Secondary metabolites are compounds produced in other metabolic pathways that, although important, are not essential to the functioning of the plant whereas Primary metabolism in a plant comprises all metabolic pathways that are essential to the plant's survival. Primary metabolites are compounds that are directly involved in the growth and development of a plant. secondary plant metabolites are useful in the long term, often for defence purposes, and give plants characteristics such as colour. Secondary plant metabolites are also used in signalling and regulation of primary metabolic pathway. secondary metabolism plays a pinnacle role in keeping all the plant's system working properly. 
Types of Secondary Metabolites: Based on their biosynthetic origin, plant secondary metabolites can be divided into three major groups:
1.    Terpenes
2.    Flavonoids and allied phenolic and polyphenolic compounds,
3.    Nitrogen-containing alkaloids and sulphur-containing compounds

11.1.    Terpene
Terpenes are a large and diverse class of organic compounds, produced by a variety of plants, particularly conifers. They are often strong-smelling. Terpenes are major biosynthetic building blocks within nearly every living creature. 

11.1.1.    Biosynthesis of Terpenes:
Terpenes are derived biosynthetically from units of isoprene, which has the molecular formula C5H8. The basic molecular formula of terpenes is multiples of that, (C5H8). Where n is the number of linked isoprene units. This is called the isoprene rule or the C5 rule.

Isoprene itself does not undergo the building process, but rather activated forms, isopentenyl pyrophosphate (IPP or also isopentenyl diphosphate) and dimethylallyl pyrophosphate (DMAPP or also dimethylallyl diphosphate), are the components in the biosynthetic pathway.
11.1.2.    Isoprene Biosynthesis:
Two metabolic pathways exist for the biosynthesis of isopentenyl pyrophosphate and dimethylallyl pyrophosphate:
•    The mevalonate pathway, predominantly used by plants and in a few insect species.
•    The non-mevalonate pathway or methyl D-erythritol 4-phosphate (MEP) pathway, which occurs in plant chloroplasts, algae, cyanobacteria, eubacteria, and important pathogens such as Mycobacterium tuberculosis and malaria parasites.
11.1.3.    Mevalonate Pathway
The mevalonate pathway performs several key functions within cells and is an important central metabolic pathway in all higher eukaryotic cells. The key isomers dimethylallyl pyrophosphate (DMAPP) and isopentenyl pyrophosphate (IPP) are produced via the mevalonate pathway from (R)-mevalonate and its subsequent phosphorylated metabolites (R)-mevalonate-5-phosphate and (R)-mevalonate-pyrophosphate.
DMAPP and IPP are further utilized in condensation reactions for the biosynthesis of isoprenoids. These isoprenoids are transformed into more complex, cyclised structures through steroid and terpenoid biosynthesis.
11.1.4.    Non-mevalonate (MEP) Pathway
The mevalonate-independent pathway for the biosynthesis of IPP and DMAPP was discovered in the 1990s and consists of eight enzyme-catalyzed reactions. Synonyms for this pathway are the non-mevalonate pathway, the 1-deoxy-D-xylulose-5-phosphate pathway (DXP (or DOXP) pathway), and the 2C-methyl-D-erythritol-4-phosphate pathway, (MEP pathway).

The MEP pathway starts with the condensation of pyruvate and D-glyceraldehyde-3-phosphate to 1-deoxy-D-xylulose-5-phosphate (DXP or DOXP). The key isomers DMAPP and IPP are subsequently formed via a series of enzymatic steps starting with the conversion of DXP to 2C-methyl-D-erythritol-4-phosphate (MEP). 
11.1.5.    Role of Terpenes:
They may protect the plants that produce them by deterring herbivores and by attracting predators and parasites of herbivores. Many terpenes are aromatic hydrocarbons and thus may have had a protective function Terpenes and terpenoids are the primary constituents of the essential oils of many types of plants and flowers. Essential oils are used widely as natural flavour additives for food, as fragrances in perfumery, and in medicine and alternative medicines such as aromatherapy. Vitamin A is a terpene. The aroma and flavour of hops, highly desirable in some beers, comes from terpenes. Of the terpenes in hops myrcene, β-pinene, β-caryophyllene, and α-humulene are found in the largest quantities.
11.2.    Phenols
These are the class of naturally occurring compound with one or more phenolic compounds or benzene ring with –OH group.

Phenol - the simplest of the phenols.
They are classified on the basis of their number of phenol groups. They can, therefore, be called simple phenols or monophenols, with only one phenolic group, or di-(bi), tri and oligophenols, with two, three or several phenolic groups respectively. The largest and best studied natural phenols are the flavonoids, which include several thousand compounds, among them the flavonols, flavones, flavanones, anthocyanidins and isoflavonoids. The phenolic unit can be found dimerized or further polymerized, creating a new class of polyphenol.

11.2.1.    Biosynthesis of Phenols:
Phenols are formed by 3 different biosynthetic pathways. Most of the natural phenols are derived from secondary plant metabolism of the shikimic acid pathway, malic acid pathway or both.
11.2.2.    Shikimic Acid Pathway:
Shikimic acid, more commonly known as its anionic form shikimate, It is an important biochemical metabolite in plants and microorganisms. This pathway (unique to plants) leads to the formation of the aromatic amino acids phenylalanine and tyrosine and to the formation of many other phenyl-C3 compounds.  

11.2.3.    Formation of Shikimic acid:
Phosphoenolpyruvate and erythrose-4-phosphate react to form 3-deoxy-D-arabinoheptulosonate-7-phosphate (DAHP), in a reaction catalyzed by the enzyme DAHP synthase. DAHP is then transformed to 3-dehydroquinate (DHQ), in a reaction catalyzed by DHQ synthase. Although this reaction requires nicotinamide adenine dinucleotide (NAD) as a cofactor, the enzymic mechanism regenerates it, resulting in the net use of no NAD.

Biosynthesis of 3-dehydroquinate from phosphoenolpyruate and erythrose-4-phosphate
DHQ is dehydrated to 3-dehydroshikimic acid by the enzyme 3-dehydroquinate dehydratase, which is reduced to shikimic acid by the enzyme shikimate dehydrogenase, which uses nicotinamide adenine dinucleotide phosphate (NADPH) as a cofactor.

11.2.4.    Biosynthesis of shikimic acid from 3-dehydroquinate
The shikimate pathway is for the biosynthesis of aromatic amino acids (phenylalanine, tyrosine, and tryptophan) in bacteria, fungi, algae, parasites, and plants. This pathway is not found in animals. The first 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 phosphoenolpyruvate to give 5-enolpyruvylshikimate-3-phosphate via the enzyme 5-enolpyruvylshikimate-3-phosphate (EPSP) synthase.

Then (5EPSP) 5-enolpyruvylshikimate-3-phosphate is transformed into chorismate by a chorismate synthase.

Prephenic acid is then synthesized by a Claisen rearrangement of chorismate by Chorismate mutase.

Prephenate is oxidatively decarboxylated with retention of the hydroxyl group to give p-hydroxyphenylpyruvate, which is transaminated using glutamate as the nitrogen source to give tyrosine and α-ketoglutarate.

11.3.    Anthocyanins :
Anthocyanins are colored flavinoids that attract animals. Anthocyanins are responsible for most of the red, pink & blue color observed in plant parts. 
11.3.1.    Formation of Anthocyanidins and Anthocyanins: 

Anthocyanins are Glycosides, that have sugar at position 3 and sometimes elsewhere. Without their sugar, anthocyanins are known as anthocyanidins. The precursor for the formation of Anthocyanins is naringenin (a flavone), which is synthesized via the shikimic acid pathway by the precursor malonyl-CoA (a different starter than acetyl-CoA).
11.3.2.    Role of phenols:
As they are present in food consumed in human diets and in plants used in traditional medicine of several cultures, their role in human health and disease is a subject of research. Some phenols are germicidal and are used in formulating disinfectants. Others possess estrogenic or endocrine disrupting activity. Phenols are important raw materials and additives for industrial purposes in laboratory processes chemical industry, chemical engineering processes, wood processing, plastics processing, Tannins are used in the tanning industry. Some natural phenols can be used as biopesticides. Furanoflavonoids like karanjin or rotenoids are used as acaricide or insecticide. 
11.3.3.    Nitrogen-Containing compounds
Alkaloids, amines, nonprotein amino acids, cyanogenic glycosides and glucosinolates are the main compounds of nitrogen-containing secondary metabolites. Most nitrogen-containing secondary compounds are derived from amino acids which donate the carbon skeleton and nitrogen.

11.3.4.    Biosynthesis of Alkaloids:
Besides the 20 protein-building amino acids, others such as ornithine are also important precursors. Very often, the amino acid is decarboxylated by a pyridoxal phosphate containing decarboxylase in the first step. Other enzymes that have been found to be associated with the biosynthesis of nitrogen-containing secondary metabolites include transaminases, amine oxidases, oxidoreductases, peroxidases, hydrolases, N- or O-methyltransferases, acyl-CoA transferases, mono- and dioxygenases, phenolases and several synthases, which, in general, are specific and stereo-selective enzymes showing a high affinity for their particular substrate.

11.3.5.    Biosynthesis of Indole Alkaloids:
Biosynthesis of monoterpenoid indole alkaloids begins with the Mannich reaction of tryptamine and secologanin; it yields strictosidine which is converted to 4,21-dehydrogeissoschizine. Then, the biosynthesis of most alkaloids containing the unperturbed monoterpenoid part (Corynanthe type) proceeds through cyclization with the formation of cathenamine and subsequent reduction to ajmalicine in the presence of  NADPH. In the biosynthesis of other alkaloids, 4,21-dehydrogeissoschizine first converts into preakuammicine (an alkaloid of subtype strychnos, type Corynanthe) which gives rise to other alkaloids of subtype strychnos and of the types Iboga and Aspidosperma. Bisindole alkaloids vinblastine and vincristine are produced in the reaction involving quarantine (alkaloid of type Iboga) and vindoline (type Aspidosperma). 

11.4.    Biosynthesis of cyanogenic glycosides.
Cyanogenic glycosides are secondary plant compounds that occur widely in the plant kingdom. They are the source of HCN which can render the plant toxic if it is taken as food. The enzymes responsible for production of the HCN have long been known. More recent biosynthetic studies have established certain protein amino acids as precursors of the aglycones and indicate N-hydroxyamino acids, aldoximes, nitriles and alpha-hydroxynitriles as intermediates

11.5.    Biosynthesis of Glucosinolates: 
Biosynthesis of Glucosinolates start with help of the precursor of amino acid, which converted into the Aldoxine and at last it forms Glucosinolate via intermidiates Thiohydroximic acid and desulfoglucosinolate by the enzyme sulfotransferese.

11.6.    Role of Nitrogen containg compounds:
Most of the known functions of alkaloids are related to protection. For example, the presence of alkaloids in the plant prevents insects and chordate animals from eating it. However, some animals are adapted to alkaloids and even use them in their own metabolism. Such alkaloid-related substances as serotonin, dopamine and histamine are important neurotransmitters in animals. Alkaloids are also known to regulate plant growth some alkaloids, such as salts of nicotine and anabasine, were used as insecticides. Their use was limited by their high toxicity to humans.

Next Previous