Chapter-6

13. Bioenergetics and Biochemical

Reaction Types
13.1 Bioenergetics and Thermodynamics 490
13.2 Chemical Logic and Common Biochemical
Reactions 495
13.3 Phosphoryl Group Transfers and ATP 501
13.4 Biological Oxidation-Reduction Reactions 512

PART II
BIOENERGETICS AND METABOLISM

Why we need to study this part ?

Metabolism is a highly coordinated cellular activity in which many
multienzyme systems (metabolic pathways) cooperate to:
1. obtain chemical energy by capturing solar energy or degrading
energy rich nutrients from the environment;
2. convert nutrient molecules into the cells own characteristic
molecules, including precursors of macromolecules;
3. polymerize monomeric precursors into macromolecules: proteins,
nucleic acids, and polysaccharides;
4. synthesize and degrade biomolecules required for specialized
cellular functions, such as membrane lipids, intracellular
messengers, and pigments.

Energy vs Carbon source

Types of
Trophs

Energy
source

Carbon
source

Microorganisms

PhotoAutotroph

UV light

CO2

algae, cyanobacteria,
sulphur bacteria, ..

Photo
Heterotroph

UV light

Chemo
Autotroph

Inogranics: CO2
NH4+,
NO2-, H2S,
H2, Fe2+

Chemo
Heterotroph

Organics

Plants

Animals

Organics Purple bacteria, green

bacteria
Nitrification bacteria,
Sulphur oxidative
bacteria, hydrogen
producing bacteria

Organics Fermentative bacteria,

Enterobacteria

Autotrophs - (such as photo-synthetic bacteria, green algae, and vascular plants) can
use carbon dioxide from the atmosphere as their sole source of carbon, from which they
construct all their carbon-containing biomolecules (see Fig. 15). Some autotrophic
organisms, such as cyanobacteria, can also use atmospheric nitrogen to generate all
their nitrogenous components.
Heterotrophs cannot use atmospheric carbon
dioxide and must obtain carbon from their
environment in the form of relatively complex
organic molecules such as glucose. Multicellular
animals
and
most
microorganisms
are
heterotrophic,
In our biosphere, autotrophs and heterotrophs
live together in a vast, interdependent cycle in
which autotrophic organisms use atmospheric
carbon dioxide to build their organic biomolecules,
some of them generating oxygen from water in
the process. Heterotrophs in turn use the organic
products of autotrophs as nutrients and return
carbon dioxide to the atmosphere

Interdependent Cycle

Definitions
Metabolism, the sum of all the chemical transformations taking place in a cell or
organism, occurs through a series of enzyme-catalyzed reactions that constitute
metabolic pathways. Each of the consecutive steps in a metabolic pathway brings
about a specic, small chemical change, usually the removal, transfer, or addition of a
particular atom or functional group.
Metabolites are series of metabolic intermediates formed during conversion of the
precursor into a product.
Catabolism is the degradative phase of metabolism in which organic nutrient molecules
(carbohydrates, fats, and proteins) are converted into smaller, simpler end products
(such as lactic acid, CO2, NH3). Catabolic pathways release energy, some of which is
conserved in the formation of ATP and the electron carriers (NADH, NADPH, and
FADH2); the rest is lost as heat.
Anabolism, also called biosynthesis, small, simple precursors are built up into larger
and more complex molecules, including lipids, polysaccharides, proteins, and nucleic
acids. Anabolic reactions require an input of energy, generally in the form of the
phosphoryl group transfer potential of ATP and the reducing power of NADH, NADPH,
and FADH2.

FIGURE 3 Energy relationships

between catabolic and anabolic
path ways.

Three types of nonlinear metabolic pathways.

See VIDEO CLIP: metabolic pathway

Anabolism

Catabolism

13. Bioenergetics and Biochemical

Reaction Types
13.1 Bioenergetics and Thermodynamics 490
13.2 Chemical Logic and Common Biochemical
Reactions 495
13.3 Phosphoryl Group Transfers and ATP 501
13.4 Biological Oxidation-Reduction Reactions 512

13.1 Bioenergetics and Thermodynamics

Bioenergetics is the quantitative study of energy transductionschanges of
one form of energy into an otherthat occur in living cells, and of the nature
and function of the chemical processes underlying these transductions.
Biological Energy Transformations Obey the Laws of Thermodynamics
Gibbs free energy, G, expresses the amount of energy capable of doing work during
a reaction at constant temperature and pressure. When a reaction proceeds with the
release of free energy (that is, when the system changes so as to possess less free
energy), the free-energy change, DG, when <0 is said to be exergonic reactions;
when > 0 is said to be endergonic reactions.
Enthalpy, H, is the heat content of the reacting system. It reects the number and kinds
of chemical bonds in the reactants and products. When a chemical reaction releases
heat, it is said to be exothermic; the heat content of the products is less than that of the
reactants and DH <0. Reacting systems that take up heat from their surroundings are
endothermic and have positive values of DH.

DG = DH - TDS

Entropy, S, is a quantitative expression for the randomness or disorder in a system (see

Box 13). When the products of a reaction are less complex and more disordered than
the reactants, the reaction is said to proceed with a gain in entropy. DS is the change in
entropy of the system.
DS >0 when entropy increases and DH, as noted above, < 0 when heat is released by
the system to its surroundings DG <0.

Free energy change, DG

When a reacting system is not equilibrium,
the tendency to move toward
equilibrium represents a driving force,
the magnitude of which can be
expressed as the free-energy change
for the reaction, DG.
< 0: exergonic: release free energy
> 0: endergonic: require energy

Ea

Ea : Activation energy, at that state

transition stateIn biosystem: living cells and
organisms, however, are open
systems, exchanging both materials
and energy with their surroundings;
living systems are never at equilibrium
with their surroundings.
Notes:
Endogenic : action or object coming from inside
Exogenic : action or object coming from out side

DG

Standard (transformed) free-energy changes, DGo

DGo = -RT ln Keq

KEY
CONVENTION:
For
convenience
of
calculations,
biochemists define a standard state
different from that used in
chemistry and physics: in the
biochemical standard state, [H+] is
10-7 M (pH 7.0) and [H2O] is 55.5
M. For reactions that involve Mg+2
(which include most of those with
ATP as a reactant), [Mg2+] in
solution is commonly taken to be
constant at 1 mM.

Keq=

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

DG0: in the standard chemical

condition: Temp. 25oC = 298K, 1 atm
(101.3 kPa), concentration of reactants
= 1 M.
DGo : biochemical reaction does not
occur in 1 M concentration, thus it is
the transformedDGo.
Keq thus is the transformed Keq

Actual Free-Energy Changes (DG ) Depend on Reactant

and Product Concentrations
aA + bB

v1

cC+ dD

v2

DG =DGo + RT ln [products]
[reactants]
vR : gas constant = 8.315 J/mol or = 1.987 cal/mol
vT : absolute temperature (Kenvin temp (Ko) , 25oC = 298oK)

Standard Free-Energy Changes Are Additive

In the case of two sequential chemical reactions, A B and B C, each
reaction has its own equilibrium constant and each has its characteristic
standard free energy change, DGo 1 and DGo 1.

For an example

The overall reaction is exergonic. In this case, energy stored in ATP is used to drive the
synthesis of glucose 6-phosphate, even though its formation from glucose and
inorganic phosphate (Pi) is endergonic.

SUMMARY 13.1 Bioenergetics and Thermodynamics

1. Living cells constantly perform work. They require energy for maintaining
their highly organized structures, synthesizing cellular components,
generating electric currents, and many other processes.
2. Bioenergetics is the quantitative study of energy relationships and energy
conversions in biological systems. Biological energy transformations obey
the laws of thermodynamics
3. All chemical reactions are inuenced by two forces: the tendency to achieve
the most stable bonding state (for which enthalpy, H, is a useful expression)
and the tendency to achieve the highest degree of randomness, expressed
as entropy, S. The net driving force in a reaction is DG, the free-energy
change, which represents the net effect of these two factors: DG =D H-TDS.
4. The standard transformed free-energy change, DGo, is a physical constant
that is characteristic for a given reaction and can be calculated from the
equilibrium constant for the reaction: DGo = RT ln Keq.

SUMMARY 13.1 Bioenergetics and Thermodynamics

5. The actual free-energy change, DG, is a variable that depends on DGo and on
the concentrations of reactants and products: DG = DGo + RTln
([products]/[reactants]).
6. When DG is large and negative, the reaction tends to go in the forward direction;
when DG is large and positive, the reaction tends to go in the reverse direction;
and when DG = 0, the system is at equilibrium.
7. The free-energy change for a reaction is independent of the pathway by which
the reaction occurs. Free-energy changes are additive; the net chemical reaction
that results from successive reactions sharing a common intermediate has an
overall free-energy change that is the sum of the DG values for the individual
reactions.

13.2 Chemical Logic and Common Biochemical Reactions

Cellular chemistry does not encompass every kind of reaction learned in a typical
organic chemistry course. Biological reactions are determined by (1) their relevance
to that particular metabolic system and (2) their rates.
Most of the reactions in living cells fall into one of ve general categories:
(1) reactions that make or break carboncarbon bonds;
(2) internal rearrangements, isomerizations, and eliminations;
(3) free-radical reactions;
(4) group transfers;
(5) oxidation-reductions.
Note that: the ve reaction types are not mutually exclusive; for example, an
isomerization reaction may involve a free -radical intermediate.

Two basic chemical principles:

1) a covalent bond can be broken in two general ways: homolytic cleavage and
heterolytic cleavage;
2) biochemical reactions involve interactions: nucleophiles or electrophiles.

FIGURE 131 Two mechanisms

for cleavage of a CC or CH
bond. In a homolytic cleavage,
each atom keeps one of the
bonding electrons, resulting in the
formation of carbon radicals
(carbons having unpaired
electrons) or uncharged hydrogen
atoms. In a heterolytic cleavage,
one of the atoms retains both
bonding electrons. This can result
in the formation of carbanions,
carbocations, protons, or hydride
ion.
(Carbon anion )

(Carbon cation )

Formation of a C C bond involves

the combination of a nucleophilic
carbanion and an electrophilic
carbocation. Carbanions and
carbocations are generally so
unstable that their formation as
reaction intermediates can be
energetically inaccessible even
with enzyme catalysts.

A anion donates electrons

A cation pulls electrons

FIGURE
132
Common
nucleophiles and electrophiles
in
biochemical
reactions.
Chemical reaction mechanisms,
which trace the formation and
breakage of covalent bonds, are
communicated with dots
and curved arrows, a convention
known informally as electron
pushing. A covalent bond
consists of a shared pair of
electrons. Nonbonded electrons important to
the reaction mechanism are
designated
by dots (:). For movement of a
single electron (as in a free
radical reaction), a single-headed
(shhook-type) arrow is used ( ).
Most reaction steps involve an
unshared electron pair.

The carbon of a carbonyl group has a

partial positive charge due to the
electron-withdrawing property of the
carbonyl oxygen, and thus is an
electrophilic carbon.

FIGURE 133 Chemical properties of carbonyl groups.

(a) The carbon atom of a carbonyl group is an electrophile by virtue of the electron
withdrawing capacity of the electro negative oxygen atom, which results in a
resonance hybrid structure in which the carbon has a partial positive charge. (
(b) Within a molecule, delocalization of electrons into a carbonyl group stabilizes a
carbanion on an adjacent carbon, facilitating its formation.
(c) Imines function much like carbonyl groups in facilitating electron withdrawal.
(d) Carbonyl groups do not always function alone; their capacity as electron sinks often
is augmented by interaction with either a metal ion (Me2+, such as Mg2+) or a
general acid (HA)

aldolase

converts a six-carbon
compound to two threecarbon compounds in
glycolysis

synthesis of citrate in the

citric acid cycle (TCA)

FIGURE 134 Some

common reactions that
form and break CC
bonds in biological
systems.
For both the aldol condensation and the Claisen condensation, a carbanion serves
as nucleophile and the carbon of a carbonyl group serves as electrophile. The carbanion
is stabilized in each case by another carbonyl at the adjoining carbon.
In the decarboxylation reaction, a carbanion is formed on the carbon shaded blue as
the CO2 leaves. The reaction would not occur at an appreciable rate without the
stabilizing effect of the carbonyl adjacent to the carbanion carbon.

Internal Rearrangements, Isomerizations, and Eliminations

FIGURE 135 Carbocations in
carboncarbon bond
formation. In one of the early
steps in cholesterol
biosynthesis, the enzyme prenyl
transferase catalyzes
condensation of isopentenyl
pyrophosphate and dimethylallyl
pyrophosphate to form geranyl
pyrophosphate (see Fig. 2136).
The reaction is initiated by
elimination of pyrophosphate
from the dimethylallyl
pyrophosphate to generate a
carbocation, stabilized by
resonance with the adjacent
CPC bond.
Polymeration

Isomerization

Elimination

FIGURE 136 Isomerization and elimination reactions.

(a) The conversion of glucose 6-phosphate to fructose 6-phosphate, catalyzed by
phosphohexose isomerase.
(b) The reaction proceeds through an enediol intermediate. B1 and B2 are ionizable
groups on the enzyme; they are capable of donating and accepting protons (acting as
general acids or general bases) as the reaction proceeds. Pink screens indicate
nucleophilic groups; blue, electrophilic.

Free radical reactions

FIGURE 137 A free radicalinitiated decarboxylation reaction.

Groups transfer reactions

FIGURE 138 Alternative ways of showing the structure of inorganic

orthophosphate (Pi) (a) In one (inadequate) representation, three oxygens are singlebonded to phosphorus, and the fourth is double-bonded, allowing the four different
resonance structures shown here. (b) The resonance structures can be represented
more accurately by showing all four phosphorusoxygen bonds with some double-bond
character; the hybrid orbitals so represented are arranged in a tetrahedron with P at its
center. (c) When a nucleophile Z (in this case, the OH on C-6 of glucose) attacks ATP,
it displaces ADP (W). In this SN2 reaction, a pentacovalent intermediate (d) forms
transiently.

FIGURE 1310 An oxidationreduction reaction.

FIGURE 139 The oxidation states of

carbon in biomolecules. Each
compound is formed by oxidation of the
red carbon in the compound shown
immediately above. Carbon dioxide is
the most highly oxidized form of carbon
found in living systems.

SUMMARY 13.2 Chemical Logic and Common Biochemical

Reactions
Living systems make use of a large number of chemical reactions that can be
classied into ve general types.
Carbonyl groups play a special role in reactions that form or cleave C C bonds.
Carbanion intermediates are common and are stabilized by adjacent carbonyl groups
or, less often, by imines or certain cofactors.
A re-distribution of electrons can produce internal rearrangements, isomerizations,
and eliminations. Such reactions include intramolecular oxidation-reduction, change in
cis-trans arrangement at a double bond, and transposition of double bonds.
Homolytic cleavage of covalent bonds to generate free radicals occurs in some
pathways, such as in certain isomerization, decarboxylation, reductase, and
rearrangement reactions.
Phosphoryl transfer reactions are an especially important type of group transfer in
cells, required for the activation of molecules for reactions that would otherwise be highly
unfavorable.
Oxidation-reduction reactions involve the loss or gain of electrons: one reactant
gains electrons and is reduced, while the other loses electrons and is oxidized.
Oxidation reactions generally release energy and are important in catabolism.

13.3 Phosphoryl Group Transfers and ATP

ATP Donates Phosphoryl, Pyrophosphoryl,
and Adenylyl Groups

18O:

isotope

Free Energy from hydrolysis of ATP

g-b phosphoanhydride: 30.5 kJ/mol

ab phosphoanhydride: 45.6 kJ/mol

+ H20

Adenosine triphosphatase
(ATPase)

(-)30.5 kJ/mol
H+ v

Other compounds are energy rich

BPP

: Bis-phosphoglycerate

+ H20
(-) 49.3 kJ/mol

Bis-phosphoglycerate

+ Pi

Other compounds are energy rich

PEP: Phosphoenolpyruvate

+ H20
(-) 61.7 kJ/mol
Pyruvate kinase
(ATPase)

Phosphoenolpyruvate

+ Pi

FIGURE 1319 Ranking of biological phosphate

compounds by standard free energies of hydrolysis.

SUMMARY 13.3 Phosphoryl Group Transfers and ATP

1. ATP is the chemical link between catabolism and anabolism. It is the energy
currency of the living cell. The exergonic conversion of ATP to ADP and Pi or to AMP
and PPi, is coupled to many endergonic reactions and processes.
2. Direct hydrolysis of ATP is the source of energy in some processes driven by
conformational changes, but in general it is not ATP hydrolysis but the transfer of a
phosphoryl, pyrophosphoryl, or adenylyl group from ATP to a substrate or enzyme
that couples the energy of ATP breakdown to endergonic transformations of
substrates.
3. Through these group transfer reactions, ATP provides the energy for anabolic
reactions, including the synthesis of informational macromolecules, and for the
transport of molecules and ions across membranes against concentration gradients
and electrical potential gradients.
4. To maintain its high group transfer potential , ATP concentration must be held far
above the equilibrium concentration by energy-yielding reactions of catabolism.
5. Cells contain other metabolites with large, negative, free energies of hydrolysis,
including phosphoenolpyruvate, 1,3-bisphosphoglycerate, and phosphocreatine.
These high-energy compounds, like ATP, have a high phosphoryl group transfer
potential. Thioesters also have high free energies of hydrolysis.
6. Inorganic polyphosphate, present in all cells, may serve as a reservoir of
phosphoryl groups with high group transfer potential.

13.4 Biological Oxidation-Reduction Reactions

1. Directly as electrons. For example, the Fe2"/Fe3"redox pair can transfer an
electron to the Cu"/Cu2" redox pair
2. As hydrogen atoms. Recall that a hydrogen atom consists of a proton (H")
and a single electron (e-). In this case we can write the general equation

3 As a hydride ion (:H-), which has two electrons.This occurs in the case of
NAD-linked dehydrogenases, described below

4. Through direct combination with oxygen. In this case, oxygen combines

with an organic reductant and is covalently incorporated in the product, as
in the oxidation of a hydrocarbon to an alcohol:

NADH and NADPH act with dehydrogenases as soluble electron

carriers

FIGURE 1324 NAD and NADP. (a) Nicotinamide adenine dinucleotide, NAD +, and its
phosphorylated analog NADP+ undergo reduction to NADH and NADPH, accepting a
hydride ion (two electrons and one proton) from an oxidizable substrate. The hydride ion
is added to either the front (the A side) or the back (the B side).

FADH2

SUMMARY 13.4 Biological Oxidation-Reduction Reactions

1. In many organisms, a central energy-conserving process is the stepwise oxidation of
glucose to CO2,in which some of the energy of oxidation is conserved in ATP as
electrons are passed to O2.
2. Biological oxidation-reduction reactions can be described in terms of two halfreactions, each with a characteristic standard reduction potential, Eo.
3. The standard free-energy change for an oxidation-reduction reaction is directly
proportional to the difference in standard reduction potentials of thetwo half-cells:
DGo ' = -n J DEo
4. Many biological oxidation reactions are dehydrogenations in which one or two
hydrogen atoms (H+ + e-) are transferred from a substrate to a hydrogen acceptor.
Oxidation-reduction reactions in living cells involve specialized electron carriers.
5. NAD and NADP are the freely diffusible coenzymes of many dehydrogenases. Both
NAD+ and NADP + accept 02 electrons and 01 proton.
6. FAD and FMN, the avin nucleotides, serve as tightly bound prosthetic groups of
avoproteins. They can accept either 01 or 02 electrons and 01 or 02 protons.
Flavoproteins also serve as light receptors in crytochromes and photolyases.

Oxidative phosphorylation or ATP synthesis by ATPsynthase

driven by the protons motive force generated through the
electrons transport chain
See VIDEO CLIP

F1

Fo

ATP synthase
(F-type: FoF1- ATPase)

See VIDEO CLIP

ATP synthase

FIGURE 1919 Chemiosmotic model. In this simple representation of the

chemiosmotic theory applied to mitochondria, electrons from NADH and other
oxidizable substrates pass through a chain of carriers arranged asymmetrically in the
inner membrane. Electron ow is accompanied by proton transfer across the membrane,
producing both a chemical gradient (DpH) and an electrical gradient (D y). The inner
mitochondrial membrane is impermeable to protons; protons can reenter the matrix only
through proton-specic channels (Fo). The proton-motive force that drives protons back
into the matrix provides the energy for ATP synthesis, catalyzed by the F1Fo complex.

SUMMARY 19.2 ATP Synthesis

The ow of electrons through Complexes I, III, and IV results in pumping of protons
across the inner mitochondrial membrane, making the matrix alkaline relative to the
intermembrane space. This proton gradient provides the energy (the proton-motive
force) for ATP synthesis from ADP and Pi by FoF1- ATP synthase in the inner
membrane.
ATP synthase carries out rotational catalysis, in which the ow of protons through Fo
causes each of three nucleotide-binding sites in F1 to cycle from (ADP + Pi)bound to
ATP-bound to empty conformations.
ATP formation on the enzyme requires little energy; the role of the proton-motive force
is to push ATP from its binding site (release off) on the synthase.
The ratio of ATP synthesized per reduced to H2O (the P/O ratio) is about 2.5 when
electrons enter the respiratory chain at Complex I (NADH), and 1.5 when electrons enter
at ubiquinone. (FADH2)
Energy conserved in a proton gradient can drive solute transport uphill across a
membrane.
The inner mitochondrial membrane is impermeable to NADH and NAD+ but NADH
equivalents are moved from the cytosol to the matrix by either of two shuttles. NADH
equivalents moved in by the malate-aspartate shuttle enter the respiratory chain at
Complex I and yield a P/O ratio of 2.5; those moved in by the glycerol 3-phosphate
shuttle enter at ubiquinone and give a P/O ratio of 1.5.