Download Chapter 5 - San Diego Mesa College

SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): 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. But what exactly is energy and what type of energy are we talking about?
Since life forms do not operate with batteries to supply the necessary life energy,
which energy is keeping the different forms of life going and alive?
Definition: Energy
 Energy is per definition the ability to perfom 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 interconvertable

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
maall eenneerrggyy
Body temperature
E
l
e
c
t
r
o
m
a
g
n
e
t
i
c
(
=
l
i
g
h
t
)
Electromagnetic (= light)
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. Solar energy is utilized by
photosynthesizing life forms, such as green plants and algae, to produce complex
high energy carbon molecules, such as glucose and sucrose. Since the carbon
molecules are taking up by all heterotrophic life forms, including fungi, animals and
humans, as part of their food, literally all life on planet earth is dependent on the sun’s
abundantly emitted solar energy.
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
The Rules of Thermodynamics or The Laws of Energy

In order to understand how the different forms of life - as the truly most 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, to movement, to flight and
reproduction, it is important to first understand the nature of energy

Our scientific understanding of energy came a long way and major contributions to
our modern understanding 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
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): 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 are due to their permanent flow and conversions of energy and due to
their highly organized structures in a thermodynamic sense open, low entropic
systems. Open means that they permanently take up some for of energy. Low
entropic means that parts of the taken up energy is used to create highly ordered (low
entropy) structures.

To perform their many tasks, cells require transfusions of energy from outside
sources. In most ecosystems, energy enters as sunlight. Light energy trapped in
organic molecules is available to both photosynthetic organisms and others that eat
them.
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
“Living organisms are the strict opposite of disorder ..”

Cells convert chemical energy (which is a form of potential energy), usually stored in
the form 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 the ATP molecule), into
kinetic energy to accomplish their life processes, e.g. cell division, growth,
biosynthesis, and active transport. This flow of energy maintains the organized
structures, order and the 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
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
in an ordered fashion into kinetic energy = driving force

Organic molecules existing in or being taken up by a living cell possess potential
energy due to the arrangement of their electrons in their chemical bonds. Organic
molecules store energy in their arrangement of atoms. This chemical energy is
permanently transformed into other forms of energy. Enzymes catalyze the
systematic degradation of organic molecules that are rich in energy to simpler waste
products with less energy. Some of the released energy is in most cases stored in
other forms of chemical energy again (mostly in form of ATP), used to do work and
the rest is dissipated as heat.
- 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 (= bioluminsecence); e.g. in the bioluminescent abdomen of fire-flies
or 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 structures from less
ordered starting material, they increase the entropy in their surrounding

In living systems, energy stored in organic molecules is released in a step-wise
fashion along so-called metabolic pathways. The release of the energy stored in
complex organic molecules is called catabolic. One type of catabolic process,
fermentation, which leads to the partial degradation of sugars in the absence of
oxygen. A more efficient and widespread catabolic process, cellular respiration,
uses oxygen as a reactant to complete the breakdown of a variety of organic
molecules.
- Most of the processes in cellular respiration occur in mitochondria.

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 in form of disordered energy, of which heat is the most common
one.
 cells haven’t developed a mechanism to re-use this escaped heat energy for
biological work.
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
4.2. 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, is converted into a structurally different molecule,
called the pprroodduucctt

If the product is not removed, the reaction reaches a so-called equilibrium, which is
unique for each chemical reaction. Each chemical reaction has an equilibrium
constant (Keq).

Chemists divide chemical reactions into 2 major reaction types which both occur
and can be observed in a living cell:
11.. E
Ennddeerrggoonniicc reactions

These are chemical reactions where the energy content (Gibbs Free Energy) of the
products is higher than the energy content of the reactants. They also require
energy to be added to the reactions to start them and to keep them going. The most
important endergonic chemical reactions in biological organisms are:
1. the formation of polypeptides and proteins from amino acids
2. the build-up of the nucleic acids DNA and RNA from precursor
molecules (= nucleotides), and
3. the build-up of fat from the precursor molecule acetyl-CoA

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, which builds up high energy-containing glucose
molecules from the simple precursor molecules carbon dioxide (CO2) and water
(H2O)
e.g. Photosynthesis
solar energy
Energy:
+
6 CO2 + 6 H2O

C6H12O6 + 6 O2
(glucose)
rreeaaccttaannttss

pprroodduuccttss
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
22.. E
Exxeerrggoonniicc reactions

These are generally chemical reaction which release energy during the chemical
process. 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

Important examples of exergonic chemical reactions are:
e.g. Combustion
wood
or
(cellulose)
gasoline
+ 6 O2

6 CO2 + 6 H2O + energy
(hydrocarbons)
e.g. Cellular Respiration
- Cellular respiration is similar to the combustion of gasoline in an automobile engine.
- The overall process is:
Organic compounds + O2 -> CO2 + H2O + energy
- Carbohydrates, fats, and proteins can all be used as the fuel, but it is traditional to
start learning with glucose.
C6H12O6 + 6 O2

6 CO2 + 6 H2O + energy
(glucose)
rreeaaccttaannttss

pprroodduuccttss

If 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, e.g. in a calorimeter, 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)

Unlike the explosive release of heat energy that would occur when H 2 and O2
combine, cellular respiration uses several small metabolic steps and an electron
transport chain to break the fall of electrons to O2 into several steps.
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
E
Enneerrggyy pprrooffiillee ooff cchheem
miiccaall rreeaaccttiioonnss
eexxeerrggoonniicc
eennddeerrggoonniicc
Energy Barrier
Energy Barrier

R
Reeaaccttaanntt

P
Prroodduucctt
R
Reeaaccttaanntt
P
Prroodduucctt
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
S
Sppoonnttaanneeoouuss aanndd nnoonn--ssppoonnttaanneeoouuss cchheem
miiccaall rreeaaccttiioonnss

Chemical reactions rarely start or ignite suddenly, but rather have to be “jumpstarted” by adding some form of “activation energy”, mostly in form of heat, 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!

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
Non-spontaneous, exergonic reaction
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)
Spontaneous, endergonic reaction
2 N2O5
+ eenneerrggyy 
4 NO2 + O2
 Dinitrogen pentoxide decomposes spontaneously under consumption of energy
 ergo: something other than the heat change is driving this chemical reaction; the
other driving force is known in thermodynamics as Entropy (degree of disorder)
 2 molecules of reactant (less disordered state) are transformed into 5 molecules of
product (more disordered state), which in total represents a higher magnitude of
disorder
C
Coonncclluussiioonn:: 22 m
maajjoorr ffoorrcceess aarree ddrriivviinngg cchheem
miiccaall rreeaaccttiioonnss
1. Difference in heat content (= Δ
ΔH
H)
2. Difference in disorder or Entropy (= Δ
ΔS
S)
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.

Chemists combine these two driving forces of chemical reactions in the concept of
Gibbs Free Energy (G)
G
Giibbbbss FFrreeee E
Enneerrggyy

the Gibbs free energy 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
reaction partners is used to determine whether a certain chemical reaction will occur
spontaneously

the change in Gibbs Free Energy between reactants and resulting products of a
distinct chemical reaction is represented by G and called free energy change

the ffrreeee eenneerrggyy cchhaannggee ((ΔΔG
G)) 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)

A reaction that gives off Gibbs free energy is considered as exergonic:
eexxeerrggoonniicc & spontaneous:
ΔG = minus (-)
 the sign of ΔG is negative

A reaction that consumes Gibbs free energy is referred to as endergonic:
eennddeerrggoonniicc & non-spontaneous: ΔG = plus (+)
 the sign of ΔG is positive
E
Exxaam
mpplleess ooff G
Giibbbbss FFrreeee E
Enneerrggyy cchhaannggeess ((G
G)) ooff
eennddeerrggoonniicc aanndd eexxeerrggoonniicc cchheem
miiccaall rreeaaccttiioonnss
INPUT
OUTPUT
non-spontaneous, endergonic
(1) Glutamic acid + NH3 + energy

Glutamine + H2O
ΔG
(Δ
G == ++ 33..44 kkccaall//m
moollee)
10
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
spontaneous, exergonic

(2) Glucose-6-PO4 + H2O
Glucose + PO4 + energy
ΔG
(Δ
G == -- 33..33 kkccaall//m
moollee)
spontaneous, exergonic

(3) ATP + H2O
ADP + PO4 + energy
ΔG
(Δ
G == -- 77..33 kkccaall//m
moollee)
FFrreeee eenneerrggyy ccoouupplliinngg iinn bbiioollooggiiccaall cceellllss

(1)
biological organisms couple endergonic with exergonic chemical reactions with
the help of the energy-rich ATP molecule
ATP + H2O

ADP + PO4 + energy
ΔG
(Δ
G == -- 77..33)
ΔG
(2) Glutamic acid + NH3 + energy

Glutamine + H2O
(Δ
G == ++ 33..44)
---------------------------------------------------------------------------------------------Glutamic acid + NH3 + ATP

Glutamine + PO4+ ADP + energy
ΔG
(Δ
G == -- 33..99)
 the coupled reaction is ssppoonnttaanneeoouuss and eexxeerrggoonniicc !

burning is only one, very fast and uncontrolled, way to release energy (solely as heat
and light) from chemical compounds

in living organisms and cells, chemicals are burned in a slow, step by step and highly
controlled way in a ‘biological burning process’, called cellular respiration

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 part 3 of this UNIT for more details)

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
11
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
Role of the ATP molecule in cellular energetics

All biological activities, such as muscle contraction, ion transport across cell
membranes, or glucose uptake into cells, require energy which is collected from the
exergonic degradation of nutritional sugar or other food sources. Part of the released
(chemical) energy is conversed into the synthesis of the most important molecule of
biological systems, into Adenosine Triphosphate (= ATP)

ATP, adenosine triphosphate, is the pivotal molecule in cellular energetics, because
in donates chemical (Gibbs free) energy to endergonic chemical reactions to allow
them to proceed. The ATP molecule is the chemical equivalent of a loaded spring.

The close packing of three negatively-charged phosphate groups is an unstable,
energy-storing arrangement. Loss of the end (or gamma) phosphate group “relaxes”
the “spring”. Whenever, the gamma phosphate of ATP is hydrolyzed to form ADP, 7.3
kcal or energy is released for every mol (see Table below)
Table: Examples of the Standard Free Energy (G)
of different biomolecules
Phosphoenolpyruvate
1,3Diphosphoglycerate
ATP
Glucose -1-PO4
Glucose -6-PO4
14.8 kcal/mole
11.8 kcal/mole
7.3 kcal/mole
5.0 kcal/mole
3.3 kcal/mole

Due to this relatively high energy donating capacity, ATP (= Adenosine-TrisPhosphate) is surely one of the most important molecules in biological organisms. It
is of crucial importance in all biological energy transfer and coupling reactions It is not
surprising that all living cell contain high (milli-molar) concentrations of ATP at any
given time.

The ATP molecule, is made up of adenine, ribose and three covalently linked
phosphate groups.
12
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
TThhee cchheem
miiccaall ssttrruuccttuurree ooff A
Addeennoossiinnee--TTrriisspphhoosspphhaattee ((== A
ATTP
P))
A
Addeenniinnee
R
Riibboossee
γ
β
α

33 xx P
h
o
Phosspphhaatteess

During the diverse biological energy coupling reactions, the energy conserved in
the three high-energy phosphate groups of the ATP molecule is released after
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 frees up approx. 31 kJ/mol of usable
Energy (see Graphic below)
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
The ATP molecule & Exergonic cleavage of the γ-phosphate
ΔG = - 7.3 kcal/mole
γ-Phosphate
H
Adenosine Triphosphate
(ATP)
Pi
Adenosine Diphosphate
(ADP)
Phosphate

It is the chemical reaction (= hydrolysis reaction) of ATP which powers almost all
forms of cellular work , 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 transfer of the terminal phosphate group from ATP to another molecule which
is called phosphorylation plays an important role in regulation of important
cellular processes, such as insulin receptor functioning, cell communication and
gene activation. This phosphate transfer changes the shape of the receiving
molecule, (in most cases a protein) therefore performing work in form of transport,
mechanical, or chemical. When the phosphate groups leaves the phosphorylated
molecule again, the molecule returns to its alternate shape and its original
biological function.
•
In a very special cellular process called protein phosphorylation, the 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.
- examples are: phosphorylation of myosin protein in muscle cells during
contraction
- phosphorylation of so-called receptor kinases after binding of hormones or
14
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
growth factors

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 free 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 UNIT 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
15
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.

ATP is a renewable source of chemical energy, which cells can regenerate by two
major mechanisms. The regeneration of ATP can happen via:
1.
2.
new synthesis starting from ADP in mitochondria via a process called
oxidative phosphorylation (see UNIT 6)
fast regeneration of ATP from ADP in the presence of phosphocreatine,
which is the major chemical ‘reserve fuel’ in many cells (e.g. skeletal
muscle cells)
“A working cell consumes and regenerates its entire pool of ATP approx. 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

The life activities of biological organisms are due to thousands of biochemical
reactions, which are essentially energy transfers in form of moved electrons from
one molecule to another

In catabolic pathways electrons stored in food molecules are relocated between
different chemical reaction partners, releasing energy that is used to synthesize
ATP.

Reactions that result in the transfer of one or more electrons from one reactant to
another are oxidation-reduction reactions, or redox reactions.

The most important chemical reactions in living organisms are indeed rreedductionooxxidation reaction or for short redox reactions!

During redox reactions, outer shell electrons of functional groups of certain
molecules are moved from one molecule to another
1. Removal of an electron (= e¯) from an atom or molecule is an ooxxiiddaattiioonn
reaction
 Dehydrogenation (= removal of a hydrogen atom) is also
an oxidation reaction
Lactic acid

Pyruvic acid + ee¯¯
16
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
2. Addition of an electron (= e¯) is a rreedduuccttiioonn reaction
 Hydrogenation (= addition of a hydrogen atom) is also a
reduction reaction
Pyruvic acid + ee¯¯

Lactic acid

In reduction/oxidation reactions, one molecule (the reducing agent or reductant)
is oxidized, and its electrons are passed on to another (usually neighboring)
molecule (the oxidizing agent or oxidant), which becomes reduced

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 redox reactions
 in the Krebs cycle, the molecule succinate is oxidized to fumarate under release
of two electrons (and two protons)
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
Conversion of succinate into fumarate
(Krebs cycle, Mitochondrion)

Redox reactions also occur when the movement of electrons is not complete but
involve a change in the degree of electron sharing in covalent bonds. For
example, in the combustion of methane to form water and carbon dioxide, the
nonpolar covalent bonds of methane (C-H) and oxygen (O=O) are converted to
polar covalent bonds (C=O and O-H).
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.

However, the energy of most moved electrons within living cells is trapped and
rearranged in a series of important and highly abundant biological compounds
(redox molecules), such as NAD+ or FAD+.
Reminder:
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
or reductant. Conversely, the reception of electrons during a redox reaction is called
reduction; the molecules which receives the electrons is called the electron acceptor
or oxidant.

Electron transfer during redox reactions requires both a donor and an electron
acceptor; redox reactions are always coupled together
 during degradation of glucose it loses its electrons in form of hydrogen (H)atoms, 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!

When during cellular redox reactions, bonds shift from nonpolar to polar, the
electrons move from positions equidistant between the two atoms for a closer
position to oxygen, the more electronegative atom.
Key Information: Oxygen is one of the most potent oxidizing agents.

An electron looses energy as it shifts from a less electronegative atom to a more
electronegative one. A redox reaction that relocates electrons closer to (the very
electronegative) oxygen releases chemical energy that can do work.

In biological systems the electrons are almost always removed from the covalent
bonds of food molecules (e.g. glucose or fatty acids) in connection with a transfer
of H-atoms from the involved molecules to either 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
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
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
Chemical structures & Redox reactions
of NAD+ or NADP+

The removal of H-atoms in biological systems is accelerated by special proteins
called Dehydrogenases. A protein with the capability to accelerate a certain
chemical reaction is also called an enzyme. Dehydrogenase enzymes strip two
hydrogen atoms from the fuel molecule (e.g., glucose or fatty acid), pass two
electrons and one proton to NAD+ and release one proton (H+) into the
surrounding water.
H-C-OH + NAD+  2 e-, 2 H+ 

C=O + NADH + H+
This electron and proton transfer changes the oxidized form (NAD+) to the reduced
form (NADH + H+). NAD+ functions as the oxidizing agent in many of the redox
steps during the catabolism of glucose and fatty acids.
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
Chemical structure & Redox reactions
of the FAD molecule
FAD
(oxidized form)
2 e- + 2 H+
FADH2
(reduced form)

Summarized, Dehydrogenases transfer two H-atoms (2 protons and 2
electrons) 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.
 many enzymes are known to work or to be enzymatically active only in
combination with their co-enzymes
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SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.
 many vitamines e.g. vitamine B12 or folic acid are co-enzymes of important
cellular enzymes

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!

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
(for more details see UNIT 6)
 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

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 UNIT 6)

At the end of this enzyme-bound electron cascade, the electrons finally are
transferred to molecular oxygen (= O2), which is the final electron acceptor
 O2 gets reduced to water

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!
22
SAN DIEGO MESA COLLEGE
SCHOOL OF NATURAL SCIENCES
General Biology (BIOL 107): Instructor: Elmar Schmid, Ph.D.

Other important cellular redox molecules, which means, molecules which play
crucial roles in cellular redox processes are:
1. Ubiquinones (e.g. Q10)
 important redox molecule of the electron transport chain (ETC) located in the
inner mitochondrial membrane
2. Plastoquinones
 important redox molecule of the electron transport chain (ETC) located between
the light-tapping photosystems in the thylacoid membranes of plant
chloroplasts
3. Cytochromes (e.g. cytochrome c)
 these are heme iron-containing proteins which are integrated or associated
with biological membranes, such as the inner mitochondrial or the thylacoid
membranes of the chloroplasts
 in mitochondria and chloroplasts, cytochromes are integral part of the ETCs or
these two important cell organelles
4. Iron-Sulfur (Fe-S) proteins
 these type of redox molecules are found throughout the kingdoms of life
 they contain clusters of several iron and sulfur atoms which reversible take
up 2 or 4 electrons during cellular redox reactions
 a prominent example belong this group of redox molecules is ferredoxin
4. Glutathione
 this molecule is the co-substrate of many enzymes involved in cellular
detoxification and protection mechanisms
 it is a so-called tri-peptide and consists of three amino acids; it contains a
cysteine, which (in its reduced form) has a characteristic so-called
sulfhydryl- (SH-) group
 this functional 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 GS-SG.
 the glutathione redox system plays an important role in the cellular defense
and protection against toxic molecules (e.g. in cigarette smoke) or irradiation
(e.g. after intensive sun exposure)

In the context of reduction-oxidation reactions in the cell we heard about biological
molecules e.g. NAD, GSH, which are essential parts (as prosthetic groups or cosubstrates) of specific proteins, called enzymes
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