Biochemical Pathways

Chapter 6 and 7 from text

book

Energy:
All living organisms require a constant supply of energy to
sustain life.
This energy is obtained through enzyme mediated chemical
reactions that release the internal potential energy stored in
the chemical bonds of molecules.
eg: burning of wood. Chemical reaction that results in
breaking of bonds and releasing energy in the form of heat.
The organic molecules are broken down to CO2 and water.
there is less potential energy in the chemical bonds of CO 2
and water than the complex organic compounds.
Living organisms carry out a series of such complex
reactions in a controlled manner to release the right amount
of energy necessary for the particular process.
energy is required for all the processes from anabolism, to
growth, movements and reproduction.

Autotrophs: self feeding organisms, use simple inorganic

molecules to produce complex organic compounds. ( fix
carbon dioxide)
Photoautotrophs: they use sunlight as the source of energy
and use simple inorganic molecules to produce complex
organic compounds.
Chemoautotrophs: they use inorganic chemical reactions as
the source of energy and use simple inorganic molecules to
produce complex organic compounds.
Heterotrophs: they require organic molecules as the source
of carbon and energy to produce complex organic molecules
In eukaryotic cells organelles like chloroplast and
mitochondria are the sites of photosynthesis and
respiration.
In prokaryotes, since these organelles are absent,
photosynthesis and respiration occurs in the cell cytoplasm
and inner surfaces of the cell membranes.

Photosynthesis:
Some organisms like plants, algae trap the radiant energy from
sunlight and convert it into the energy of chemical bonds in
large molecules such as carbohydrates.
Respiration:
All organisms must carry out respiration for survival.
Cellular respiration is of two types:
Aerobic cellular respiration: organisms require the presence of
oxygen to carry out respiration.
Anaerobic cellular respiration: organisms that do not require
oxygen for respiration. ( reduction of sulphates to sulphides..
It is a redox reaction required for the functioning of ETC).

Aerobic cellular respiration:

Aerobic cellular respiration is a series of enzyme controlled
chemical reactions in which oxygen is involved in the breakdown
of glucose to carbon dioxide and water and the chemical-bond
energy from glucose is released to the cell in the form of ATP.
The following equation summarizes the net result of the reaction
between sugar and oxygen to form carbon dioxide and water :
Glucose + Oxygen
energy
C6H12O6 + 6O2
heat)

carbon dioxide + water +

6CO2 + 6H2O + energy (ATP +

Of all the covalent bonds in glucose, the ones that are easiest to
break are the C-H and O-H bonds which are present on the
outside of the molecule.
When these bonds are broken, two things happen:
1. The energy of the electrons can be used to phosphorylate ADP
molecules to produce higher-energy ATP molecules and

The ATP is used to power the metabolic activities of the cell. The
chemical activities that remove electrons from glucose result in
the glucose being oxidized.
These high energy electrons must be controlled. Electron
transfer molecules like NAD+ and FAD temporarily hold the
electrons and transfer them to other electron carriers.
ATP is formed when these transfers take place.
In aerobic cellular respiration oxygen serves as the terminal
electron acceptor. When the electrons are added to oxygen it
becomes a negatively charged ion
(O--) and hence becomes reduced.
The positively charged hydrogen ions that are released from
glucose molecule combine with the negatively charged oxygen
ions to form water.
Once all the hydrogen are removed from the glucose molecule,
the remaining carbon and oxygen atoms are rearranged to form
individual molecules of CO2. The redox reactions are complete.
All the hydrogen removed from glucose combines with oxygen to

In eukaryotic cells, the process of releasing energy from food

begins in the cytoplasm and is completed in the mitochondria.
There are three distinct enzymatic pathways involved:
Glycolysis, Krebs cycle and Electron transport chain.
Glycolysis:

Glycolysis (glycos = sugar; lysis = split) takes place in the

cytoplasm of the cells and results in the breakdown of
glucose with the release of electrons and the formation of
ATP.

Glucose has energy added to it from 2 ATP molecules. This

extra energy makes some of the bonds in glucose unstable
and glucose is more readily broken down.

After passing through four enzymatic reactions, 6-C is

cleaved into 2, 3-C molecules, glyceraldehyde-3-Phosphate
and dihydroxyacetone phosphate.

These undergo 5 more reactions to form Pyruvic acid or

Energy released by these 10 step reactions produces 4 ATP

molecules.

Since 2 ATP molecules are consumed in starting the reaction,

the net gain of ATP is 2 ATP per molecule of glucose in
glycolytic pathway.

Electrons released from the bond splitting are picked by NAD +

and transferred to a series of electron transfer reactions (ETC).

2 NADH2 are formed.

These have large potential energy that can be used to form

ATP through ETC.

Thus the generalized reaction that summarizes the events of

glycolysis is:
Glucose + 2 ATP + 2 NAD+
Pyruvic acid
Summary:

4 ATP + 2 NADH + 2

Glycolysis steps

Krebs cycle:

These reactions take place in the mitochondria. The Krebs cycle is

also known as citric acid cycle and the tricarboxylic acid cycle
(TCA).

The 3-carbon pyruvic acid molecules released from glycolysis

enter the mitochondria and are acted upon by enzymes in
conjunction with coenzyme A to form 2-carbon acetylcoenzyme A, CO2 and 2 NADH.
The acetyl-coenzyme A proceeds through the Krebs cycle and is
completely oxidized.
The acetyl portion of the molecule is transferred to 4-carbon
compound, oxaloacetate and a new 6-C compound, citrate is
formed. The CoA is released to participate in another reaction
with pyruvic acid.
The citrate formed is broken down in a series of reactions which
ultimately produce oxaloacetate, which is again used in the first
reaction to form citrate.
The series of compounds formed here are called keto acids.
In the process, electrons are removed and get attached to NAD +
or FAD. The electrons are picked by NAD+ to form NADH and FAD
to form FADH2. Whichever the electron acceptor/ carrier, the
electrons are sent to the ETC.

Two molecules of CO2 are liberated at two steps of

decarboxylation.
1. Conversion of isocitrate to -ketoglutarate
2. Conversion of -ketoglutarate to succinyl CoA.
Thus the overall reaction in the Krebs cycle is:
2 Pyruvic acid+ 8NAD+ + 2FAD + 2ADP + 2H3PO4 6CO2 + 8 NADH +
8H+ + 2FADH2 + 2ATP

Hence, when both the pyruvate molecules are processed

through the Krebs cycle:
3. All the original carbons from the glucose molecule are
released as CO2
4. All the hydrogen originally found on the glucose molecule
are transferred either to NAD+ to form NADH and FAD to
form FADH2
5. 2 ATPs are formed from the addition of phosphates to ADP.

3. Electron transport system:

This is the final stage of aerobic cellular respiration and is dedicated

to generating energy, ATP.
These are a series of redox reactions with oxygen as the final
electron acceptor. The negatively charged oxygen combines with
hydrogen ions to form water. This step makes the process aerobic.

Addition of the third phosphate to the ADP molecule, increases

its potential energy.
The mitochondria consists of two membranes; an outer
enclosing membrane and an inner folded membrane.
The reactions of the ETC are associated with this inner
membrane. The production of ATPs involves two separate but
connected processes.
Electrons carried by NADH enter reactions in complex I, where
they lose some energy and are eventually transferred to
Coenzyme Q. Electrons from FADH2 enter complex II and are
also transferred to Coenzyme Q.
Coenzyme Q transfers the electrons to complex III. In complex
III, the electrons lose additional energy and are transferred to
cytochrome c, which transfers electrons to complex IV.
In complex IV, the electrons are eventually transferred to
oxygen.

Electron transport:

As the electrons lose energy in complex I, complex II,

complex III and complex IV, additional protons are pumped
into the inner membrane space.
When these protons flow down the concentration gradient
through special channels in the membrane, phosphorylase
enzymes (ATPase) in the membrane are able to use the
energy to generate ATP.
A total of 12 pairs of electrons and hydrogen are transported
to the ETC from glycolysis and Krebs cycle for each glucose
molecule.
In prokaryotes:
2 pairs carried by NADH generated during glycolysis.
6 ATPs
8 pairs carried by NADH generated during Krebs cycle..
24 ATPs
2 pairs carried by FADH2 generated during Krebs cycle..
4 ATPs
ATP formed during glycolysis..
ATPs

In eukaryotes:
2 pairs carried by NADH generated during glycolysis.
ATPs

The electrons released during glycolysis are carried by NADH and converted to
2FADH2 in order to shuttle them into the mitochondria

8 pairs carried by NADH generated during Krebs cycle..

ATPs
2 pairs carried by FADH2 generated during Krebs cycle..
ATPs
ATP formed during glycolysis..
ATP formed during Krebs cycle.
Total:
38 ATPs
Energy utilized
During glycolysis
ATPs
During Krebs cycle
Total net energy gain.
ATPs

24
4

4 ATPs
2 ATPs
2
NIL
36

Anaerobic cellular respiration:

Some organisms do not have the necessary enzymes
required for Krebs cycle or ETC.
Most of these are prokaryotes. However all these cells still
require a constant supply of ATP.
These organisms do not require oxygen as the final electron
acceptor and hence are called anaerobic and they perform
anaerobic cellular respiration.
These organisms utilize certain inorganic and organic
molecules as their final electron acceptors.
The acceptor molecules can be sulfur, nitrogen, or
other inorganic atoms or ions. Organic molecules like
pyruvic acid can also do the needful.
Anaerobic pathways that oxidize glucose to generate ATP by
using organic molecule as the ultimate hydrogen acceptor
are called fermentation.

Anaerobic respiration is the incomplete oxidation of glucose:

C6H12O6 + (H+ and e- acceptor)
smaller hydrogen
containing
molecules + energy (ATP +
heat)
Typically glucose proceeds through glycolysis producing
pyruvic acid.
The pyruvic acid then undergoes several alternative changes
depending on the kind of organism and the specific enzymes
it possesses.
In some organisms pyruvic acid is reduced to lactic acid,
while in some organisms, it is reduced to alcohol and carbon
di oxide.
NADH

Pyruvic acid
NADH

NAD+

Lactic acid
NAD+

ethanol + carbon di oxide

Used in making bread, trapped gas. Leavened. Alcohol

produced evaporated during baking.
Ethanol is also desired for wine making.
Champagne, other sparkling wines are products of that contain
carbon di oxide and alcohol.
Lactic acid fermentation:
Pyruvate is converted to lactic acid.
Here also net profit is 2ATPs per glucose.
Seen in curd, sour cream, cheeses, and other fermented dairy
products.
Lactic acid makes the milk protein coagulate and become solid.
In human body, different cells have different metabolic
capabilities.
RBCs lack mitochondria, and hence, depend on lactic acid
fermentation for energy. Muscle cells can do both aerobic and

Accumulation of lactic acid results in cramping of muscles with

pain.
As the oxygen level increases due to stoppage of activity, the
lactic acid concentration decreases and the muscle cells relax.
Metabolic processing of Molecules Other than
Carbohydrates:
Fat respiration:
Before fats can be broken down to release energy, they must be
converted to smaller compounds by digestion.
Glycerol forms the backbone of most fatty acids. It is converted
to glyceraldehyde-3-phosphate, which directly enters glycolysis.
The remaining fatty acids are often long molecules that also
must be processed before they are metabolized.
First they need to enter the mitochondria, where each long
chain of carbons is hydrolyzed into 2-carbon fragments.
Next, each 2-carbon fragment is converted to acetyl which
enters krebs cycle.

Protein respiration:
Proteins..digested to individual amino acids.
Each amino acid then needs to have the amino group removed by
deamination that take place in liver.
The non-nitrogenous part of the protein is converted to keto-acids
Acids enter Krebs cycle..keto acids.
In the Krebs cycle the electrons are removed and sent to ETS, where
their energy is converted into chemical bond energy of ATP.
Amino group that was removed is converted into ammonia
All toxic products are released from the cell through blood and
kidneys. In case of high protein diet, excess fluid intake will allow the
kidney to remove the urea or uric acid efficiently.
Proteins cannot be stored.

Photosynthesis:
Chlorophyll is a green pigment that absorbs light energy
for the process of photosynthesis.
Through the process of photosynthesis, plants, algae and
certain bacteria transform light energy to chemical bond
energy in the form of ATP and then use ATP to produce
complex organic molecules like glucose.
Photosynthesis occurs in organelles called chloroplasts.
Chloroplasts have two distinct regions: grana and stroma.
Granum consists of stacks of membranous sacks, thylakoids,
containing chlorophyll and the stroma consists of the
intervening spaces between the membranes.
Equation to summarize photosynthesis:
Light energy + carbon dioxide + water

glucose + oxygen

There are three distinct events in the photosynthetic

pathway;
1. Light capturing events:
The energy of light comes in discrete packages called photons.
Photons of light having different wavelengths have different
amounts of energy.
Chlorophyll absorbs red or blue light best and reflects green
light.
When a chlorophyll molecule is struck by and absorbs a photon
of the correct wavelength, its electrons get excited to a higher
energy level.
The energy of these excited electrons is used to split water
molecules and form ATP.
These reactions take place in the thylakoids.
Many molecules (photosystems) are involved and are embedded
in the membrane of the thylakoid.

The antenna complex is a network of hundreds of chlorophyll

and accessory pigments molecules whose main role is to capture
photons of light energy and transfer the energy to the reaction
center.
When light strikes a chlorophyll molecule, an electron
becomes excited. The energy of the excited electron is passed
from one pigment to another through the antenna complex.
The series of excitations continues until the combined energies
from several excitations are transferred to the reaction center,
which consists of chlorophyll a and protein molecules.
An electron is excited and passed to a primary electron acceptor
molecule, oxidizing chlorophyll and reducing the acceptor.
Ultimately, the oxidized chlorophyll then has its electron replaced
with another electron from a different electron donor.
Thus in summary:
a. chlorophyll and other pigments of the antenna complex capture light
energy and produce excited electrons
b. The energy is transferred to the reaction center
c. Excited electrons from the reaction center are transferred to a primary

2. Light dependent reactions:

Both photosystem I and photosystem II have antenna complexes
and reaction centers.
PS II occurs first and feeds its excited electrons to PS I.
One special attribute of the PS II is that it possesses an enzyme
responsible for splitting of water molecules (H2O
2H+
O)
The oxygen is released into the environment as O2 and the
electrons of the hydrogens are used to replace the electrons that
previously had been lost by the chlorophyll.
The remaining protons are released to participate in other
reactions.
Thus, the light energy captured by the antenna complex is used
to split water into H and O.
The excited electrons from PS II are sent through a series of

This is similar to the ETC described for aerobic respiration.

While the electrons are being transported, protons are
pumped from the stroma into the space inside the thylakoid.
Eventually, these protons move back across the membrane and
while doing so ATPase is used to produce ATP (ADP is
phosphorylated to ATP).
Thus, energy of sunlight is also used to produce ATP.
In PS I, light is trapped and the energy is absorbed in the same
manner as in PS II. But the PS I lacks the enzymes necessary for
splitting of water into oxygen, protons and electrons and hence
O2 is not evolved / released from PS I.
The high energy electrons leaving the reaction center of PS I
make their way through a different series of oxidationreduction reactions.
During these reactions, the electrons are picked up by NADP+,
which is reduced to NADPH.

In summary, the light-dependent reactions of photosynthesis

take place in the thylakoids of the chloroplast:
a. Excited electrons from PS II are passed through an ETC and
ultimately enter PS I.
b. The ETC is used to establish a proton gradient that produces
ATP.
c. Excited electrons from PS I are transferred to NADP+ to form
NADPH.
d. In PS II, an enzyme splits water into hydrogen and
oxygen. The oxygen is released as O2.
e. Electrons from the hydrogen of water replace the electrons
lost by chlorophyll in PS II.

PS II and PS I and
how they interact.

3. Light independent reactions:

These reactions take place within the stroma of the
chloroplast.
ATP, NADPH, CO2 and a 5-C starter molecule called
ribulose are the materials required for light independent
reactions.
ATP and NADPH are made available from the light dependent
reactions in PS II and I.
CO2 molecules come from the atmosphere and the ribulose
starter molecule is already present in the stroma of the
chloroplast from the previous reactions
CO2 undergoes carbon fixation through Calvin cycle.
ATP and NADPH from the light dependent reactions are used
along with CO2
to synthesize larger organic molecules in the Calvin cycle.
The fixation of carbon begins with CO combining with 5-C

The newly formed 6-C molecule immediately breaks into two 3-C
molecules each of which undergo a series of reactions that involve a
transfer of energy from ATP and a transfer of hydrogen from
NADPH.
This results in formation of two molecules of glyceraldehyde-3phoshate.
Since this is the first 3-C stable compound this pathway is referred to
as C3 photosynthetic pathway.
Some of the glyceraldehyde-3-phosphate is used to synthesize glucose
and some is used to regenerate ribulose molecule which again
combine with CO2 in a cyclic manner.
The general equation for light independent reactions is
CO2 + ATP + NADPH + Ribulose
phosphate + NADP+ + ADP + P

Glyceraldehyde-3-

In summary:
1. ATP and NADPH from the light dependent reactions leave the
grana and enter the stroma.
2. The energy of ATP is used in the Calvin cycle to combine CO2 to
a 5-C molecule (ribulose) to form a 6-C compound.
3. The 6-Cmolecule immediately divides into 3-C molecule
(glyceraldehyde-3-phosphate)
4. Hydrogens from NADPH are transferred to molecules in the Calvin
cycle.
5. 5-C ribulose is regenerated.
6. ADP and NADP+ are returned to the light dependent reactions.

Glyceraldehyde-3-Phosphate: the product of

photosynthesis
When a plant goes through photosynthesis, it produces 12
glyceraldehyde-3-phosphate molecules.
10 of these molecules are rearranged by a series of reaction
to regenerate the 5-C ribulose, needed to operate the light
independent reactions.
The other 2 molecules are considered as a profit from the
process and are changed into a hexose.
Hence, G-3-P and not sugar is the initial product of
photosynthesis.
G-3-P can be converted to glucose molecules, which can be
combine to form complex carbohydrates like starch or
cellulose.
Other simple sugars formed can be used as building blocks for
ATP, RNA, DNA, or other carbohydrate containing materials.

G-3-P can also serve as a carbon skeleton for construction of

amino acids needed to form proteins.
G-3-P can be broken down during cellular respiration to form
ATP.
Other Aspects of Plant Metabolism:
Photosynthetic organisms are able to manufacture organic
molecules from inorganic molecules.
They have the ability to form a variety of complex molecules
like fats, proteins etc for their own needs.
Amongst the complex molecules formed, some compounds
could be toxic to animals which would use plants as food.
Many such complex compounds could have medicinal
properties.
Vitamins are another important group of molecules formed by
plants.

Interrelationships between Autotrophs and

Heterotrophs:
Autotrophs are able to capture energy to manufacture new
organic molecules from inorganic molecules.
Heterotrophs use organic molecules as source of energy.
Plants and other autotrophs obtain energy from food
molecules, in the same manner as animals. And also require
oxygen for the ETC for cellular respiration.
Plants utilize oxygen during respiration and evolve it during
photosynthesis.
Thus, animals supply the raw materials- CO2, H2O and nitrogen,
needed by the plants and
the plants supply the raw materials- sugars. Oxygen, amino
acids, fats and vitamins, needed by animals.
This constant cycling is essential to life on Earth.

END

Common Mechanisms used in Processing Energy and Matter:

Biochemical Pathways:
In living organisms, the same amount of energy is released
that would have been released by breaking of the chemical
bond otherwise. But the release of energy in the living
systems is in a series of small steps.
Each of the steps is controlled by an enzyme. The substrate
is converted into the product by one enzyme. A second
enzyme acts on this product as a substrate and converts it
into another product, which is acted upon by a third enzyme.
Such controlled reaction are often called a biochemical
pathway or a metabolic pathway.
Catabolism: Metabolic pathways that result in breakdown of a
complex compound
Anabolism: synthesis of new, larger compounds.

Most of the organisms use the same biochemical pathway, but

the enzymes involved may slightly vary.
The fact that so many organisms use essentially the same
biochemical pathway is a strong argument for the idea of
evolution from a common ancestor.
Generating energy in a useful form: ATP
The transfer of chemical energy within living systems is handled
by a molecule known as Adenosine tri phosphate (ATP).
Chemical energy is stored when ATP is made and released when
it is broken apart.
ATP molecule is formed by combining adenine ( a nitrogenous
base), ribose (sugar) and 3 phosphates.
AMP, ADP and ATP are the three forms, depending on the
number of phosphates present.
The addition of phosphate to a molecule is called a

The bonds holding the last 2 phosphates to the molecule are easily
broken to release energy for energy requiring cellular processes.
This bond is called the high energy phosphate bond.
These bonds are often shown as curved lines in the diagrams.
Both ADP and ATP contain the high energy bonds and hence are
unstable molecules and lose their phosphates readily..
When this occurs, the energy held in the high energy bond of the
phosphates is transferred to a lower energy molecule or released
to the environment.
When energy is being harvested from a chemical reaction or
another energy source like sunlight, it is stored when a phosphate
is attached to an ADP to form ATP.

Adenosine Tri phosphate (ATP)

Electron Transport is another process that can be applied to

many different organisms.
The electrons in the outer energy level are lost easily to the
surroundings, if they receive additional energy.
When electrons receive additional energy they move to the
higher energy level.
These electrons fall back to their original position and give
up the extra energy they had acquired.
In living systems, such changes in the energy are harnessed
by special molecules that capture such excited electrons and
transfer them to other chemical reactions. These electron
transfer reactions are called oxidation-reduction reactions or
redox reactions.
Redox reactions are electron transfer reactions in which a
molecules losing electrons become oxidized and those
gaining the electrons become reduced.

Proton Pump:
In most of the redox reactions, the electrons transferred come from
the hydrogen atoms. A hydrogen nucleus (proton) is formed when
the electrons are removed from hydrogen atoms.
When these high-energy electrons are transferred to the low energy
state, protons are pumped across the membranes, creating a
region with high concentration of protons on one side of the
membrane.
Therefore, this process is referred to as a proton pump.
The pressure created by this high concentration of protons is
released when protons flow through special pores in the membrane
back to the side from which they were pumped.
As they pass through the pores, an enzyme, ATPase (a
phosphorylase), speeds the formation of an ATP molecule by
bonding a phosphate to an ADP molecule.
Thus, the establishment of a proton gradient is an important step
for the production of much of the ATP produced in the cells.