Metabolic Concepts

The term metabolism applies to assembly of biochemical reactions which are

employed by the organisms for the;
 synthesis of cell materials and
 the utilization of energy from their environments.
The metabolism of an organism (or of a cell) may be defined as ‘the sum total
of all the enzyme-catalyzed reactions that occur in an organism (or in a cell)’.
The large number of reactions in a cell are organized into a relatively small
number of sequences or pathways. It is a highly coordinated and purposeful cell
activity, in which multienzyme systems cooperate.
The magnitude of metabolism may be appreciated by
taking the examples of microorganisms and the human beings :
(a) Microorganisms like bacteria (e.g., Escherichia coli) can double in
number every 40 minutes in a culture medium containing only glucose and
inorganic salts, or in 20 minutes in a rich broth. Each cell contains hundreds
to thousands of molecules of each of about 2,500 different proteins, about
1,000 types of organic compounds and a variety of nucleic acids. It is, thus,
apparent that the bacterial cells participate in a variety of metabolic activities
in a remarkable way.
(b) Human adults maintain a constant weight for about 40 years, during
which period a total of about 60 quintals of solid food and 45,000 litres of
water are metabolized. And yet both body weight and body composition
remain almost constant.
Terminology of Metabolism
The various processes constituting metabolism may be divided, arbitrarily,
into
 catabolism &
 anabolism.
Catabolism: the processes, whose major function is the generation of chemical
energy in forms suitable for the mechanical and chemical processes of the cells, are

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termed as catabolism (cataG = down ; balleinG = to throw). The various activities
such as;
 mechanical movement,
 growth,
 reproduction,
 accumulation of foods,
 elimination of wastes,
 generation of electricity &
 maintenance of temperature.

Anabolism: the processes, which utilize the energy generated by catabolism for the
biosynthesis of cell components, are termed as anabolism (anaG = up). It is
exemplified;
 food manufacture.

Amphibolism: Some processes can be either catabolic or anabolic, depending on

the energy conditions in the cell are referred as amphibolism. For example
 The Krebs cycle.
In all cells, metabolism enables the cell to perform its vital functions.
Metabolism performs following 4 specific functions:
(a) to obtain chemical energy from the degradation of energy-rich nutrients
or from captured solar energy.
(b) to convert nutrient molecules into precursors of cell macromolecules.
(c) to assemble these precursors into proteins, lipids, polysaccharides,
nucleic acids and other cell components.
(d) to form and degrade biomolecules required in specialized functions of
cells.

Since the synthesis of the molecules, that are a component of cell, requires an
input of energy, while at the same time it is obvious that the cell components (such

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as cell membrane and its constituent transport proteins) are needed to provide the
energy supply and to control intracellular solute concentrations.
The specialized functions such as;
 movement,
 the secretion of a particular type of molecule or
 stimulation of an adjacent cell also require biosynthetic processes as
well as a supply of energy.

The processes of anabolism or assimilation (also synonyms) utilize food

materials (or intermediates from catabolism) and energy to synthesize cell
components as shown in Fig 1.

Fig. 1. Energy relations between catabolic and anabolic pathways

In dealing with the energy relations of the biological processes, the term
exergonic is used to denote a chemical reaction which liberates chemical-free
energy. The term exothermic refers to the total energy liberated including heat.
Although the magnitude of heat energy is small and also that it cannot drive

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biological reactions, the biochemists are more interested in free energy changes and
often use the term exergonic. The corresponding energy-consuming term
endergonic refers to the processes which require an input of free energy while the
term endothermic denotes a total energy requirement including heat.

The organisms which reduce oxygen are said to be aerobic. The route or
pathway by which this reaction is accomplished (esp., its terminal steps) is called
respiration or defined as the terminal processes involved in the reduction of
molecular oxygen. The organisms which reduce not oxygen but other compounds
are said to be anaerobic.

Fermentation is a natural process through which microorganisms like yeast and bacteria
convert carbohydrates such as starch and sugar into alcohol or acids. The alcohol or acids
act as a natural preservative and give fermented foods a distinct zest and tartness.
Fermentation also promotes the growth of beneficial bacteria, known as probiotics.

Functions of Metabolism
An arrays of enzyme-catalyzed chemical reactions, that bring about
transformations of certain organic compounds vital to the organism, constitute
metabolic pathways or metabolic routes.
The molecules or the compounds which participate in these reactions are
called as metabolic intermediates or metabolites. The synthesis of cell constituents
begins with the metabolic pathways which supply the building blocks. The major
cell constituents are;
 complex carbohydrates,
 the proteins,
 the lipids, and
 the nucleic acids.
In mammalian cells, these key metabolites come from one of the following 3
sources.
(a) Absorption of the metabolites from outside the cell and by implication,
if we consider the organism as a whole, by absorption of the metabolites as
dietary constituents from the alimentary tract.
(b) Release of the metabolite from a source stored with the cell. The
metabolite may be released either from a molecule used solely for storage
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 (such as glycogen or triacylglycerol), or from a molecule that has another
function within the cell (such as an enzyme or a membrane lipid).
(c) The metabolite may be formed by the metabolism of a simple precursor.
However, the precursor must be absorbed by the cell or derived from a source
stored within the cell.
Following are the key functions of metabolism:
A. Metabolism enables the cell to convert some of the energy found in
nutrients into a form which will support biosynthesis, the maintenance of
homeostasis and the cell’s other energy-requiring processes.
Biosynthetic reaction sequences or pathways in the cell require an input of
energy in the form of ATP or a reduced coenzyme (NADH, NADPH). It is
noteworthy that the usefulness of ATP as an energy source is not a consequence of
any special or ‘high energy’ form of the phosphate bond, but a function of how far
the hydrolysis of ATP is displaced from equilibrium.
Mammalian cells have 5 reaction schemes which are capable of supplying
cells with adequate amounts of energy in one of these forms. These energy
conserving pathways (or energy-supplying processes) are listed below:
The glycolytic pathway: This converts glucose into 3-c compounds, pyruvate
or lactate.
The citric acid cycle (CAC): This converts 2-c acetate units into carbon
dioxide.
The pentose phosphate pathway (PPP): This converts glucose-6-phosphate
into pentose phosphate, and reduces the NADP+ coenzyme.
The β-oxidation of fatty acids: This converts fatty acids into 2-c units, and
reduces the coenzymes FAD and NAD+.
Oxidative phosphorylation: This is the electron transport phosphorylation
process in which molecular oxygen is used to oxidize the coenzymes, which
are reduced in the other 4 pathways, with the production of water and the
conversion of ADP plus phosphate into ATP.
The glycolytic pathway, can be distinguished from the others because it is
capable of operating independently of a supply of oxygen out of 5 energy-supplying
processes. It can operate as an anaerobic pathway even oxygen is plentifully

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available i.e. in an oxygen-independent mode. However all other (4)
energy-supplying pathways lack this flexibility since they can only function in the
presence of oxygen.

B. Metabolism provides key metabolites which are required for the synthesis of
many essential cell components.In addition to supplying the cell with energy, these
central pathways provide precursors required for the formation of;
 carbohydrates,
 proteins,
 lipids and
 nucleic acids
Glycolysis, which is responsible for the conversion of glucose into 3-C
compounds, illustrates the dual role of these central metabolic pathways. The
glycolytic pathway supplies the cell;
 ATP and
 Acetyl-coenzyme A (acetyl-CoA) + glycerol-3-phosphate required (to
form the phospholipids needed for the cell membranes).
The pentose phosphate pathway (PPP) provides a different sort of example
since it is responsible for supplying energy (as NADPH) for fatty acid synthesis, but
it also supplies the phosphoribosyl-1-pyrophosphate needed for the formation of
nucleotides, the precursors of the nucleic acids.
The Metabolic Roles of ATP
The energy produced by one biological reaction or process, such as the
synthesis of X – Y in is often coupled to a second reaction, such as the hydrolysis
of ATP. The first reaction would not otherwise occur spontaneously;

The sum of the Gibbs free energy (available energy) changes for the coupled
reactions must be negative for the reactions to proceed. This does not mean that both
of the individual reactions have to be favored in isolation (ΔG < 0). The advantage

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of coupled reactions is that the energy released from one of them can be used to drive
the other even when the second reaction is unfavorable by itself (ΔG > 0).
Energy flow in metabolism depends on many coupled reactions involving
ATP. In many cases, the coupled reactions are linked by a shared intermediate such
as a phosphorylated derivative of reactant X.
Transfer of either a phosphoryl group or a nucleotidyl group to a substrate
activates that substrate (i.e., prepares it for a reaction that has a large negative Gibbs
free energy change). The activated compound (X - P) can be either a metabolite or
the side chain of an amino acid residue in the active site of an enzyme. The
intermediate then reacts with a second substrate to complete the reaction.
Experimental Methods for Studying Metabolism
The complexity of many metabolic pathways makes them difficult to study.
Reaction conditions used with isolated reactants in the test tube (in vitro) are often
very different from the reaction conditions in the intact cell (in vivo). The study of
the chemical events of metabolism is one of the oldest branches of biochemistry, and
many approaches have been developed to characterize the enzymes, intermediates,
flux, and regulation of metabolic pathways.
A classical approach to unraveling metabolic pathways is to add a substrate
to preparations of tissues, cells, or subcellular fractions and then follow the
emergence of intermediates and end products. The fate of a substrate is easier to
trace when the substrate has been specifically labeled. Since the advent of nuclear
chemistry, isotopic tracers have been used to map the transformations of metabolites.
For example, compounds containing atoms of radioactive isotopes such as 3H
or 14C can be added to cells or other preparations, and the radioactive compounds
produced by anabolic or catabolic reactions can be purified and identified. Nuclear
magnetic resonance (NMR) spectroscopy can trace the reactions of certain isotopes.
It can also be employed to study the metabolism of whole animals (including
humans) and is being used for clinical analysis.
By determining the substrate specificity and kinetic properties of a purified
enzyme, it is possible to draw some conclusions regarding the regulatory role of
that enzyme. It’s the approach that allows us to understand the relationship between
structure and function. However, a complete assessment of the regulation of a
pathway requires analysis of metabolite concentrations in the intact cell or organism
under various conditions.
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 Typically, a defective enzyme results in a deficiency of its product and the
accumulation of its substrate or a product derived from the substrate by a branch
pathway. This approach has been extremely successful in identifying metabolic
pathways in simple organisms such as bacteria, yeast, and Neurospora. In humans,
enzyme defects are manifested in metabolic diseases. Hundreds of single-gene
diseases are known. Some are extremely rare, and others are fairly common; some
are tragically severe. In cases where a metabolic disorder produces only mild
symptoms, it appears that the network of metabolic reactions contains enough
overlap and redundancy to allow near-normal development of the organism.
In instances where natural mutations are not available, mutant organisms can be
generated by treatment with radiation or chemical mutagens (agents that cause
mutation). Biochemists have characterized entire pathways by producing a series
of mutants, isolating them, and examining their nutritional requirements and
accumulated metabolites. Bacterial and yeast systems have been the most widely
used for introducing mutations because large numbers of these organisms can be
grown in a short period of time. It is possible to produce animal models—
particularly insects and nematodes—in which certain genes are not expressed. It is
also possible to delete certain genes in vertebrates. “Gene knockout” mice, for
instance, provide an experimental system for investigating the complexities of
mammalian metabolism.
In a similar fashion, investigating the actions of metabolic inhibitors has helped
identify individual steps in metabolic pathways. The inhibition of one step of a
pathway affects the entire pathway. Because the substrate of the inhibited enzyme
accumulates, it can be isolated and characterized more easily. Intermediates formed
in steps preceding the site of inhibition also accumulate. The use of inhibitory drugs
not only helps in the study of metabolism but also determines the mechanism of
action of the drug, often leading to improved drug variations.