Bioenergetics
The tiny hummingbirds can store enough fuel to fly a
distance of 500 miles without resting. This achievement is
possible because of the ability to convert fuels into the
cellular energy currency, ATP.
Thermodynamics and Metabolism
A biochemical pathway must satisfy minimally two criteria:
(1) the individual reactions must be specific and
(2) the entire set of reactions that constitute the pathway
must be thermodynamically favored.
A reaction that is specific will yield only one particular
product or set of products from its reactants.
A function of enzymes is to provide this specificity.
The thermodynamics of metabolism is
approached in terms of free energy, G.
most readily
A reaction can occur spontaneously only if G, the
change in free energy of products and reactants, is
negative.
Free-Energy Change
• Free-energy change (G) is a measure of the
chemical energy available from a reaction
G = Gproducts - Greactants
-G = a spontaneous reaction in the direction
written
+G = the reaction is not spontaneous
G = 0 the reaction is at equilibrium
The Standard State (Go) Conditions
• Reaction free-energy depends upon conditions
• Standard state (Go) - defined reference
conditions
Standard Temperature = 298K (25oC)
Standard Pressure = 1 atmosphere
Standard Solute Concentration = 1.0M
• Biological standard state = Go’
Standard H+ concentration = 10-7 (pH = 7.0)
rather than 1.0M (pH = 1.0)
Equilibrium Constants and
Standard Free-Energy Change
• For the reaction: A + B
C+D
Greaction = Go’reaction + RT ln([C][D]/[A][B])
Thus, the actual free energy change (G) of a reaction
depends on the nature of the reactant and products
(expressed by the G°' term, the standard free-energy
change) and on their concentrations (the ratio of products
to substrates expressed by the second term).
R is the gas constant. T is the absolute temperature.
• At equilibrium: Keq = [C][D]/[A][B] and
Greaction = 0, so that:
Go’reaction = -RT ln Keq
An important thermodynamic fact is:
the overall free-energy change for a chemically
coupled series of reactions is equal to the sum of
the free-energy changes of the individual steps
AB
BD
AD
G°' = +5 kcal mol-1
G°' = -8 kcal mol-1
G°' = -3 kcal mol-1
Under standard conditions, A cannot be spontaneously
converted into B, because G is positive.
The conversion of B into D under standard conditions is
thermodynamically feasible (G is negative).
Because free-energy changes are additive, the conversion
of A into D has a G°' = -3 kcal mol-1, which means that it
can occur spontaneously under standard conditions.
Thus, a thermodynamically unfavorable reaction
can be driven by a thermodynamically favorable
reaction to which it is coupled.
In the example
AB
G°' = +5 kcal mol-1
BD
G°' = -8 kcal mol-1
AD
G°' = -3 kcal mol-1
the chemical intermediate B, common to both reactions,
couples the reactions.
Thus, metabolic pathways are formed by the
coupling of enzyme-catalyzed reactions such
that the overall free energy of the pathway is
negative.
ATP Is the Universal Currency of Free
Energy in Biological Systems
The commerce of the cell — metabolism — is
facilitated by the use of a common energy currency,
adenosine triphosphate (ATP).
Energy from oxidation of metabolic fuels is
transformed into highly accessible ATP molecule, which
acts as the free-energy donor in most energy-requiring
processes such as motion, active transport, or
biosynthesis.
ATP is a nucleotide consisting of an adenine, a ribose, and a
triphosphate unit.
The active form of
ATP is usually a
complex of ATP with
Mg2+ or Mn2+.
ATP is an “energy-rich” compound
• ATP is an energy-rich molecule because its triphosphate
unit contains two phosphoanhydride bonds
• A large amount of free energy is liberated when ATP is
hydrolyzed to adenosine diphosphate (ADP) and
orthophosphate (Pi) or when ATP is hydrolyzed to
adenosine monophosphate (AMP) and pyrophosphate
(PPi).
ATP + H2O  ADP + Pi
ATP + H2O  AMP + PPi
G°' = -7.3 kcal mol-1
G°' = -10.9.3 kcal mol-1
ATP is an “energy-rich” compound
ATP + H2O  ADP + Pi
ATP + H2O  AMP + PPi
G°' = -7.3 kcal mol-1
G°' = -10.9.3 kcal mol-1
The precise G°' for these reactions depends on the ionic
strength of the medium and on the concentrations of
Mg2+ and other metal ions
Under typical cellular concentrations, the actual G for
these hydrolyses is approximately -12 kcal mol-1
• Hydrolysis
of ATP
The role of ATP in energy metabolism is paramount
But some biosynthetic reactions are driven by hydrolysis of
nucleoside triphosphates that are analogous to ATP — namely,
guanosine triphosphate (GTP), uridine triphosphate (UTP), and
cytidine triphosphate (CTP).
The diphosphate forms of these nucleotides are denoted by GDP,
UDP, and CDP, and the monophosphate forms by GMP, UMP, and CMP.
Enzymes can catalyze the transfer of the terminal phosphoryl group
from one nucleotide to another.
All of the nucleotide triphosphates have nearly equal standard free
energies of hydrolysis, but ATP is the primary cellular energy carrier.
ATP Hydrolysis Drives Metabolism by
Shifting the Equilibrium of Coupled Reactions
How does coupling to ATP hydrolysis make possible an otherwise
unfavorable reaction?
Suppose that the standard free energy of the conversion of compound A into
compound B is + 4.0 kcal mol-1. The reaction A  B is thermodynamically
unfavorable.
AB
G°' = + 4.0 kcal mol-1
Go’ = -RT ln Keq or Go’ = -2.303RT log10 Keq
Keq = 10-Go’/(2.303RT)
G°' = + 4.0 kcal mol-1, R = 1.987 x 10-3 kcal mol-1 deg-1, T = 298 K (25oC)
The equilibrium constant is related to G°' by:
Keq = 10-Go’/1.36
Keq = [B]/[A] = 1.15 x 10-3
Thus, net conversion of A into B cannot occur when the molar ratio of B to A is equal
to or greater than 1.15 X 10-3.
A can be converted into B if the reaction is coupled to the
hydrolysis of ATP.
AB
G°' = + 4.0 kcal mol-1
ATP + H2O  ADP + Pi
G°' = -7.3 kcal mol-1
The new overall reaction is:
A + ATP + H2O  B + ADP + Pi + H+
G°' = -3.3 kcal mol-1
The equilibrium constant of this coupled reaction is:
Keq = ([B]/[A]) X ([ADP]x[Pi]/[ATP])
Keq = 10-Go’/1.36
Keq = 103.3/1.36 = 2.67 x 102
At equilibrium, the ratio of [B] to [A] is given by:
[B]/[A] = Keq x ([ATP]/[ADP]x[Pi])
The ATP-generating system of cells maintains the
[ATP]/[ADP][Pi] ratio at a level of 500 M-1. For this ratio,
[B]/[A] = 2.67 x 102 x 500 = 1.34 x 105
which means that the hydrolysis of ATP enables A to be
converted into B until the [B]/[A] ratio reaches a value
of 1.34 X 105.
In the absence of ATP hydrolysis this value was 1.15 X
10-3.
Coupling the hydrolysis of ATP with the conversion of A
into B has changed the equlibrium ratio of B to A by a
factor of about 108
Thermodynamic essence of ATP's action: ATP acts as an
energy coupling agent:
AB
ATP + H2O  ADP + Pi
A + ATP + H2O  B + ADP + Pi + H+
G°' = + 4.0 kcal mol-1
G°' = -7.3 kcal mol-1
G°' = -3.3 kcal mol-1
Cells maintain a high level of ATP by using oxidizable substrates or
light as sources of free energy.
The hydrolysis of an ATP molecule in a coupled reaction then changes
the equilibrium ratio of products to reactants by a very large factor,
of the order of 108.
The hydrolysis of n ATP molecules changes the equilibrium ratio of a
coupled reaction by a factor of 108n.
For example, the hydrolysis of three ATP molecules in a coupled
reaction changes the equilibrium ratio by a factor of 1024.
A thermodynamically unfavorable reaction sequence can be
converted into a favorable one by coupling it to the
hydrolysis of a sufficient number of ATP molecules in a new
reaction.
ATP has High Phosphoryl Transfer Potential
ATP can transfer the phosphoryl group to many substrates.
Compare the standard free energy of hydrolysis of ATP with that of the
phosphate ester, glycerol-3-phosphate:
ATP + H2O  ADP + Pi
G°' = -7.3 kcal mol-1
Glycerol 3-phosphate + H2O  glycerol + Pi
G°' = -2.2 kcal mol-1
G°' for the hydrolysis of glycerol 3-phosphate
is much smaller than that of ATP, which means
that ATP has a stronger tendency to transfer
its terminal phosphoryl group to water than
does glycerol 3-phosphate.
ATP has a higher phosphoryl transfer
potential (phosphoryl-group transfer
potential) than does glycerol 3-phosphate.
WHY? What is the structural basis of the
high phosphoryl transfer potential of ATP?
The structures of both ATP and its hydrolysis products, ADP and Pi, must be
examined to answer this question.
Three factors are important:
1) resonance stabilization,
2) electrostatic repulsion, and
3) stabilization due to hydration.
1. ADP and, particularly, Pi, have greater resonance stabilization than
does ATP. Orthophosphate has a number of resonance forms of
similar energy.
Products are more stable than reactants. There are more
delocalized electrons on ADP, Pi or AMP, PPi than on ATP.
2. Electrostatic repulsion among negatively charged oxygens of
phosphoanhydrides of ATP.
At pH 7, the triphosphate unit of ATP carries about four negative
charges. These charges repel one another. The repulsion between
them is reduced when ATP is hydrolyzed.
3. Solvation of products (ADP and Pi) or (AMP and PPi) is better than
solvation of ATP.
Water can bind more effectively to ADP and Pi than it can to the
phosphoanhydride part of ATP, stabilizing the ADP and Pi by hydration.
Phosphoryl Transfer Potential Is an Important
Form of Cellular Energy Transformation
ATP is not the only compound with
a high phosphoryl transfer
potential
Some compounds in biological
systems (phosphoenolpyruvate
(PEP), 1,3-bisphosphoglycerate
(1,3-BPG), and creatine
phosphate) have a higher
phosphoryl transfer potential
than that of ATP
Phosphoryl Transfer Potential Is an Important
Form of Cellular Energy Transformation
These compounds can transfer
its phosphoryl group to ADP to
form ATP
The phosphoryl transfer from
PEP and 1,3-BPG is one of the
ways in which ATP is generated in
living system in the breakdown of
carbohydrates - substrate level
phosphorylation
It is significant that ATP has a phosphoryl transfer
potential that is intermediate among the biologically
important phosphorylated molecules.
Standard free energies of hydrolysis of some
phosphorylated compounds
Compound
Phosphoenolpyruvate
1,3-Biphosphoglycerate
Creatine phosphate
ATP (to ADP)
Glucose 1-phosphate
Pyrophosphate
Glucose 6-phosphate
Glycerol 3-phosphate
kcal mol-1
-14.8
-11.8
-10.3
-7.3
- 5.0
- 4.6
-3.3
- 2.2
Such intermediate position enables ATP to function
efficiently as a carrier of phosphoryl groups.
Creatine phosphate in vertebrate muscle serves as a reservoir of highpotential phosphoryl groups that can be readily transferred to ATP.
Creatine phosphate regenerates ADP to ATP every time we exercise
strenuously. This reaction is catalyzed by creatine kinase.
Creatine kinase
Creatine phosphate + ADP + H+  ATP + creatine
The amount of ATP in muscle
suffices to sustain contractile
activity for less than a second.
The amount of creatine
phosphate, as the major source
of phosphoryl groups for ATP
regeneration in muscles, is
enough to sustain intensive
contractile activity for 4
seconds.
After that, ATP must be
generated through metabolism.
Source of Cellular Energy
 In a typical cell, an ATP molecule is consumed within a minute of its
formation.
The total quantity of ATP in the body is approximately 100 g,
 The turnover of ATP is very high. A resting human being consumes about
40 kg of ATP in 24 hours.
 During strenuous exertion, the rate of utilization of ATP may be as high
as 0.5 kg/minute. For a 2-hour run, 60 kg of ATP is utilized.
It is vital to have mechanisms for
regenerating ATP.
Motion, active transport, signal
amplification, biosynthesis etc. can
occur only if ATP is continually
regenerated from ADP.
The generation of ATP is one of the primary roles of catabolism.
The carbon in fuel molecules — such as glucose and fats — is oxidized to
CO2, and the energy released is used to regenerate ATP from ADP and Pi.
There are two ways of ATP synthesis in living systems:
1. Oxidative phosphorylation
2. Substrate-level phosphorylation
Oxidative phosphorylation
The electrochemical
potential of ion
gradients across
membranes, produced
by the oxidation of
fuel molecules,
ultimately powers the
synthesis of most of
the ATP in cells (90%
in animal cells)
The oxidation of fuels can power the formation
of proton gradient. This proton gradient can in
turn drive the synthesis of ATP
Substrate-Level Phosphorylation
High Phosphoryl Transfer Potential Compounds Can Couple
Carbon Oxidation to ATP Synthesis
EXAMPLE
Glyceraldehyde 3-phosphate
is a metabolite of glycolysis
Oxidation of the aldehyde to an acid will release energy.
Oxidation
However, the oxidation does not take place directly.
The carbon oxidation generates 1,3-bisphosphoglycerate (1,3-BPG).
The electrons released are captured by NAD+
1,3-bisphosphoglycerate has a high phosphoryl transfer potential (standard
free energies of 1,3-BPG hydrolysis is -11.8 kcal mol-1).
Standard free energies of ATP hydrolysis is -7.3 kcal mol-1.
Thus, the cleavage of 1,3-BPG can be coupled to the synthesis of ATP
The oxidation energy of a carbon atom is transformed
into phosphoryl transfer potential, first as 1,3bisphospoglycerate and ultimately as ATP