Biosynthesis, Chemistry tutorial


The simple fact that plants have roots results in very different selective pressures than those driving the evolution of animal metabolism. After all, very few plants have the ability to run away when another organism sees them as food. As a result, plants have evolved ways to repel or, in several cases, attract other organisms. Their lack of movement as well permits them to produce rigid compounds (such as cellulose or lignin) that, among other things, allow them to grow upward into new ecological niches.

To make these compounds as sugars, waxes, lignin, starch, pigments, or alkaloids, plants utilize precise enzymes, each of which catalyses an exact metabolic reaction. Enzymes are proteins, which act as organic catalysts. They are coded via exact genes in the plant's DNA and are made via processes we call transcription (conversion of DNA to RNA via the enzyme RNA polymerase) and translation (conversion of RNA to protein via the enzymatic action in complex structures said ribosomes). When there is a series of enzymatically catalysed reactions in a well-described series of steps, we have what is phrased a metabolic pathway. Several enzymes might be included in metabolic pathways requiring just a few enzymatic steps (as in synthesis of starch from the sugar nucleotide, adenosine diphosphate [ADP]-glucose) or many enzymatic steps (as in the synthesis of gibberellins hormones from mevalonic acid).

Various enzymes might be involved in pathways that break down compounds (as in the hydrolysis of starch to sugars via α- and β-amylases). Still other enzymes might be involved in making storage shapes of specified compounds these as glucosides, amides, or esters of the plant hormone indole-3-acetic acid (IAA).

Such dissimilar enzymatic pathways involved in the synthesis, breakdown, and formation of storage shapes of a compound regulate the level of the specified compound. The regulation of each pathway and of each of its enzymes is, though, tremendously complicated. Please note that not all proteins are enzymes. Many proteins inside a specified cell may be purely structural in function.

In the sections that follow, we aim to provide the reader an understanding of the primary biosynthetic pathways that are recognized to take place in plants. We then provide an overview of what is recognized about several of the best-known plant compounds and how they function inside the plant. It should be noted, though, that there is a huge amount of information on such subjects, and new discoveries continue to be made. 

Biosynthesis of Some Plant Metabolites

Alkaloid biosynthesis

So far, we tried to touch upon each of the main categories of products generated via plants in general. We discussed the biosynthesis of the major cellular components found in the majority of plants, including primary storage compounds and key compounds that start the carbon fixation process (chlorophylls). We utilized carotenoids to illustrate the production of terpenoids and anthocyanins to provide instances of phenolic compounds.

Now we will say a few words about nitrogen-containing compounds, which will be symbolized via the alkaloids. Most of such products aren't considered to be necessary to the expansion and development of the plant, but several these as pyrimidine nucleotides and tetrapyrroles, are essential. There are thousands of different plant products that have nitrogen in their structures. Perhaps the most diverse of these kinds of compounds (found in 20 to 30% of vascular plants) are the alkaloids that, like most other nitrogen-containing compounds, are synthesized from amino acids. 

Alkaloids are particularly interesting since they are toxic to together herbivores and humans; yet they have several extremely significant medicinal properties for humans. The nitrogen atom, which in such substances is almost always part of a heterocyclic ring origin, is originate innately in the structure of the amino acids from that they came or are the effect of the circularization of the specified amino acid. This is the case by aspartic acid that combines with glyceraldehyde-3-phosphate in the production of nicotinic acid (a precursor of the alkaloid, nicotine) in plants these as tobacco (Nicotiana tabacum). Nicotine is well recognized as a toxic component of tobacco smoke. There are many categories of alkaloids, as well as pyrrolidine, tropane, piperidine, pyrrolizidine, quinolizidine, isoquinoline, and indole alkaloids. Much of the carbon skeleton of several of such alkaloids is derived from the mevalonic acid pathway, but it is beyond the scope of this unit to go into the features of the biosynthesis of all kinds of alkaloids. An old thought about the function of alkaloids in plants depicted them as waste products of plant metabolism. Nevertheless, plants are energetically proficient organisms. They merely don't waste their energy in the production of compounds that they don't require - there always seems to be a reason for their production. The predominant activity of alkaloids in plants seems to be the deterrence of herbivores. Many livestock deaths are caused via ingestion of alkaloid-containing plants such as lupines (Lupinus spp.), larkspur (Delphinium spp.), and groundsel (Senecio spp.). They were as well exposed to be toxic to insects, bacteria, and fungi. 

Chlorophyll biosynthesis

There are 3 major locations of pigments inside the cell: (1) plastids, (2) vacuoles, and (3) cell walls. The chemistry of the pigments varies through the location. Chlorophyll is a porphyrin that constitutes the primary photoreceptor pigment for the procedure of photosynthesis in plants. It is generated in the chloroplasts and is responsible for the green appearance of leaves and stems, aerial and prop roots, many kinds of floral bracts, and green fruits before they ripen. The chlorophyll molecule is made up of 4 pyrrole rings, made from aliphatic amino acids that are ligated to form a tetrapyrrole ring through a magnesium atom in its centre. Ring IV is esterified by a hydrophobic long-chain phytol molecule (C20H39) made in the terpenoid pathway. For light harvesting, plants utilize 2 shapes of chlorophyll- a and b. Chlorophyll a is in all plants and is the only chlorophyll at the reaction centres. It has a methyl group at C3. Chlorophyll b, found in most plants, has a formyl group at this position and, like other accessory pigments, functions to absorb the energy from wavelengths of light that fluctuate from chlorophyll a. The biosynthesis of the chlorophylls is compound and has only recently been worked out in feature within the model plant angiosperm, Arabidopsis thaliana. It creates through the synthesis of L-glutamic acid 1-semialdehyde from L-glutamyl-tRNA through the action of the enzyme glutamyl-tRNA reductase.

This is then switched to δ-aminolevulinic acid through the enzymatic activity of glutamate 1-semialdehyde amino transferase. Such are dangerous steps, since the porphyrin ring containing conjugated double bonds is assembled in the chloroplast from eight molecules of δ-aminolevulinic acid. Subsequent steps lead to the formation of protochlorophyllide, insertion of a Mg2+ ion in the centre of the tetrapyrrole ring, and addition of the phytol tail to form chlorophyll a and chlorophyll b. Please note that it isn't uncommon for each plant species to have more than one copy of a given gene. 

In the chloroplasts, the chlorophyll pigments are link to proteins of the photosynthetic membranes.  (Stacks of thylakoid membranes inside chloroplasts are said grana stacks.) Such proteins, said chlorophyll a/b binding proteins, are arranged into huge complexes through many other proteins, cytochromes, and quinones to form the photosynthetic electron-transport chain that, as its primary function, generates the ATP required fixing carbon dioxide. The pigment chlorophyll absorbs the energy of the sun and shuttles consequential free electrons to this all-significant series of chemical events.

Chlorophyll absorbs photons of light energy from the sun or from artificial lamps (for example, incandescent lamps, high-pressure lamps, and light-emitting diodes) in the red and blue portions of the electromagnetic spectrum, with peaks of maximal absorption occurring at 660 and 450 nm, correspondingly. This is said its absorption spectrum. Absorption spectra are commonly utilized to characterize pigment kinds. Maximal rates of photosynthesis (measured by the rate of CO2 uptake or O2 evolution) as well take place in the red and blue portions of the electromagnetic spectrum.

This is said its action spectrum. When the action spectrum peaks, as that for photosynthesis, matches the absorption spectrum for a specified pigment, as that for chlorophylls, one can figure out that the pigment is needed for the absorption of light for the exacting procedure under consideration. Another way to prove pigment type is to find plants that lack the pigment of interest and determine which processes are functional. For example, albino mutants and parasitic plants such as Indian pipe (Monotropa uniflora), that are devoid of chlorophyll pigments, cannot carry out photosynthesis. As well, please note that not all plants photosynthesise.  Parasitic plants feed off the nutrients and sugars provided by their hosts.

Carotenoid biosynthesis

Plant carotenoids are dependable for the red, orange, and yellow pigments originate in fruits and roots, involving tomatoes, red peppers, pumpkins, and carrots. They can be seen in the petals of many flowers and are the primary pigments in charge for the fall colouration of deciduous trees. Carotenoids are manufactured in the terpenoid pathway as C40 tetraterpenes obtained from the condensation of eight isoprene units starting throughout isopentenyl diphosphate. There are 2 necessary types of carotenoids: (1) carotenes that enclose no oxygen atoms and (2) xanthophylls that enclose oxygen. At the centre of each carotenoid molecule, the linkage order is annulled, consequential in a molecule that is symmetrical. A set of double links in the molecule is accountable for the absorption of light in the visible portion of the spectrum. As mentioned above, this has a significant contact on the absorption of a wider range of light wavelengths for utilize in photosynthesis. As a result, in photosynthetic organisms, carotenoids are an integral structural component of photosynthetic antenna and reaction centre complexes, but they as well defend against the damaging results of Photooxidation procedures. As chlorophyll, carotenoids are established in the thylakoids of green leaves and stems. In fruits and flowers, they are as well originated in plastids, but such plastids have structural dissimilarities and are termed to as chromoplasts to point out that they enclose pigments other than chlorophyll. β-carotene is the orange pigment in carrot (Daucus carota) roots, sweet potato (Ipomoea batatus) tuberous roots, pumpkin (Cucurbita Pepo) fruits, leaves of deciduous trees, and several flower petals. Zeaxanthin and violaxanthin are originated in autumn-coloured leaves and flower petals and are responsible for the bright yellows that are sometimes seen. Colouration of flowers is extremely significant to the survival accomplishment of the plants producing them. The colour of the flowers is one of the primary factors included in attracting pollinators. β-carotene is significant in the human diet since of its purported anticancer activity, its utilize as a food colouring, and it is an significant source of vitamin A (an alicyclic alcohol), that is synthesized from β-carotene and other carotenoids. Vitamin A produced by animals is, in turn, converted to the pigment, retinal. This pigment is one of the necessary components in the light receptors of the eye that allow us to see. Carotenoid pigments can as well function in fruit and seed dispersal via attracting animals that in turn, spread seeds. 

Most fruits generate odor compounds such as monoterpenes, to assist attract such organisms, and the sugars generated and stored in the fruits act as a positive reward. In ripening fruits, as in leaves turning colour in autumn, chlorophyll pigments steadily break down in chloroplast thylakoid membranes, revealing the carotenoid pigments that were masked through the chlorophyll pigments. During ripening, there is important synthesis of new carotenoid pigments. In the case of ripening tomatoes and peppers, for instance, the unripe fruits are typically bright green. As ripening developments (triggered by the plant hormone, ethylene), diverse carotenoid pigments appear and, newly synthesized, account for the colour of the ripe fruits. Lycopene is the red pigment seen in mature tomato and red pepper fruits. Tomatoes (Lycopersicon esculentum) can contain together red and yellow fruits depending on the genotype of the parent. In several peppers, ripe fruits are green (sold as sweet bell peppers) but turn red or yellow at maturity (Capsicum frutescens var, grossum). Other ripe peppers, often very "hot" to the taste ("hot" due to the presence of the alkaloid, capsaicin), might be green, orange, yellow, or red at maturity, depending again on the genotype of the parents. Similar kinds of colour changes take place in ripening cucurbit fruits (squash, gourds, and pumpkins in the Cucurbitaceae family) and in the fruits of egg plant (Solanum melongena var, esculentum).

Several plants, these as red maple (Acer rubrum) trees, generate red-coloured flowers or leaves, yet they are wind pollinated. It is obvious that such plants don't have to attract pollinators - so, why the colour? One interesting theory behind why they spend their energy to do this is that the pigments assist to warm the flowers in early spring or the leaves during early spring or late fall. This extra heat would greatly aid seed expansion and photosynthetic processes in early spring, permitting the plant to obtain a head start on growth over other plants in addition to providing a longer period during that to create energy reserves in the fall. Red colouration in many plants isn't due to carotenoids, but rather, to anthocyanin pigments originate in the vacuoles of plant cells.

Other natural products of pharmaceutical importance Prostaglandins, Thromboxanes & Leukotrienes

The members of this collection of structurally related natural hormones contain an extraordinary range of biological consequences. They can lower gastric secretions, stimulate uterine contractions, lower blood pressure, influence blood clotting and induce asthma-like allergic responses. Since their genesis in body tissues is tied to the metabolism of the necessary fatty acid arachidonic acid (5,8,11,14-eicosatetraenoic acid) they are classified as eicosanoids. Many properties of the general drug aspirin effect from its effect on the cascade of reactions associated with these hormones.

The metabolic pathways via that arachidonic acid is exchanged to the diverse eicosanoids are compound and won't be discussed here. A rough outline of some of the transformations that take place is provided below. It is useful to observation arachadonic acid in the coiled conformation revealed in the shaded box

2330_Rough Outline of some of the Metabolic Pathways by.jpg

Fig: Rough Outline of some of the Metabolic Pathways by which Arachidonic Acid is converted to the Various Eicosanoids 

Leukotriene A is a precursor to other leukotriene derivatives by epoxide opening reactions. The prostaglandins are given systematic names that reflect their structure. The initially formed peroxide PGH2 is a common intermediate to other prostaglandins, as well as thromboxanes such as TXA2


The alkaloids aren't the only group of secondary metabolites that are derived from amino acids. Amino acids not only form the building blocks for the huge peptides and proteins but as well for smaller peptides that are converted into the β-lactam antibiotics these as the penicillins and cephalosporins. The diketopiperazine antifungal agents produced through Trichoderma and Gliocladium species, such as gliotoxin, are also obtained from amino acids.


There are a number of natural products that are necessary for life but that can't be generated via the body. The recognition via Hopkins and others at the start of the 20th century that diseases these as scurvy, rickets and beriberi, which arose from deficiencies in the diet, might be connected through a requirement for particular compounds present in foods, led to the search for such necessary factors. Such natural products became recognized as vitamins. As each vitamin was isolated, it was identified via a letter of the alphabet. As their structures became known, such compounds obtained a trivial name.

A number of vitamins play a role as co-enzymes in the function of particular enzymes these as those engaged in biological oxidation, diminution and carboxylation. This biological function of the vitamins places them in the class of primary metabolites. Though, the clarification of their structures and traits of their chemistry and biosynthesis bond them through secondary metabolites. In the period subsequent in the year 1920, bioassay-guided fractionation using test animals led to the isolation of diverse vitamins. They are present in their natural sources in low concentrations, and consequently extremely small amounts of material were available for structural studies. Nevertheless, the structures of many of the vitamins were established in the year 1930s and verified via synthesis. Material then became available for biological studies and dietary supplements. The presence of the fat-soluble vitamin A in egg and in fish oils was established in 1913-1915, and its structure was elucidated by Karrer in 1931. The recognition that the disease beriberi, which was prevalent in South East Asia, was a deficiency disease and that it could be cured by an extract obtained from rice polishing, led Funk in 1911 to coin the name vitamin for these essential dietary factors. Vitamin B1 (thiamine) was isolated in 1926 and in quantity by Williams in 1934. Its structure was established in 1936 and confirmed by synthesis. Other members of this group of vitamins comprise riboflavin (vitamin B2), pyridoxamine (vitamin B6), biotin, folic acid and vitamin B12. Vitamin BI2 was isolated in 1948 and its structure established by a combination of chemical work and X-ray crystallography in the year 1954. It is one of the most potent of the vitamins, being active in the treatment of pernicious anaemia at the level of micrograms. Vitamin C (ascorbic acid) is important in the prevention of scurvy. Its structure was established in the year 1932. Vitamin D, a steroid, has already been revealed. Vitamin E, tocopherol, is an antioxidant and vitamin K, a quinone, is an antihaemorrhagic factor.


The flavonoids have 2 benzene rings divided through a propane unit and are obtained from flavone. They are usually water-soluble compounds. The more conjugated compounds are frequently brightly coloured. They are usually originated in plants as their glycosides, which can complicate structure determinations.  The different classes within the group are distinguished by additional oxygen-enclosing heterocyclic rings and hydroxyl groups. These comprise the chalcones, flavones, flavonols, flavanones, anthocyanins, and isoflavones. 

Other general flavonoid groups comprise aurones, xanthones, and condensed tannins. The catechins and leucoanthocyanidins are structurally similar and only hardly ever exist as their glycosides. They polymerise to shape condensed tannins that assist provide tea its colour. They as well are adequately prevalent to darken the colour of streams and rivers in several woody areas, including the black waters of the Okefenokee Swamp in Georgia and the Suwannee River in Georgia and Florida. The flavanones and flavanonols are rare and normally exist as their glycosides. The flavones and flavonols are the most extensively distributed of all the phenolics. The anthocyanins are the general red and rare blue pigments of flower petals and can make up as much as 30% of the dry weight of various flowers. The red pigment of beet (Beta vulgaris) is anthocyanin. The anthocyanins exist typically as glycosides. Flavanones often coexist in plants with their corresponding flavones (e.g., hesperidin and diosmin in the bark of Zanthoxylum avicenna). The flavone, acacetin, isolated from black locust (Robinia pseudoacacia), shows anti inflammatory activity. Galangin, a flavonol from galanga root (Alpina officinarum) illustrated antibacterial activity against antibiotic-resistant strains of Staphylococcus aureus.

Isoflavones possess a rearranged flavonoid skeleton. A variety of structural modifications of this skeleton lead to a large class of compounds that includes isoflavones, isoflavanones, and rotenone. The isoflavonoid compounds are common constituents of the legume family Fabaceae (formerly called Leguminosae family). Such compounds displayed estrogenic, insecticidal, and antifungal activity. Some are potent fish poisons. Therefore, for instance, the isoflavones biochanin A from red clover (Trifolium pratense), genistein from soybean (Glycine max), and coumestrol from alfalfa (Medicago sativa) are phytoestrogens, in addition to exhibiting antifungal activity. The isoflavanone rotenone is the principal insecticidal constituent of the Flavonoid classes.  Piscicidal plants Derris elliptica and Lonchocarpus nicou. It is a powerful inhibitor of mitochondrial electron transport. The chalcones, these as butein, lack the pyran ring found in flavonoids, even though this is frequently subject to pH-controlled equilibria. The chalcone is more fully conjugated and normally brightly coloured.

Phlorizin is a strong inhibitor of apple seedling expansion. The aurones are golden yellow pigments that are general in assured flowers. Sulfuretin is an aurone pigment responsible for the yellow colour of certain species of the aster family (Asteraceae), for instance, cosmos (Cosmos sulphureus) and dahlia (Dahlia variabilis). Many of such phenols come from familiar sources. The condensed biflavonoids santalins A and B are the main pigments of red sandalwood (Pterocarpus santalinus). The flowers of the hawthorn tree provide hyperoside, one of the principal flavonoids from this source (Crataegus laevigata).  Neohesperidin is responsible for the bitter taste of orange peels (Citrus aurantium), while the dihydrochalcone derivative is one of the sweetest-tasting chemicals recognized. Quercetin, a flavonoid present in numerous plants, has antioxidant activity. It is presently popular at health food stores, although any benefits are speculative. Silybin, one of the silymarins, a mixture of diverse flavanone derivatives (flavonolignans), is present in the fruit of the milk thistle (Silybum marianum). It is utilized to treat several liver disorders. Similarly, silymarin is the active antihepatotoxic complex used for the treatment of liver damage, and it enhances the rate of synthesis of ribosomal ribonucleic acids. It is as well utilized to prevent skin cancer. The secoiridoid glucoside centapicrin is an ultrabitter (bitterness value ca. 4,000,000) secoiridoid glycoside from the century plant (Centaurium erythraea). The isoflavones genistein and daidzein are originated in high concentrations in kudzu (Pueraria montana), soybeans (Glycine max), in addition to several other legumes. Both genistein and daidzein have anticancer activity.

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