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Dr.

Ghanshyam R Parmar
 All organisms need to transform and interconvert
a vast number of organic compounds.
 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.
 Primary
◦ Carbohydrates
◦ Protein
◦ Lipids
 Secondary
◦ Metabolic products of Primary metabolites
 C1 from S-methyl of l-methionine.
 C2 from acetyl-CoA.
 C5 ‘isoprene’ from mevalonate or
methylerythritol phosphate.
 C6C3 phenylpropyl from l-phenylalanine or l-
tyrosine.
 C6C2N from l-phenylalanine or l-tyrosine
 C4N cyclic pyrrolidine from l-ornithine
 C5N from C4N l-lysine
 Alkylation Reactions: Nucleophilic Substitution
 Alkylation Reactions: Electrophilic Addition
 Wagner–Meerwein Rearrangements
 Aldol and Claisen Reactions
 Imine Formation and the Mannich Reaction
 Amino Acids and Transamination
 Decarboxylation Reactions
 Oxidation and Reduction Reactions
 Phenolic Oxidative Coupling
 Halogenation Reactions
 Glycosylation Reactions
 The various organized structures in the cells eg: chloroplast,
mitrochondria plays an important role in metabolic reactions.
 The growing seedlings first of all develop the rich foliage which
produces large quantities of carbohydrates by photosynthesis.
 During a phase of growth and differentiation most of these
carbohydrates are metabolized for the sake of energy requirements
in the metabolic process and also for building the cellular
organization or it is stored in the cells as a reserve polysaccharide
like starch.
 During the metabolism of starch, or
monosaccharides like glucose it is broken down to
glycerates, pyruvates and later to acetyl Co A
which is finally consumed in the TCA cycle.
 During the course of this breakdown glycerates
and pyruvates gives rise to aliphatic and aromatic
amino acids which further produce the proteins.
 Pyruvates are broken down to acetyl CoA which yield through fatty
acids fixed oils and fats.

 All these primary products are termed as primary metabolites


because of their direct utilization in biological system at the
developmental stages of the plant.

 Once the developmental necessities of the plant are fulfilled, these


excessive quantities of carbohydrates, proteins and fats are stored
in the cells as starch grains, aleurone grains or fixed oils and fats
respectively which represent food storage products.
 During the biosynthetic reactions, many by products of metabolism
are produced.

 Most of these by products are stored in various morphological part


of the plant.

 These by products which do not have any primary function in the


plants and are in fact secondary products of metabolism are called
secondary metabolites.

 The secondary metabolites derived through one single or mixed


pathways gives rise to other compounds like carbohydrates,
proteins, fixed oils, fats, alkaloids, glycosides, resins, tannins, gums
and mucilages etc.

 These by products are used as food material, colourants, pesticides


and as medicinal agents.
 Carbohydrates are the products of photosynthesis, a biological
process that converts light energy into chemical energy.

 The general process of photosynthesis can be described by

CO2 + H2O Green Plants Sugars + O2


uv
 All green plants and certain algae and becteria have the capacity to
synthesize Adenosine Tri-phosphate (ATP) and Nicotine Adenine
Dinucleotide phosphate (NADPH).

 These compounds mediate most of the biosynthetic reactions in


plants.
 These are basically two primary light mediated processes in
photosynthesis which are

a) Absorption of light by chlorophyll or energy transfer to chlorophyll


by other light absorbing pigments leading to production of ATP and
NADPH.

b) Photolysis of water to produce oxygen and electrons which are


transferred via carrier species and produces ATP and NADPH, two
reactive molecules which work as activating and reducing agents
respectively during biosynthetic reactions.
 Acetate Mevalonate Pathway:
 Since a long time biochemists were aware of the involvement of
acetic acid in the synthesis of cholesterol, squlene and rubber like
compounds.
 The discovey of acetyl co enzyme A called as “active acetate” in
1950, further supported the role of acetic acid in biogenesis
pathways.
 Later, mevalonic acid was found to be associated with the acetate.

 Mevalonic acid further produced isopentenyl pyrophosphate (IPP)


and its isomer Dimethylallyl Pyrophosphate (DMAPP).
 These two main intermediates IPP and DMAPP set the „active
isoprene‟ units as a basic building block of isoorenoid compounds.
 Both of these units yield geranyl pyrophosphate (C10-
monoterpenes) which further association with IPP produces fernesyl
pyrophosphate (C15- sesquiterpenes).
 Fernesyl pyrophosphate with one more unit of IPP develops into
geranyl-geranyl pyrophosphate (C20- diterpenes).

 The fernesyl pyrophosphate multiplies with its own unit to produce


squalene and sunsequent cyclization gives rise to
cyclopentanoperhydrophenantherene skeleton containing steroidal
compounds like cholesterol and other groups like triterpenoids.

 The acetate mevalonate pathway thus works through IPP and


DMAPP via squalene to produce two different skeleton containing
compounds i.e. steroids and triterpenoids.

 It also produces vast array of monoterpenoids, sesquiterpenoids,


diterpenoids, carotenoids, polyprenols and also the compounds like
glycosides and alkaloids in association with other pathways.
The Mevalonate Pathway to
Isopentenyl Diphosphate
●Begins with conversion of
acetate to acetyl CoA
●Claisen condensation
yields acetoacetyl CoA
●Second Claisen
condensation reaction with
third molecule of acetyl
CoA yields six-carbon
compound 3-hydroxy-3-
methylglutaryl CoA
●3-Hydroxy-3-methylglutaryl
CoA is reduced to
mevalonate
●Phosphorylation with loss
STEP 1 OF FIGURE CLAISEN CONDENSATION
First step in mevalonate biosynthesis is a Claisen condensation to
yield acetoacetyl CoA
●Catalyzed by acetoacetyl-CoA acetyltransferase
●Acetyl group is first bound to enzyme by nucleophilic acyl
substitution reaction with cysteine –SH group
●Formation of enolate ion from second molecule of acetyl CoA
followed by Claisen condensation yields product
STEP 2 OF FIGURE : ALDOL CONDENSATION
Acetoacetyl CoA undergoes an aldol-like addition of an
acetyl CoA enolate ion
●Reaction catalyzed by 3-hydroxy-3-methylglutaryl-
CoA synthase
●Occurs by initial binding of substrate to cysteine –SH
group followed by enolate addition and hydrolysis
STEP 3 OF FIGURE: REDUCTION
Reduction of HMG-CoA to give (R)-mevalonate is catalyzed by 3-
hydroxy-3-methylglutaryl-CoA reductase
●Requires 2 equivalents of NADPH
●Reaction occurs in two steps and proceeds through an aldehyde
intermediate
○Nucleophilic acyl substitution involving hydride transfer from
NADPH to thioester carbonyl group of HMG-CoA
○CoA is expelled and aldehyde undergoes second hydride
addition to give mevalonate
STEP 4 OF FIGURE : PHOSPHORYLATION AND

DECARBOXYLATION

Three additional reactions convert mevalonate to isopentenyl

diphosphate

●Two phosphorylations on terminal phosphorus of ATP catalyzed by


mevalonate kinase

●Phosphorylation of tertiary hydroxyl group followed by


decarboxylation and loss of phosphate ion
●Final decarboxylation is catalyzed by mevalonate-5-diphosphate

decarboxylase

○Substrate is phosphorylated on tertiary –OH group by ATP

○Tertiary phosphate spontaneously dissociates

○Tertiary carbocation acts as electron acceptor to facilitate

decarboxylation
Conversion of Isopentenyl Diphosphate to Terpenoids

Conversion of isopentenyl diphosphate (IPP) to terpenoids

begins with its isomerization catalyzed by IPP isomerase to

dimethylallyl diphosphate (formerly called dimethylallyl

pyrophosphate and abbreviated DMAPP)

●Proceeds through carbocation pathway


●Isopentenyl
diphosphate (IPP)

and dimethylallyl

diphosphate

(DMAPP) combine

to give C10 geranyl

diphosphate (GPP)

●Combination of GPP
with another IPP

gives C15 farnesyl

diphosphate (FPP)

●Reductive
Mechanism of coupling DMAPP with IPP to give GPP catalyzed
by farnesyl diphosphate synthase
●Process requires Mg2+ ion
●Key step is a nucleophilic
substitution reaction
●IPP double bond
acts as nucleophile
displacing PPi
●Further conversion of geranyl diphosphate into
monoterpenoids involves carbocation intermediates

○Catalyzed by terpene cyclases


○Geranyl diphosphate isomerizes to allylic isomer linalyl
diphosphate (LPP)

■Catalyzed by monoterpene cyclases


■Isomerization converts C2-C3 double bond of GPP into a
single bond
■Makes cyclization possible
■Allows E/Z isomerization of double bond

○Dissociation and cyclization by electrophilic addition of


Acetate Malonate Pathways:

 Acetate pathway operates functionally 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 (arachidc
acid). The synthesis of fatty acids is thus explained by following
reaction.
M
o
It II
OOC-CH2-C- Co A
113C--C-CO_A

~
o o
11
OOC-CH2-C--S-ACP
n
H3C--C--S-ACP

A.cetyJACP Malonyl ACP

C> 0
11 II
H3C-C-C~-C--S-ACP Acetoacetyl ACP
..
.
'. Palmit:oyl-A.CP Palmitic acid

". o
.
_H3C-(C~)"\6-C--S-ACP
II
Stearoyl ACP Stearic acid
1
I H3C-(CH2>7-CH=CH-(CH:z.>7--C-5-ACP

Oleoyl ACP
o
11 -
Oleic acid (16:1)

Linoleioy' ACP
l -2H
Li noleic acid (16:2)

,I
( Linolenoyl
~ -2H

ACP Linolenic aCid(16:3)

I
I ~
i

• Arachidonyl ACP Arachidonic

---------------------------
Fig 1.0_3: Acet:.a~e~alona.e
--- -- ----
Pathwa
---- -
Polyacetate Malonate Pathway:

 Acetate pathway is also actively involved in the biosynthesis of


endocrocin, an intermediate of anthraquinone group of compounds
via polyketide formation.

 Endocrocin after decarboxylation yield emodin.

 Acetyl CoA first produces malonyl CoA and then engaged in chain
lengthening from the combination of malonyl CoA and terminal
acetate.

 This pathwaay is termed as polyacetate malonate pathway which


produces variety of anthraquinone derivatives in higher plants.
 Shikimic acid pathway is an important route for the biosynthesis of
phenylpropanoid (C6-C3 compounds)derivatives.
 Two important starters for these compounds of ubiquitous nature
are phosphoenolpyruvate, a metabolite of glucose and a tetrose
sugar, erythrose $-phosphate derived via photosynthesis.
 Both of these intermediates are condesend together to yield 2-keto
3-deoxy-7-phospho D-glucoheptanoic acid which further afford 3-
dehydroquinic acid, 3-dehydroshikimic acid and shikimic acid 3-
phosphate.
 The later gets condensed with an unit of phosphoenolpyruvate to
yield phenylpyruvic or p-hydroxy phenyl pyruvic acis which in turn
undergo reductive amination to afford two important amino acids
phenylalanine and tyrosine respectively.
 Chorismic acid through some other chains of reaction produces
anthranilic acid which gives rise to tryptophen.

The shikimic acid pathway is used for the biogenesis of phenolic
compounds, tannins, lignans and phenylpropane units of flavonoids
and coumarins.
t'~

H~ ;- jH20P03H2

O~"""OH
OH
Eryt:.h.rose-4-P

J, ,.
Phenyla lan ine

o
OH
Tryosine

r o
1 OH
eOOH eOOH
, ..
H.
O

I
OH
2-ket<>-3-deoxy-7-phospho- I - lucoheptanoic
acid
-
HO ! Phenylpyruvic acid OH
p-HY<!roxyphenylpYTU
acid
eOOH
OH
OH
-Dchydroquinic acid

.!. eH3
N
H
I• H CH3
Tryptophan
I 0
I 3-Dehy~shim:i1cic
OH

acid r
Prephenic acid
Phosp~ori
pyropho

! C:OOH
CC>C>H COOH Serine

OH
HO OH
OH OH
OH
Shiklfn:ac ,d Slnkimic cid-_ -phosphan:: Chorismjc acid Ant:hranilic acid
Fig. 0.4: Bios nth 0" Aromat:ic
i<e ; compounds by Shikimic acid ~.at:h'¥Va_y_._...I"..:.IIII"
 The precursors for the flavonoids are the unstable chalcones which
are derived from the shilimic acid pathways and acetate pathways.

 The C6-C3 unit of phenylpropane formed by shikimate pathway


undergo chain building by the asociation of acetate units via malonyl
CoA to produce polyketide.

 A polyketide by ring closure gives rise to various types of flavonoids


derivatives.
 In plants amino acids are formed and found in the free state or as
the fundamental units of proteins.

 Some aromatic amino acids like that of phenylalanine, tyrosine and


tryptophen are biosynthesized via shikimic acid pathway.

 The aliphatic and heterocyclic amino acids have some different


route of biogenesis.

 Nitrogen enters in the metabolic reactions by reductive amination of


α-keto acids like pyruvic, oxaloacetic and α-ketoutaric acids to afford
the aliphatic amino acids like alanine, aspartic acid and glutamic
acid respectively.
 Peptides and proteins are biosynthesized from the amino acids.

 The molecules of amino acids gets condensed with each other by


forming a peptide linkage to form dipeptide, tripeptide and
subsequently polypeptide with more than three amino acids.

 Protein synthesis generally takes place in association with the


ribosomes present in the endoplasmic reticulum.