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Bioenergetics
January 15, 2003
Bryant Miles
Basis of Thermodynamics
Every living cell and organism must perform work to stay alive, to grow and to reproduce. The
ability to harvest energy from nutrients or photons of light and to channel it into biological work
is the miracle of life. Living organisms carry out a remarkable variety of energy transductions.
The biological energy transductions obey the physical laws that govern all natural processes,
including the laws of thermodynamics.
1st Law of Thermodynamics
The energy of the universe remains constant.
2nd Law of Thermodynamics
All spontaneous processes increase the entropy of the universe.
State functions depend only on the initial and final conditions not on path taken between the
initial and final conditions. They are independent of path. The important state functions for
the study of biological systems are:
G, the Gibbs free energy which is equal to the total amount of energy capable of doing work
during a process at constant temperature and pressure.
• If ∆G is negative, then the process is spontaneous and termed exergonic.
• If ∆G is positive, then the process is nonspontaneous and termed endergonic.
• If ∆G is equal to zero, then the process has reached equibrium.
H, the Enthalpy which is the heat content of the system.
• When ∆H is negative the process produces heat and is termed exothermic.
• When ∆H is positive the process absorbs heat and is termed endothermic.
S, the Entropy is a quantitative expression of the degree of randomness or disorder of the
system.
• When ∆S is positive then the disorder of the system has increased.
• When ∆S is negative then the disorder of the system has decreased.
The conditions of biological systems are constant temperature and pressure. Under such
conditions the relationships between the change in free energy, enthalpy and entropy can be
described by the expression where T is the temperature of the system in Kelvin.
∆G = ∆H − T∆S
Equilibrium Constants
All spontaneous processes proceed until equilibrium is reached. Consider the following
chemical reaction.
k1
A + B
C + D
k2
The forward rate of product formation is = k1[A][B]
The reverse rate of reactant formation is = k2[C][D]
At equilibrium the concentrations of products and reactants are such that forward and reverse
rates are equal
k1[Aeq][Beq] = k2[Ceq][Deq].
A little algebra and presto
[C eq ][ Deq ]
k
K eq = 1 =
k 2 [ Aeq ][ Beq ]
At equilibrium ∆G = 0.
The biochemist standard state the concentration of reactants and products are initially set at 1 M,
the temperature is 298 oK, the pressure is 1 atm, the pH is 7.0 and the concentration of water is
55 M. The biochemists constants are written as ∆Go’ and K’eq. This is the only standard state we
will work with in this class so forgive if I occasionally drop the prime. ∆Go’ is a constant
characteristic for each reaction just as K’eq is a constant characteristic for each reaction. These
two constants have a simple relationship.
∆G o ' = − RT ln K 'eq or K 'eq = e
 − ∆G o ' 


 RT 
The actual free energy change depends on the reactant and product concentrations.
[C ][ D] 
∆G = ∆G o '+ RT ln 

 [ A][ B] 
Reactions can be coupled together. The standard free energy changes are additive. Cool feature
of state functions. Multiply the equilibrium constants
Ie.
(1)Glucose + Pi glucose-6-phosphate + H2O
∆Go’ = 13.8 kJ/mol; K’eq = 3.9 X 10-3 M-1.
(2)ATP + H2O ADP + Pi
∆Go’ = -30.5 kJ/mol; K’eq = 2 X 105 M.
(Sum)ATP + glucoseglucose-6-phosphate + ADP ∆Go’ = 13.8 kJ/mol + -30.5 kJ/mol = -16.7 kJ/mol
K’eq = (3.9 X 10-3 M-1)X(2 X 105M)=7.8X102
Given
∆Go’ = -61.9 kJ/mol
(1) Phosphoenolpyruvate (PEP) + H20 pyruvate + Pi
(2) ATP + H2O ADP + Pi
∆Go’ = -30.5 kJ/mol
What is the free energy change for: PEP + ADP ATP + pyruvate ?
(1) PEP + H20 pyruvate + Pi
∆Go’ = -61.9 kJ/mol
(2) ADP + Pi ATP + H2O
∆Go’ = 30.5 kJ/mol *
(Sum) PEP + ADP ATP + pyruvate ∆Go’ = -61.9 kJ/mol + 30.5 kJ/mol = -31.4 kJ/mol
*Note: change the direction of the reaction change the sign of the ∆Go’, invert equilibrium
constant. 1/K’eq.
Thermodynamics of ATP Hydrolysis
ATP is the principle energy currency of the cell that links catabolism to anabolism. ATP has a
large negative standard free energy change of hydrolysis.
ATP + H2O ADP + Pi
∆Go’ = -30.5 kJ/mol
What is the chemical basis of the large, negative free energy change?
1. The hydrolytic cleavage of the γ-phosphate anhydride bond relieves electrostatic
repulsion in ATP.
2. The phosphate formed is stabilized by several resonance forms that are not possible in
ATP.
3. The ADP product, immediately ionizes, releasing H+ in a medium with low hydrogen ion
concentration, pH 7.
4. ATP has a small solvation energy compared to the solvation energies of ADP, Pi and H+.
Thus the products of hydrolysis are stabilized more by solvation than then reactant ATP.
ATP hydrolysis
NH2
H
N
O
O
-
O
N
H
O
P
O
P
O
-
N
O
O
-
O
P
O
N
O
O-
H
H
OH
OH
H
H
N
H
2
O
-
N
P
O
O
O-
O
+
H
O
N
O
P
O
O-
O-
P
O
P
O
H
H
H
OH
OH
+
H
OO
H
NH2
O-
-
N
O
OH
O
N
H
O
P
O
O
H
-
O
P
O-
N
N
O
O
P
O
N
N
O
O-
H
H
OH
OH
H
H
O-
O
P
O
O
H
ATP4- + H2O ADP3- + Pi 2- + H+
∆Go’ = -30.5 kJ/mol
In cells, the concentration of ATP, ADP and Pi are not 1M. For example in human erythrocytes
the concentration of ATP is 2.25 mM, [ADP] = 0.25 mM and [Pi] = 1.65 mM
 [2.5 × 10 − 4 M ][1.65 × 10 − 3 M ] 
[ ADP][ Pi ] 
o
o
∆G = ∆G o '+ RT ln 
=
−
30
.
5
kJ
/
mol
+
8
.
315
J
/
mol
K
×
298
K
×
ln



 [ ATP ] 
[2.25 × 10 − 3 M ]


∆G = −30.5 kJ/mol − 21,300 j/mol = −51.8 kJ/mol
This ∆G for ATP hydrolysis in the cell is designated ∆Gp. For intact cells, ∆Gp ranges from -50
to -65 kJ/mol. This is known as the phosphorylation potential.
Other High Energy Phosphorylated compounds.
Phosphoenolpyruvate – PEP
PEP3- + H2O Pyruvate- + Pi2- ∆Go’ = -61.9 kJ/mol
O
O
O
C
-
O
C
P
O
O
O
-
C
-
CH2
O
-
H
O
O
C
O
H
+ HO
P
O
CH2
O
-
H
O
C
-
O
C
O
H2C
H
Phosphoenolpyruvate contains one phosphate ester bond that can under go hydrolysis to yield the
enol form of pyruvate which immediately tautomerizes to the more stable keto form of pyruvate.
The reactant PEP has only one stable form while the product pyruvate has two possible forms.
This extra stabilization of the product is the greatest contributor to the high standard free energy
of hydrolysis.
1,3-Bisphosphoglycerate
1,3-Bisphosphoglycerate2- + H2O 3-Phosphoglycerate3- + Pi2- + H+ ∆Go’ = -49.3 kJ/mol
O
-
O
P
O
C
H2
O-
OH
O
C
C
O
O
This high energy compound contains one
phosphoanhydride bond.
O-
P
O-
H
H
O
H
O
-
O
P
O
C
H2
O-
OH
O
C
C
O
+
OH
H
O
O-
P
-
O
H
The product 3-phosphoglyceric acid
immediately ionizes to produce a carboxylate
anion.
H+
O
-
O
P
O-
O
C
H2
OH
O
C
C
H
O-
The removal of the 3-phosphoglyceric acid and
the resonance stabilized phosphate favor the
forward reaction.
Phosphocreatine
Phosphocreatine2- + H2O Creatine + Pi2- ∆Go’ = -49.3 kJ/mol
O
H
O
O
H
C
O
-
O
P
O-
C
O
CH2
N
H
C
N
NH2
H
+
O
-
-
CH2
H2N
CH3
C
N
NH2
H
O
CH3
+ H
+
O
P
O-
O
-
O
C
O
-
CH2
+
H2N
C
N
NH2
H
CH3
The release of Pi and the resonance stabilized creatine favor the forward reaction.
Note for all of these phosphate releasing reactions, the phosphate formed is stabilized by
resonance favoring product formation.
Standard Free Energies of Phosphate Ester Hydrolysis of Some Biological Compounds
Compound
∆Go’ (kJ/mol)
Phosphoenolpyruvate (PEP)
-61.9
1,3-Bisphosphoglycerate
-49.4
Acetyl phosphate
-43.1
Phosphocreatine
-43.1
ADPAMP + Pi
-35.7
PPi
-33.5
ATPAMP + PPi
-32.2
ATPADP + Pi
-30.5
Glucose-1-phosphate
-20.9
Fructose-6-phosphate
-15.9
Glucose-6-phosphate
-13.8
Glycerol-3-phosphate
-9.2
AMPadenosine + Pi
-9.2
The compounds with more negative free energy of phosphate ester hydrolysis than ATP can
phosphorylate ADP to form ATP. Ie. PEP + ADP ATP + pyruvate ∆Go’ = -31.4 kJ/mol
ATP provides energy by group transfers, not simple hydrolysis.
Ie.
∆Go’ = 13.8 kJ/mol; K’eq = 3.9 X 10-3 M-1.
(1)Glucose + Pi glucose-6-phosphate + H2O
(2)ATP + H2O ADP + Pi
∆Go’ = -30.5 kJ/mol; K’eq = 2 X 105 M.
(Sum)ATP + glucoseglucose-6-phosphate + ADP ∆Go’ = 13.8 kJ/mol + -30.5 kJ/mol = -16.7 kJ/mol
K’eq = (3.9 X 10-3 M-1)X(2 X 105M)=7.8X102
NH2
N
O
-
O
P
O
O
-
O
P
-
O
N
O
P
O
O
H
H
H
OH
OH
H
:B
O
H
N
O
OH
CH2O
N
H
H
H
OH
OH
OH
H
OH
NH2
O
O
H 2C
N
O
-
O
O
H
H
-
+
O
N
O
P
O
P
O
H
O
-
O-
H
H
H
OH
OH
H
OH
OH
N
O
HH
OH
N
O-
P
H
OH
Another example
Glutamate + NH3 + ATP Glutamine +ADP + Pi
O
H2N
CH
C
OH
N
H
CH2
2
CH2
C
N
O-
O
O
-
O
P
O
O
P
O
-
O
N
O
P
-
O
H
H
OH
OH
H
O
CH
C
N
O
OH
H2N
N
O
NH2
OH
N
N
CH2
CH2
H3N:
C
O
+
O
O
-
O
P
-
O
P
O
N
O
O
P
-
O
O
O-
H
H
OH
OH
H
O
OO
Pi
H2N
CH
C
CH2
CH2
C
NH2
O
OH
H
N
NH2
Three Positions on ATP for Nucleophilic Attack
Most of the group transfer
reactions of ATP are SN2
nucleophilic substitutions. In the
examples above the nucleophile
:OR
is an oxygen of an alcohol. Each
ADP
:OR
:OR
of the three phosphates of ATP
AMP
are susceptible to nucleophilic
attack. Nucleophilic attack at the
PPi
γ-phosphate results in ADP and
the transfer of phosphate to the
nucleophile. Nucleophilic attack
at the β-phosphate results in
AMP and the transfer of a
pyrophosphate group to the
nucleophile. Nucleophilic attack at the α-phosphate results in pyrophosphate and the
adenylylation of the nucleophile.
N
-
O
γ
β
O
O
P
-
O
P
-
O
O
N
O
P
O
N
α
O
N
O
O-
H
H
OH
OH
H
H
NH2
N
O
RO
P
O
N
-
O
O
RO
P
O
O-
P
O-
N
O
O-
R
O
P
O-
O
N
O
O-
H
H
OH
OH
H
H
Inorganic Pyrophosphatase
The nucleophilic attack at the α-phosphate of ATP results in an adenylylated nucleophile and
pyrophosphate. The ubiquitous enzyme inorganic pyrophosphatase provides an additional
thermodynamic push for the adenylylation reaction by catalyzing the hydrolysis of
pyrophosphate into two molecules of phosphate (∆Go’ = -33.5 kJ/mol). This enzyme makes
adenylylation reactions very favorable thermodynamically.
NH2
Fatty acyl-CoA synthetase
N
O
O
-
O
P
P
O
O-
O-
N
O
O
P
-
O
N
Example: Fatty acyl-CoA synthesis.
O
O-
O
O
N
H
H
OH
OH
H
H
ATPAMP + PPi ∆Go’ = -32.2 kJ/mol
PPi2Pi
∆Go’ = -33.5 kJ/mol
C
CH3(CH2)14
H
O
H
O
-
O
P
O
O-
P
NH2
O-
O-
N
inorganic pyrophosphatase
O
CH3(CH2)14
C
O
P
O
O
-
O
P
O
H
N
O
H
H
OH
OH
H
-
CoA—SH + PalmitatePalmitoyl-CoA
∆Go’ = 31.4 kJ/mol
N
N
O
O-
2
ATPAMP + 2Pi ∆Go’ = -65.7 kJ/mol
O
H
CoA
S
NH2
ON
N
O
-
O
CH3(CH2)14
C
S
CoA
+
O
P
O
N
N
O
O-
H
H
OH
OH
H
H
Palmitate + ATP + CoASHpalmitoyl-CoA + AMP + 2 Pi
∆Go’ = −65.7 kJ/mol +31.4 kJ/mol= −34.3 kJ/mol
RNA Synthesis
NH2
N
N
Rna
N
O
N
NH2
P
O
O
O
H
O-
H
N
H
H
OH
:
OH
O
-
O
O
P
O
P
-
O
P
O
O
-
O
-
O
N
O
O
O-
O
H
OH
OH
H
O-
P
-
H
H
O
P
-
O
O
O
NH2
O
H2O
N
N
Rna
N
O
O
O
2 O
P
P
O
H
N
H
H
O-
H
O
O
OH
P
N
O
O
O-
H
H
OH
OH
H
Activation of an aminoacid for aminoacyl-tRNA synthesis
H
NH2
N
O
O
-
O
P
O
N
O
P
O
-
O
P
-
O
O
N
N
O
O-
H
H
OH
OH
H
H
O
H2N
CH
O-
C
NH2
CH3
N
O
H2N
CH
N
O
C
O
P
CH3
O
O
O-
H
H
OH
OH
H
+
O
-
O
P
H
O
O
O-
P
-
-
O
O
Inorganic phosphatase
H2O
O
2
-
O
OH
P
-
O
NH2
O
O-
OH
N
N
N
O
Transphosphorylation
There are other nucleoside triphosphates (GTP, CTP, UTP, dATP, dGTP, dCTP and dTTP).
These are all energetically equivalent to ATP. These nucleotides are generated and maintained
by phosphoryl group transfer to the corresponding nucleoside diphosphates and
monophosphates. ATP is the primary high energy nucleoside produced by catabolism. Several
enzymes catalyze the transfer of the phosphoryl group from ATP to the other nucleotides. There
are called nucleoside diphosphate kinases.
ATP + NDP (or dNDP)
ADP + NTP (or dNTP)
∆Go’ ≈ 0
Note that this reaction is fully reversible.
When ADP accumulates as a result of phosphoryl group transfers from ATP, such as when the
muscles are vigorously exercising. Adenylate kinase removes the ADP by the reaction:
ATP + AMP ∆Go’ ≈ 0
2ADP
Note this reaction is also fully reversible, so that the enzyme can also convert AMP to ADP
when AMP and ATP concentrations are high. There is a similar enzyme four guanosine
nucleotides, Guanylate kinase.
Phosphocreatine (PCr) serves as a ready source of phosphoryl groups for quick synthesis of
ATP from ADP. It is found in the skeletal muscle at a concentration 10 times greater than the
cellular concentration of ATP. It is also found in smooth muscle, the brain and the kidney at
lower concentration. Creatine Kinase catalyzes the following reaction.
ADP + PCr
∆Go’ = -12.5 kJ/mol
ATP + Creatine
When a sudden demand for energy depletes the concentration of ATP, the PCr reservoir is used
to replenish ATP at a much faster rate than ATP can be synthesizes by catabolic pathways.
When the demand for ATP diminishes, ATP synthesized by catabolism replenishes the PCr
reservoir.
H
O
H
C
S
CH3
O
H3C
NH
C
CH2
C
O
O
H
NH
C
H+
CH 2
H3C
C
O
CH2
-
NH
O
C
H
C
H2C
NH
NH2
C
N
CH 3
O
P
O-
N
O
O
P
O
H
H
O
C
H
N
C
O
H3C
C
H
H2C
CH3
O
O
P
O-
N
O
O
P
O
P
N
O-
Acetyl-CoA + H2O Acetate- + COA-SH + H+
H
H
O
OH
H
OH
O-
N
O
O-
H
O
O
O
N
H3 C
O
H
O-
NH2
C
N
HO
O
O
CH2
O
CH 2
H3C
H
CH2
CH 2
CH 2
HO
High Energy Thioesters
Thioesters have a large
negative free energyh of
hydrolysis. As an example,
acetyl-CoA is one of many
thioesters important in
metabolism.
O
S
O
H
P
O-
O-
∆Go’ = −32.2 kJ/mol