Bioenergetics

Martin Knneke
(10/2009)

Energetic Considerations

Introduction
Definitions
Calculation of free energy changes
Examples of different biological
processes
Role of ATP
Free energy and reduction potential

Why do microorganisms need

energy?
Maintain the highly defined cellular
order
Active Movement
Detoxification
Signaling/Communication
Storage
Growth / Reproduction

Metabolism
Phototrophy

Chemotrophy

Catabolic Reactions
ATP
Biosynthesis
Anabolic Reactions
Heterotrophy

Autotrophy

Free Energy of Chemical Reactions

A+B

C+D

Free Energy

C+D

!G
A+B

A+B

!G
C+D

Progress of Reaction

!G >0 (positive)
endergonic reaction

Progress of Reaction

!G < 0 (negative)
exergonic reaction
Yield energy

Free Energy

Catabolic reactions are in

general exergonic reactions

A+B

Conserved as

!G
C+D

Progress of Reaction

ATP

( or other high-energy bonds)

= -32kJ/mol

!G < 0 (negative)
exergonic reaction

Free Energy

!G provides no information
about the rate of a reaction

A+B

!G
C+D
Progress of Reaction

!G < 0 (negative)
exergonic reaction

Free Energy

!G provides no information
about the pathway of the
reaction

A+B

!G
C+D
Progress of Reaction

!G < 0 (negative)
exergonic reaction

Definitions
Free-energy change of a reaction

!G = !G0 + RT ln

!G
!G0
R
T
[ A,B ]
[ C,D ]
a,b,c,d

aA + bB

cC + dD

[C]c [D]d
[A]a [B]b

= Free-energy change under specific conditions (in KJ=kiloJoule)

= Standard free-energy change (25C, unit activities; 1atm, 1M)
= Gas constant (8.314 J/mol/K)
= Absolute temperature (K; K=C+273.15)
= Molar Concentration of reactants (Activity)
= Molar Concentration of products (Activity)
= Stoichiometric coefficients

!G of a reaction depends on
a) the nature of the reactants
!G = !G0 + RT ln

[C]c [D]d
[A]a [B]b

and
b) on their concentrations
!G = !G0 + RT ln

[C]c [D]d
[A]a [B]b

Standard free-energy changes

A) Can be calculated from standard free energies of formation
!G0 = " !Gf0 (products) - !Gf0 (reactants)
B) Can be calculated from equilibrium constant
At equilibrium !G = 0
0 = !G0 + RT ln

[C]c [D]d
[A]a

[B]b

!G0= - RT lnK

Enthalpies of
formation !G'(f) of
biologically relevant
compounds

Standard free-energy changes

B) Can be calculated from equilibrium constant
At equilibrium !G = 0
0 = !G0 + RT ln
!G0 = - RT ln

K=

[C]c [D]d
[A]a [B]b

!G0= - RT lnK

[C]c [D]d
[A]a [B]b

[C]c [D]d
[A]a [B]b
(K = equilibrium constant)
0
- !G0/ 2.3RT
K = e - !G / 2.3RT= 10

Conditional (biochemical) standard

free-energy changes !G0
!G0 = Free-energy change under biochemical standard
condition at pH=7, unit activities, 25C = 298 K
!G0 = !G0 + m !Gf (H+)
!G0 = !G0 + mRT ln [H+] = !G0 + 39.95kJ m
m = net number of protons in the reaction
m < 0; when more protons are consumed than formed
m > 0; when more protons are formed than consumed

Redox potential E and

free-energy change
A+ + ne2H+ + 2e1/2 O2 + 2eH2 + 1/2O2

A
H2
O2H2O

; E = reduction potential

! E0

= Difference in potentials of half-reactions

= E0 electron-accepting - E0 electron-donating

n
E0

= Number of electrons
= Standard potential for redox-half-reaction
(in V,25 C, 1M)
= E0 at pH 7

E0

The electron tower

Couple
CO2/glucose(-0.43) 24e2H+ /H2 (-0.42) 2eNAD+/NADH (-0.32) 2eCO2/acetate (-0.28) 8eSO42-/H2S (-0.28) 8e-

NO3-/NO2- (+0.42) 2eNO3-/1/2N2 (+0.74) 5eFe3+/Fe2+ (+0.76) 1e-,(pH 2)

1/2O2/H2O (+0.82) 2e-

E0 (V)
-0.50

0.0

+0.50

+0.90

The standard free-energy change !G0 is

proportional to the redox-potential
difference between e--donor and
e--acceptor ! E0
!G0 = - nF ! E0
!G0 = - nF ! E0
n
F

= Number of electrons
= Faradays constant (96.48 kJ/V)

The electron tower

Couple
2H+ + 2e1/2 O2 + 2eH2 + 1/2O2

H2
O2H2O

!G0= -237 kJ
!G0 = - nF ! E0

CO2/glucose(-0.43) 24e2H+ /H2 (-0.42) 2eNAD+/NADH (-0.32) 2eCO2/acetate (-0.28) 8eSO42-/H2S (-.028) 8e-

NO3-/NO2- (+0.42) 2eNO3-/1/2N2 (+0.74) 5eFe3+/Fe2+ (+0.76) 1e-,(pH 2)

1/2O2/H2O (+0.82) 2e-

E0 (V)
-0.50

0.0

+0.50

+0.90

The substrate with lower E0 provide the electrons (e- donor)

Calculating free-energy changes for

hypothetical reactions

10

Balancing of chemical reactions

Oxidation-reduction (redox) balance
All electrons removed from a substance on one side must be
transferred to another substance on the other side
Ionic balance
Total ionic charge of all molecules must be equal on both sides
In aqueous medium, ionic balance can be achieved by adding
H+ or OH-, and H2O (for elemental balance)
Elemental balance
Total number of each element must be equal on both sides
of the equation

Determining the oxidation state

Oxidation state of elements in elementary substance or
combined with itself is 0 (H2, O2, N2, S(s)0)
Except when combined with itself, H has the oxidation state +1
Except when combined with itself, oxygen has the oxidation
state -2
Oxidation state of an ion of an element is equal to its charge
(O2-, Na+, Fe3+)
Sum of the oxidation states of all atoms in neutral molecule is 0
(H2O, 2 x +1, 1x -2)
Sum of oxidation states of all atoms in an ion is equal to its
charge (OH- = -1)
The oxidation state of individual carbon atoms in organic
compounds can vary (average ox-state can be calculated by
assuming that: N is usually -3, S is usually -2)

11

Calculating free-energy yields

Biological examples
Aerobic respiration
Fermentation
Anaerobic respiration: e.g., Methanogenesis
Syntrophic ethanol oxidation at anaerobic conditions

Aerobic Respiration of Glucose:

Glucose + Oxygen

Carbon dioxide

C6H12O6 + O2

CO2

12

Aerobic Respiration of Glucose:

Glucose + Oxygen

Carbon dioxide

C6H12O6 + O2

CO2

Elemental balancing
(6xC, 12xH, 18xO)

(1xC; 2xO)

C6H12O6 + 6O2

6CO2 + 6H2O

Aerobic Respiration of Glucose:

Glucose + Oxygen

Carbon dioxide

C6H12O6 + O2

CO2

Elemental balancing
(6xC, 12xH, 18xO)

(1xC; 2xH; 3xO)

C6H12O6 + 6O2
Redox balancing
C (0);H 12(+I);O 6(-II);
O 6(0)

6CO2 + 6H2O
C 6(+IV) O 12(-II); H 12(+I);O 6(-II)

13

Aerobic Respiration of Glucose:

Glucose + Oxygen
C6H12O6 + 6O2

Carbon dioxide + Water

6CO2 + 6H2O

!G0 = " !Gf0 (products) - !Gf0 (reactants)

= 6(-394.4)+6(-237.17) - (-917.22) = -2872.2 kJ

Aerobic Respiration of Glucose:

Glucose + Oxygen
C6H12O6 + 6O2

Carbon dioxide + Water

6CO2 + 6H2O

C 6(0); H 12(+I); O 6(-II)

C 6(+IV); O 18(-II); H 12(+I)

C6H12O6
6CO2+ 24 eGlucose (e- donor);

-0.43 V

6O2 + 24e6 H 2O
Oxygen (e acceptor)

+0.82V

!G0 = - nF ! E0
= -24 (96.48 kJ/V)(+0.82V -(-0.43V))= -2894.4 kJ

14

Fermentation of Glucose:
Glucose

Ethanol + Carbon dioxide

C6H12O6

C2H6O + CO2

Elemental balancing
(6xC, 12xH, 6xO) (3xC, 6xH, 3xO)
C6H12O6
Redox balancing
C (avg. 0)

2C2H6O + 2CO2
C 2(avg. -II); C 2(+II)

!G0 = (2(-394.4)+2(-181.75)) - (-917.22) = -234.28 kJ

Anaerobic Respiration (i.g.: Methanogenesis)

Hydrogen + Carbon dioxide
Methane
H2 + CO2

CH4

Redox Balance
C +IV; H 0

C -IV; H 4(+I) 8 e-

4H2 + CO2
(e- donor) (e- acceptor)

CH4

Elemental Balance
8xH, 1xC, 2xO

4xH, 1xC

4H2 + CO2

CH4 + 2H2O

!G0 = -50.75 + 2(-237.17) - (-394.4) = -130.7 kJ

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Ethanol fermentation
Ethanol
C2H6O

Acetate + Hydrogen
C2H3O2- + H2

Ionic Balance
C2H6O

C2H3O2- + H2 + H+

Elemental Balance
C2H6O + H2O

C2H3O2- + 2H2 + H+

Redox Balance
C 2(-II); H 6(+I); O (-II)

C 2(0); H 3(+I); O 2(-II) + H (+I)

Ethanol fermentation
Ethanol
C2H6O

Acetate + Hydrogen
C2H3O2- + H2

Ionic Balance
C2H6O

C2H3O2- + H2 + H+

Elemental Balance
C2H6O + H2O

C2H3O2- + 2H2 + H+

Redox Balance
C 2(-II); H 6(+I); O (-II)

C 2(0); H 3(+I); O 2(-II) + H (+I)

!G0 = -369.41 + (-39.83) - [(-181.75) + (-237.17)] = 9.68 kJ

16

Effect of hydrogen partial pressure

on free-energies
Ethanol fermentation:
ethanol + H2O
acetate + 2H2 + H+
[C]c [D]d
!G = !G0 + RT ln
[A]a [B]b

!G = !G0 + RT ln

[H2]2 [acetate] [H+ ]

[ethanol] [H2O]

at 10-4 atm H2
!G = !G0 + mRT ln [H2]
!G = 9.68 + 2RT ln [10-4 ] = -36.03 kJ/mol

Syntrophic ethanol oxidation at

anaerobic conditions
Ethanol fermentation
2 ethanol + 2H2O

!G0 (kJ/reaction)

2 acetate + 4H2 + 2H+

+ 19.4

Methanogenesis
4H2 + CO2

CH4 + 2H2O

- 130.7

Syntrophic coupled reaction

2 ethanol + CO2

2 acetate + CH4 + 2H+

- 111.3

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Syntrophic co-culture Methanobacillus omelianskii

ethanol

CO2

Interspecies Hydrogen-transfer

H2

H2

CH4

acetate
Strain S

Strain
MoH
Methanobacillus omelianskii

Syntrophic co-cultures
Interspecies hydrogen transfer
Hydrogen-producer

Hydrogen-consumer

Fermentation
fatty-acids
(e.g., butyrate, propionate)
alcohols
(e.g.,ethanol)

Anaerobic Respiration
CO2, SO4-2, NO3-

H2

H2

acetate + CO2

acetate, methane, HS-, N2O,

NO, N2

Syntrophomonas
Syntrophobacter

Methanogens
Sulfate-reducing bacteria
Homoacetogens
Denitrifyers

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Adenosintriphosphate (ATP)

Free enthalpy of ATP

Hydrolysis of ATP, AMP and pyrophosphate

ATP + H2O ! ADP + Pi
ATP + H2O ! AMP + PPi +

"G' = -32 kJ/mol

H+

"G' = -45 kJ/mol

AMP + H2O ! Adenosin + Pi

"G' = -13 kJ/mol

PPi + H2O ! 2 Pi

"G' = -29 kJ/mol

ATP + AMP ! 2 ADP

"G' = 0 kJ/mol

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How much ATP is in a cell?

ATP

Energy charge, EC of the cell

EC =

[ATP] + 0.5 [ADP]

[ATP] + [ADP] + [AMP]

> 0.8

e.g. [ATP] # 10 mM, ADP # 1 mM, AMP # 1 mM

EC = 10.5/12 = 0.875

The cell is energetically loaded. (During starvation?)

What is the value of ATP in the cell?

ATP

Consideration of concentrations for

energetical calculations:
Multiply reactant concentrations, if
there is more than 1 reactant:
"G = "G + RT ln(cProduct/cReactant)
"G = "G + RT ln(C C / C C )

P1

P2

R1

R2

Textbook (standard conditions)

ATP + H2O ! ADP + Pi
"G' = -32 kJ/mol
In the cell: [ATP]#0.01 M, [H2O]='1', ADP#0.001 M, [Pi] #0.01 M
Product-reactant ratio is (0.001*0.01)/(0.01 * 1) = 0.001
"Gbiol. = "G0' + RT ln 0.001
"Gbiol. = 32 kJ/mol + (8,315 J/K mol) (298 K)(ln 0.001)
"Gbiol. = "G0' + RT ln 0.001 = "G0' -17 = -49 kJ/mol
For Regeneration of ATP spent: mostly about 75 kJ/mol ATP

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What is the value of ATP in the cell?

ATP

Consideration of concentrations for

energetical calculations:
Multiply reactant concentrations, if
there is more than 1 reactant:
"G = "G + RT ln(cProduct/cReactant)
"G = "G + RT ln(C C / C C )

P1

P2

R1

R2

Textbook (standard conditions)

ATP + H2O ! ADP + Pi
"G' = -32 kJ/mol
In the cell: [ATP]#0.01 M, [H2O]='1', ADP#0.001 M, [Pi] #0.01 M
Product-reactant ratio is (0.001*0.01)/(0.01 * 1) = 0.001
"Gbiol. = "G0' + RT ln 0.001 = "G0' -17 = -49 kJ/mol

"Gbiol= -50 kJ/mol

For Regeneration of ATP spent: mostly about 75 kJ/mol ATP

In the cell ATP has a higher value than under standard

conditions, and requires even more energy to be regenerated.

Mechanisms of ATP regeneration

There are only two possibilities.
Substrate level Phosphorylation
b + a (last slide) backwards, coupled to an exergonic reaction,
e.g. redox reaction
Ion transport Phosphorylation (H+ or Na+)
(membrane bound, driven by electrical membrane potential +
chemical gradient)
Terms:
Energy conservation
Substrate level phosphorylation, dt. Substratketten-Phosphorylierung ?
There is

no oxidative phosphorylation, neither electron transport-

driven phosphorylation, nor photophosphorylation

Do not get stupefied by obsolete terms!

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Gibbs free energy and reduction potential

!G0 = - nF ! E0

24

Gibbs free energy and reduction potential of NAD

NAD+ + 2H+ + 2e- ! NADH + H+ E0 = -0.32 V
0.5O2 + 2H+ + 2e- ! H2O

E0 = 0.82 V

NADH + 0.5O2 + H+ ! NAD+ + H2O

!E0 = E0O2- E0NADH = 0.82 V - (-0.32 V) = 1.14 V

!G0 = - nF ! E0
!G0 = -(2) (96.48kJ/V mol) (1.14V) = -220kJ/mol

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