 middle Hydrogen electron
- at bottom
79
Q

how do redox couple interact

A

electrons will flow from the redox couple with the lower reduction potential to another with higher reduction potential

80
Q

how does the reduction potential vary

A

depending on the percentage of the reduced and oxidised species in the solution

81
Q

what is midpoint potential

A

50% of each oxidised and reduced species at pH7

82
Q

what is the Nernst equation

A

describes the curve

E = Eo + (RT / nF) ln (oxidised / reduced)

83
Q

what is E in the nernst equation

A

the actual potential at any point on the curve

84
Q

what is Eo in the nernst equation

A

midpoint potential

85
Q

waht is F in the nernst equation

A

faraday constant

86
Q

when are 2 electrons transferred

A

in NADH reactions

87
Q

what does a free energy change calculation require

A

concentration of redox couples

88
Q

how is the redox potentials and free energy changes calculated

A

ΔG° = nF ΔEo’

89
Q

what does n stand for in the free energy changes calculation

A

number of electron transferred

90
Q

what occurs in the electron transport chain

A

two redox couples involved include 1/2 O2/h2O and NAD+NADH

potential difference of 1.14V between NADH and O2 drives electron through electron transport chain

91
Q

what happens when NADH is oxidised

A

Free Energy is ‘released’

but some is ‘saved’ in ATP

92
Q

what do enthalpy values do

A

Enthalpy values give the amount of energy which can be released on complete oxidation of a foodstuff

93
Q

what is E = Q - W

A

Internal Energy (E) is related to heat (Q) and work (W (PΔV))

94
Q

what is ΔG° = ΔH° - TΔS°

A

Changes in standard Free Energy (G), Entropy (S) and Enthalpy (H) are related by the expression

95
Q

what is ΔH = Σ (ΔH reactants) - Σ (ΔH products)

A

Enthalpy changes are best measured by the bomb calorimeter using the expression

96
Q

what is ΔG° = - R.T.ln Keq

A

Standard Free Energy changes are measured from equilibrium studies

97
Q

what in ΔG° = -nF ΔEo

A

Standard Free energy (G) changes are related to Potential Difference (ΔE) between REDOX couples

Biochemistry (13 decks)

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