Comprehensive Study of Metabolic Pathways and Secondary Metabolite Biosynthesis in Higher Plants

Comprehensive Study of Metabolic Pathways and Secondary Metabolite Biosynthesis in Higher Plants

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  UNIT-I  Metabolic pathwaysin higher plants and their determination  Brief study of basic metabolic pathways and formation of different secondary metabolites through these pathways- Shikimic acid pathway, Acetate pathways and Amino acid pathway.  Study of utilization of radioactive isotopes in the investigation of Biogenetic studies.
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  30/07/2026 2 Metabolites arethe small molecules that are formed as intermediates or end products during metabolic reactions in living organisms.
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  30/07/2026 3 As aresult of metabolic process in plants, plant synthesizes primary plant metabolites and secondary plant metabolites. Feature Primary Plant Metabolites Secondary Plant Metabolites Definition Basic plant constituents essential for life processes. Compounds derived from primary metabolites with specific ecological functions. Examples Sugars, amino acids, lipids, Coenzyme A, mevalonic acid, starch. Alkaloids, glycosides, tannins, flavonoids, terpenoids, volatile oils, quinine.
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  30/07/2026 4 Feature PrimaryPlant Metabolites Secondary Plant Metabolites Distribution Found in all plants and plant parts; widely distributed. Found in specific plant species or families; limited distribution. Quantity Present in large quantities. Present in small or trace amounts. Involvement in Plant Functions Directly involved in growth, development, and reproduction. Not directly involved in growth or development. Biological/ Pharmacologica l Action Generally, do not have biological or pharmacological activity. Have specific biological or pharmacological effects on humans, animals, or pathogens. Function in Nature Provide energy, structural components, and primary metabolic functions. Help in defense, protection, stress response, and interaction with environment
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  30/07/2026 5  "Metabolicpathways in higher plants and their determination" usually covers two things:  What those pathways are — the biochemical routes by which plants produce, transform, and store primary and secondary metabolites.  How we determine them — the experimental methods scientists use to trace and study these pathways.
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  30/07/2026 6 Pathway FunctionExample in Higher Plants Photosynthesis Convert light → glucose Sugarcane storing sucrose in stems Respiration Break down glucose → ATP Germinating wheat seeds Pentose Phosphate Pathway NADPH & nucleotides synthesis Actively dividing meristem cells in pea shoots Nitrogen Assimilation Convert nitrate → amino acids Spinach leaves converting soil nitrate into glutamate Amino Acid Biosynthesis Build proteins & precursors Soybean producing methionine & lysine Lipid Biosynthesis Membranes, oils Sunflower seeds producing oil during ripening A. Primary Metabolism (Growth & Energy)
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  30/07/2026 7 B. SecondaryMetabolism (Specialized Compounds) Pathway Products Example Shikimic Acid Pathway Phenolics, flavonoids, tannins Tea leaves producing catechins Acetate Pathway Fatty acids, polyketides (anthraquinones, flavonoids) Senna pods producing anthraquinones Amino Acid Pathway Alkaloids derived from specific amino acids Datura producing atropine from ornithine
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  30/07/2026 8 BASIC METABOLICPATHWAY
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  30/07/2026 9  Theshikimate pathway provides an alternative route to aromatic compounds, particularly the aromatic amino acids L-phenylalanine, L-tyrosine, and L-tryptophan.  This pathway is employed by microorganisms and plants, but not by animals, and accordingly the aromatic amino acids feature among those essential amino acids for human beings, to be obtained from the diet.  Shikimic acid is named after the highly toxic Japanese shikimi (Illicium anisatum) flower from which it was first isolated. SHIKMIC ACID PATHWAY
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  30/07/2026 10  TheShikimic acid pathway is a key intermediate from carbohydrate for the biosynthesis of C -C units (phenyl propane derivative). ₆ ₃  The Shikimic acid pathway converts simple carbohydrate precursors derived from glycolysis and the pentose phosphate pathway to the aromatic amino acids.
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  30/07/2026 12 SHIKMIC ACID PATHWAY
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  30/07/2026 14  Usesof the Shikimic Acid Pathway 1. Biosynthesis of Aromatic Amino Acids Shikimic acid pathway is to synthesize the aromatic amino acids: Phenylalanine Tyrosine Tryptophan These amino acids are precursors for proteins and secondary metabolites.
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  30/07/2026 15 2. Productionof Secondary Metabolites •It provides precursors for: • Alkaloids • Flavonoids • Tannins • Lignin • Coumarins • Phenolic acid (eg., gallic acid, ferulic acid) These compounds are important for: • Plant defense mechanisms • Antioxidant properties • Medicinal uses
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  30/07/2026 16  Inthe pharmaceutical industry, shikimic acid from the Chinese star anise (Illicium verum) is used as a base material for the production of oseltamivir  Shikimate can be used to synthesize (6S)-6-Fluoroshikmic acid, an antibiotic which inhibits aromatic biosynthetic pathway.  Glycophosphate, the active ingredient in the herbicide Roundup, kills plant by interfering with the shikimate pathways in plants.  More specifically glycophosphate inhibits the enzyme 5-enolpyurvlshikimate-3- phosphate synthase (EPSPS). “Roundup Ready” genetically modified crops overcome that inhibition
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  30/07/2026 17 Acetate Pathway Theacetate pathway (also called the acetyl-CoA pathway or polyketide pathway) is a biosynthetic route primarily responsible for the formation of fatty acids, polyketides, and other important secondary metabolites. It is widely found in plants, fungi, bacteria, and animals.
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  30/07/2026 21 Acetate Pathway 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 pathway begins with acetyl CoA molecule produced from pyruvic acid, which is the end product of glycolysis.
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  ACETATE PATHWAY Glycolysis Pyruvate Endproduct Acetyl Co-A TCA Acetate mevalonate pathway Acetate melonate pathway- Mevalonic acid Malonyl Co-A terpenes & steroids Long chain fatty acids & polyketides Isoprenoids Squalene Steroids Lipids, fats , waxes
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  30/07/2026 23 Acetate-Mevalonate Pathway
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  30/07/2026 24 1. TerpenoidBiosynthesis • Produces isopentenyl pyrophosphate (IPP), the universal precursor of all isoprenoids (terpenes). • Terpenoids are important in: • Essential oils (aroma, flavors → e.g., menthol, eugenol). • Medicinal compounds (artemisinin, taxol, guggulsterone). • Resins & rubber 2. Steroid Formation • Provides precursors for steroids and sterols such as cholesterol, phytosterols, and steroidal glycosides. • Steroids are essential for: • Cell membrane stability • Hormones
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  30/07/2026 25 3. Quinonesand Electron Carriers • Produces ubiquinone (coenzyme Q) and dolichols, which are vital for: • Mitochondrial electron transport (energy production). • Glycoprotein synthesis (via dolichol phosphate). 4. Plant Growth Regulators 5. Commercial & Pharmaceutical Uses • Essential oils in perfumes and flavors. • Industrial products: natural rubber, carotenoids (colorants, vitamin A precursor).
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  30/07/2026 26  References Medicinal Natural Products: A Biosynthetic Approach, Paul M. Dewick, 3rd Ed. 2009, John Wiley & Sons, Ltd. England .  The Biosynthesis of secondary metabolites, R.B. Herbert, 1st Ed. 1981, Chapman & hall, London.  Pharmacognosy, C.K. Kokate, A.P. Purohit, S.B. Gokhale, 54th Ed. 2017, Nirali Publication, New Delhi  Trease and Evans Pharmacognosy, W.C. Evans, 15th Ed. Elsevier, 2002.
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  30/07/2026 27 Amino acidPathway 1.Amino acid are molecules that combine to form proteins. 2.There are total 20 amino acids which are needed in our body 3.Plants and bacteria can synthesize all 20 of the amino but humans can not synthesize 9- 10 of them. 4.Those amino acids which can not synthesized in our body are known as essential amino acids. 5.Those amino acids which can synthesized in our body are known as non-essential amino acids. 6.These amino acids must come from our diet. 7.The non-essential amino acids are synthesized by simple pathways, whereas biosynthesis of the essential amino acid are complex
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  30/07/2026 28  EssentialAmino Acids  Isoleucine  Leucine  Lysine  Methionine  Phenylalanine  Threonine  Tryptophan  Valine  Histidine  Non-Essential Amino Acids:  Alanine  Asparagine  Aspartic acid (Aspartate)  Glutamic acid (Glutamate)
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  30/07/2026 30 30 PPP α-acetyl serine Glycine cysteine Shikimicacid pathway α-ketoisovaleric acid valine Transamination α-ketoiso caproic acid Leucine Alanine NH 3 Hydroxy proline Ornithine, citrulline, arginine NH3 NH3 NH3
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  30/07/2026 31 Amino acidsPrecursor Glutamate, Glutamine, Proline, Arginine α-Ketoglutarate Serine, glycine, cystine 3- phosphoglycerate Aspartate, aspargine, methionine, threoline, lysine Oxaloacetate Alanine, valine, leucine, isoleucine Pyruvate Histidine Ribose-5-phosphate Tryptophan, phenylalanine, tyrosine Phosphoenol pyruvate List of Precursors for amino acid biosynthesis
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  30/07/2026 32  Sourceof Energy & Metabolic Intermediates • Amino acid catabolism produces pyruvate, acetyl-CoA, oxaloacetate, α- ketoglutarate, fumarate, succinyl-CoA → all enter the TCA cycle for energy. • Useful during fasting, starvation, or exercise when glucose is low.  Medical & Pharmaceutical Uses • Disorders studied through pathways: Phenylketonuria (phenylalanine metabolism), Alkaptonuria (tyrosine metabolism), Maple syrup urine disease (branched-chain AA metabolism). • Drug development → Pathways targeted in cancer, infections, and metabolic diseases (e.g., enzymes in tryptophan or methionine metabolism are drug targets). • Biotechnology → Microbes are engineered to overproduce amino acids (glutamate for MSG, lysine for supplements).
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  30/07/2026 33  Agricultural& Industrial Uses • Fertilizers & Plant Growth: Amino acid derivatives act as growth stimulators. • Food Industry: Flavor enhancers (e.g., glutamate → MSG). • Nutritional Supplements: Lysine, methionine, arginine for animal feed and human health.
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  30/07/2026 39 Methods ofintroduction: 1.Root feeding 1. Labelled compound is dissolved in water and absorbed by plant roots. 2. Example: Radioactive phosphate (³²P) given via soil solution. 2.Stem feeding 1. Labelled solution is injected or supplied directly into the stem. 2. Useful for woody plants. 3.Floating method 1. Plant leaves or parts are floated in labelled solution for absorption. 2. Example: Leaf discs floated in radioactive glucose solution. 4.Spray technique 1. Labelled compound is sprayed on leaves, absorbed through stomata. 2. Example: Urea labelled with ¹ N sprayed on crops. ⁵ 5.Direct injection 1. Labelled precursor is injected directly into plant tissue or organ. 2. Example: Radioactive amino acid injected into fruit/leaf.
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  30/07/2026 42 1. PrecursorProduct Sequence  Meaning: The compound that comes first (precursor) in a metabolic pathway gets converted into the final compound (product).  How tracer is used: If we add a radioactive isotope to the precursor, we can see where it goes in the pathway and confirm which product it forms.  Example: If we label acetate with C¹ , it gets incorporated into ⁴ cholesterol → shows acetate is a precursor of cholesterol.
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  30/07/2026 43 2. Doubleand Multiple Labelling  Meaning: Two or more atoms in a molecule are tagged with different radioactive isotopes to track how they behave.  Why: Helps understand complex reactions where more than one atom changes place.  Example: Labeling glucose with both C¹ and H³ (tritium) → helps study ⁴ whether carbon or hydrogen atoms are retained or lost during glycolysis.
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  30/07/2026 44 3. CompetitiveFeeding  Meaning: A radioactive precursor and a non-radioactive (normal) precursor are given together.  Purpose: To see which one the organism prefers or which pathway is more active.  Example: Feeding plants C¹ -labeled phenylalanine ⁴ along with normal phenylalanine → helps know if phenylalanine really converts into alkaloids.
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  30/07/2026 45 4. SequentialAnalysis  Meaning: The isotope-labeled precursor is given, and samples are collected at different time intervals.  Purpose: To check the sequence of intermediates formed step by step.  Example: Giving C¹ acetate to yeast and then analyzing after 5, 10, 20 ⁴ minutes → we see it first appears in citric acid, then α-ketoglutarate, then succinate, etc. → reveals the TCA cycle steps.
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  30/07/2026 46  Precursor-productsequence: Tells who makes whom.  Double labelling: Tracks more than one atom.  Competitive feeding: Finds pathway preference.  Sequential analysis: Finds order of reactions.
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