CHAPTER 13

Bioenergetics and Reactions

Thermodynamics applies to biochemistry, too
Organic chemistry principles are still valid
Some biomolecules are high energy with respect
to their hydrolysis and group transfers
Energy stored in reduced organic compounds can be
used to reduce cofactors such as NAD
+
and FAD,
which serve as universal electron carriers
Key topics:
Life needs energy
Recall that living organisms are built of complex
structures
Building complex structures that are low in entropy
is only possible when energy is spent in the process
The ultimate source of this energy on Earth is the
sunlight
Metabolism is the sum of all chemical
reactions in the cell
Series of related reactions form metabolic pathways
Some pathways are primarily energy-producing
This is catabolism
Some pathways are primarily using energy to build
complex structures
This is anabolism or biosynthesis

Laws of thermodynamics
apply to living organisms
Living organisms cannot create energy from nothing
Living organisms cannot destroy energy into nothing
Living organism may transform energy from one form to another

In the process of transforming energy, living organisms
must increase the entropy of the universe
In order to maintain organization within themselves,
living systems must be able to extract useable energy
from their surroundings, and release useless energy
(heat) back to their surroundings
Free energy, or the equilibrium constant,
measure the direction of processes
G = H - TS
Gibbs free energy (G): amount of energy capable of doing
work during a reaction at a constant temperature and
(absolute) temperature.
Exergonic: G is negative
Endergonic: G is positive



G must be negative (energetically favorable) for a process
to be spontaneous.
Exergonic: G is negative
Endergonic: G is positive

H: change in enthalpy (heat content of the system).
Reflects the number and kinds of chemical bonds in the
reactants and products.
Exothermic: H is negative
Endothermic: H is positive
Free energy, or the equilibrium constant,
measure the direction of processes
G = H - TS
Exergonic: G is negative
Endergonic: G is positive

Exothermic: H is negative
Endothermic: H is positive

S is the entropy (disorder) in a system. When S is positive,
the entropy of the system has increased.


Free energy, or the equilibrium constant,
measure the direction of processes
G = H - TS
Free energy, or the equilibrium constant,
measure the direction of processes
G = H - TS

S is negative

S is positive


H is negative


?

G is negative


H is positive


G is positive


?
Free energy, or the equilibrium constant,
measure the direction of processes
G = H - TS

G can be related to K
eq
by:

G = -RT ln K
eq


Standard conditions: 298 K (25C) and 101.3 kPa (1 atm)
Free energy, or the equilibrium constant,
measure the direction of processes
Energetics of Some Chemical Reactions
Hydrolysis reactions tend to be strongly favorable
(spontaneous)
Isomerization reactions have smaller free-energy
changes
Isomerization between enantiomers: G = 0
Complete oxidation of reduced compounds is
strongly favorable
This is how chemotrophs obtain most of their energy
In biochemistry the oxidation of reduced fuels with O
2
is
stepwise and controlled
Recall that being thermodynamically favorable is not the
same as being kinetically rapid
Energetics within the cell are not standard
The actual free-energy change of a reaction in the
cell depends on:
The standard change in free energy
Actual concentrations of products and reactants
For the reaction aA + bB cC + dD:



Standard free-energy changes are additive:
(1) A B G
1

(2) B C G
2

Sum: A C G
1
+ G
2



b a
d c
B A
D C
RT G G
] [ ] [
] [ ] [
ln '
Lesson in Quantum Chemistry
Most organic molecules, including the reduced fuels, are in
the singlet spin state
All electrons are paired into electron pairs
Molecular oxygen is in the triplet spin state
Two electrons are unpaired
Direct electron transfer from a singlet reduced species to a
triplet oxidizing species is quantum-mechanically forbidden
This is why direct oxidation (spontaneous combustion) of
biomolecules does not occur readily
Few cofactors, such as transition metal ions, and flavin
adenine dinucleotide are able to catalyze consecutive single-
electron transfers needed for utilization of O
2
Review of Organic Chemistry
Most reactions in biochemistry are thermal
heterolytic processes
Nucleophiles react with electrophiles
Heterolytic bond breakage often gives rise to
transferable groups, such as protons
Oxidation of reduced fuels often occurs via transfer of
electrons and protons to a dedicated redox cofactor
Chemical Reactivity
Most reactions fall within few categories:
Cleavage and formation of CC bonds
Cleavage and formation of polar bonds
Nucleophilic substitution mechanism
Additionelimination mechanism
Hydrolysis and condensation reactions
Internal rearrangements
Eliminations (without cleavage)
Group transfers (H
+
, CH
3
+
, PO
3
2
)
Oxidations-reductions (e

transfers)
Chemistry at Carbon
Covalent bonds can be broken in two ways
Homolytic cleavage is very rare
Heterolytic cleavage is common, but the products
are highly unstable and this dictates the chemistry
that occurs

Homolytic vs. Heterolytic Cleavage
Nucleophiles and Electrophiles
in Biochemistry
Examples of Nucleophilic Carbon-Carbon
Bond Formation Reactions
Isomerizations and Eliminations:
No Change in Oxidation State
AdditionElimination Reactions
Substitution from sp
3
carbon proceeds normally via
the nucleophilic substitution (S
N
1 or S
N
2) mechanism
Substitution from the sp
2
carbon proceeds normally
via the nucleophilic additionelimination mechanism
Nucleophile adds to the sp
2
center giving a
tetrahedral intermediate
Leaving group eliminates from the tetrahedral
intermediate
Leaving group may pick up a proton
AdditionElimination Reactions
Group Transfer Reactions
Proton transfer, very common
Methyl transfer, various biosyntheses
Acyl transfer, biosynthesis of fatty acids
Glycosyl transfer, attachment of sugars
Phosphoryl transfer, to activate metabolites
also important in signal transduction
Nucleophilic Displacement
Substitution from sp
3
phosphorous proceeds via the
nucleophilic substitution (usually associative, S
N
2-like)
mechanism
Nucleophile forms a partial bond to the
phosphorous center giving a pentacovalent
intermediate or a pentacoordinated transition state
Nucleophilic Displacement
Phosphoryl Transfer from ATP
ATP is frequently the donor of the phosphate in the
biosynthesis of phosphate esters.
Hydrolysis of ATP is highly favorable
under standard conditions
Better charge separation
in products
Better solvation of
products
More favorable resonance
stabilization of products

Actual G of ATP hydrolysis
differs from G
The actual free-energy change in a process depends on:
The standard free energy
The actual concentrations of reactants and products
The free-energy change is more favorable if the reactants
concentration exceeds its equilibrium concentration
True reactant and the product are Mg-ATP and Mg-ADP,
respectively
G also Mg
++
dependent
] MgATP [
] P [ ] MgADP [
ln '
2
i

RT G G
G of ATP hydrolysis is
Mg
++
dependent
Cellular ATP concentration is usually far above the equilibrium
concentration, making ATP a very potent source of chemical energy.
Several phosphorylated compounds have large
G for hydrolysis
Again, electrostatic repulsion within the reactant
molecule is relieved
The products are stabilized via resonance, or by more
favorable solvation
The product undergoes further tautomerization
Phosphates: Ranking by the Standard Free
Energy of Hydrolysis
Reactions such as

PEP + ADP =>
Pyruvate + ATP

are favorable, and
can be used to
synthesize ATP.
Phosphate can be transferred from compounds with
higher G to those with lower G.
Hydrolysis of Thioesters
Hydrolysis of thioesters is strongly favorable
such as acetyl-CoA
Acetyl-CoA is an important donor of acyl groups
Feeding two-carbon units into metabolic pathways
Synthesis of fatty acids
In acyl transfers, molecules other than water accept
the acyl group
Hydrolysis of Thioesters
Molecular Basis for Thioester Reactivity
The orbital overlap between the carbonyl group and
sulfur is not as good as the resonance overlap between
oxygen and the carbonyl group in esters.
Oxidation-Reduction Reactions
Reduced organic compounds serve as fuels from which
electrons can be stripped off during oxidation.
Reversible Oxidation of
a Secondary Alcohol to a Ketone
Many biochemical oxidation-reduction reactions
involve transfer of two electrons
In order to keep charges in balance, proton transfer
often accompanies electron transfer
In many dehydrogenases, the reaction proceeds by a
stepwise transfers of proton (H
+
) and hydride (:H

)
Reduction Potential
Reduction potential (E)
Affinity for electrons; higher E, higher affinity
Electrons transferred from lower to higher E

E

= -(RT/nF)ln (K
eq
) = G/nF

E = E
(e-

acceptor)
E
(e-

donor)


G = nFE
For negative G need positive E
E
(acceptor)
> E
(donor)



NAD and NADP are
common redox cofactors
These are commonly called pyridine nucleotides
They can dissociate from the enzyme after the
reaction
In a typical biological oxidation reaction, hydride
from an alcohol is transferred to NAD
+
giving NADH
NAD and NADP are
common redox cofactors
Formation of NADH can be monitored
by UV-spectrophotometry
Measure the change of absorbance at 340 nm
Very useful signal when studying the kinetics of
NAD-dependent dehydrogenases
Flavin cofactors allow
single electron transfers
Permits the use of molecular oxygen as an ultimate electron acceptor
flavin-dependent oxidases
Flavin cofactors are tightly bound to proteins
Chapter 13: Summary
The rules of thermodynamics and organic chemistry still apply to
living systems
Reactions are favorable when the free energy of products is much
lower than the free energy of reactants
Biochemical phosphoryl transfer reactions are favorable when:
The phosphate donors are destabilized by electrostatic repulsion,
and the reaction products are often stabilized by resonance
Unfavorable reactions can be made possible by chemically coupling
a highly favorable reaction to the unfavorable reaction
Oxidation-reduction reactions commonly involve transfer of
electrons from reduced organic compounds to specialized redox
cofactors
Reduced cofactors can be used in biosynthesis, or may serve as a source of energy for
ATP synthesis
In this chapter, we learned: