Metabolic pathways for synthesis of primary and secondary metabolites

1. Basic metabolic pathways and the
origin of secondary metabolites.

2. Introduction
• Living organism need to transform organic compounds for
life, growth, and reproduction.
• Enzymes are needed to mediate these transformations =
metabolic pathways
• The fundamental molecules: carbohydrates, proteins, fats
and nucleic acids.
• The metabolic pathways: degrading materials, whilst others
are then required to synthesize.
• This metabolism requires and energy

3. • Primary metabolism demonstrates a fundamental unity is all
organisms.
• i.e photosynthesis = sugars (carbohydrates) + energy
• Carbohydrates/sugars via glycolysis/Kreb’s cycle = energy
• Oxidation of fatty acids = energy
• Aerobic organisms optimise via phosphorylation = energy
• Degradation of the unrequired amino acids = energy
Primary metabolism = biochemistry

4. • Secondary metabolism uses metabolites from primary
metabolism as building blocks = intermediaries.
Acetyl coenzyme A (acetyl-CoA) via acetate pathway,
• Acetate pathway = Phenols, prostaglandins, and macrolide
antibiotics, fatty acids and derivatives.
Mevalonic acid via mevalonate pathway
• Mevalonate pathway channels acetate into a different series
of compounds.
The mevalonate and methylerythritol phosphate pathways =
terpenoid and steroid metabolites
Building blocks of secondary metabolism

5. shikimic acid via shikimate pathway,
• Shikimate pathway = phenols, cinnamic acid derivatives,
lignans and alkaloids.
• Other building blocks: Peptides, proteins, alkaloids, and many
antibiotics from amino acids, employed in natural product
synthesis.
Secondary metabolism = natural product chemistry.
Note: Primary and secondary metabolisms have blurring
boundaries and considerable overlap.

6. • The biosynthesis is biological and catalysed by enzymes.
• Many reactions occurring in the cell are enzyme-dependent.
Enzymes engineer reactions at normal temperatures and at
pH values around neutral in a manner not possible in a
laboratory.
1. Oxido-reductases;
for any oxidation, there is a simultaneous reduction.
2. Hydrolases;
They hydrolyze ester bonds; they include lipases, tannase in
tannins, lipids……
Enzymes
Classes:

7. Glycoside hydrolases (lactase, maltase, amylase, cellulase,
penicillinase, β-glucosidase .etc).
3. Lyases;
Lyase-catalyzed reactions break the C-O, C-S, C-C bonds.
They include L-tryptophan-decarboxylase and L-tyrosine / L-
dopa-decarboxylase…. which work in the biosynthesis of
monoterpenoid, indole alkaloids and benzylisoquinoline
alkaloids.
4. Isomerases; These also work in formation of terpenoids. E.g.
diphosphate isomerase and chalcone isomerase.

8. Coenzymes.
• Some enzymes require the presence of smaller organic
molecules (coenzyme) before they can participate in a
biochemical reaction.
• One group of coenzymes consists of esters of phosphoric
acid and various nucleosides. E.g. ATP, ADP, UTP, NADP, FAD,
FMN.
• Adenosine and Uridine phosphates serve to transport energy
in the form of high-energy phosphates bonds and

9. ….this energy is made available for biochemical reactions in
presence of appropriate enzymes.
• Other coenzymes are the decarboxylation coenzymes;
thiamine, biotin and pyridoxine.
• CoA (Coenzyme A).

10. 1. PHOTOSYNTHESIS (Biosynthesis of Carbohydrates).
Photosynthesis is a process by-which carbondioxide of the
atmosphere is converted into sugars by the green plant. The
mechanism of this carbon reduction follows this overall
reaction.
CO2 + H2O (CH2O) + O2
Photosynthesis occurs in the chloroplasts which are bounded by
definite membrane and are auto reproductive (separated
from the rest of the cell, chloroplasts can carry out the
complete process of photosynthesis)..
Light

11. • Chlorophyll is the principal pigment plus phycobilins.
• The result of photosynthesis is the production of ATP from
ADP and a phosphate and then decomposition of water to
hydrogen and oxygen.
• These two processes require light.

12. The process of photosynthesis:
• ATP is a coenzyme and the high energy of the terminal
phosphate bond is available to the organism for the supply of
energy.
• Decomposition of water produces free oxygen and hydrogen
ions which convert the electron carrier, NADP, to its reduced
form NADPH.
• In photosynthesis, there’re two systems; photosystem I and II.
• Photosystem I produces NADPH & some ATP & photosystem II
produces ATP.

13. • These systems involve two chlorophyll complexes which
absorb light at different wavelengths (above and below λ =
685 nm).
• The chlorophyll molecule captures solar energy & electrons
become excited and move to higher energy levels; on
returning to the normal low energy state, the electrons give
up their excess energy which is passed through a series of
carriers to generate NADPH & some ATP.

14. • Note: It has been proved that the oxygen liberated during
photosynthesis is derived from water and not carbon
dioxide.
• Following the light reactions, a series of dark reactions then
utilize NADPH in the reduction of CO2 to carbohydrates.

15. • The path of carbon in photosynthesis.
Photosynthesis
2molecules, 3-
phosphoglyceric acid
3-Phospho -
glyceraldehyde
Fructose 1:6 –di P
Fructose 6-P
CO2 Dihydroxyacetone-
P
Xylulose 5-P
Ribulose 1:5 - di P
Ribulose 5 - P
Ribose 5-
P
Erythrose 4-P
Sedoheptulose 7-P
Sedoheptulose 1:7 -di P

16. C -3 plants.
• These are green plants that produce 3-phosphoglyceric acid,
a C-3 Compound, during photosynthesis.
• There is the reaction of ribulose 1:5 –diphosphate that
combines with CO2 to produce two molecules of 3-
phosphoglyceric acid.

17. CAM-Plants.
• CAM stands for ‘Crassulacean Acid Metabolism’, called so
because it was in the Crassulaceae family.
• When water is not available, respiratory CO2 is recycled
under conditions of darkness, with formation of malic acid
as an intermediate.
• CO2 and H2O loss to the atmosphere are eliminated, a
condition which would be fatal for normal C-3 plants.

18. C-4 plants.
• These plants synthesize in presence of light, oxalo-acetic
acid & other C-4 acids. Carbon assimilation is based on a
modified leaf anatomy & biochemistry.
• They usually grow in semi-arid regions in a high light
intensity and possess an additional carbon-fixation system.
• In the mesophyll cells; pyruvate is converted via
Oxaloacetate to Malate.
• They are effective in their use of CO2 so cutting down on
photorespiration and loss of water.

19. Carbohydrate storage and utilization.
Storage carbohydrates such as starch of plants or glycogen of
animals is made available for energy production by a process
which involves conversion of glycogen or starch to pyruvate
and then to acetate (acetyl coenzyme A).
The latter is passed into the TCA cycle

20. 2. BIOSYNTHESIS OF GLYCOSIDES:
• Glycosides are certain molecules in which a sugar part
(glycon/genin) is bound to some other part which is non a
sugar (aglycon).
• The biosynthetic pathways of glycosides are widely variable
depending on the type of units present.
• The aglycone and glycon parts are biosynthesized separately,
then coupled to form a glycoside.
20

21. • Phosphorylation of a sugar yields a sugar1-phosphate,
which reacts with a Uridine Diphosphate (UDP) to form a
Uridine Diphosphate sugar (UDP-sugar) and inorganic
Phosphate.
• This UDP-sugar reacts with the aglycone to form the
glycoside and a free UDP.
• Sugar Phosphorylation = Sugar 1-phosphate + UDP
UDP-sugar + PPi + Aglycone = Sugar-aglycone + UDP.
(Glycoside)

22. 3. BIOSYNTHESIS OF PHENOLIC COMPOUNDS:
• These are a group of plant secondary metabolites.
Widespread in nature and found in most classes of natural
compounds having several hydroxyl groups attached to
aromatic moieties (benzene ring).
Acetate pathway of biosynthesis (hypothesis) :
• “The central position of acetate (C2H3O2) in relation to the
general metabolism of plants indicates a possibility by which
acetate condensation could occur to give a variety of
aromatic compounds.”

23. Shikimate pathway:
• The synthesis of phenolic compounds starts from the level of
aromatic amino acids; phenylalanine, tyrosine, tryptophan.
• These acids in themselves are synthesized starting with
phosphoenlopyruvate (PEP) (from respiration of pentose
sugars) and erythrose 4-P (from glycolysis) during a series of
successive reactions in schikimic acid pathway.
Note: This pathway is common to bacteria, fungi and plants but
absent in animals hence making these amino acids among the
10 essential ones.

24. • The pathway starts with condensation of erythrose 4-P and a
molecule of phosphoenolpyruvate (PEP).
• The resulting 7-C atom molecule (3-deoxyarabino-
heptulosonate 7C) undergoes cyclisation then a reduction
reaction to give a shikimate compound, from where the
name of the pathway is obtained.
• Subsequent reactions lead to a compound called 3-
enolpyruvylschikimate 5-P, that in turn will lead to the
formation of chorismate compound.

25. The enzyme responsible for this reaction is inhibited by a
herbicide =glyphosate.
• The Chorismate is situated at cross roads that lead to the
formation of phenylalanine and tyrosine from one part and
tryptophane from another part.

26. The phenolic compounds;
• The synthesis of the secondary phenolic compounds starts
by the deamination of phenylalanine in to cinnamic acid by
the enzyme phenylalanine ammonialyase.
• Another alternative path is the deamination of tyrosine to
coumaric acid.
• Sequential addition of the hydroxyl radical to coumaric acid
to form cafeic acid and a methoxyl= ferulic acid respectively.

27. Note: Non of these 4 simple phenolic compounds accumulate
in high quantities in the plants, their principal function is to
serve as precursors of the complex phenolic derivatives;
coumarin,
lignins,
tannins,
flavonoids e.t.c.

28. .
Schikimic pathway
Respiration; Pentose
phosphate path
Glycolysis
Erythrose 4-P Phosphoenopyruvate-P (PEP)
Gallic acid
Hydrolysable
Tannins
Tyrosine
Phenylalanine
Tryptophane
Alkaloids
Indole Acetic
Acid
Coumaric acid
Cinnamic acid Flavonoids
Condensed
Tannins
Cafeic acid Ferulic acid
Lignin Coumarins

29. • Despite their diversity, all the terpenic compounds and their
derivatives posses a common biosynthetic pathway called
‘mevalonic acid or mevalonate pathway’, due to the
intervention of an intermediary = melavonic acid.
• These compounds are considered to be polymers of a 5C
((5C)n) compound = 2-methyl1,3-buta-diene or isoprene.
• Hence they are often designated by the term ‘isoprenic
compounds’.
4. BIOSYNTHESIS OF TERPENIC COMPOUNDS.

30. NB: Infact, the units that constitute the terpenic compounds
are not the real isoprenes but the two phosphorylated
derivatives= isopentenyldiphosphate (IPP)= active isoprene
and its isomer = dimethylallyldiphosphate (DMAPP).
• The biosynthesis starts at the condensation of 3 molecules of
acetyl CoA to form the 3-hydroxy3-methylglutaryl-CoA (a 6C
molecule) which is transformed to mevalonic acid. This acid
is an efficient precursor of the terpenes.

31. • Mevalonic acid then undergoes phosphorylation (twice)
forming mevalonate diphosphate.
• A decarboxylation transforms this molecule to a 5C -
isopentenyldiphosphate (IPP) which by reversible
isomerization forms dimethylallyldiphosphate (DMAPP).
• The DMAPP undergoes a head-tail condensation with IPP
to form a 10C- geranyldiphosphate (GPP) which is the
origin of all the monoterpens. E.g. Iridoids
• More condensations form an intermediary=
fernesyldiphosphate (FPP), The FPP is at cross roads which
lead to the production of 15C – the sesquiterpens.
Among them is the abscissic acid.

32. • then gives geranylgeranyldiphosphate-20C (GGPP).
• The GGPP leads to the diterpens, for example the phytol.
The triterpens, for example the steroids, gibberellins and
the tetraterpens like the carotenoids.
• NB: Some of the terpenic compouds play the role of
primary metabolites, however the majority are secondary
and act as toxins or as persuasive elements for herbivore
insects.

33. • Terpenoids are biosynthesized from activated isoprene
units (C5H8).
Isoprene (Hemiterpenoid)
units
C5H8
Mono-terpenes C10H16
Sesqui-terpenes C15H24
Diterpenes
Sesterpenes
Triter-terpenes
Tetra-terpenes
Poly-terpenes
C20H32
C25
C30-derived
C40
Cn, n>40

34. H3C
C
H2C
C H
C H2
HO
C O O H
O
2
n
O
Limonene Camphor
Monoterpenes (C10)
-Carotene
Carotenoids
Rubber
Isoprene (C5)
Triterpenes (C30)
Squalene
Steroids
Sesquiterpenes (C15)
Zingiberene
Glycyrrhetinic acid
Poly-terpenes (C>40)
Tetra-terpenes (C40)
n
Diterpenes (C20)
Phytol

35. NB: In nature, there are a few chemicals which are found to
be composed of both isoprenoid and non-isoprenoids
moieties.
They are called as meroterpenoids.
Such meroterpenoid structures of natural origin reported
are;
quinine,
phylloquinone (vitamin K),
tocopherols (vitamin E, cannabinoids),
and various ergot alkaloids.

36. S/N Primary metabolites Secondary metabolites
1 Simple in nature Complex in nature
2 Widely distributed in nature, in
all organisms and present in large
quantities
Restricted to taxonomic groups and
present in small quantities
3 Generally, do not have biological
activity
Have biological activities. E.g Quinine-
antimalarial
4 Occur in growth phase of a plant Occur in stationary phase of a plant
5 Directly involved in growth,
development and reproduction
of plant
Responsible for properties like colour,
poisonous, taste and therapeutic
6 Are primary compounds Derived from primary compounds
7 Generally not expensive to
produce. E.g potato starch
Expensive to produce or isolate E.g
Quinine in cinchona back

37. Resource:
Medicinal Natural Products: A Biosynthetic Approach.
3rd Ed.