Download Chapter 5: chemical reactions in the living cell

SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.
CHAPTER 5: CHEMICAL REACTIONS IN THE LIVING CELL
- PART I -
“All living beings need some form of energy to maintain their complex
structures and to stay alive …”

without a steady flow of energy through their bodies, living organisms would not able
to maintain their complex carbon-based structures and life-supporting chemical
activities
Definition: Energy
 energy is per definition the ability to perform work

work and energy are measured in the same units (= Joule); or in older text books in
calorie (cal)
 energy is one of the two fundamental ideas in physics; the other one is matter
 A. Einstein taught us with his famous formula E = m x c2, that
energy and matter are closely related and inter-convertable

energy exists in many forms, but only some energy forms are tapped and used by
biological organisms
Form of energy
Biological Use
P
Pootteennttiiaall
Proton/ion gradients
M
e
c
h
a
n
i
c
a
l
(
=
k
i
n
e
t
i
c
)
Mechanical (= kinetic)
Movement/Flying
C
Chheem
miiccaall
Metabolism
TThheerrm
a
l
e
n
e
r
g
y
mal energy
Body temperature
E
Elleeccttrroom
maaggnneettiicc ((== lliigghhtt))
Photosynthesis
E
Elleeccttrriiccaall
Electrical organs
M
a
g
n
e
t
i
c
Magnetic
Orientation/Navigation
G
Grraavviittaattiioonn
N
Nuucclleeaarr
M
Maassss
 = these forms of energy are relevant to most biological organisms;
 = these forms of energy play a role and are used by some organisms

all biological, including human life strictly depends upon the energy in the universe, of
which the solar light energy is the most important one
- light energy emitted by the sun (a form of electromagnetic radiation) is absorbed
by the chlorophyll molecules of photosynthetic organisms, such as green plants
and algae, and ultimately converted into other types of energy, most prominently
into the formation of new covalent bonds of sugar molecules during
photosynthesis (see Chapter 7)
- the importance of sugar molecules produced by agricultural plants for human
nutrition and food supply proves the prime importance of solar energy and
photosynthesis to human life on this planet
1
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.
The Rules of Thermodynamics or The Laws of Energy

In order to understand how the different forms of life on earth - as the most (and
currently only known) complex organized form of matter in the universe - are able to
use different forms of energy to sustain their amazing life processes, such as growth,
movement, flight, bioluminescent light generation and reproduction, it is important to
first understand the “true nature” of energy

Our scientific understanding of energy came a long way in human history and it’s
better understanding is associated with names of humankind’s brightest and most
ingenious scientists, such as Maxwell, Gibbs, Lorentz, Einstein, Planck, and many
others

Major contributions to our modern understanding of the “true nature” of energy have
been made by the field of thermodynamics, which is an important sub-discipline of
physics

Thermodynamics is the scientific study of energy transformation that occurs
between a defined collection of matter or a so-called system and its surroundings
 a system can be, e.g. a water turbine, the engine of a car
or the living cells of biological organisms

The field of thermodynamics lead to the discovery of two laws, the first and second
law of thermodynamics or laws of energy

What are the 2 laws of thermodynamics and what exactly do they say?
First law of energy (= law of the conservation of energy)
 it states, that energy can be changed (= transformed) from one form into another, but
it cannot be created or destroyed
 e.g. Pendulum experiment
 e.g. light emission in fire flies
 the total amount of energy and matter in the Universe remains constant, merely
changing from one form to another
S
Seeccoonndd llaaw
w ooff eenneerrggyy
 it states, that every system and its surroundings spontaneously tend toward a higher
degree of disorder (= entropy);
 one prominent form of disorder is heat (= thermal energy)
 it also states that any form of energy conversion reduces the order in the universe
and leads to an increase in disorder (= entropy), in many cases in form of released
thermal energy (= heat)
 in all energy exchanges, if no energy enters or leaves the system, the potential
energy of the state will always be less than that of the initial state
2
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.

biological organisms and its cells are so-called open systems, which strictly
underlay the 2 laws of thermodynamics
 open systems means that they exchange both matter and energy with its
surroundings; a living organism takes up matter in form of food, oxygen and water
and (after multiple transformations releases matter and energy in form of urea,
water, CO2 and heat
 they follow the first law of energy since they don’t create energy de-novo but rather
transform or convert pre-existing forms of energy into new forms of mostly
chemical energy
 the follow the second law of energy since the energy conversion processes in
living organisms do not occur with 100% efficiency
“Biological organisms as open systems with enormously complex carbon-based
structures obey the two laws of thermodynamics; they are not any different than any
other energy-converting open systems, such as machines and engines …”

living cells due to their permanent flow and conversions of energy and due to their
highly organized structures are in a thermodynamic sense open, low entropic
systems
“Living organisms are the strict opposite of disorder ..”

cells convert chemical energy (which is a form of potential energy), usually in the
from of carbon-carbon (C – C) covalent bonds (as in glucose or a fatty acid) or in the
form of phosphorus-oxygen (P – O) covalent bonds (as in phosphocreatine or the
ATP molecule), into kinetic energy to accomplish their life processes, e.g. cell
division, growth, biosynthesis, and active transport

chemical energy is recognizable (measurable) when molecules undergo energyreleasing reactions often indicated by the parallel release of heat energy
“Living organisms depend on a permanent flow of energy within their cells to
survive …”

this continuous flow of energy in living organisms assures the maintenance of the
highly organized structures, cellular order and the synchronization of life activities
 Entropy wins when organisms cease to take in energy and die

as a consequence of the permanent energy transformations, e.g. on our sun, in
biological organisms, and in our intensively used cars and machineries, the entropy in
the universe increases steadily
 consider this: a car turns about 75% of the chemical energy of the
molecules of gasoline into the unordered energy = heat; only 25% is transformed
in an ordered fashion into kinetic energy = driving force
3
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.

molecules in a living cell possess potential energy due to the arrangement of
their electrons in their covalent bonds
 this chemical energy is permanently transformed into other forms
of energy, which is in most cases chemical energy again
 in many cases it is transformed into mechanical or kinetic energy
e.g. swimming, running, flying, sliding, etc.
 in some cases it is transformed into light energy which can be seen as light
emission (= bioluminescence);
e.g. luminescent abdomen of fire-flies of the luminescent extensions of
deep-sea fish
 in some cases it is transformed into warmth/heat
e.g. in brown fat tissue of polar inhabitants
or in form of warm muscles after prolonged exercise

since cells and biological organisms create highly ordered (low entropic) structures
from less ordered starting material, they increase the entropy in their surrounding

the second law of thermodynamics also explains that energy transfers in a cell cannot
be 100% efficient; some energy retrieved from the chemical reactions always
escapes the cells as heat
- cells haven’t developed a mechanism to re-use this escaped heat energy for
biological work
- however, cells or tissues of certain organisms purposely uncouple the efficiency
of their chemical transformations to generate more heat (disordered energy)
instead of ordered chemical structures
 e.g. the brown fat tissue in human infants or in hibernating animals
ENERGY TRANSFER IN BIOLOGICAL SYSTEMS, FREE ENERGY COUPLING &
THE FUNDAMENTAL ROLE OF THE ATP MOLECULE TO LIFE

there is thousands of chemical reactions and energy conversions happening every
second in any cell of any form of life

during any chemical reaction, a starting molecule, called the rreeaaccttaanntt (R) is
converted into a structurally different molecule, called the pprroodduucctt (P)

if the product is not removed, the reaction reaches a so-called chemical equilibrium,
which is unique for each chemical reaction
- each chemical reaction (see Figure below) has a unique equilibrium constant
(Keq)
- the larger the number for Keq, the more the chemical reactions goes into the
direction of the chemical products and the more the equilibrium of that specific
chemical reaction will be on the side of the products (P)
4
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.
Reactants
Products
O
H3C – C
O
Keq
+
H3C – CH2 – OH
H3C – C – O – C2H5
(Ethanol)
(Acetic acid ethylester)
+ H2O
OH
(Acetic acid)
A

B
C
(Water)
D
the concentration of the reactants and the products in chemical equilibrium (at
standard conditions) can be calculated with the help of the equation (1) below
- the equation tells that a chemical reaction involving the molecules A and B is
more energetic (reactive), the more the chemical equilibrium concentrations is on
the side of the products C and D
c (C) x c (D)
c (A) x c (B)
= Keq
(1)
c = concentration of reactant or product
(in mole/l)
Keq = chemical equilibrium constant
“Chemical reaction partners with a large equilibrium constant Keq have a
high energy potential ΔG0”

the correlation between the difference in energy potential or change in free
energy of a chemical reaction and its chemical equilibrium constant is described
by following formula as shown below
ΔG0 = Gproducts - Greactants = - R T ln Keq
ΔG0 = Gibbs free energy difference
R = universal gas constant
T = temperature (in Kelvin)
Keq = chemical equilibrium constant
5
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.
“ A chemical mixture at equilibrium is in a state of minimal free energy and
no free energy is being generated or released;
in chemical equilibrium ΔG0 = 0 …”

generally, the formulas above help to predict the direction of a chemical reaction
(from left to right towards the products or in the opposite direction) and help to
calculate the amount of energy released alongside the chemical reaction

since biological systems, i.e. cells, are generally operating at constant temperature T
and pressure p, it is possible to use the considerations and deduced equations above
to predict the direction of chemical reactions
The term “free energy” as a measure for the amount of potential energy released along
side chemical reactions and to give a prediction for the direction of chemical reactions,
was introduced by the American biochemist Josiah Willard Gibbs (1839 – 1903), one of
the great pioneers of the science of thermodynamics (= science about the laws of
energy); in honor of him, the potential energy release connected to chemical reactions is
referred to as Gibbs free energy “G”

Gibbs stated that under constant pressure p and temperature T (a situation generally
found within living organisms), “all systems change in such a way that free energy is
minimized”. ( Gibbs’ law)

As we will see further below, at any constant temperature and pressure, two factors
determine the difference in energy potential or change in free energy ΔG0 of a
chemical reaction: enthalpy (or bond energy) and entropy (or the degree of
randomness or chaos of a system)
Types of chemical reactions

today, chemists divide chemical reactions into 2 major reaction types which both
occur and can be observed in a living cell:
11.. E
Ennddeerrggoonniicc reactions

are chemical reactions where the Gibb’s free energy of the products is larger than G
of the reactants (see Figure below); endergonic reactions require an energy input
into the system, in living organisms usually in form of sunlight or the chemical bond
energy of ATP
 the most important chemical reactions in biological organisms, e.g. :
1. the formation of polypeptides and proteins from amino acids
 a biochemical synthesis reaction which requires ATP
2. the build-up of the nucleic acids DNA and RNA from precursor
molecules (= nucleotides)
 a biochemical synthesis reaction which requires ATP
3. the build-up of fat from the precursor molecule acetyl-CoA
 another biochemical synthesis reaction which requires ATP
All of the above given examples are strict endergonic chemical reactions
6
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.

the rreeaaccttaannttss have less energy than the pprroodduucctt & extra energy must be supplied
from the surrounding

another important example of an endergonic chemical reaction is the biological
process called photosynthesis (see Chapter 7 for more detail), which builds up high
energy-containing glucose molecules from the simple precursor molecules carbon
dioxide (CO2) and water (H2O)
e.g. Photosynthesis
solar energy
+
6 CO2 + 6 H2O

C6H12O6 + 6 O2
(glucose)
rreeaaccttaannttss

pprroodduuccttss
Energy:
22.. E
Exxeerrggoonniicc reactions

are chemical reactions where the Gibbs free energy of the products is smaller than
the free energy of the reactants; endergonic reactions are accompanied with the
release or energy during the chemical process (see Figure below)

the rreeaaccttaannttss contain more potential (= chemical) energy than the pprroodduuccttss
 since the equilibrium constant for an exergonic reaction is greater than
1, the concentration of products is greater than the concentration of
reactants at equilibrium

e.g. Combustion
wood
or
gasoline
+ 6 O2
(cellulose)
(hydrocarbons)


6 CO2 + 6 H2O + energy

6 CO2 + 6 H2O + energy
e.g. Cellular respiration
C6H12O6 + 6 O2
(glucose)
rreeaaccttaannttss

pprroodduuccttss

when 1 mol (180 g) of glucose reacts with oxygen under standard conditions,
686 kcal of energy is released

if glucose is simply burned in air, all or most of this energy is released as heat

in the cell, however, this important exergonic chemical reaction is tightly
coupled to the synthesis of ATP from ADP (see:  free energy coupling in
cellular chemical reactions)
7
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.
Two types of chemical reaction profiles
Exergonic reaction
Endergonic reaction
E
N
E
R
G
Y
Activation
Energy EA
G
-
E
N
E
R
G
Y
+ ΔG0
Go
Time
Time
R
P
ΔG0
=
R
P
Gibbs’ free energy difference
Spontaneous and non-spontaneous chemical reactions & Gibbs’ free energy

chemical reactions rarely start or ignite suddenly, but rather have to be “jump-started”
by adding some form of “activation energy (EA)” (see Figure above), mostly in form
of heat, irradiation of pressure, to the reactants
- think of your car and the important role of the spark plugs in starting the
combustion reaction in the combustion chambers of your car’s engine
- your car wouldn’t go anywhere without that extra “energy push” given to the
gasoline (= the reactant) in your combustion chambers!
- think of the wax molecules of a candle which require the flame of a match to
trigger the combustion reactions which is accompanied (with the wished)
generation of light and heat of course ( second law of energy)

in order to become a new product, the molecules of the reactant have to overcome a
the so-called energy potential barrier to make the transition toward the new energy
state of the products of that chemical reaction

a very low energy barrier of a distinct chemical reaction favors a spontaneous
transition toward the new energy state; it favors a spontaneous chemical reaction

if the energy barrier of a chemical reaction is high, a transition event is unlikely; if the
reaction only occurs and proceeds under addition of external energy, e.g. heat,
pressure, light, etc., chemists speak of a non-spontaneous chemical reaction
8
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.

an example of a non-spontaneous, exergonic reaction is given below
C6H12O6 + 6 O2

6 CO2 + 6 H2O + eenneerrggyy
 in this chemical reaction 676 kcal/mole glucose of energy, mostly in form of heat,
is given off during this reaction
 the released heat energy (= free enthalpy) donates the further required activation
energy to keep the chemical reaction going until chemical equilibrium has been
reached
 it is a typical example of an exothermic reaction (= release of heat)

an example of a typical spontaneous, endergonic reaction is given below
2 N2O5
↑
Dinitrogen
pentoxide
+
eenneerrggyy

4 NO2 + O2
 dinitrogen pentoxide decomposes spontaneously under consumption of energy
and the chemical equilibrium is strongly located on the side of the products (= NO2
and O2)
 consequently, some other force other than the heat change ΔH connected to the
Breaking of bonds and the release of bond energy is driving this chemical
reaction;
 the other driving force is known in thermodynamics as entropy S
Definition: Entropy
Entropy is a measure of the degree of randomness or disorder (chaos) of a system;
entropy S increases as a system becomes more disordered and devreases as it
becomes more structured and organized
-
-
in our dinitrogen pentoxide example above, 2 molecules of reactant (= less
disordered state) are transformed into 5 molecules of products (= more disordered
or more chaotic state), which in total represents a higher magnitude of disorder or
a larger entropy S for this chemical reaction
this explains, why despite the fact that the chemical reaction above requires an
energy input (= endergonic reaction), its equilibrium is located on the side of the
products
C
Coonncclluussiioonn:: 22 m
maajjoorr ffoorrcceess aarree ddrriivviinngg cchheem
miiccaall rreeaaccttiioonnss
1. Difference in heat content or bond energy (= Δ
ΔH
H)
AND
2. Difference in disorder or Entropy (= Δ
ΔS
S)

chemists combine these two driving forces of chemical reactions in the concept of
Gibb’s Free Energy (G)
9
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.
“Thermodynamically seen, life is the opposite of chaos and all life forms due
to their highly structured components are “low-entropic systems”
Gibbs Free Energy

the Gibbs free energy G0 is a number which gives the intrinsic potential energy (in
kJ/mole) of a substance or a system

this information - experimentally retrieved from calorimetric measurements of
individual chemical reaction partners - is used to determine whether a certain
chemical reaction will occur spontaneously and in which direction the chemical
reaction will proceed

the change in Gibbs Free Energy between reactants and resulting products of a
distinct chemical reaction is represented by G0 and called Gibbs’ free energy
change

the G
Giibbbbss’’ ffrreeee eenneerrggyy cchhaannggee ((ΔΔG
G000)) is equal to the change in heat content or
enthalpy (ΔH) minus the entropy change (ΔS):
Δ
ΔG
G =Δ
ΔH
H – T xΔ
ΔS
S
 T= temperature in degrees Kelvin (= oK)
 enthalpy difference ΔH is the difference of the total bond energy of the
products minus the total bond energy of the reactants
“Chemical reactions tend to proceed towards their product side if they
liberate energy (= ΔH < 0) and if there is a strong increase in entropy S”

A reaction that gives off Gibb’s free energy is considered as exergonic (see left
panel of Figure above)
eexxeerrggoonniicc & spontaneous:
ΔG0 = minus (-)
 the sign of ΔG0 is negative

A reaction that consumes Gibb’s free energy is endergonic (see right panel of
Figure above)
eennddeerrggoonniicc & non-spontaneous: ΔG0 = plus (+)
 the sign of ΔG0 is positive

The introduction of the difference of Gibbs’ free energy gives the biochemist a clear
idea about the direction of a certain chemical reaction (from left to right or vice versa)
in even complex (biological) systems
10
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.
-
-

due to the fact that most chemical reactions in living organisms happen at
constant temperatures (especially in endothermic organisms, e.g. humans),
constant pressure (air pressure)
however, most chemical reactions – especially the ones in biological organisms
which take place in an aqueous environment – are affected by the pH of the
solution
The most commonly used measure is the standard Gibb’s free energy change
ΔGo’ of chemical reaction partners to estimate the direction of chemical reactions
under standard chemical conditions
Definition: Standard Gibb’s free energy change ΔGo’
The standard Gibb’s free energy change ΔGo’ of a chemical reaction is the value of the
change in free energy under the experimental conditions of 298 oK (25oC), 1 atm air
pressure, pH 7.0 and initial concentrations of 1M for all reactants and products
 concentration conditions, which are of course never fulfilled in a living system, e.g. an
average living cell
 the Table below gives values for the standard Gibb’s free energy changes G 0’ for
some cellular important chemical reactions
Examples of Standard Gibb’s Free Energy changes (G0’) of
endergonic and exergonic chemical reactions
INPUT
OUTPUT
non-spontaneous, endergonic
(1) Glutamic acid + NH3 + energy

Glutamine + H2O
ΔG
(Δ
G000’’ == ++ 33..44 kkccaall//m
moollee)
spontaneous, exergonic
(2) Glucose-6-PO4 + H2O

Glucose + PO4 + energy
ΔG
(Δ
G000’’ == -- 33..33 kkccaall//m
moollee)
spontaneous, exergonic
(3) ATP + H2O

ADP + PO4 + energy
ΔG
(Δ
G000’’ == -- 77..33 kkccaall//m
moollee)
11
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.
spontaneous, exergonic
(4) Glyceraldehyde 3-phosphate

Dihydroxyacetone phosphate +
energy
ΔG
(Δ
G000’’ == -- 11..8844 kkccaall//m
moollee)
Non-spontaneous, endergonic
(5) Malate
+
energy

Fumarate + H2O
ΔG
(Δ
G000’’ == ++ 00..7755 kkccaall//m
moollee)
spontaneous, exergonic
(6) Palmitic acid + 23 O2

16 CO2 + 16 H2O + energy
ΔG
(Δ
G000’’ == -- 22338888 kkccaall//m
moollee)
 the metabolic – highly exergonic - degradation of fatty acids (such as palmitic
acid) is a accompanied with a very high release of Gibbs’ free energy, which
explains the biological role of fatty acids as important energy storage
molecules in animals and in the human body
Free energy flow and free energy coupling in biological cells

There is millions of chemical reactions happening at any given time in living cells of
biological organisms; all of them with the desire to reach chemical equilibrium
where the chemical systems would reach a stable energy minimum – and (as we
learned in the previous sections above) the Gibbs’ free energy change would become
“zero”

But since chemical reactions in cells happen not solitary but rather are directly
connected with other chemical reactions via chemical “follow-up reaction” (=
reactions where a product of one chemical reaction immediately becomes the
reactant of a new chemical reaction and will be removed from the previous one),
chemical reactions in living systems never actually reach their chemical equilibrium

We rather see a permanent flow of energy along defined chemical reaction
pathways (for more detail on that look into Chapters 6 and 7), with permanent
changes in Gibbs’ free energies; in living systems ΔG0 is always < or > “zero”
“In living systems, chemical reactions are permanently away from their
chemical equilibrium which assures the permanent flow of energy which
assures the ongoing of the important processes of life…”
12
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.

Another important aspect to understand the energy-related processes in living
systems, e.g. a cell, is the concept of Gibbs’ free energy coupling

In order to assure the anabolic, endergonic build-up of new molecules, such as
proteins, nucleic acids, polysaccharides or fats, biological organisms couple
endergonic with exergonic chemical reactions
 these thermodynamic coupling reactions happen usually in the tight, “nanoenvironment” of the substrate binding – and active sites of enzymes or complex
enzyme systems within cells (see  enzymes)

Cells primarily rely on the highly exergonic reaction of a handful of molecules, such
as pyrophosphate, phosphocreatine and ATP, which they harbor in high
concentrations in the cytosol

But it is especially the ATP molecule which has the key position to be coupled to
endergonic reactions within cells (see section below for further detail); the conversion
of ATP to its hydrolysis product ADP by dephosphorylation of the terminal gammaphosphate (PO42-) is a highly exergonic chemical reaction; the exergonic reaction is
accompanied with the Gibbs’ free energy release of 7.3 kcal for each mole of ATP
hydrolyzed
(1)
ATP + H2O

ADP + PO4 + energy
ΔG
(Δ
G000’’ == -- 77..33)
ΔG
(2) Glutamic acid + NH3 + energy

Glutamine + H2O
(Δ
G000 == ++ 33..44)
---------------------------------------------------------------------------------------------Glutamic acid + NH3 + ATP

Glutamine + PO4+ ADP + energy
ΔG
(Δ
G000’’ == -- 33..99)
 due to the negative prefix of ΔG0’, the coupled reaction is ssppoonnttaanneeoouuss
and eexxeerrggoonniicc
 its chemical equilibrium is located on the product side
“Without ATP in living cells and its exergonic hydrolysis into ADP, anabolic
chemical reactions – which are endergonic reactions - would be
impossible..!”

One of the most commonly perceived experiences with exergonic chemical reactions
is the burning of materials, such as wood, oil, gasoline or gas; but burning or
combustion reactions is only one, very fast and uncontrolled, way to release the
intrinsic energy of chemical compounds, which happens in most cases, such as in the
interior spaces of combustion chambers (of cars or power plants) solely as heat and
light

in living organisms and within their cells, however, fed in nutritional molecules (which
are chemicals in the most general sense) are “burned” in a slow, step by step and
highly controlled way in a ‘biological burning process’, called cellular respiration
- as you will hear more in Chapter 6, cellular respiration is the gradual, step-bystep dismantling of food molecules by a series of exergonic and coupled
endergonic chemical reactions
13
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.

during this process, part of the energy released during the exergonic breakdown of
sugar molecules into water and CO2, is conserved into high-energy-containing
molecules

one of the most important molecules into which cells store chemical energy is ATP =
adenosine-triphosphate (see sections of this chapter further below for more details)
- other important “Gibbs’ free energy-storing” molecules are phosphocreatine
and phosphoenol pyruvate (PEP) which cells harbor in high, milli-molar
concentrations

every working cell simultaneously carries out thousands of endergonic and exergonic
chemical reactions; the sum of which is called cellular metabolism

with help of this cellular metabolism together with cellular respiration, living organisms
stay capable to keep all their vital functions running
e.g. eating, digesting, escaping predators, repair of damaged tissue or growing

all these biological activities require energy which is collected from exergonic
degradation of nutritional molecules, such as monosaccharides, amino acids or fatty
acids; part of the released (chemical) Gibbs’ free energy is conversed into the
synthesis of the most important molecule of biological systems; into Adenosine
Trisphosphate (= ATP)
Table: Examples of the Standard Gibb’s Free Energy differences (ΔG0’)
of some important biochemical reactions
Chemical reaction partners
Reactants
Products
Phosphoenol pyruvate
1,3Diphosphoglycerate
Pyruvate + PO423-Phosphoglycerate +
PO42Creatine + PO42
Acetate + Coenzyme A
PO42- + PO42ADP + + PO42Glucose + PO422 glucose
Alanine + Glycine
Glucose + PO42
2 glycine
Phosphocreatine
Acetyl-Coenzyme A
Pyrophosphate (PPi) + H2O
ATP + H2O
Glucose -1-PO4
Maltose + H2O
Alanylglycine
Glucose -6-PO4
Glycylglycine + H2O
Gibbs’ free energy
change (ΔG0’)
[kcal/mole]
- 14.8
- 11.8
- 10.3
- 8.4
- 8.0
- 7.3
- 5.0
- 4.0
- 4.0
- 3.3
- 2.2
 values determined at 25oC and at pH 7.0
14
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.
The ATP molecule

ATP (= Adenosine-Tris-Phosphate) is surely one of the most important molecules in
biological organisms, a statement which is supported by the fact that this high-energy
molecule is found in literally all forms of life on planet earth

this molecule, made up of adenine, ribose and three covalently linked phosphate
groups, is of crucial importance in all biological energy transfer and free energy
coupling reactions (see Figure below)
The chemical structure of Adenosine-Trisphosphate (= ATP)
A
Addeenniinnee
R
Riibboossee
γ
β
α

33 xx P
Phhoosspphhaatteess

during the diverse biological energy coupling reactions, the energy conserved in
the three high-energy phosphate groups of the ATP molecule is released after
exergonic cleavage of the last (or so-called gamma phosphate group) and used to
drive coupled endergonic synthesis reactions within the cell
- the gamma (= γ) phosphate cleavage (chemically a hydrolysis reaction) frees
up approx. 31 kJ/mol (or 7.3 kcal/mole) of usable Gibbs’ free energy under
standard conditions (see Graphic below)

Besides being of crucial importance for major free energy coupling reactions in
metabolic activities of living systems, ATP also plays a major role in a series of
other biological processes such as:
1. Regulation of enzyme and protein functions via an ATP-dependent process
called protein phosphorylation
2. Execution of muscle contraction in skeletal muscle fibers
3. Active transport of molecules across biological membrane
15
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.
The ATP molecule & Exergonic hydrolysis of the γ-phosphate
ΔG0’ = - 7.3 kcal/mole
γ-Phosphate
H
Adenosine Triphosphate
(ATP)
Pi
Adenosine Diphosphate
(ADP)
Phosphate

it is the chemical reaction of hydrolysis of the ATP molecule which powers almost
all forms of cellular work in living organisms, such as:
1. muscle contraction ( moving, flying, swimming, crawling)
2. light perception ( seeing)
3. neural activities ( thinking)
4. transport of nutrients ( food resorption)
5. or light generation ( fire fly bioluminescence)

the chemical structure of ATP shows three phosphate groups which each
contain a high amount of chemical reaction energy in their chemical bonds
 after cleavage of either one of these phosphate groups, the earlier conserved
energy gets released in an exergonic reaction

in cells, this exergonic ATP cleavage reaction is coupled with other endergonic
biological reactions in a so-called energy coupling reaction

Energy coupling reactions are the chemical driving force behind the many
metabolic activities of cells
 in Glycolysis, one of the most important biological metabolic reactions
(see Chapter 6 for more details), the exergonic energy released from the
breakdown of glucose molecules is transferred and stored in the high-energy
phosphate groups of ATP (see structural formula of ATP below)
 at other places in the cell, this ATP-conserved energy will be released again by
a chemical process called hydrolysis; it is especially the third, so-called
gamma-phosphate of the ATP which is usually hydrolyzed in this highly
exergonic reaction
16
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular & Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.

in a very special cellular process called protein phosphorylation, this gammaphosphate of ATP is transferred to certain amino acid residues of proteins, e.g.
serine or tyrosine; this phosphorylation event changes the 3D structure of the
affected protein which is usually accompanied with a change in protein function or
in case of an enzyme with a change in enzymatic activity (for more details see
Chapter: Cell Signaling);
e.g. phosphorylation of myosin protein in muscle cells during contraction
phosphorylation of so-called receptor kinases after binding of hormones or
growth factors

ATP is a renewable source of chemical energy, which cells can regenerate by two
major mechanisms:

the regeneration of “used” ATP within cells happens by two major processes:
1.
2.
through new synthesis starting from ADP in mitochondria via a process
called oxidative phosphorylation with help of an enzyme called ATP
synthase (see Chapter 6 for more details)
fast regeneration of ATP from ADP via free energy coupling with the
cellular high-energy molecules phosphocreatine and pyrophosphate
(PPi), which both are major chemical ‘reserve fuel’ molecules in many
cells (e.g. skeletal muscle cells)
“A working cell consumes and regenerates its entire pool of (~ 1mM) ATP
approximately once every minute!!”

another important chemical reaction where energy coupling plays a fundamental
role are the so-called reduction/oxidation reactions, which we will look up and
discuss in more detail in the next chapter
Reduction-Oxidation (= Redox) reactions

as you read earlier, there is millions of chemical reactions happening at any given
time in living cells of biological organisms, which are essentially energy transfers

many of these chemical reactions result in the transfer of moved electrons from
one atom or molecule to another
- in most studied cases these electron transfer reactions are accompanied with
the formation of new chemical bonds

the most important chemical reactions in living organisms are so-called rreedductionooxxidation reaction or also short redox reactions!

during redox reactions, outer shell electrons of atoms or of functional groups of
certain molecules are moved from one molecule to another
17
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular & Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.
1. Removal of an electron (= e¯) from an atom or molecule is defined as an
oxidation reaction
- Dehydrogenation (= removal of a hydrogen atom) is also an oxidation
reaction, since during the transfer of a hydrogen atom one electron is
removed from the reactant
- An example of a typical oxidation reaction is the conversion of lactic acid
into pyruvate, a reaction which is accompanied by the loss of two electrons
and two hydrogen ions H+ (= protons)
The dehydrogenation of lactic acid to pyruvate
 a typical oxidation reaction
“Dehydrogenation”
 oxidation
OH
O
C – C – CH3
HO
O
O
C – C – CH3
HO
H
Pyruvic Acid
Lactic Acid
H+
2
2 e-
2. Addition of an electron (= e¯) is a rreedduuccttiioonn reaction
- Hydrogenation (= addition of a hydrogen atom) is also a reduction reaction,
since during the transfer of a hydrogen atom one electron is added to the
chemical reactant
- An example of a typical reduction reaction is the conversion of the 4-carbon
molecule fumarate into succinate, a reaction which is accompanied by the
gain of two electrons and two hydrogen ions H+ (= protons) by fumarate
- We will encounter this important reduction reaction in Chapter 6 again,
when we look up the individual chemical reactions of the Krebs cycle
The hydrogenation of fumarate to succinate
 a typical reduction reaction
2H
2 eH
H
COOH
C
HOOC – C – C – COOH
C
HOOC
H
Fumarate
H
“Hydrogenation”
 reduction
H
H
Succinate
18
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular & Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.

in reduction/oxidation or redox reactions, one molecule is oxidized, and its
electrons are passed on to another (usually neighboring) molecule, which becomes
reduced (see Figure below)
The principle of redox reactions

Redox reactions play a major role in the most significant chemical reaction
pathways and processes in living organisms, such as in photosynthesis, during
glycolysis, in the Krebs cycle and in the mitochondrial electron transport chain
 e.g. glucose gets dismantled to CO2 and water during cellular respiration in a
series of sequential, step-by-step redox reactions
 in the Krebs cycle, the molecule succinate is oxidized to fumarate under release
of two electrons (and two protons)
19
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular & Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.
Conversion of succinate into fumarate
(Krebs cycle, Mitochondrion)

the energy of the moved electrons is trapped and rearranged in a series of
important biological compounds, such as NAD+ or FAD+ (see Chapter 6 for more
detail)

the release of electrons from a molecule is commonly called oxidation; the
molecule which donates these electron during the chemical reaction is called an
electron donor

conversely, the reception of electrons during a redox reaction is called reduction;
the molecules which receives the electrons is called the electron acceptor

electron transfer during redox reactions requires both a donor (= electron spender)
and an electron acceptor; in living systems, such as a cell, redox reactions are
always tightly coupled together
- during degradation of glucose it loses its electrons in form of hydrogen (H)atoms during a series of dehydrogenation reactions, while molecular oxygen
(O2) gains electrons (again in form of H-atoms!);
- we say: glucose becomes oxidized, while O2 is reduced to water!
- at this point it may be easier to understand now when we always spoke about
burning of glucose during cellular metabolism; since burning (on a molecular
level) is nothing else than oxidation of a compound!

in biological systems the electrons are almost always moved in connection with a
transfer of H-atoms from the involved molecules to three crucial cellular redox
molecules, which (in abbreviated form) are called NAD+, NADP+ or FAD+ molecules, which we will study in more detail in the following chapter
NAD+
NADP+
FAD
=
=
=
Nicotineamide Dinucleotide
Nicotineamide Dinucleotide Phosphate
Flavinadenine Dinucleotide
20
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular & Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.

all three molecules, which cells stock-pile in high (milli-molar) concentrations,
undergo typical redox reactions involving 2 electrons and 2 protons; the abstraction
or dissociation of the electrons and protons during the redox reactions occurs at a
defined functional region – the nicotinamide part - of the molecules (for redox
reactions and chemical structures  see Figure below)
Redox reactions of the Dinucleotides NAD+, NADP+ & FAD



NAD+ + 2e¯ + 2 H+
NADP+ + 2e¯ + 2 H+
FAD + 2e¯ + 2 H+



NADH + H+ (NADH2)
NADPH + H+ (NADPH2)
FADH2
Chemical structures & Redox reactions
of NAD+ or NADP+
-
-
as you can see in the chemical structures of NAD+ and NADP+, the only
structural difference between both redox molecules is the presence of a
phosphate (= P) group at the adenosine group in NADP+
despite this minor structural difference, both molecules have completely
different roles in the cellular metabolic activities
NAD+ is involved in dehydrogenation reactions of catabolic chemical reactions,
while NADP+ is crucial in cellular anabolic chemical reactions
21
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular & Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.
Chemical structure & Redox reactions of the FAD molecule
FAD
(oxidized form)
2 e- + 2 H+
FADH2
(reduced form)

in biological systems, the removal of H-atoms from molecules (= dehydrogenation)
during metabolic activities is accelerated (= catalyzed) by special class of proteins
called dehydrogenases, most of which are in close association with the redox
molecules NAD+, NADP+ or FAD (see Figure below)
- a protein with the capability to accelerate a certain chemical reaction is also
called an enzyme; we will here about enzymes in more detail in the last section
of this Chapter

Dehydrogenases transfer H-atoms with the help of the molecule NAD+ or FAD,
which are closely attached to the protein; NAD+ and FAD are then referred to as
the prosthetic group or the co-enzyme of that specific dehydrogenase
- the Graphic below shows the enzyme isocitrate dehydrogenase (IDH) with its
tightly associated co-enzyme NAD+, which is actively involved in the redox
reaction catalyzed by the IDH enzyme
- many enzymes are known to work or to be enzymatically active only in
combination with their co-enzymes
- other important co-enzymes of enzymes are molecules belonging to the vitamin
class, such vitamin B12 , biotin or folic acid
22
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular & Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.
The position of the associated coenzyme NAD+ in the active site pocket of the
enzyme isocitrate dehydrogenase (IDH)
Blue
Red
=
=
Structure of IDH enzyme
Location of NAD+ molecule

the NAD+ molecule within the dehydrogenase complex is the part of the enzyme
which actually shuttles the electrons during the catalyzed redox reaction
 e.g. during several steps along glycolysis, NAD+ receives two hydrogen atoms
(= including 2 electrons!) from glucose and becomes reduced to NADH + H+;
glucose loses two electrons contained in the two H-atoms and is oxidized!
(for more detail  see Chapter 6)

in the course of this coupled redox process, NAD+ is loaded with energy; NADH +
H+ carries this chemical energy over to specialized proteins located in the inner
mitochondrial membrane

the tightly packed proteins in the mitochondrial membrane are also called electron
carrier proteins; they form a so-called electron transport chain
 one example of these proteins is cytochrome c reductase

at the electron transport chain, NADH + H+ gives up its bound H-atoms (and
electrons!) and regenerates to NAD+ again, while the first electron carrier protein
of the electron transport chain receives the liberated electrons
 members of the electron transport chain are enzymes which all have specific
so-called prosthetic groups (= co-enzymes), each with a slightly higher affinity
for electrons than the uphill neighbor
23
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular & Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.

therefore the released electrons from NADH + H+ begin a journey along a socalled electron cascade, while the H+ ions (= protons) are left behind and shuttled
through the membrane into the mitochondrial matrix
 this separation of H+-ions from the electrons along this cascade and its
accumulation in the mitochondrial matrix is of crucial importance for the
cellular synthesis of ATP (see Chapter 6)

at the end of this enzyme-bound electron cascade, the electrons are transferred in
a final redox reaction of cellular respiration over to molecular oxygen (= O2),
which is the final electron acceptor
 O2 gets reduced to water
2 e- + 2 H+ +
½ O2

H2O

in summary, the many redox-steps along the breakdown (= oxidation) of glucose to
CO2 and H2O release energy in amounts small enough to be utilizable by the cell;
most of this energy is used to build up a gradient of H+-ions along the
mitochondrial membrane for ATP synthesis
 if oxygen would be reduced all at one step with hydrogen, a chemical
explosion would occur and the released energy in form of heat and light
could not be used by the cell!

Besides the just introduced cellular redox molecules NAD+, NADP+ and FAD,
there is a series of other important cellular molecules which play crucial roles
in redox processes occurring within cells; these molecules are:
1. Ubiquinones (e.g. Q10)
- important redox molecule of the electron transport chain (ETC) located in the
inner mitochondrial membrane (for chemical structure and redox reactions see
Figure below)
- ubiquinones are found in high concentrations in the phospholipid environment
of bacterial and mitochondrial membranes where they easily embed
themselves due to the highly lipophilic isoprenoid chain which is crucial part of
this class of redox molecules
- it is a crucial and highly mobile carrier molecule which operates within the
phospholipid bilayer membrane of the inner mitochondrial membrane
- it serves as a “molecular shuttle or carrier molecule” for 2 electrons and 2
hydrogen ions between other protein components (complex I and II) of the
mitochondrial electron transport chain (ETC) (see Chapter 6 for more detail)
2. Plastoquinones (PQs)
- plastoquinones are an important class of redox molecules which are found in
high concentrations in the thylacoid membranes of the chloroplasts of plants
(for chemical structure and redox reaction see Figure below)
- they play a crucial role as molecular redox components of the electron
transport chain (ETC) which is operating between the light-harvesting
complexes (LHCs) or photosystems of these fascinating plant organelles
(for more detail see Chapter 7)
24
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular & Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.
The Co-enzyme Q (Ubichinone) molecule & Cellular redox reactions
2 e- + 2 H+
Isoprenoid chain
– OH
H
HO –
Co-enzyme Q10
Co-enzyme Q10
(oxidized form)
(reduced form)
CoQ
CoQH2
The plastoquinone molecule (PQ-9) & Cellular redox reactions
2 e2 H+
OH
OH
Plastoquinone (PQ)
 redox molecule of thylacoid membranes
25
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular & Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.
3. Cytochromes
-
Cytochromes are a unique class of redox active proteins, which have ironcontaining heme groups as redox active centers embedded into their protein
structure
- It is the complexed iron of the heme group which undergoes the important oneelectron redox reactions of this important class of redox proteins (see Figure
below)
- Prominent examples of cytochromes are:
Cytochrome c
=
important redox protein of the mitochondrial
Electron transport chain
Cytochrome b/f
=
important redox protein of the thylacoid
electron transport chain which links
the two photosystems within the chloroplast
4. Iron-sulfur proteins
-
-
Iron-sulfur proteins are proteins which show characteristic iron-sulfur
complexes as part of their protein structure (see Figure below)
It is the iron of this class of proteins, which is responsible for the one electron
redox reactions these proteins perform as part of catalytic activities
Iron is complexed with the help of the negative charges of the sulfhydryl groups
of critical cysteine residues (= Cys-SH) located within the active centers of
these proteins (see Figure below)
Iron sulfur proteins play crucial roles as components of electron transport
chains in animals and plants; they also have been isolated from different
bacteria, where they are important for metabolic activities
26
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular & Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.
Heme group of cytochromes with complexed redox active iron
Fe3+
Fe2+
oxidized form
reduced form
1 eIron
Porphyrine ring
27
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular & Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.
Iron Sulfur (Fe-S) proteins & Cellular redox reactions
1 e-
Redox reaction
of iron
Cys
Cys
S
S
Fe
FeII
FeIII
Cys – S
Fe
S
S
S
Fe
S
Cys
S
Cys
Fe
Fe
S
S
S – Cys
Fe
S
Cys – S
Graphics©E.Schmid/2003
Protein
[ 2Fe + 2S ] Center of
Iron-Sulfur protein
 enzymes of the ETC
 Nitrite reductase
Protein
[ 4Fe + 4S ] Center of
Iron-Sulfur protein
 e.g. bacterial enzymes
4. Glutathione
-
-
-
this molecule is the co-substrate of many enzymes involved in cellular
detoxification and protection mechanisms
 e.g. glutathione peroxidase, glutathione transferase
it is a so-called tri-peptide, which is made up from the three amino acids
glutamic acid, cysteine and glycine; it is the cysteine with (in its reduced form)
characteristic sulfhydryl- (SH-) group, which is involved in the reversible redox
reactions (see Figure below)
reduced glutathione is abbreviated GSH, where the “SH” stands for the critical
cysteine-SH group of this redox molecule
this functional SH-group (like with NAD+/NADH + H+) can easily donate or
accept electrons, depending on the cellular pH and environment
in the case of a high demand of free electrons in the cell, e.g. to combat
invaded or generated so-called free radicals, reduced glutathione (= GSH)
becomes oxidized and forms a so-called disulphide bridge between two
molecules of glutathione to become the oxidized version of glutathione (=
GSSG) (see Figure below)
28
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular & Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.
The redox reaction of the cellular antioxidant glutathione
2 e- + 2 H+
Glutamate
2x
Glu
Cysteine
Glycine
Cys
Gly
Glu
Gly
S
S
SH
Glu
GSH
Cys
-
Cys
Gly
+
2e +2H
Reduced glutathione
GSSG
Graphic©E.Schmid/2004
Oxidized glutathione
Definition: Free radical & Oxidation
A free radical is any molecule which has one unpaired electron in its outermost
electron shell; this unpaired electron is responsible for the strong tendency of these
chemical enitites to strongly oxidize other molecules in their immediate surroundings
and to initiate so-called oxidative chain reactions in cells; the oxidative chain reactions
initiated by free radicals (if unprotected) lead to the destruction of cellular structures
-
the glutathione redox system plays an important role in the cellular defense and
protection from free radicals generating molecules or factors, such as in
cigarette smoke, generated after irradiation (X-rays) or after intensive sun
exposure
6. Antioxidants
-
-
-
-
-
Antioxidants is a class of molecules which are able to reversibly take up
(abstract) single electrons (free radicals) in typical one electron redox
reactions
Cellular antioxidants, such as vitamin C (ascorbic acid) or vitamin E
(tocopherols) play a major role in the protection of cellular structures, such as
protein, lipids or DNA, from free radical attack and modification
The chemical structures and redox transitions for ascorbic acid and tocopherol
are shown in the two Figures below
 the redox active functional (hydroxyl) group which is the site of attack of free
radicals is indicated by the purple circle in both molecules
Due to the long isoprenoid tail, the tocopherols are potent lipophilic antioxidants
which are primarily found in the lipophilic environment of the cellular
phospholipid bilayer membranes
The tocopherols protect the cells from oxidative damage of cell membranes,
e.g. lipid peroxidation, caused by free radicals, UV irradiation, etc.
29
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular & Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.
-
-
L-ascorbic acid (= vitamin C) is a highly water soluble (= hydrophilic)
antioxidant which occurs in high (milli-molar) concentrations within cells
 ascorbic acid concentrations are especially high in the inner liquid area of
the human eye, where it protects the eye structures from (UV) light-induced
oxidative damage
 in the presence of free iron in can function as a pro-oxidant and lead to
generation of free radicals
Ascorbic acid is a strong scavenger of free radicals, especially the oxygenderived free radicals OH. and O2-., of aqueous cellular environments, e.g. the
cytosol
Chemical structure & Redox reaction of the lipophilic antioxidant vitamin E
Chromane ring
Phospholipid
bilayer
Isoprenoid tail
CH3
HO
CH3
H3C
reduced
O CH
3
CH3
CH3
CH3
α-Tocopherol
CH3
(= Vitamin E)
H2O
Free radicals
( R. )n
-
2 e- + 2 H+
+
2e +2H
OH
CH3
O
C16H33
CH3
R–H
neutralized
H3C
O
CH3
oxidized form
α-Tocopherylquinone
Graphic©E.Schmid/2004
30
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular & Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.
Chemical structure of the antioxidant L-ascorbic acid
H2C – OH
Cytosol
HC – OH
O
O
L-Ascorbic Acid
(= Vitamin C)
HO
OH
reduced form
Graphic©E.Schmid/2004
2 e- + 2 H+
2 e- + 2 H+
H2C – OH
HC – OH
O
O
O
O
oxidized form
L-DehydroAscorbic Acid

in the context of reduction-oxidation reactions in the cell we heard about biological
molecules, such as NAD, FAD, biotin, GSH, which are essential parts (as
prosthetic groups or co-substrates) of specific proteins, called enzymes

in the very last section of this Chapter we want to have a little closer look at this
tremendously important class of proteins.
31
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular & Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.
Redox reactions & Standard redox potential

To get a better overview and a better description of the events of reductionoxidation (redox) reactions, an easy approach is to divide the them into two
separate half reactions, as shown for the reaction of ferrous iron (Fe 2+) and oxygen
(O2) in the Equation below
- this redox reaction is of prime importance to all forms of aerobic life since it is
the crucial terminal chemical reaction of the mitochondrial electron transport
chain (see Chapter 6 for more details)
2 Fe2+
2 e- + ½ O2


(1) Oxidation
(2) Reduction
H2O
(3)
Adding two protons to each side of equation (2), the complete redox reaction for
the reduction of oxygen can be written out as shown in equation (4)
2 e- + ½ O2 + 2 H+

2 Fe3+ + 2 eO2-
In this case, the reduced oxygen O2- readily reacts with two protons (H+) to form
one molecule of water (H2O), as written out below
2 H+ + O2-




H2O
(4)
The readiness with which a certain atom or molecule gains an electron (reduction)
or gives it off (oxidation) is given by chemists with a number; the reduction
potential E
Definition: Reduction potential
The reduction potential E is a quantitative measure for the tendency of elements or
molecules to give off electrons. Reduction potentials of redox active reaction partners
(for examples see Table below) are measured with the help of a platinum electrode in
volts (V) from an arbitrary zero-point set at the known reduction potential of the
reduction of hydrogen under standard conditions (25oC, 1atm, reactants at 1M
concentrations).
H+ + e

½ H2
The measurement and knowledge of the reduction potentials for different redox
partners helps the chemist and (more importantly in our field) the biochemist to
give a prediction to the direction of flow of electrons within complex
systems, such as a biological cell, where there is more than only two redox
partners present
- as you will hear more in Chapter 6, the directed flow of electrons between a
series of interconnected cellular redox partners is of prime importance for the
understanding of the molecular events at the mitochondrial electron transport
chain
32
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular & Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.
“The redox potential dictates the direction of flow of electrons and is one
of the major driving forces of life…”

The value of E for a molecule or an atom under standard lab conditions is called
the standard reduction potential E0 , and these tabulated (see Table below)

To calculate the reduction potential for chemical reaction partners which are not
adjusted to 1M standard concentrations, biochemists use the so-called “Nernstequation” (see Figure below), to calculate the standard reduction potentials E at
different concentrations c1 and c2 of the redox partners
- within the Nernst equation several important natural constants are considered:
R
=
universal gas constant
F
=
Faraday constant
T
=
absolute temperature (in 0K)
n
=
number of electrons transferred

The experimentally determined ( platinum electrode) standard reduction
potentials E0 also differ significantly from the “true” reduction potentials E0’ found
under the “physiological” conditions within a cell for biologically relevant redox
partners (see Graphic below)
- the standard reduction potentials usually differ from the “true” reduction
potentials being valid within cells due to the fact that the cell interior is a
complex environment with significant differences in pH, salinity and
temperature to the standard platinum electrode system
- keep in mind that the standard reduction potential E0 is determined at the
platinum electrode with 1M concentration of each redox partner, a condition
which is certainly not fulfilled within a cell, where concentrations of molecules
are in the lower milli-molar range!

In order to calculate the “true” reduction potential or redox potential E’ for two
redox partners with concentrations cox for the ixidant and cred for the reductant
within a living system, biochemist use the formula as shown in the Graphic below,
an equation which is derived from the Nernst equation

A reduction potential E can have either a positive (+) or a negative (-) value:
- a negative reduction potential means that a molecule, for example acetate (CH 3
– COO-) in its reduction to acetaldehyde (CH3 – CHO), has a lower affinity for
electrons
- this means that in a system with different redox partners each with different
reduction potentials, consequently, there is a directed flow of electrons in
certain direction dictated by the involved redox partners
“In reduction-oxidation (redox) reactions, electrons move spontaneously
toward atoms or molecules having a more positive reduction potential…!”
33
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
Intro Molecular & Cell Biology (BIO 210): Instructor: Elmar Schmid, Ph.D.

In the Graphic below, the spontaneous electron flow (see green dashed arrow)
between the depicted redox partners (purple colored text) goes from the
NAD+/NADH + H+ redox partner system (E0’ = - 0.32 V), via FAD/FADH2 and
various iron-containing cytochromes (Cyt b, c and a), down to molecular oxygen
(O2) with its very positive reduction potential of + 0.82 volts
The scales of the “true” and standard reduction potential
Platinum
Electrode
H 2 ↔ 2 H + + 2 e-
(25oC, pH 0; pH2 = 1.013 bar) E0 = 0
at E0: cox = cred
Standard Redox Potential
E ’0
H2
NAD/NADH+H+
Lactate
At physiological pH
(pH = 7.0, 30oC)
In biological systems
FAD/FADH2
E0 (Volt)
- 0.4
- 0.2
n
Cyt. b
Cyt. c
Cyt. a
6
lg
5
4
3
2
1
Pt/H2Electrode
- 0.08
+ 0.2
+ 0.27
+ 0.29
“Nernst Equation”
cox
E = E0 +
cred
O2

pH
- 0.08
“True Redox Potential”
0.06
- 0.2
0.0
Flow of
electrons e-
E’ = E0’ +
- 0.4
- 0.32
+ 0.81
RxT
nxF
ln
+ 0.4
c1
c2
Graphics©E.Schmid/2003
+ 0.6
+ 0.8
With this important background information about types of energy, types of
chemical reactions, redox reactions and the flow of electrons between redox
partners, we should be ample prepared to better understand and appreciate the
enormously complex and fascinating chemistry behind important cellular metabolic
activities, such as glycolysis, Krebs cycle, electron transport chain and
photosynthesis, which we look up in the two following chapters (Chapters 6 and 7)
34