Welcome to an interactive course in Biotechnology.

The field of biotechnology is entering an exciting new era. With the advent of newer tools, genomic
information is being integrated into molecular level descriptions of life process. Our current
understanding of how biomolecules work at the level of atoms has enabled us to make rapid
progress in molecular medicine. Harnessing the tools and insights into developing a life saving drug
at the present covid time is all the more fascinating for every student of biotechnology!
Let us consider all the growth and development in various areas of science, engineering, medicine,
agriculture, communications, space exploration, warfare technologies, social progress, and
economical advancement: But the greatest impact result from our eagerness to know the truth and
quest to learn how living organisms operate at the molecular or atomic level.
Metabolism is a vast subject. Every lesson deals with related and highly complicated topics. With all
the complicated pathways, its it the most fascinating subject to study.
Let me begin with certain study tips. The subject requires a lot of memorization of names,  and
structures. Do not equate understanding of the subject with memorization of structures.  You have
to pay special attention to logic that permeate throughout the course. You should establish
relationship of function to structures or relate work of a molecule to its composition and
arrangement. Pay attention to the operation of various regulatory mechanism by which a cell or
organism control its own activities. You know that these themes cannot be learned by
memorization. When you understand this, you begin to appreciate why football is round, why each
lock requires a specific key, why left shoe does not fit the right foot, why the cap of the pen has a
tiny hole at the top.  You know that though there is a reason for each of these observations, the
reasons are very simple.
In order to study metabolism well, you must have a pencil and paper to solve problems. Carry the
knowledge from one chapter to the next and reinforce your knowledge. You must talk metabolism
with others, dream metabolism and live metabolism!
Biochemistry is termed as ‘Chemistry of Life’. Metabolism is the chemistry that takes place in
cells. Within a volume of less than a µl, the cell carries out thousands of enzymatic reactions. A
metabolic pathway consists of a series of reactions in which a precursor is converted to a product
in one or more steps. It consists of, on the one hand, of a maze of converging degradative pathways
by which exogenously supplied food stuffs and endogenous reserves are converted to a relatively a
few simple products, and on the other hand, of a maze of diverging and interlocking biosynthetic
pathways by which the catabolic end products are converted to simple metabolites, viz., amino
acids, sugars, nucleotides and fatty acids.  The latter, in turn, are utilized for the synthesis of
macromolecules such as proteins, nucleic acids, complex lipids and polysaccharides which are
finally assembled into the structural elements of the cell. 
We study not individual reactions; but how they interact. In other words, there is nothing that
exists in isolation. Therefore, Biochemistry is ‘biology of molecules. This is a new way to look at
metabolism.  Cell is a ‘community’ of molecules.  There are different ways of looking at community
of molecules. In a metabolite centric view, Substrate, each intermediate and product is given
importance. Whereas in the protein centric view of metabolism, metabolites are not given
importance, rather, enzymes are given importance.  So metabolism is a series of consecutive
enzymatic reactions that produce specific products. Their reactants intermediates and products are
referred to as metabolites. Since an organism utilizes many metabolites, it has many metabolic
pathways.

In the given chart, the numbers (eg. 2.3.1.47 etc.) is representative of:
Protein centric view
There are remarkable differences between living and non living beings. All living beings have
directed and  life sustaining reactions occurring in every cell . Further these  have high rate of
reaction achieved under mild conditions of temperature, pH and concentration of substrates. All
reactions in a cell show high degree of specificity. Finally reactions are functionally related. This
awareness has a great value in understanding biochemical principles. It becomes clear to us that
reactions are highly coordinated and directed. Many pathways operate simultaneously in a cell, as
a community of molecules. Each pathways must sense the status of other pathways,  and operate
optimally to be a unit of life. All biochemical activities have a purpose; a purpose of maintenance
and propagation of a system.
At this stage students are encourage to read the following article
The origin of Intermediary metabolism. Harold J Morowitz., et al., PNAS, July 5, 2000. Vol 97, No.14.
P 7704-7708.
At this juncture, it is important to ask, what are the functions of metabolism? It can be listed as:
To obtain chemical energy by capturing solar energy or by degrading energy rich nutrients from
environment or exchange of energy either from sunlight or organic nutrients.
To convert nutrient molecules to cell own molecules or to synthesize building blocks
To polymerize monomeric precursors to proteins, Nucleic acids, lipids polysaccharides etc.
To synthesize or degrade biomolecules required for specialized cellular functions.
Synthesizing glycoproteins, antibodies, histamines, niacin  etc. suits which of the functions of
metabolism?
Extraction of energy from various sources
Polymerize monomeric precursors to polymeric forms
Synthesizing of biomolecules for carrying out specialized cellular functions

The question that can arise in students is how do cells extract energy, substrates and reducing
power from the environment? How do cells synthesize the building blocks of their
macromolecules? How cells operate with coherence inspite of having thousands of reactions? It is
important to note that, though there are thousands of reactions happening in a cell, the number of
kinds of reactions are limited to about six. They are:

Type of reaction Description

Oxidation-Reduction Electron transfer

Ligation requiring ATP cleavage Formation of covalent bonds (C-C

bonds)

Isomerization Rearrangement of atoms to form

 isomers

Group Transfer Transfer of a functional group from

one molecule to another

Hydrolytic Cleavage of bonds by the addition of

water

Addition or removal of functional Addition of functional groups to

groups double bonds or their removal to form
double bonds

It is also important to note that about a hundred molecules play central role in all forms of life. Out
of there are 30 crucial molecules. Intermediary metabolism supplies energy needed for the
synthesis of macromolecules and furnishes with as steady supply of these biomolecules and their
activated intermediates. The concentration of intermediates are kept stable. It is achieved by
maintaining a rate of synthesis for each intermediate that is equivalent to its utilization. The term
steady state is used to describe this nonequilibrium situation.
Organisms differ in source of energy, reducing power and starting materials for biosynthesis. To
maintain the steady state and to permit growth and reproductions well, all living cells require
energy (obtained from ATP) and starting materials for biosynthesis. They also require reducing
power (NADPH) since most biosynthesis involves converting compounds to a more reduced state.
The need of different organisms for source of energy, reducing power and starting materials for
biosynthesis are quite similar, the way in which organisms satisfy their needs can be quite different.

No Types of Organism Source of ATP Source of Source of

NADPH Carbon

1 Chemoautotrophs Oxidation of Oxidation of CO2

inorganic inorganic
compounds compounds

2 Photoautotrops Sunlight H2O CO2

3 Photoheterotroph sunlight Oxidation of Organic

s organic compounds
compounds

4 Heterotrophs Oxidation of Oxidation of Organic

organic organic compounds
compounds compounds

A biomolecule crucial for life is Choline

Reactions are organized into sequences or pathways. It is the sequence that serves a function, not
the individual reactions (eg. Conversion of glucose to pyruvate). There are 3 types of metabolic
pathways:
Linear: e.g. catabolism and biosynthesis of monosaccharides and amino acids, ETC.
Cyclic: TCA cycle, urea cycle.
Spiral: They are neither linear nor cyclic but share some features of both. The same set of enzymes
is used over and over for step-by-step lengthening or breakdown of a given molecule. E.g. protein
synthesis, fatty acid synthesis and degradation.
Sequentially related enzymes are frequently clustered.
The three types of clustering seen are linear (as in glycolysis), cyclic (as seen in fatty acid synthesis)
and trans membrane (as seen in ETC)
Enzymes of linear pathway are generally soluble and cyclic enzyme at times exist as a Multi enzyme
complex. A multienzyme complex has several advantages as being efficient, faster with minimum
loss of intermediates. In this case, there is high concentration of enzyme in small area. It also gives
better regulation as precursors can be short supplied.
Metabolic pathways are irreversible. Overall equilibrium of a pathway is towards final product
formation. How a cell achieve this? In a multistep reaction, there will be one or more reactions
where there is a large free energy change is associated with. Therefore, this will pull the pathway to
Let us consider A is converted to B and C with a free energy change of +5Kcal and B is converted to
D with a free energy change of -8Kcal. The net transaction of the conversion of A to D+C  is -3Kcal.
Therefore in any pathway there should be a highly exergonic step with a large negative free energy
change. This will ensure that  the reaction goes to completion.  Those steps that pull the pathway
to a definite product is called committing step. A committing step gives, pathway a direction. Look
at the above example and identify the committing step.
At this state it is important to know the difference between delta Gzero and delta G zeroprime.
Students are encouraged to read about it from any book available
If two metabolites are interconvertible, it is exactly not the reversal.  If the first pathway is
exergonic, energy must be supplied to bring it back to make it uphill. That is to say, at least some of
the reactions in a pathway must be different. There fore catabolic and anabolic pathways must
differ. It has a huge advantage. Independent pathways allows independent control. For example,
product B is required by a cell it is necessary to turn off the pathway no.2 and turn on pathway 1.
ΔG° is best defined as: Standard condition at 27C, 1 Atm and 1M
Every metabolic pathway has a committing step, which is normally the step which has maximum
negative ΔG.  You are advised to read page 576 from Voet and Voet, ed 2 or to go through the steps
of glycolysis and identify the committing step. Then answer the question below
Reactions within mitochondria provide most to the energy needed by a typical cell.
Many of the reactions necessary to keep cells and organisms alive must run against their
thermodynamic potential. It means in the direction of a positive delta G. Among these are the
synthesis of ATP and creation of ion gradients in all mammalian cells. These processes are driven in
the thermodynamically unfavorable direction via coupling with highly favourable process.
We can predict whether pairs of coupled reactions will proceed spontaneously by simply summing
the free energy changes for each reaction. In the example, PEP is converted to Pyruvate. Hydrolysis
of Pep is energetically favourable and it is used to drive phosphorylation of ADP to form ATP, a
process that is energetically unfavourable.
The net reaction catalyzed by pyruvate kinase depends upon coupling between the first two
reactions. So the fundamental biological purpose of ATP as an energy coupling agent is to drive
thermodynamically unfavourble reactions to that overall free energy charge for the coupled
process  is negative (ie. Favourable). To put this in another way, the role of ATP is to change the
equilibrium ratio of [reactant] to [products]for a reaction.
The role of ATP in metabolism is two fold.
1. Make metabolic sequences thermodynamically favourable
2. It is an important allosteric effector in the kinetic regulation of metabolism
In organisms, the energy needed to start a chemical reaction is typically provided by some energy
input from the surrounding environment such as ATP