Primary and Secondary Metabolism PDF

Natural products Primary and secondary metabolism Primary metabolism -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 co...

Natural products Primary and secondary metabolism Primary metabolism -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 (metabolic pathways).  -Some of crucially important molecules of life are carbohydrates, proteins, fats, and nucleic acids. Apart from fats, these are polymeric materials. -Carbohydrates are composed of sugar units, whilst proteins are made up from amino acids, and nucleic acids are based on nucleotides. -Organisms vary widely in their capacity to synthesis and transform chemicals. -For instance, plants are very efficient at synthesizing organic compounds via photosynthesis from inorganic materials found in the environment, whilst other organisms such as animals and microorganisms rely on obtaining their raw materials in their diet, e.g. by consuming plants.  -Thus, many of the metabolic pathways are concerned with degrading materials taken in as food, whilst other metabolic pathways are required to synthesize specialized molecules from the basic compounds so obtained. -Despite the extremely varied characteristics of living organisms, the pathways for generally modifying and synthesizing carbohydrates, proteins, fats and nucleic acids are found to be essentially the same in all organisms, apart from minor variations. -These processes demonstrate the fundamental unity of all living matter, and are collectively described as primary metabolism, with the compounds involved in these pathways being termed primary metabolites.  - Thus degradation of carbohydrates and sugars generally proceeds via the well characterized pathways known as glycolysis and the Krebs cycle, which release energy from the organic compounds by the oxidation reactions. -Oxidation of fatty acids from fats by the sequence of β-oxidation also provides energy. -Protein taken in via diet provide amino acids.  PRIMARY METABOLISM Primary metabolism comprises the chemical processes that every plant must carry out every day in order to survive and reproduce its line. Photosynthesis Glycolysis Citric Acid Cycle Synthesis of amino acids Transamination Synthesis of proteins and enzymes Synthesis of coenzymes Synthesis of structural materials Duplication of genetic material Reproduction of cells (growth) Absorption of nutrients  Secondary metabolism -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, -Secondary metabolites are not necessarily produced under all conditions, and in the vast majority of cases the function of these compounds and their benefits to the organism is not yet known.  -Some are undoubtedly produced for easily appreciated reasons, e.g. toxic materials providing defense against predators, as volatile attractants towards the same or other species, or as colouring agents to attract or warn other species, but it is logical to assume that all do plays some vital role for the well-being of the producer. -It is this area of secondary metabolites that provides most of the pharmacologically active nature products. -It is thus fairly obvious that the human diet could be both unpalatable and remarkably dangerous if all plants, animal and fungi produced the same range of compounds.  - Secondary metabolism comprises the chemical processes that are unique to a given plant, and are not universal. - Secondary metabolism is the chemistry that leads to the formation of a natural product. -Sometimes portions of this chemistry are common to a number of different plants or plant families, but the actual chemical produced (natural product) is usually different in one plant than in another. - Common chemical precursors can lead to different results. - Secondary metabolites (in most cases) do not appear to be necessary to the survival of the plant, but they may give it a competitive advantage.  A TYPICAL PLANT h Glycolysis Photosynthesis (daytime) CO2 Respiration (nighttime) H2O O2 N2 bacteria TRACE METALS “N” Na, Ca, K, Mg NO2-/NO3-/NH4+ Fe, Cu, Co, Mo H2O  CO2 + H2O h PRIMARY METABOLISM Photosynthesis Glucose Carbohydrates SECONDARY SECONDARY G METABOLISM L METABOLISM Building Blocks Y C O Phenyl- L Y propanoids Amno Acids S Fatty Acids Flavonoids I Lipids Proteins S Alkaloids synthesis enzymes Acetyl CoA regulation Acetogenins Nucleic Terpenes Acids Citric Acid Steroids reproduction Cycle RNA DNA CO2 + H2O + ATP  Glucose h CH2OH (6 carbons) CH2OH CH2OH CH2OH O O O O OH OH OH OH HO OH HO O O O CO2 OH OH OH OH photosynthesis starch n glycolysis CHO CH OH CHO CH2OH HC OH C O CH OH polyketides CH2OP CH2OP CH2OP erythrose- acetogenins 4-phosphate CH2 phosphoenol O O lipids C OP COOH pyruvate (PEP) H3C C CH2 C CH2 fatty acids COOH shikimic (3 carbons) acid anthanilic acid HO OH COOH O acetyl- OH H3C C SCoA coenzymeA NH2 (2 carbons) HO CH3 mevalonic phenylpropanes lysine oxalo- acid O phenylalanine ornithine acetate citric O energy (ATP) tyrosine acid tryptophan + CO2 + H2O cycle terpenes NH3 steroids nicotinic aspartic alkaloids acid acid carotenoids glutamic acid  The buildings blocks -The building blocks for secondary metabolites are derived from primary metabolism. - The most important building blocks employed in the biosynthesis of secondary metabolites are derived from the intermediates acetyl coenzyme A (Acetyl-CoA), shikmic acid, mevalonic acid, and 1-deoxyxylulose 5- phosphate. - Acetyl-CoA is formed by oxidative decarboxylation of pyruvic acid and β-oxidation of fatty acids. It used for synthesis of phenols, prostaglandins, and macrolide antibiotics.  -Shikimic acid is produced from a combination of phosphoenolpyruvate and erthro 4-phosphate. The shikimate pathway leads to a variety of phenols, cinnamic acid deravatives, lignans, and alkaloids. -Mevalonic acid is formed from three molecules of acetyl-CoA. - Deoxyxylulose phosphate arises from a combination of pyruvic acid and glyceraldehyde 3-phosphate.  -The mevalonate and deoxyxylulose phosphate pathways are together responsible for the biosynthesis of vast array of terpenoid and steroid metabolites. - Some amino acids (phenylalanine, tyrosine, tryptophane, ornithine, and lysine) are employed in natural product synthesis, peptides, proteins, alkaloids, and many antibiotics.  The strucrural features of the building blocks: 1- C1: The simplest of the building blocks is composed of a single carbon atom, usually in the form of a methyl group, and most frequently it is attached to oxygen or nitrogen -X-CH3 (X= O,N), it derived from methionine. 2- C2: A two carbon unit may be supplied by acetyl-CoA (C=C). It could be a simple acetyl group forms part of ester.  3- C5: The branched-chain C5 'isoprene' is formed from mevalonate or deoxyxylulose phosphate. Mevalonate itself is the product from three acetyl-CoA molecules, but only five of six carbons are used, the carboxylic group being lost.  head C tail C C C C isoprene isoprene unit  4- C6C3: This refers to a phenylpropyl unit and is obtained from L-phenylalanine or L-tyrosine, two of the shikimate- derived aromatic amino acids. This requires loss of amino groups. Sometimes the side chain is cleaved, removing one or two carbons (C6C2 or C6C1). 5- C6C2N: derived from L-phenylalanine and L-tyrosine. This requires loss of carboxyl groups. 6- Indol.C2N: derived from tryptophan. This requires loss of carboxyl groups.  CH2 CH COOH CH2 CH COOH NH2 NH2 HO tyrosine phenylalanine C C C C Phenylpropyl C6C3 or C6C1  COOH NH2 NH2 N N H H Tryptophane Indol.C2N  7- C4N; derived from L-ornithine. The carboxylic and α-amino nitrogen groups are lost. 8- C5N: derived from lysine. The carboxylic and amino nitrogen groups are lost. These eight building blocks will form the basis of many of the natural product structures.  N N N N H H H pyrrolidine pyrrole piperidine pyridine N N N N H H quinoline isoquinoline indole dihydroindole C4N & C5N  Terpenoids Terpenoids are secondary metabolites synthesized by plants, marine organisms and fungi by head to tail joining isoprene units (5 carbon atoms). They are also found to occur in rocks, fossils and animal kingdom.  Terpenoids find wide applications in industry. For example, linalool along with phenyl-ethyl alcohol is used in perfumery. Citral is used as a mosquito repellant and the starting material for the synthesis of vitamin A, menthol and artemisinin in pharmaceutical industries. Farnesol and juvabione are insect juvenile hormones whereas ecdysones are insect anti-moulting hormones. Gibberellic acids and brassinolides are the plant growth regulators. Salannin and azadirachtins are insect antifeedant and growth inhibitors.  Taxol and cucurbitacins are anti-tumor compounds. Forskolin is a unique adenylate cyclase stimulator, which displays a variety of biological activities including blood pressure lowering, positive inotropic, hypolipidemic, antiglucoma. Artemisinin is a sesquiterpene peroxide with potent antimalarial activity. Panaxadiol and panaxatriols are immunostimulants. Natural rubber is a polymer of isoprene. Moreover insects use many terpenoid-derived molecules for their communications.  Classification Terpenoid are classified according to the number of isoprene units involved in their biosynthesis. The terpenoid skeletons occur as open chain as well as in various cyclised forms. 1 unit of isoprene C5 (meroterpenoids) 2 units of isoprene C10 (monoterpenoids) 3 units of isoprene C15 (sesquiterpenoids) 4 units of isoprene C20 (diterpenoids) 5 units of isoprene C25 (sesterterpenoids) 6 units of isoprene C30 (triterpenoids) 8 units of isoprene C40 (carotenoids) Many of isoprene (natural rubber)  Biosynthesis Biosynthesis of terpenoids consists of the following steps: 1- Photosynthesis converts 6 molecules of carbon dioxide and molecules of oxygen to the glucose molecule, which breaks down through glycolysis to pyruvate. 2- Pyruvate is further converted to acetyl-CoA and two molecules of acetyl-CoA couple each other to form acetoacetyl-CoA. 3- Acetoacetyl-CoA reacts with another molecule of acetyl-CoA to produced hydroxymethylglutaric acid which turn to mevalonic acid (MVA) (key- intermediate). 4- MVA is phosphorylated by ATP to give mevalonic acid -5-diphosphate. 5- MVA-5-diphosphate undergoes decarboxylation with the simulantaneous elimination of pyrophosphate to isoprene unit, isopenetenyl diphosphate (IDP). 6- IDP is isomerised by the catalytic action of sulphhydryl enzyme IDP-isomerase to dimethylallyl diphosphate (DMADP). 7- Condensation of DMADP and IDP catalyzed by the enzyme geranyl transferase results in the formation of geranylpyrophosphate (C10) and further addition of IDP units afford farnesyl pyrophosphate (C15) and geranyl-geranyl pyrophosphate (C20), which are precursors of sesquiterpenes and diterpenes, respectively. 8- Two molecules of farnsyl pyrophosphates couple with each other through the cyclopropane intermediate and by the transfer of hydrogen from NADPH to furnish squalene. 9- Squalene is the precursor of all triterpenoids (C30). 10- Condensation of geranyl-geranyl pyrophosphates with IDP leads to C25 skeletone, which is precursor of sesterterpenoids. 11- Two molecules of geranyl-geranyl pyrophosphates couple with each other to afford carotenoids (C-40-isoprenoids). 12- Cyclization in terpenoids: using The complex terpene cyclase reaction.  MEVALONIC ACID PATHWAY FORMATION OF MEVALONIC ACID FROM ACETYL UNITS O O HO CH2 C SCoA HO CH2 C SCoA 3 acetylCoA C NADPH C H H3C H3C CH2 C SCoA CH2 C SCoA O :.. O: - O O O HO CH2 C SCoA HO CH2 C OH HO CH2 C SCoA C C C H3C H3C H2O H3C NADPH CH2 C H CH2 CH2 OH CH2 CH2 OH O mevalonic acid (continued next slide)  MEVALONIC ACID PATHWAY The isopentenyl and 3,3-dimethylallyl pyrophosphate intermediates ADP :B-Enz O O 2 ATP AMP HO CH2 C OH P O CH2 C O H C C H3C H3C CH2 CH2 OH CH2 CH2 O P P mevalonic acid These five-carbon intermediates are responsible for the formation of all the CH3 CH3 terpenes. Enz-B: H+ H CH3 H CH2 P P O CH2 P P O CH2 DMAPP IPP 3,3-dimethylallyl isopentenyl pyrophosphate pyrophosphate  TERPENES The Czech chemist Leopold Ruzicka ( born 1887) showed that many compounds found in nature were formed from multiples of five carbons arranged in the same pattern as an isoprene molecule (obtained by hydrolysis of natural rubber). natural rubber head  C tail. C C C C C C C C C isoprene isoprene unit He called these compounds “terpenes”.  JOINING ISOPRENE UNITS individual isoprene units Head-to-Tail join head-to-tail an extra bond Tail-to-Tail The terms head-to-tail and tail-to-tail are often used to describe how the isoprene larger terpenoid units are joined. units dimerize tail-to-tail ….. explained later  SESQUITERPENES CH3 CH3 CH CH3 CH3 guaiazulene geranium oil CH3 CH3 CH3 caryophyllene oil of cloves  TRITERPENES CH3 CH3 OH CH3 CH3 CH3 TAIL-TO-TAIL CH3 CH3 ambrein ambergis  TETRATERPENE head-to-tail tail-to-tail head-to-tail -carotene carrots HOW THE TERPENES ARE FORMED  CONCATENATION OF C5 (ISOPRENE) UNITS CH3 CH3 IPP H CH2 H CH3 DMAPP OPP CH2 OPP CH2 HEAD CH3 C5 C10 :B CH2 OPP C5 H isopentenyl-PP CH2 OPP 3,3-dimethylallyl-PP OPP CH2 H TAIL C10 OPP geranyl-PP C20 C15 C15 farnesyl-PP CH2 OPP again C20 geranyl-geranyl-PP CH2 OPP EACH NEW UNIT IS JOINED HEAD-TO-TAIL  C30 AND C40 UNITS ARE FORMED DIFFERENTLY Number Isoprene Class of Carbons Units Origin HEMITERPENES C5 1 IPP or DMAPP MONOTERPENES C10 2 geranyl-PP x2 SESQUITERPENES C15 3 farnesyl-PP x2 DITERPENES C20 4 geranyl-geranyl-PP SESTERTERPENE C25 5 uncommon TRITERPENES C30 6 2 x (farnesyl-PP) C35 7 uncommon TETRATERPENES C40 8 2 x (geranyl-geranyl-PP)  Occurrence -Mono (C10)and sesquiterpenoids (C15): These are generally present in many plant species but more concentrated in plants yielding volatile or essential oils. Essential oil containing plants belong to both Gymnospermae and Angiospermae (flowering plants). -Diterpenoids (C20): These are commonly present in the conifer resins, and trees of the families Cistaceae, Leguminoseae and Burseraceae. Some plants belonging to the family solanaceae such as tobacco is found to be a rich source of diterpenoids.  -Sesterterpenoids (25): Sesterterpenoids are quite rare in nature, generally, they are found to occur in the protective waxes of insects and fungi. They are phytotoxic. -Triterpenoids (C30) They are commonly to found in plant families as Leguminoseae and Cucurbitaceae.  -Carotenoids (C40): Due to the presence of long chain of conjugated double bonds the carotenoids are coloured yellow, orange and red. Most of them are fat-soluble pigments. Carotenoids occur in many plants and their distribution is found in almost all parts of the plants such as roots (carrot), leaves (Spinach), fruits (Tomato) and seeds (palm).