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BCM301

Chapter 1:

Bioenergetics


By: Zatilfarihiah Rasdi

Biochemistry II

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.


1. Open
system: Living organisms, which take up
nutrients, release waste products and generate work and
heat.

2. Closed
system: If an organism were sealed inside an
uninsulated

box.

3. Isolated
system: If the box perfectly insulated.

A.
Energy


The 1
st

law of thermodynamics is a mathematical
statement of the law of conservation of energy.


Energy can be neither created nor destroyed
.




∆ U =
U
final



U
initial

=
q



w


here
U

is energy,
q

represents the heat absorbed by
the system from surroundings and
w

is the work done
by the system on the surroundings.


Processes in which a negative
q
, are known as
exothermic processes

(Greek:
exo
, out of); those in
which the system gains heat (positive
q
) are known as
endothermic processes

(Greek:
endon
, within).


The SI unit of energy, the
joule (J),

is steadily
replacing the
calorie (cal)

in modern scientific usage.

Voet
Biochemistry

3e

© 2004 John Wiley & Sons, Inc.

Table 3
-
1

Thermodynamic Units and Constants.

Page 52

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
.

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.


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.


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

2
nd

law

of

thermodynamics

expresses

this

phenomenon,

provide

the

criterion

for

determining

whether

a

process

is

spontaneous
.

1. Second Law of Thermodynamics:

The universe tends toward maximum
disorder

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.

Page 53

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 = k
B

ln

W


that increases with W but in more manageable way. Here
k
B

is
the Boltzman constant. Eg. For twin bulb system,
S = k
B
N
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 O
2

is higher than in
venous blood passing through them, more O
2

enters
the blood than leaves it. On the other hand, in the
tissues
-

where the O
2

concentration is lower than in
arterial blood, there is net diffusion of O
2

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 energy
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 + P
i

+ 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
°
’.

Voet
Biochemistry

3e

© 2004 John Wiley & Sons, Inc.

Table 3
-
2

Variation of Reaction Spontaneity
(Sign of
D
G
) with the signs of
D
H

and
D
S
.


Page 56

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.

Voet
Biochemistry

3e

© 2004 John Wiley & Sons, Inc.

Table 3
-
3

Variation of
K
eq
with
D
G
°

at 25
°
C.

Page 57

Table 3
-
4

(
top
) Free Energies of Formation of
Some Compounds of Biochemical Interest.

Page 58

Voet
Biochemistry

3e

© 2004 John Wiley & Sons, Inc.

Table 3
-
4

(
middle
) Free Energies of
Formation of Some Compounds of
Biochemical Interest.

Page 58

Voet
Biochemistry

3e

© 2004 John Wiley & Sons, Inc.

Table 3
-
4

(
bottom
) Free Energies of
Formation of Some Compounds of
Biochemical Interest.

Page 58

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


∆G
1


(2)

D + E F + G


∆G
2


If ∆G
1
≥ 0, reaction (1) will not occur spontaneously.


However, if ∆G
2

is sufficiently
exergonic

so that ∆G
1
+ ∆G
2

< 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



∆G
3



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 many
otherwise
endergonic

biological processes to completion.