Secondary Metabolites and Their Effect on Human Health

Secondary Metabolites And Their Effect On Human Health

Metabolites are different kinds of substances that are essential to the metabolism of an organism. Plants produce a huge variety of metabolites, which can be broadly categorized into primary metabolites and secondary metabolites. Primary metabolites have a key role in the survival of the plant and generally play an active role in respiration and photosynthesis, while secondary metabolites are not involved in the normal growth and development of the plant. Although the absence of secondary metabolites doesn’t cause an immediate death, it can lead to the impairment of the survivability of the plant in the long run.

Secondary metabolites are mostly produced by plants for defense purposes. They include alkaloids, steroids, phenolics, resins, essential oils, tannins, flavonoids, lignins, etc. examples of primary metabolites include lipids, carbohydrates, and proteins. In plants, secondary metabolites are limited to an occurrence, and some are restricted to specific taxonomic groups’ species, genus, or family. They are generally accumulated by the plant cells in much smaller quantities than the primary metabolites and are synthesized in specialized cells at different developmental stages. As such, their extraction and purification are often difficult.

We call air that has a substantial number of secondary metabolites “Paleo Air®” as we believe that this air is closer to the air that our ancestors breathed, and is, therefore, healthier for us.

A simple classification of secondary metabolites includes three main groups:

  •    Terpenes (such as carotenoids, cardiac glycosides, and sterols)
  •    Phenolics (such as lignans, lignins, flavonoids, phenolic acids, stilbenes, and coumarin)
  •    Alkaloids or nitrogen-containing compounds (such as glucosinolates)

Terpenes (Isoprenoids)

This is the largest and most diverse class of metabolites, ranging in structure from linear to polycyclic molecules, and in size from a single isoprene unit (C5H8) to natural rubber, containing up to 5,000 isoprene units. Terpenoids are usually synthesized by condensing isoprene units and are classified based on the number of isoprene units present in the core structure.

Many aromatic and flavor molecules such as linalool, menthol, caryophyllene, and geraniol are formed by monoterpenes (C10H16) which have two isoprene units, and sesquiterpenes (C15H24), made up of 3 isoprene units. Other subsequent terpenes such as triterpenes (C30H48) and diterpenes (C20H32), and tetraterpenes (C40H64) exhibit special properties as discussed below.

Plant volatiles: Monoterpenes and Sesquiterpenes

These are typically lipophilic liquids with very high vapor units. The non-conjugated volatiles is able to freely cross membranes and evaporate into the atmosphere when barriers to diffusion are absent.

Many derivatives of monoterpenes are essential in plant defense against pathogens. For example, pyrethroids are a form of monoterpene esters produced in the leaves of Chrysanthemum species, and typically have neurotoxic and insecticidal activities for many kinds of insects such as wasps, moths, bees, and beetles. When isolated, they are used in the production of commercial insecticides, since they have low toxicity for mammals. Monoterpenes are also present in the ducts of gymnosperms, occurring in the form of limonene, alpha-pinene, beta-pinene, and myrcene, which are toxic for serious pests like the bark beetle.

Sesquiterpenes are present in essential oils, and some of their derivatives serve as phytoalexins. Phytoalexins are antibiotic compounds that are produced by plants during microbial attacks and act as antifeedants to deter herbivorous prey. The Asteraceae family has costunolides with 5-membered lactone ring, which provides a strong deterrence to prey.


These include phytol, which is a hydrophobic tail of chlorophyll that helps anchor plants in thylakoid membranes. It’s essentially a reduced form of geranylgeraniol, which forms a lipophilic side chain of chlorophyll. Gibberellin hormones are forms of diterpenes, which are involved in leaf expansion, seed germination, and act as growth promoters with important roles in CO2 fixation, biomass production, assimilate translocation, stomatal conductance, and phloem loading. Other diterpenoids include abietic acid, the pharmacologically active metabolites like taxol, found in the barks of plants in the Taxus species, and phytoalexins, resins found in legumes and conifers are diterpenes.


Squalene is the most common triterpene and is mostly isolated from shark’s liver oil. It’s also found in the livers of other fish species, vegetable oils, and even human sebaceous secretions. The skeletal modification of squalene units side chains results in a number of biologically active products like bile acids, steroidal saponins, cardioactive glycosides, mammalian sex hormones, and corticosteroids.


These constitute a large group of natural dyes with a variety of functions. Carotenoids are the most important tetraterpenes and are biosynthesized by plants, fungi, algae, bacteria, and yeast. When absorbed through the human diet, some varieties of carotenes, such as beta-carotene are pro-vitamin A. Others like lycopene are very important due to their antioxidant properties.

Benefits of Terpenoids to Human Health

The essential oils give certain plants their fragrance. For centuries, human beings have extracted these essential oils for use in aromatherapy and medicine. In aromatherapy, the oils are believed to improve the mental functioning and uplift the mood. In alternative medicine, essential oils are thought to possess a number of health benefits.

Taxol, which is extracted from the bark of the Pacific Yew Tree, has become very important in the medical field. Taxol is used in the treatment of breast and ovarian cancer.

Phenolic Compounds

These compounds are characterized by having at least one aromatic ring, which is attached to one or more hydroxyl group. Phenols can be found in almost all parts of the plant, in nearly every plant species on the plant.

Phenolics range from simple compounds with low molecular weight to large, very complex tannins and other multi-ringed derived polyphenols. They can generally be categorized based on the arrangement and the number of carbon atoms present. Phenolics are commonly found conjugated to organic acids and sugars and can be broadly classified into flavonoids and non-flavonoids.


These polyphenolic compounds are made up of 15 carbon atoms, with a three-carbon bridge linking them to two aromatic rings. Flavonoids are the most common phenolics, and they can be found throughout the plant kingdom. In plants, these metabolites are involved in a number of processes, such as pigmentation, UV protection, disease resistance, and the stimulation of nitrogen-fixing nodules.

The major subclasses of flavonoids are flavonols, flavones, isoflavones, flavan-3-ols, and anthocyanidins. Other flavonoid groups such as coumarins, dihydroflavonols, chalcones, aurones, flavan-3, 4-diols, and dihydrochalcones are in comparison quantitatively minor.

The majority of flavonoids are sugars, which naturally exist as glycosides. Although both hydroxyl groups and sugars help to increase the solubility of flavonoids in water, other components such as the isopentyl units and methyl groups make them lipophilic.


These have a very close relationship to flavonols in terms of their structure. Unlike the flavonols, flavones are not as widely distributed, though they have significant occurrences in plants like parsley, celery, and a few other herbs. Moreover, polymethoxylated flavones like tangeretin and nobiletin have been found in a few species of citrus. In West Africa, flavones found in millet have been linked with goiter.


these have a B-ring structure, and they are commonly found in leguminous plants. They are in their highest concentration in soya bean.


The C6-C1 phenolic acids are the major non-flavonoids with dietary significance to humans. Most notable of these is gallic acid, which is a precursor to the C6-C3 hydroxycinnamates, the hydrolysable tannins, and their conjugated derivatives.

 Phenolic acids

Also known as hydroxybenzoates, the principal component of phenolic acids is gallic acid. The name refers to a swelling that occurs due to the accumulation of carbohydrates and other nutrients that support the growth of larvae.

Gallic acid forms the base unit for the gallotannins, which are hydrolysable tannins. Hydrolysable tannins and condensed tannins can bind to and precipitate the collagen protein contained in animal hides. The process changes animal hide into leather, making them more resistant to putrefaction. Therefore, plant-derived tannins paved the way for the tanning industry many years ago. Tannins also bind to the salivary proteins, which produces a taste humans identify as astringency. Mild astringency ideally enhances the texture and taste of a number of beverages and food, most notable, red wines and tea.


the base unit for hydroxycinnamates is cinnamic acid (C6-C3), which can be converted to a wide range of compounds. As products of the phenylpropanoid pathways, these compounds are generally referred to as phenylpropanoids. Caffeic, p-coumaric, and ferulic acids are the most common hydroxycinnamates, which often accumulate as their respective tartrate esters, caftaric, coutaric, and fertaric acids.

Quinic acids, which are conjugates of caffeic acids, are common substituents of fruits and vegetables. Chlorogenic acids form about 10% of the green Robusta coffee beans and the leaves of green mate plant. Regular coffee consumers may have an intake exceeding 1 gram of this compound per day.


Just like flavonoids, members of the stilbene family are polyphenolic compounds, with a C6-C2-C6 structure. Stilbenes are important phytoalexins that are produced by plants in response to an attack by bacterial, fungal, and viral pathogens.

The most common stilbene is resveratrol. It occurs in both the trans and the cis isomers and is commonly present in plant tissues as trans-resveratrol-3-O-glucoside, also referred to as polydatin and piceid. There’s also a family of resveratrol polymers known as viniferins. The main dietary sources of stilbenes include wine, grapes, peanuts, and soy products. The itadori plant (the Japanese knotweed) is known to contain high amounts of trans-resveratrol and is glucosides.


Alkaloids are a huge, structurally diverse group of compounds derived from amino acids such as lysine, tryptophan, tyrosine, and aspartic acid. They occur as secondary metabolites in about 20% of the total plant species and have an important defensive role against pathogenic and herbivory attacks. A huge number of different biologically active alkaloids have been successfully isolated from their plant sources. At the cellular level, the action of alkaloids is quite varied, with some affecting the nervous system, others influencing membrane transport, others protein synthesis, and some enzyme activities.

From their varied biological activities, over 12,000 alkaloids are used in pharmaceuticals, narcotics, and poisons. Some of the most common alkaloids from plants include vinblastine, vincristine, and camptothecin, which are used as anticancer medications, morphine and codeine as analgesics, colchicine as a gout suppressant, and scopolamine as a sedative.  

Alkaloids can be broadly categorized into three groups:

  • Typical alkaloids: these are derived from amino acids and have a heterocyclic ring with a nitrogen atom. They include pyrrolizidine, pyrrole and Pyrrolidine, quinolone, tropane, pyridine and piperidine, terpenoid, isoquinoline, imidazole, steroid, purine, aporphine, indolizidine, indole, and norlupinane.
  • Biological alkaloids: amines that are not heterocyclic
  • Steroidal alkaloids: these are not derived from amino acids, but they contain a heterocyclic ring with a nitrogen atom

Benzylisoquinoline alkaloid

These pharmacologically active alkaloids are present in Papaveraceae, Fumariaceae, Ranunculaceae, and Magnoliaceae, families of angiosperms. Most of them help to protect plants against pathogenic attacks. Some important examples of alkaloids in this group include morphine, berberine, colchicines, sanguinarine, tubocurarine, etc.

Tropane alkaloids

These typically have an 8-azabicyclo octane nucleus and are commonly found in Solanaceae, Convolvulaceae, and erythroxylaceae angiosperms families. However, most of them are toxic, and they are seldom potent pharmaceutically. Some examples of this group include hyoscine, atropine, and hyoscyamine.


Nicotine is a simple alkaloid that makes up the active component of most Nicotiana species, including tobacco. Tobacco is an American native plant that human beings have been cultivating since 3000 BC. The plant is sniffed, chewed, drunk, eaten, smoked, and even used to kill parasites.

Pyrrolizidine alkaloids

These are commonly very toxic and can pose as a deleterious effect on animals. They are therefore a deterrent to herbivores from plants. Pyrrolizidine alkaloids are present in certain families of angiosperms, including Asteraceae, Boraginaceae, Orchidaceae, and Fabaceae.

Purine alkaloids

These include caffeine, coffee, and theobromine. Coffee is usually obtained from Camellia sinensis, Coffea Arabica, and ilex paraguariensis. Tea and coffee are some of the most widely consumed beverages on the planet.

Quinolizidine alkaloids

These are generally toxic and are usually present in leguminous plants. Most of them are produced by Lupinus, whose seed are used as sources of protein in human and animal foods. To remove the toxic alkaloids, the seeds are first soaked in water for a few hours before consumption.

Effects of Secondary Metabolites on Human HealthSecondary Metabolites on Human Health


Secondary metabolites, such as the alkaloids, have been in use for many years as analgesics, anti-malarial drugs, and other antibiotics in order to prevent microbial infections and other health-related issues.  Codeine from papaver, quinine from cinchona, scopolamine from datura, and atropine from Atrop are other secondary metabolites used in the pharmaceutical industry.

Morphine, which is extracted from the plant Papaver somniferum otherwise known as the opium poppy, is used as a pain reliever for patients experiencing severe pain.1 It’s also used as a cough suppressant. Another alkaloid, cocaine is quite addictive and dangerous to human health. However, it has been previously used as an anesthetic.

The people of South America have culturally used cocaine to alleviate hunger. Workers chew on the leaves of the coca plant while working. Nonetheless, this is not as dangerous as using cocaine because the leaves only contain a small amount of cocaine. Still, most cocaine derivatives are dangerous to human health, especially when used habitually, and can be fatal.

Salicylic acid is a medically active phenol, which serves as the active ingredient of aspirin. It’s extracted from the bark of the willow tree and has been successfully used as a pain reliever and has treated fevers since ancient times. It also has some cosmetic uses and is used in a number of skin care products to aid in the treatment of acne, dermatitis, and large pores.

Preventing Disease

The caffeic acid produced in some plant species is an effective substance against bacteria, viruses, and fungi. Other phenolic compounds with essential oils such as Eugenol are an effective antibacterial agent for use against bacteria and fungi. Aloe vera produces a combination of such secondary metabolites, along with latex, which is effective against bacteria such as salmonella, streptococcus, and staph aureus. Cashew produces phenolic compounds including salicylic acid, which helps to inhibit the growth of fungi and bacteria.

Saponins help to protect the body from cholesterol-related illnesses and conditions. They are a group of terpenoids commonly found in the allium plant species like garlic and onions and are abundant in tea, legumes, and spinach. They help to promote a cardiovascular health by binding to and removing cholesterol from cell membranes.1

LDC cholesterol is harmful to the body in the sense that it intercalates the cell membranes and decreases their flexibility. Rigidity in the vascular system can put pressure on the heart, and increase the risk for problems. Saponins help to prevent this by binding to the cholesterol and removing it from the arterial membranes.  

Fragrance and Insect repellents

Secondary metabolites are also used as fragrances. Terpenoids are very volatile and evaporate easily to release isoprene gas. Isoprene is believed to protect the plant from excess heat. Essential oils ideally give a plant its fragrance. In some plants, the scent is a deterrent to insects and/or herbivores and protects it from dangerous pathogens.

Since the ancient times, humans have used essential oils for medicine and aromatherapy. Essential oils have a wide variety of uses in aromatherapy, including relaxing the mind, enhancing mood, improving respiration, and boosting the mental function. Essential oils are thought to have a number of benefits in alternative medicine as well.

Nonetheless, essential oils can be dangerous if consumed. As such, they are mostly inhaled, applied topically or more recently breathed using retronasal olfaction, and if need be, consumed internally in very low doses. Some oils can be very helpful for treating skin problems, respiratory illnesses, and wounds as antiseptics.


Caffeine is perhaps the most popular and loved alkaloid. Human beings have used caffeine to stay alert for centuries. As an alkaloid, caffeine has a protective role in the plants it comes from; coffee, cocoa, and tea. The seedlings of the coffee plant contain high concentrations of caffeine, which is toxic in nature and protects the seedlings from insects. The high concentration of caffeine also has an interesting defense mechanism; they prevent other plants from germinating in the area. This phenomenon is referred to as allelopathy.

In human beings, caffeine acts as a stimulant and boosts moods while improving physical performance. This is quite helpful in keeping people alert enough to face the long days of work and school. It works by blocking the adenosine receptors in the brain. Adenosine is usually responsible for slowing down nerve activity, as well as regulating neurotransmitters such as dopamine, which leads to a heightened brain activity. Caffeine is also thought to reduce the risk of heart disease and diabetes. And although it’s a drug, it can bring positive effects to the efficiency and mood of humans, if consumed in moderate amounts.2


Many secondary metabolites from plants are toxic to humans and animals. For example, cyanogenic glycosides that occur in cassava, strychnine from strychnos, and coniine from conium are toxic to both man and animals.

The phytotoxicity of certain coumarins by the name furanocoumarins are of special interest. These compounds are only toxic when they are exposed to light, and can cause skin related diseases and even cancers. Furanocoumarins are commonly abundant in the members of the Umbelliferae family such as celery.

Maintaining Good Health

Carotenoids occur naturally in certain plants, photosynthetic bacteria, and algae. Vegetables and fruits are the main source of carotenoids in the human diet and occur in red, yellow, or orange colors. They are actually the source of the bright color in papayas, pumpkins, tomatoes, cantaloupes, and sweet potatoes. Leafy greens like spinach are also a great source of carotenoids in the body. The two main carotenoids are zeaxanthin and lycopene. A high zeaxanthin and lycopene intake is helpful in the prevention of cancers. This is because they contain high amounts of antioxidants, which essentially scavenge the body for reactive nitrogen and oxygen species.

Flavonoids, just like carotenoids, have antioxidant properties in the body. The major sources of flavonoids in the human diet are chocolate, tomatoes, and red wine. The existence of free radicals in the body can injure the walls of the vascular system, and lead to atherosclerotic changes. By removing these free radicals, flavonoids, and carotenoids, it helps reduce the risk of heart disease, prevents inflammation tumor growth, viral infections, and osteoporosis.3

Anthocyanins, which range in color depending on the pH levels of their environment, are plant secondary metabolites commonly present in berries and grapes. They have a range of medical benefits and are believed to help protect against diabetes, heart disease, and cancer when consumed. They are also often used in skin care products to help slow the aging process.4

Glucosinolates, a group of compounds that are derivatives of amino acids, can promote good health in the human body. Dietary sources include collard greens, broccoli, cabbage, and mustard. They play an important role in preventing cancers through the induction of apoptosis. Glucosinolates essentially help to regulate the number of reproducing cells in an area experiencing uncontrollable cell growth and also have antioxidant properties.

What we can conclude here is that humans and plants are meant to work alongside each other for optimum support. It’s a relationship that takes work on both sides. If we take the time to understand and cultivate plant life, then those plants will provide us with delicious aromas, antioxidants, terpenoids, flavonoids and much more!

There is a whole microcosm of molecules and compounds working behind the scenes that we sometimes take for granted. Taking the time to incorporate more plant matter, whether, through diet, forest bathing or the use of a personal essential oil diffuser into our lives can be just the infusion needed to promote longevity in our bodies and support our overall well being.



By Aaron Williams

Aaron is an freelance writer and avid fan of anything having to do with essential oils. In his spare time he can be found taking care of his 2 cats and exploring the world of virtual reality.

Favorite MONQ blend: Sleepy

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The above information relates to studies of specific individual essential oil ingredients, some of which are used in the essential oil blends for various MONQ diffusers. Please note, however, that while individual ingredients may have been shown to exhibit certain independent effects when used alone, the specific blends of ingredients contained in MONQ diffusers have not been tested. No specific claims are being made that use of any MONQ diffusers will lead to any of the effects discussed above.  Additionally, please note that MONQ diffusers have not been reviewed or approved by the U.S. Food and Drug Administration. MONQ diffusers are not intended to be used in the diagnosis, cure, mitigation, prevention, or treatment of any disease or medical condition. If you have a health condition or concern, please consult a physician or your alternative health care provider prior to using MONQ diffusers.

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