Biosynthetic pathways of

secondary metabolites
Introduction :
• All organisms need to transform and interconvert a vast number of organic
compounds to enable them to live, grow, and reproduce.

• They need to provide themselves with energy in the form of ATP, and a
supply of building blocks to construct their own tissues.

• An integrated network of enzyme-mediated and carefully regulated chemical

reactions is used for this purpose, collectively referred to as ‘intermediary
metabolism’, and the pathways involved are termed ‘Metabolic pathways’
Biosynthesis :

It is a multistep enzyme catalysed process where substrate are converted into more complex

products in living organisms. In biosynthesis simple compounds are modified and converted

into other compounds are joined together to form macromolecules.

Metabolites

• Metabolites are the intermediate products of metabolic reactions catalyzed by various enzymes

that naturally occur within cells.

• They are the intermediate end product of metabolism . The term metabolites is usually restricted to
small molecules.

• During the process of metabolism many intermediate metabolites are formed which is used to
denote the chemical pathways of metabolism. Cellular metabolism has four functions.

1. To obtain chemical energy i.e ATP through degradation of energy reach biomolecules.

2. To transform biomolecules into building blocks or precursors needed for the synthesis of
macromolecular cell components.
3. To assemble building blocks into proteins, nucleic acids, lipids and other cell
components.

4. To form and degrade biomolecules required in the specialized functions of cells.

• As a result of metabolic process in plants, plant synthesizes primary plant metabolites and
secondary plant metabolites.
 Primary plant metabolites-

• These are considered as basic plant constituents like sugars, amino acids,

coenzyme A, mevalonic acid and lipids.

• They are widely distributed in plants in large quantities and are directly involved

in growth, development and reproduction, non-expensive to isolate from plant

• e.g starch from potato and do not possess biological or pharmacological action.
 Secondary plant metabolites-

• These are biosynthesized from the primary metabolites e.g- alkaloids, glycosides, tannins,

flavonoids, terpenoids and volatile oils.

• They are more limited in distribution , restricted to taxonomic group , not directly involved in the

growth and development.

• Possess biological or pharmacological action on humans and animals , involved in chemical

adaptation to environmental stress .

• Serve as defensive, protective chemicals against microorganisms, insects and higher herbivorous

animals and present in small quantities.

• Generally expensive to isolate from plant compared to primary metabolites e.g- quinine form

cinchona bark.
• In contrast to these primary metabolic pathways, which synthesize, degrade, and generally
interconvert compounds commonly encountered in all organisms, there also exists an area
of metabolism concerned with compounds which have a much more limited distribution
in nature. Such compounds, called ‘secondary metabolites’, are found in only specific
organisms, or groups of organisms, and are an expression of the individuality of species.

• Secondary metabolites are not necessarily produced under all conditions, and in the vast
majority of cases the function of these compounds and their benefit to the organism is not
yet known.
 Basic Metabolic Pathway:

• The building blocks for secondary metabolites are derived from primary metabolism.

• This outlines how metabolites from photosynthesis, glycolysis, and the Krebs cycle are tapped off from

energy-generating processes to provide biosynthetic intermediates.

• The most important building blocks used in the biosynthesis of secondary metabolites are derived from the

intermediates acetyl coenzyme A (acetyl-CoA), shikimic acid, mevalonic acid, and 1-deoxyxylulose 5-

phosphate.

• These are utilized respectively in the acetate, shikimate, mevalonate, and deoxyxylulose phosphate

pathways.
• Living plants are solar-powered biochemical and biosynthetic laboratory which

manufactures both primary and secondary metabolites from air, water, minerals and

sunlight.

• The primary metabolites like sugars, amino acids & fatty acids that are needed for general

growth & physiological development of plant which distributed in nature & also utilized as

food by man.

• The secondary metabolites such as alkaloids, glycosides, Flavonoids, volatile oils etc. are

biosynthetically derived from primary metabolites.

Schematic representation of the primary and secondary metabolites derived from carbon
metabolism in plants as follows.
Carbohydrates Glycosides(sugar moiety
SUGAR (Polysaccharides
Photosynthesis Complex polysaccharides
Nucleic acid)

Glycolysis pathways Pentose phosphate pathways

Shikimic acid metabolites
Phenylpropanoids - Tannins ,Lignin
Phosphoenol pyruvate
SHIKIMIC ACID Flavonoids, coumarin
PATHWAY
pyruvate

TCA cycle Aromatic amino acids

Proteins
Aliphatic amino acids
Malonyl CoA Acetyl CoA

Fatty acids Mevalonic acids , Steroids ,

Lipids Terpenoids , isoprenoids
 Biosynthetic pathway of secondary metabolites

 Shikimic acid pathway

 Acetate pathways

Amino acid pathways

Shikimic Acid Pathway

• It is also known as biosynthesis of aromatic amino acids.

• This occurs mainly in plants , fungi and bacteria but animals do not synthesize the same.

• Its name came from Japanese flower Shikimi ( Illicium anisatum) from which shikimic acid was first
isolated in 1885 by john Fredrick.

• The majority of the aromatic compounds are biosynthesized via shikimic acid pathways.

• This pathway is the key intermediate from carbohydrates (derived from glycosides and pentose
phosphate pathway) for biosynthesis of phenyl propane derivatives (C6-C3 units),

• Shikimic acid pathway is the Precursors for synthesis of aromatic amino acids (phenyl alanine , tyrosine
, and tryptophan) and also acts as intermediates for synthesis of secondary metabolites like
phenylpropanoids like tannins , flavonoids , coumarins , vanillin etc.
 The shikimic acid pathways consists of several enzymatic steps.

1. Shikimic acid pathway starts with the Erythrose 4-Phosphate (obtained from the pentose
phosphate pathways) and Phosphoenol pyruvate (obtained from glycolysis pathway)
on aldol condensation to yield DAHP ( 2-Keto-3-Deoxy-7- Phospho D-
glucoheptonicacid).

2. Elimination of phosphoric acid from DAHP followed by intermolecular aldol reaction

generates the first carbocyclic intermediate DHQ (3-Dehydroquinic acid) in the
presence of DHQ synthase.

Condensation -H3Po4
-cyclization
3. DHQ which on dehydration to form 3-dehydroshikimic acid by the enzyme DHQ dehydratase
which is reduced to shikimic acid by the enzyme DHQ dehydrogenase.

NADPH NAD+
Reduction

-H20

4. The next enzyme involved is shikimate kinase, an enzyme that catalyzes the ATP dependent
phosphorylation of shikimate to form shikimate 3-phosphate. Shikimate 3-phosphate is then
coupled with phosphoenol pyruvate to give 5-enolpyruvylshikimate-3-phosphate via the
enzyme 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase.
5. The next product chorismic acid is formed from the product 5-enol pyruvyl shikimate-3 phosphate via the
enzyme chorismate synthase.

H3PO4

ATP ADP

6. Clasien rearrangement reaction occurs with chorismic acid in the presence of enzymes chorismate mutase give
rise to prephenic acid .

Chorismate mutase
7. Prephenic acid on decarboxylation gives P-hydroxy phenyl pyruvic
acid which on reductive amination forms Tyrosine.

• Phenyl pyruvic acid on reductive amination forms Phenylalanine , this

-H20 and –CO2 –CO2
reaction is catalysed by the enzyme transaminase.

• Chorismic acid in presence of enzyme anthranilate synthase forms

anthranilic acid , which inturn isomerizes to form Tryptophan.

Transamination
 Condensation -H3Po4 Reduction
-cyclization -H20

NADPH

NAD+
ATP
ADP

-H20 and –CO2 –CO2

 Role of Shikimic Acid Pathway:

• Starting Point in the Biosynthesis of Some Phenolics Phenyl alanine and tyrosine are the
precursors used in the biosynthesis of phenylpropanoids.

• The phenylpropanoids are then used to produce the flavonoids, coumarins, tannins and lignin.

Gallic acid biosynthesis, Gallic acid is formed from 3-dehydroshikimate by the action of the
enzyme shikimate dehydrogenase to produce 3,5- didehydroshikimate. The latter compound
spontaneously rearranges to gallic acid.

 Other compounds

• Shikimic acid is a precursor for indole, indole derivatives and aromatic amino acid tryptophan and
tryptophan derivatives such as the psychedelic compound dimethyltryptamine.

• Many alkaloids and other aromatic metabolites.

 Acetate pathways: Acetate-Mevalonate Pathway / Isoprenoid pathway

• Isoprenoid pathway is also known as terpenoid pathway or acetate mevalonate pathway.

• This pathway contributes one-third of all known secondary metabolites .

• The isoprene units from this pathway is contributed in biosynthesis of many other metabolites such as
anthraquinones , napthaquinones , terpenoids and indole alkaloids.

• Since a long time it was believed that acetic acid is involved in the synthesis of cholesterol, squalene and
rubber-like compounds.

• The discovery of Acetyl coenzyme A further supported the role of acetic acid in biogenetic pathways. Later,
mevalonic acid was found to be associated with the acetate.

• The Acetate Malonate pathway is important in the formation of various important phytoconstituents like
fatty acids, polyketides, prostaglandins, aflatoxin, tetracycline and other various important phytoconstituents
• The pathway begins with acetyl CoA molecule produced from pyruvic acid, which is the
end product of glycolysis.

• First 2 molecules of acetyl CoA forms acetoacetyl CoA through Claisen condensation.

• Third molecule of acetyl CoA coupled with Acetoacetyl CoA forms an important
intermediate β-hydroxy β-methylglutaryl-CoA (HMG-CoA) by aldol reaction.

-CoA

-H2O
• Next on reduction gives rise to mevalonic acid, during this reaction CoA is liberated which is the
main precursor for biosynthesis of terpenoids.

• Mevalonic acid on ATP mediated phosphorylation gives mevalonic acid diphosphate which on
oxidative decarboxylation and elimination of phosphate gives the 1st isoprene unit, isopentyl
pyrophosphate (IPP).

• By the isomerase enzyme, the IPP gives 2nd isoprene unit Dimethyl allyl pyrophosphate (DMAPP)

-CoA

Isomerase enzyme
• Electrophilic addition of IPP with DMAPP via enzyme prenyl transferase yield C10 unit, geranyl
pyrophosphate (GPP), which is the precursor for synthesis of monoterpenes.

• Combinations of another IPP unit with GPP give rise to form farnesyl pyrophosphate (FPP), C15
unit which acts as a precursor for the synthesis of sesquiterpene.

-Pyrophosphate
• Further addition of IPP unit to FPP gives C20 geranyl geraniol pyrophosphate (GGPP) to produce a
range of Diterpenes.

• On further addition of IPP unit gives C25 geranyl farnesyl pyrophosphate called Sesterterpenes.

• The tail to tail addition of two FPP units yields C30 unit, triterpene. Similarly 2 units of GGPP yield
C40 unit, tetraterpene.
The acetate mevalonate pathway thus
works through IPP and DMAPP via
squalene to produce two different
skeleton containing compounds, that is,
steroids and triterpenoids. It also
produces vast range of
monoterpenoids, sesquiterpenoids,
diterpenoids, carotenoids, polyprenols,
and also the compounds like
glycosides .
Acetate-Malonate Pathway:

• Acetate pathway operates with the involvement of acyl carrier protein (ACP) to yield
fatty acyl thioesters of ACP.

• These acyl thioesters forms the important intermediates in fatty acid synthesis.

• These C2 acetyl CoA units at the later stage produces even number of fatty acids from n-
tetranoic (butyric) to n-ecosanoic (arachidic acid).

• Unsaturated fatty acids are produced by subsequent direct dehydrogenation of saturated

fatty acids. Enzymes play important role in governing the position of newly introduced
double bonds in the fatty acids.
Acetate-Malonate Pathway:
Significance of Acetate Mevalonate pathway :

1. Mevalonic acid is the biosynthetic precursor for Isoprene units (C5H8).

2. Mevalonic acid serves as precursor for various steroidal and terpenoidal molecules.

3. The main products of the acetate malonate pathway are the fatty acids (saturated and

unsaturated).

4. This pathway makes an important contribution to plant aliphatic and aromatic

compounds.
Amino acid pathway
• Amino acids occur in plants in free state . They are the basic units of proteins and other
metabolites.

• It is the set of metabolic pathways by which the various amino acids are produced from other
compounds.

• All amino acids are derived from intermediates from glycolysis , TCA cycle , Pentose phosphate
pathway.

• Nitrogen enters these pathway by way of glutamate and glutamine.

• Plants are able to synthesize all 20 of the amino acids necessary for protein synthesis by
themselves and categoried into two types .
• Around 20 amino acids are important for the synthesis of protein in the plant. The transamination
reaction along with other like acids, alanine, glutamic acid and aspartic acid with amino transferase
enzyme transfer the amino group.

• The amino acid can be differentiated into five different groups:

1. The Glutamate family-α-ketoglutarate is the precursor for this family. Glutamate, glutamine,
arginine, and proline are the main amino acids belonging to this family.

2. Aspartate family- Oxaloacetate is the starting material for this group. The main examples of amino
acid of this group are aspargine, isoleucine, threonine, aspartate and methionine.

3. Another example is Alanine-valine - leucine group.(Pyruvate)

4. The amino acid of serine glycine group.(3-Phosphoglycerate).

5. Aromatic amino acids with pyruvate 3-phosphoglycerate phosphoenol pyruvate and erythrose 4-
phosphate as starting material
Acetyl CoA
α ProlineKetoglutarate Gives Rise to Glutamate, Glutamine,
Proline, and Arginine

• Proline is a cyclized derivative of glutamate. In the first

step of proline synthesis, ATP reacts with the side chain
carboxyl group of glutamate to form an acyl phosphate,
which is reduced by NADP or NADH to glutamate
semialdehyde. This intermediate undergoes rapid
spontaneous cyclization and is then reduced further to yield
proline.