Ch01 bcm 311

BCM301

Biochemistry II

Chapter 1:
Bioenergetics

By: Zatilfarihiah Rasdi

By the end of the lecture, students
should be able to know/define/state:

 The first and second law of thermodynamics
 The enthalpy, entropy and free energy
 Exothermic, endothermic, exergonic and endergonic
reactions
 Coupled reactions

Do revise this topic and refer to
textbook of biochemistry!!!

A Review: Thermodynamic
Principles
 Living things require a continuous throughput of
energy. eg. Photosynthesis process – plants convert
radiant energy from the Sun, the primary energy
source for life on Earth, to the chemical energy of
carbohydrates and other organic substances.
 The plants/ animals that eat them, then metabolize
these substances to power such functions as the
synthesis of biomolecules, the maintenance of
concentration gradients and the movement of
muscles.

 These processes transform the energy to heat, which is
dissipated to the environment and must be devoted to the
acquisition and utilization of energy.
 Thermodynamics (Greek: therme, heat + dynamics,
power) is a description of the relationships among the
various forms of energy and how energy affects matter on
the macroscopic as opposed to the molecular level.
 With a knowledge of thermodynamics we can determine
whether a physical process is possible. Thermodynamics
is essential for:
 understanding why macromolecules fold to their native
conformations
 how metabolic pathways are designed, why molecules cross
biological membranes
 how muscles generate mechanical force

1. First Law of Thermodynamics:
Energy Is Conserved
 A system is defined as that part of the universe that is of
interest, such as reaction vessel or an organism; the rest
of the universe is known as the surroundings.
 A system is said to be open, closed or isolated according
to whether or not it can exchange matter and energy
with its surroundings, only energy.
 Living organisms, which take up nutrients, release waste
products and generate work and heat (open system).
 If an organism were sealed inside an uninsulated box, it
would, together with the box, constitute a closed
system.
 If the box perfectly insulated, the system would be
isolated.

 Processes in which a negative q, are known as exothermic processes (Greek: exo, out of); those in which the

 The SI unit of energy, the joule (J), is steadily replacing the calorie (cal) in modern scientific usage.

Voet Biochemistry 3e Page 52
© 2004 John Wiley & Sons, Inc.

Constants.
Table 3-1 Thermodynamic Units and

a. State functions are independent of the path a systems
follow
• Experiments have invariably demonstrated that the energy of a
system depends only on its current properties or state, not on how
it reached that state.

B. Enthalpy
- any combination of only state functions must also be a state
function. One such combination, known as enthalpy (Greek: to
warm in) is defined
H = U + PV
where V is the volume and P is its pressure.
 is a particularly convenient quantity with which to describe
biological systems because under constant pressure, a condition
typical of most biochemical processes, the enthalpy change
between the initial and final states of a process, ∆H, is the easily
measured heat that it generates or absorbs.

 In general, the change of enthalpy in any
hypothetical reaction pathway can be
determined from the enthalpy change in any
other reaction pathway between the same
reactants and products.

1. Second Law of
Thermodynamics: The universe
tends toward maximum disorder

 Spontaneous processes are characterized by the
conversion of order ( in this case the coherent motion
of the swimmer’s body) to chaos ( here the random
thermal motion of the water molecules)
 The 2nd law of thermodynamics expresses this
phenomenon, provide the criterion for determining
whether a process is spontaneous.

A. Spontaneity and disorder
 The spontaneous processes occur in directions
that increase the overall disorder of the universe
that is, of the systems and its surroundings.
 Disorder, in this context, is defined as the
number of equivalent ways, W, of arranging the
components of the universe.
 (Note: Find the equation that involved with W)

Figure 3-1 Two bulbs of equal volumes connected
by a stopcock.

B. Entropy
 In a chemical systems, W, the number of equivalent ways of
arranging a system in a particular state, is usually
inconveniently immense.
 In order to be able to deal with W more easily, we define, as

Ludwig Boltzman in 1877, a quantity known as entropy
(Greek: en, in + trope, turning):
S = kB ln W
that increases with W but in more manageable way. Here kB is
the Boltzman constant. Eg. For twin bulb system, S = kBN ln 2,
so the entropy of the system in its most probable state is
proportional to the number of gas molecules contains.
Note: Entropy is a state function because it depends only on the
parameters that describe a state.

 The conclusions based on the twin-bulb apparatus
may be applied to explain, why blood transports
between the lungs and the tissues. Solutes in
solution behave analogously to gases in that they
intend to maintain a uniform concentration
throughout their occupied volume – this is their
most probable arrangement.
 In the lungs-concentration of O2 is higher than in
venous blood passing through them, more O2 enters
the blood than leaves it. On the other hand, in the
tissues- where the O2 concentration is lower than in
arterial blood, there is net diffusion of O2 from
blood to the tissues.

Figure 3-3 Relationship of entropy and temperature.
The structure of water or any other substance becomes
increasingly disordered, that is, its entropy increases, as its
temperature rises.

3. Free energy change, ∆G – indicator of spontaneity
• Thermodynamic view: metabolism is an energy
transforming process whereby catabolism provides
energy for anabolism.
• What is energy?- “the capacity to cause or
undergo change”
• Cell and organisms are able to harness forms of
energy and convert them to other suitable forms to
support movement, active transport and
biosynthesis.

 The most important medium of energy exchange
is ATP – “universal carrier of biological energy”
 Fundamental concept of metabolism:
i. exergonic – the overall process of catabolism
releases energy (spontaneous)
ii. endergonic – the overall process of anabolism
requires nergy input (nonspontaneous)
 Goal of thermodynamic: to predict the spontaneity
of a process or reaction. The most useful
thermodynamic terms is free energy, G or known
as Gibbs free energy.
 G is an indicator of the energy available from the
reaction to do work;composed of two components,
enthalpy (H) and entropy (S).

G = H – TS…………………………….(1)

where T = temperature in Kelvin (K)
units for G = joules/mol or kJ/mol
∆G = ∆H –T ∆S……………………....(2)

whether a reaction is spontaneous may be predicted from the following
values of ∆G:

If ∆G < 0 energy is released;reaction is spontaneous and exergonic
∆G = 0 reaction is at equilibrium
∆G > 0 energy is required;reaction is nonspontaneous and
endergonic

Note: it is very difficult to measure ∆G for a biochemical reaction because
the cellular concentrations of the reactants are very small and hard to
determine experimentally. In order to calculate the energy associated with
biochemical reactions, we must resort to the measurement under a set of
standard.

Standard Free Energy Change, ∆G°’
 This section focus on the most important energy

molecule, ATP.
 The breakdown of ATP must be exergonic reaction, but

what is the quantitative amount of energy released under
std. conditions?
ATP ADP + Pi + energy

In your introductory chemistry courses, std. conditions for solute
reactions were defined as:
1 atm of pressure, 25°C and initial and products concentration of 1
M. (but in biochemical process) + condition of a pH of 7 the
modified ∆G°’.

Table 3-2 Variation of Reaction Spontaneity
(Sign of ∆ G) with the signs of ∆ H and ∆ S.

4. Chemical equilibria
 The entropy (disorder) of a substance increases with its volume.
eg. Twin-bulb apparatus – a collection of gas molecules occupied
all of the volume available to it, maximizes its entropy. Entropy is
a function of concentration.
 If entropy varies with concentration, so do free energy. The free
energy change of chemical reaction depends on the concentrations
of both its reactants and products. eg enzymatic reactions which
needs substrates (reactants) and on the metabolic demand for their
products.
 The equilibrium constant of a reaction may therefore be
calculated from standard free energy data and vice versa.

Note: For more information on equilibrium constants, students may
refer to textbook and reference book of Biochemistry.

Table 3-3 Variation of Keq with ∆ G° at 25°C.

Table 3-4 (top) Free Energies of Formation of
Some Compounds of Biochemical Interest.
Page 58

Table 3-4 (middle) Free Energies of
Formation of Some Compounds of
Biochemical Interest.

Table 3-4 (bottom) Free Energies of
Formation of Some Compounds of
Biochemical Interest.

A. Coupled reactions
 The additivity of free energy changes allows an
endergonic reaction to be driven by an exergonic
reaction under the proper conditions.
(thermodynamic basis for the operation of the
metabolic pathways since most of these reaction
sequences comprise endergonic as well as
exergonic reactions.
(1) A+B C+D ∆G1
(2) D+E F+G ∆G2

 If ∆G1 ≥ 0, reaction (1) will not occur spontaneously.
 However, if ∆G2 is sufficiently exergonic so that ∆G1 + ∆G2 < 0,
then although the equilibrium concentration of D in reaction (1)
will be relatively small, it will be larger than that in reaction (2).
As reaction (2) converts D to product, reaction (1) will operate in
the forward direction to replenish the equilibrium concentration of
D.
 The highly exergonic reaction (2) therefore drives the endergonic
reaction (1), and the two reactions are said to be coupled through
their common intermediate D.
 These coupled reactions proceed spontaneously can also be seen
by summing reactions (1) and (2) to yield overall reaction
(3) A+B+E C+F+G ∆G3

As long as the overall pathway (reaction sequence) is exergonic, it
will operate in the forward direction. Thus, the free energy of
ATP hydrolysis, a highly exergonic process, is harnessed to drive

Ch01 bcm 311

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