4.3.

2013
1
THERMODYNAMICS OF THE LIVING SYSTEMS
INTRODUCTION TO METABOLISM
General Biochemistry 2013
CONCEPT OF THERMODYNAMICS
Thermodynamics, in general, studies changes of energy of the system.
A system is part of space which is separated by boundaries from its
surroundings.


Boundaries can be
Real
Fictional

The principle of changes and transfer of energy is valid for both, living and lifeless
matter.

Systems
Open
Close
Isolate


Living system = open system

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LAWS OF THERMODYNAMICS
Energy can neither be created nor destroyed. This law of energy
conservation stipulates that, although energy may be converted from one
form to another, the total energy in a system must remain constant.

AE(AU) = E
B
- E
A
= Q W

The term entropy must be defined. Entropy, which is designated by the
symbol S, is a measure or indicator of the degree of disorder or
randomness in a system. In addition, entropy can be viewed as the energy
in a system that is unavailable to perform useful work.

(AS
system
+ AS
surroundings
) > 0 for spontaneous
processes
THE FUSING THE FIRST AND THE SECOND LAWS
OF THERMODYNAMICS
(1878 Josiah Willard Gibbs)












I. First law: definition and
properties of AE
II. Second law: definition
and properties of AS
AG
Free energy, chemical potential
AG as criterion
of feasibility of
transformation
Standard
free energies
Dependence
of AG on
concentration
Energetic
coupling
Group
transfer
potentials
or high-
energy bonds
AG as a basis
for deriving
new relations
governing phy-
sicochemical
behavior
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AG AS CRITERION OF EASIBILITY

AG = 0 represents an equilibrium
AG < 0 represents an exergonic reaction
AG > 0 represents an endergonic reaction

A reaction can occur spontaneously only if AG,
the change in free energy, is negative

A THERMODYNAMICALLY UNFAVOURABLE
REACTION CAN BE DRIVEN BY A FAVOURABLE ONE
An important thermodynamic fact is that the overall free-energy change for a chemically
coupled series of reactions is equal to the sum of the free-energy changes of individual
steps.
A B + C AG
'
= + 20 kJ mol
-1

B D AG
'
= - 32 kJ mol
-1

__________________________________
A C + D AG
'
= - 12 kJ mol
-1

first reaction - A cannot be spontaneously converted into B and C because
AG
'
> 0 - endergonic reaction
second reaction - the conversion of B into D under standard conditions is
thermodynamically feasible AG
'
< 0 - exergonic reaction

The reactions are coupled by the shared chemical intermediate B.
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ATP IS THE UNIVERSAL CURRENCY OF FREE
ENERGY IN BIOLOGICAL SYSTEMS
Living things require a continual input of free energy
for three major purposes:
the performance of mechanical work in muscle contraction and
other cellular movements
the active transport of molecules and ions
the synthesis of macromolecules and other biomolecules from
simple precursors

The free energy used in these processes is derived
from the environment.
Chemotrophs obtain this energy by the oxidation of foodstuffs
Phototrophs obtain it by trapping light energy
ATP THE FREE ENERGY DONOR
The central role of ATP in energy exchanges in biological systems was perceived in 1941
by Fritz Lipmann and by Herman Kalckar.
O
H
OH
H
H
OH
H
N
N
N
N
NH
2
-
O P O P
O
O
O
O
-
O
-
P OCH
2
O
O
-
Adenosine triphosphate
(ATP)
Adenosine diphosphate (ADP)
N
N
N
N
NH
2
O
H
OH
H
H
OH
H
-
O P O
O
O
-
P OCH
2
O
O
-

N
N
N
N
NH
2
O
H
OH
H
H
OH
H
-
O P OCH
2
O
O
-


Adenosine monophosphate (AMP)
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O
H
OH
H
H
OH
H
N
N
N
N
NH
2
-
O P O P O
O O
P OCH
2
O
O
-
O
-
O
-
Mg
2+
Adenosintrifosft (ATP)
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 (P
i
)
adenosine monophosphate (AMP) and pyrophosphate (PP
i
)

ATP + H
2
O ADP + P
i
+ H
+
AG
'
= - 7.3 kcal/mol (30.5 kJ/mol)
ATP + H
2
O AMP + PP
i
+ H
+
AG
'
= - 7.3 kcal/mol (30.5 kJ/mol)

Compound phosphoryl group-transfer potential (-AG)
kJ mol
-1
kcal mol
-1

Phosphoenolpyruvate 61.9 14.8
Carbamoyl phosphate 51.5 12.3
Acetyl phosphate 43.1 10.3
Creatine phosphate 43.1 10.3
Pyrophosphate 33.5 8.0
Acetyl CoA 32.2 7.7
ATP-ADP 30.5 7.3
ATP-AMP 30.5 7.3
Glucose-1-phosphate 20.9 5.0
Fructose-6-phosphate 15.9 3.8
Glucose-6-phosphate 13.8 3.3
Glycerol-3-phosphate 9.2 2.2

ATP, AMP, and ADP are interconvertible. The enzyme adenylate kinase (also called
myokinase) catalyzes the reaction:
ATP + AMP ADP + ADP
At most physiological conditions - SUM of ATP, ADP, and AMP is constant.
Relative concentrations can be changed - always |ATP| >> |AMP|.
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Some biosynthetic reactions are driven by nucleoside triphosphates that are analogous to
ATP, namely, guanosine triphosphate (GTP), uridine triphosphate (UTP), and cytidine
triphosphate (CTP).
Enzymes can catalyze the transfer of the terminal phosphoryl group from one nucleotide to
another, as in reactions

ATP + GDP ADP + GTP
ATP + GMP ADP + GDP

R= nucleic bases


O
H
OH
H
H
OH
H
R
-
O P O P
O
O
O
O
-
O
-
P OCH
2
O
O
-

N
NH
2
N
H
O
Cytosine

HN
N
O
O
H
Uracil

N
N
N
H
NH
2
N
Adenine

HN
N
N
N
O
H
H
2
N
Guanine

ATP IS CONTINUOUSLY FORMED AND CONSUMED
ATP serves as the principal immediate donor of free energy in biological systems rather
than as a long-term storage form of free energy.
In a typical cell, an ATP molecule is consumed within a minute following its formation.
The turnover of ATP is very high.

high biochemical reactivity
Disadvantages for long-term storage
high molecular weight (M
r
=507.15)

For long-term storage of free energy have organisms others storages:

1) triacylglycerols
2) special polysaccharides - a) animals - glycogen
b) plants - starch and inuline

more developed organisms - several levels
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REDOX POTENTIALS AND FREE-ENERGY CHANGES
In oxidative phosphorylation, the electron transfer potential of NADH or FADH
2
is
converted into the phosphoryl transfer potential (phosphoryl potential) of ATP.
Reduction potential (also called the redox potential or oxidation-reduction potential) - E
0

-
the corresponding expression for the electron transfer potential.

Consider a substance that can exist in an oxidized form X and a reduced form X
-
. Such a
pair is called a redox couple.







voltmeter
agar
bridge
Solution of
1M X a 1M X
-

1M H
+
in equilibrium
with 1 atm H
2
gas
Electrons then flow from one half-cell to the other. If the reaction proceeds in the direction
X

+ H
+
X + 1/2 H
2


the reactions in the half-cells are
X

X + e
-

H
+
+ e
-
1/2 H
2

Electron flow: from the sample half-cell to the standard reference half-cell, and
consequently the sample-cell electrode is negative with respect to the standard-cell
electrode.

The reduction potential of the X:X
-
couple is the observed voltage at the start of the
experiment (when X, X
-
, and H
+
are 1M).
The reduction potential of the H
+
: H
2
couple is defined to be 0 Volts.
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IMPORTANCE OF THE REDUCTION POTENTIAL
1) A strong reducing agent (such as NADH) is poised to donate electrons and has negative
reduction potential
2) A strong oxidizing agent (such as O
2
) is ready to accept electrons and has a positive
reduction potential

A negative reduction potential means that a substance has lower affinity for electrons than
does H
2
.
A positive reduction potential means that a substance has higher affinity for electrons than
does H
2
.
STANDARD REDUCTION POTENTIALS OF SOME
REACTIONS

oxidant reductant n E
'
(V)
succinate+ CO
2
o-ketoglutarate 2 -0.67
acetate acetaldehyde 2 -0.60
feredoxin (oxid.) feredoxin (reduc.) 1 -0.43
2 H
+
H
2
2 -0.42
NAD
+
NADH + H
+
2 -0.32
NADP
+
NADPH + H
+
2 -0.32
glutathione (oxid.) glutathione (red.) 2 -0.23
acetaldehyde ethanol 2 -0.20
pyruvate lactate 2 -0.19
cytochrome b (Fe
3+
) cytochrome b (Fe
2+
) 1 0.07
fumarate succinate 2 0.03
ubiquinone (ox.) ubiquinone (red.) 2 0.10
cytochrome c (Fe
3+
) cytochrome c (Fe
2+
) 1 0.22
Fe
3+
Fe
2+
1 0.77
1/2 O
2
+ 2 H
+
H
2
O 2 0.82

Note: E
'
is the standard oxidation-reduction poteential (pH 7, 25C) and n is the number
of electrons transferred. E
'
refers to the partial reaction written
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EXAMPLE
( a ) Pyruvate + NADH + H
+
lactate + NAD
+

The reduction potential of NAD
+
: NADH couple is - 0.32 V,
pyruvate : lactate couple - 0.19 V

By convention, reduction potentials refer to partial reactions written as reductions:
oxidant + e
-
reductant

( b ) pyruvate + 2H
+
+ 2e
-
lactate AE
'
= - 0.19 V
( c ) NAD
+
+ H
+
+ 2e
-
NADH AE
'
= - 0.32 V

To obtain (a) from (b) and (c), we need to reverse the direction of reaction (c) so that
NADH appears on the left side of the arrow. In doing so, the sign of E
0

must be changed.

( b ) pyruvate + 2H
+
+ 2e
-
lactate AE
'
= - 0.19 V
( c ) NADH NAD
+
+ H
+
+ 2e
-
AE
'
= + 0.32 V

Reactions (b) and (d) can be added to get the desired reaction (a) and a AE
0

of +0.13 volt.
Calculation of the AG
'
for the reduction of pyruvate by NADH.

AG
'
= - nFAE
'


where n is the number of electrons transferred
F Faraday constant - (23.06 kcalV
-1
mol
-1
, 96.484 kJ.V
-1
mol
-1
)
AE
'
, AG
'
- related to 1 mol.

For the reduction of pyruvate, n=2

AG
'
= - 2 x 23.06 x 0.13 = - 25.1 kJ/mol

A positive AE
'
(but negative AG
'
) signifies exergonic reaction under standard
conditions.
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INTRODUCTION TO METABOLISM
SYLLABUS
Definition of Metabolism
A First Look at Metabolism
Metabolic Pathways
Central Pathways of Energy Metabolism
Distinct Pathways for Biosynthesis and Degradation
Major Metabolic Control Mechanisms
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TWO MAJOR QUESTIONS OF BIOCHEMISTRY
1. How do cells extract energy and reducing
power from their environment?

2. How do cells synthesize the building blocks
of their macromolecules?
these processes are carried out by a highly integrated
network of chemical reactions, which are collectively
known as metabolism
PURPOSES OF METABOLISM
the major role of metabolism is to oxidize food
to provide energy in the term of ATP
food molecules are converted to new cellular
material and essential components
waste products are processed to facilitate their
excretion in the urine
some specialized cells in human babies oxidize
food to generate heat. This is exceptional since
heat is, in general, a byproduct of metabolism

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METABOLISM
the sum of all reactions in organism which are
catalyzed by enzymes and which convert basic
substances into simple molecules. They are
organized, localized and controlled.
the totality of chemical reactions that occur in
living matter
Metabolic Pathway sequences of specific
reactions which form certain product
Metabolites - reaction component, intermediate
and product of metabolic pathway

Intermediary Metabolism - comprises all
reactions concerned with storing and generating
metabolic energy and with using this energy in
biosynthesis of low-molecular-weight compounds
and energy storage compounds
Energy Metabolism - part of intermediary
metabolism consisting of pathways that store or
generate metabolic energy (e.g. without metabolism
of nitrogenous compounds, nucleotide metabolism)
Central Pathways of Metabolism - are
substantially the same in many different
organisms, and they account for relatively large
amounts of mass transfer and energy generation
within a cell

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Polymers:
Proteins
Nucleic acids
Polysaccharides
Lipids
Energy Energy
1 2 3
Metabolic
Intermediates:
Pyruvate
Acetyl-CoA
Citric acid cycle
intermediates
Monomers:
Amino acides
Nucleotides
Sugars
Fatty acids
Glycerol
Simple
Small Molecules:


H
2
O CO
2

NH
3

A FIRST LOOK AT METABOLISM
Metabolism can be subdivided into two major categories
catabolism, those processes related to degradation of complex
substances
anabolism, those processes concerned primarily with the synthesis of
complex organic molecules
Both catabolic and anabolic pathways occur in three stages of
complexity
stage 1, the interconversion of polymers and complex lipids with
monomeric intermediates
stage 2, the interconversion of monomeric sugars, amino acids, and
lipids with still simpler organic compounds
stage 3, the ultimate degradation to, or synthesis from, inorganic
compounds, including CO
2
, H
2
O, and NH
3


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METABOLISM
Complex Look at Metabolism
energy-yielding pathways also generate intermediates used in
biosynthetic processes
many of the same reactions play roles in both degradive and
biosynthetic processes

Metabolic Pathway
irreversible
control mechanisms
compartmentation

METABOLISM
Organic Fuel Molecules
most organisms derive both the raw materials and the energy for
biosynthesis from organic fuel molecules such as glucose
The Central Pathways
are found in all aerobic organisms
involve the oxidation of fuel molecules
involve the synthesis of small biomolecules from the intermediates
Fundamental Distinction among Organisms
source of their fuel molecules
autotrophs - synthesize Glc and all of their other organic compounds
from inorganic carbon, supplied as CO
2

heterotrophs - can synthesize their organic metabolites only from other
organic compounds, which they must therefore consume

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MAJOR METABOLIC CONTROL MECHANISMS
4 Basic Regulatory Ways
control of enzyme levels
control of enzyme activity
control the flow of metabolite through a membrane
hormonal regulation
Other Control Mechanisms
distinct pathways for biosynthesis and degradation
compartmentation
organs specialization - the metabolic patterns of the brain, muscle,
adipose tissue, and the liver are strikingly different

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CONTROL OF ENZYME LEVELS
If you were to prepare a cell-free extract of a particular tissue and determine
intracellular concentrations of several different enzymes, you would find
tremendous variations. Some enzymes are present at many thousands of
molecules per cell, whereas enzymes that have limited or specialized
functions might be present at fewer than a dozen molecules per cell.

The level of a single enzyme (inside cells influence) depends
on:
the enzymes rate of synthesis
the enzymes rate of degradation
The set of enzyme levels (influence of outside cell factors)
enzyme induction
enzyme repression

CONTROL OF ENZYME ACTIVITY
The catalytic activity of an enzyme molecule can be controlled in principal in 4 ways:

Reversible allosteric control
the first reaction in many metabolic pathways is inhibited by its final product
Reversible covalent modification
some enzymes are effected through the ATP-dependent phosphorylation of
a specific serine (threonine or tyrosine) residue
Stimulation and inhibition by control proteins
e.g. Calmodulin as a control protein activates some protein kinases
Proteolytic activation
irreversible transformation - proenzyme to enzyme (trypsinogen to trypsin,
procarboxypeptidase to carboxypeptidase)

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CONTROL THE FLOW OF METABOLITE THROUGH
A MEMBRANE
Through the cell membrane
the membrane is not permeable for all molecules (e.g. Glc-6-P cannot go
through the membrane
some molecules have special transport systems built-in membrane (e.g.
glucose)
Through the organelle membranes inside the cell
different type of membranes for different type of organels can have
rather different permeability (e.g. membrane between cytosol and
mitochondria is impermeable to oxaloacetate)
some molecules have also special transport systems to come in (e.g.
fatty acids degradation - FA must be transported into mitochondria by
means of a specific transport system - carnitine)

HORMONAL REGULATION
The process of transmitting some messages and bringing about metabolic
changes is called signal transduction. The extracellular messengers include
hormones, growth factors, neurotransmitters, and pheromones. A hormone
is a substance synthesized in specialized cells and carried via the circulation
to remote target cells. There it interacts with specific receptors, resulting in
specific metabolic changes in the target cell.

There are 2 types of metabolic response to hormones
steroid hormones - involve changes in gene expression. Steroids enter a
target cell, where they interact with an intracellular protein receptor, and the
resultant hormone-receptor complex then migrates to the nucleus and binds
to specific sites in the genome and either activates or represses the
transcription of particular genes.
first messengers - act extracellularly by binding to receptors in the plasma
membrane. The response to binding hormone involves the synthesis of
intracellular second messengers that control metabolic reactions.

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FIRST-SECOND MESSENGERS RESPONSE
OTHER CONTROL MECHANISMS
Distinct pathways for biosynthesis and degradation
it is necessary from energetic point of view (both pathways must be
exergonic from the start to the end





Compartmentation (eukariotic cell)
FA biosynthesis x FA |-oxidation
cytosol mitochondria
Glycolysis x Citric Acid Cycle
cytosol mitochondria

1 2
A
Y X
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ENERGY STATUS OF THE CELL
many reactions in metabolism are controlled by the energy
status of the cell
energy charge as an index of the energy status





phosphorylation potential as an alternative index of the energy status

| | | |
| | | | | | AMP ADP ATP
ADP ATP
+ +
+
=
2 / 1
( 0 ; 1 ) Energy charge
| |
| | | |
i
P ADP
ATP

=
Phosphorylation potential
ENERGY STATUS OF THE CELL
Daniel Atkinson has shown that ATP-generating (catabolic) pathways
are inhibited by a high energy charge, whereas ATP-utilizing
(anabolic) pathways are stimulated by a high energy charge