Perfectly Natural: Gardeners’ Love of Chemistry and Chemists’ Love of Plants

When citrus trees are grown from seed, they revert to a wild state and they can take decades to flower. About 15 years after germination I’m still waiting to see grapefruit blossoms in our kitchen, and of course the short days of long winters at high latitudes don’t help the matter. But a few years ago I was lucky enough to visit an organic citrus farm in the Orlando, Florida region, which turned out to be a far more magical treat than any ride at nearby DisneyWorld.


On a single citrus tree we not only see fruits at various stages of ripening but also new flowers. Picture by the author.

Unlike most plants, those of the genus Citrus can simultaneously bloom while fruit is ripening elsewhere on the same tree. And the blossoms include some of the most delightful fragrances one will ever experience. And understanding how some of the compounds are synthesised by tangerines, lemons, grapefruits and plants in general makes one appreciate them even more.

At the level of citrus tissues, we see among different species variations upon a theme, the theme being what all plants of the genus have in common: bee-pollinated, bisexual flowers with usually 5 petals and 5 sepals and superior ovaries which become the fruit’s rind and flesh. Their leaves are evergreen and being part of subtropical trees, even the hardiest among them, the Meyer’s lemon, cannot survive temperatures below -5 °C.  At the biochemical level, in order to produce their special fragrance, there are variations upon themes as well.  Like many other plants they use a common precursor, the  molecule isopentenyl pyrophosphate, and with subtle changes they produce their beautiful characteristic bouquets which diffuse into our nasal receptors.

Using a process relying on thiamine(vitamin B1), among others, plants make isopentenyl pyrophosphate from acetyl coenzyme A, a metabolic byproduct of glucose known as pyruvate.   Isopentenyl pyrophosphate is a useful and ubiquitous molecule containing a 5-carbon atom-building block known as an isoprene unit. Some isopentenyl pyrophosphate molecules isomerize, meaning they rearrange with the same atoms, essentially shifting the double bond from the tail end over to the next pair of carbon atoms. The stable pyrophosphate group then leaves the molecule, leaving behind a reactive positive charge on a carbon atom at the head of the isopentenyl molecule. This is incidentally one of the many reasons plants need to absorb phosphorus from their environment.


Simplified reaction mechanism(enzyme is not shown): electron flow reveals how isopentenyl pyrophosphate bonds to a charged molecule derived from isopentenyl pyrophosphate itself. The product, geranyl pyrophosphate is then used by lemons to make geraniol. Many other fragrant molecules are also derived from geranyl pyrophosphate. See diagram below. Diagram by the author.


The backbone of geranyl pyrophosphate is highlighted in red and is found in three citrus scents.

Notice that I emphasized that only some isopentenyl pyrophosphate isomerize and become ionized. The rest then attack and stick to the positively charged molecules, creating  geranyl pyrophosphate (C10H20O7P2). This molecule can eventually be used to make an important component of cell membranes known as cholesterol, but lemons and some non-citrus plants also use the right enzyme to react it with water to produce geraniol (C10H18O). Although roses produce far more of the scent, it is also a minor component of citrus peels. In addition, lemon plants can oxidize the alcohol group of geraniol to an aldehyde to produce two isomers of citral, A and B. The former has a strong lemon scent and the latter, which has the same formula but with an aldehyde group on the other side of the carbon-double-bond, has a less intense but sweeter odor.

One 2009 study by Citrus Research and Education Center in Florida analyzed the flower scents of 15 species of citrus plants including lemons, limes, sweet oranges and mandarins. Using a relatively new solvent-less technique known as solid phase microextraction (SPME) along with mass spec-gas chromatagrophy, they identified 70 compounds, of which 29 were identified for the first time. The compounds belonged to four different groups of terpenes, compounds that are all derived from previously mentioned isoprene units. One of those oxygenated terpenes, linalool, is an alcohol derivative of geranyl pyrophosphate. Of the two possible isomers of the compound, oranges produce the R-version of linalool, which smells like lavender blended with citrus. It attracts bees and me.


A bee in a lemon flower. Linalool is one of the compounds that attracts the pollinator. Picture by the author.

geranyl pHosp deriv

More variation upon a theme at the molecular level: geranyl pyrophosphate, which is itself built up from two isoprene units, goes on to be the precursor of four other key compounds found in the floral essence of several citrus plants. Structures by the author.

Twenty four and forty five percent of  the blossom-volatiles of sweet oranges and mandarins, respectively, consist of  ß -myrcene. This compound is yet another variation upon the theme of geranyl pyrophosphate. Instead of having an allylic alcoholic head, it has a pair of conjugated double-bonded carbons and a pleasant fragrance. The same fruit blossoms and those of certain limes and lemons also produce of yet another geranyl pyrophosphate-derivative known as E-ocimene. Its aroma has been described as woody, green and tropical, an indication of how difficult it is for humans to describe smells. The difficulty becomes more pronounced when the isolated compounds of the labs force us to perceive “solo performances” while the reality of nature’s citrus blossoms present us with a symphony.


The Botanical Garden. Ryx and Phillips. Firefly.

A comparison of citrus blossom volatiles. Phytochemistry 70 (2009) 1428–1434

Principles of Biochemistry. Lehninger.

The Merck Index. Twelfth Edition

Myrcene as a Natural Base Chemical in Sustainable Chemistry: A Critical Review


Science Outreach is Alive and Well

indexTrying to explain why Canadians’ perception of science is not as favorable as it can be,  a scientist on CBC’s Cross-Canada Checkup blamed it on himself and on the rest of the scientific community. He claimed that scientists do not engage in sufficient science outreach. What an odd thing to say! And yet I have heard that unfounded complaint before.

Here is some evidence to the contrary.

Walk into any public library and you will find several shelves filled with popularizations in every scientific discipline, and a fair percentage of those books such as Oxford’s Very Short Introduction series are written by researchers. Many of those scientists may be in the twilight of their careers, but that does not make them less qualified to communicate with the public. There are also younger and active scientists who maintain blogs or youtube channels, and although some may not find the time for such a medium, it’s been my experience that most respond to emails about their research.

Every week on CBC Radio’s Quirks and Quarks, scientists share their latest endeavors . With the help of the show’s producers and host, the jargon is kept to a minimum to make things understandable. The British Broadcasting Corporation and the Australian Broadcasting Corporation have comparable quality programs such as Crowd Science and Ockham’s Razor, both of which involve active researchers. Even in pre-World-Wide-Web days, university science departments held free public lectures, which are still ongoing. In addition, accessible to anyone with an internet connection are free introductory and first year undergraduate online courses in earth sciences, chemistry, biology and physics at and at MIT (Massachusetts Institute of Technology). Other institutions such as the University of Waterloo specifically reach out to physics and chemistry teachers through their Chem13 News newsletter and the Perimeter Institute, respectively.

We can extend the list by adding popular science magazines such as Scientific American and Natural History which still have articles directly written by researchers; television programs such as Nature of Things and Nova who consult scientists; science museums such as the Exploratorium and the Boston Museum of Science and Technology who collaborate with outreaching professionals; and NASA’s astronomical efforts to educate the public. And if my list of examples seems to exclude certain continents, consider the long list of researchers involved in Science Circus Africa.  It is a pioneering science-outreach project that brings fun-filled science exhibits, shows and teacher workshops to South Africa, Botswana, Zambia and Malawi.

So why do we have a persisting belief that scientists in general don’t do enough outreach? Prejudice, if we borrow a razor-sharp definition from a recent Philosophy Now editorial, “is a preliminary opinion that is mistaken for a final conclusion.” In the same way that people of a certain ethnicity are not immune from prejudices that do not favor their native culture, scientists can also hold mistaken beliefs about their own kind.

OSCAt the root of our discussion is last year’s (August 2017) Ontario Science Center’s Canadian Science Attitude Research poll. Leger’s online panel was used, and they interviewed 1,514 Canadians. (A probability sample of the same size would yield a margin of error of 2.5%, 19 times out of 20). The poll unfortunately revealed that 75% of Canadians believe that “scientific findings can be used to support any opinion” and 43% believe that scientific findings themselves are “a matter of opinion”.


Source: National Audubon Society

Almost half of our citizens, 47%, believe that the science behind global warming is still unclear. If you consider what the poll reveals about Canadians’ sources for confirming scientific resources —-only 44% rely on scientists and professors, while 50% rely on the internet, media and family—that could be the crux of the problem. The voices of scientists and professors on the internet, in the media and within their families are often overshadowed, not because scientists don’t do enough outreach, but because their voices are largely outnumbered by those of non-scientists. Special interest groups and the general population can easily express themselves online, dominate comment threads and publish blogs and websites. And when a minority of scientists engages in disingenuous outreach, if they become effective, it’s only because their opinions resonate with political and economic viewpoints. If quality-science outreach is like the voice of a songbird amid the noise of major highway traffic, all we have to do is get away from the road.

The Science of Canada’s Symbol, the Beaver

2018BIGCOINSUB-7The beaver, Castor canadensis, is an official symbol of Canada, somehow representing our sovereignty. Each time we pick up a 5 cent-coin, the so-called nickel, which except for special collectors’ editions is about 95% steel and only 2% nickel, we see an illustration of a beaver. But how much do we know about the natural history and ecology of our icon?

Like many humans, beavers are monogamous and mate for life. They also impact both the physical landscape and biological diversity in their habitat.  Their exact impact varies from one site to another, depending on the location, relief and habitat type—again parallel to the non-uniform ecological footprint of our societies.

During dry periods, as much as 30% of  water in certain watersheds could be held in beaver ponds. This can decrease erosion when water flow increases to higher levels. If a beaver dam however collapses, the opposite effect can occur. Flooding was  caused by such an occurrence in Alberta the 1990s and in British Columbia in the summer of 2000.


A beaver chewing on a cottonwood. This will lead eventually to the tree’s production of shoots rich in protective compounds.

The presence of beavers is important for shaping the littoral communities in certain lakes of the Canadian Shield increasing the population of fish, crayfish, diving beetles, large bugs, tadpoles, newts and leeches. This happens not just from the changing water levels but because dams concentrate nutrients.

They are also engaged in a fascinating coevolutionary relationship with the type of trees they use to build dams. Regrowth of cottonwood trees felled by beavers results in the synthesis of much higher levels of phenolic glycosides. These plant compounds then serve as a defence against other mammalian herbivores and beaver themselves, ensuring the long term survival of the cottonwoods. Another beaver-target, the quaking aspen, also uses a chemical defence against beavers. Younger trees, although easier to take down, are avoided by beavers because juvenile suckers contain higher concentrations of salicin, salicortin, tremulacin, and tremuloidin. Juvenile suckers are asexual shoots produced by trees that have been cut down but which still have living roots.


Notice that each of the above compounds consists a simple sugar linked to a phenolic compound by replacement of a hydroxyl group in the sugar molecule—hence their name: phenolic glycosides, which protect trees against herbivores. The compounds’  concentrations was measured by HPLC-analysis after methanol extraction. (Structures from

In the ecological web of mammals, it’s not surprising to see beavers play a more direct role than the consequences of their influence on plant biochemistry.  The world’s second largest rodent is an important food source for wolves and black bears. Abandoned beaver lodges can provide breeding shelters for bobcats and winter shelters for badges and red foxes.


Ecological impact of beavers Castor fiber and Castor canadensis
and their ability to modify ecosystems Mammal Rev. 2005, Volume 35, No. 3&4, 248–276

Optimal central-place foraging by beavers:
Tree-size selection in relation to defensive chemicals
of quaking aspen

Beaver Behaviour and Biology

Catastrophic Failure of Beaver Dam At Chusnulida
The importance of beaver lodges in structuring
littoral communities in boreal headwater lakes

Justice Laws Website

Enduring the 5-cent coin