Fall of the House of Chlorophyll

This month inspiration came to my balcony, autumn arrived in Sulzbach, and this was the view from my apartment,

As this corner of the planet begins to receive it’s sunlight from ever more acute angles, the days get shorter, and the temperature drops.

In response, the trees leaf behind their summer wardrobe and get themselves nicely dolled up in these beautiful oranges, yellows and reds. I had always assumed this colour change simply reflected the fact that the leaves are decaying. And while that’s partly true, it turns out that there’s more to the story.

Come September and October, the oranges, reds and yellows around here actually Steven Bradbury their way to prominence.1

During spring and summer, leaves appear green because they contain a high concentration of compounds called chlorophylls. These compounds absorb light, and use the energy in light to drive their chemical production lines. Using this energy they’re able make compounds like sucrose and malic acid.

Only some of the light arriving from the sun is used by the chlorophylls. They mostly absorb light at the red and blue ends of the visible light spectrum. Green, on the other hand is largely ignored, and is simply reflected back into the surrounding environment. When light from leaves hits our eyes, it contains more of the green parts of the spectrum, and so most of us perceive them as green.

But chlorophylls are not even nearly the only compounds in a leaf that absorb light. There are a range of other light absorbing compounds, which are present in lower concentrations. In spring and summer, deciduous leaves have so much chlorophyll hanging about that the other compounds don’t make much of an impact on their overall colour. But when autumn rolls around, and deciduous trees trigger the death of their leaves, one of the first things that they do is destroy their own chlorophyll. When the chlorophyll is gone, the other coloured compounds have a much bigger impact on the colour of the leaf.

One of these coloured compounds is Quercetin. It’s part of a family of compounds called the flavones. If you would like to see proof of the Quercetin’s yellow colour, visit your local snake oil salesperson. You need to pay for jars of the powder, but the accompanying despair at the unscrupulousness of your fellow man is free. This website actually implies that the stuff will prevent cancer, have you live longer and ‘synergistically’ fuel your body.

It does none of those things.2

But it is pretty, and its biosynthesis is fascinating. So let’s leave the unpacking of the pseudoscience around superfoods to the experts, and get on with examining the chemical production line that produces the stuff from simple building blocks.

This month’s biosynthesis looks a little more complex than normal. It is certainly longer, but for each of the three reactions, the same basic process is repeating.

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In earlier posts the compounds progressed down the assembly line by themselves, and interacted only with the lego folk. Sometimes this is how biosynthesis works. But often the compounds go down the assembly line with a chaperone. In this case the chaperone is Jan. Jan is going to be a pretty regular guest in future posts, which is lovely because she’s enthiolly wonderful.

Was that a pun? Was it word play?… well, no. It was an abomination, and I’d like to make alkynes of apologies.

Anyhow, Jan has a hold of the top compound, and then weirdly, meets another identical Jan carrying a different compound. That second compound is kind of like a boardgame expansion pack. You can easily add it to your base compound and suddenly the number of things that can be done with the base compound increases dramatically.


So Jan takes her three carbon expansion compound, and with the help of Beatrice, clicks two of its carbons onto the base compound. In biological processes no building blocks are ever destroyed. In this example though, only two of the carbons of the three in the expansion are added to the base compound. The other is not destroyed, but converted to carbon dioxide, and is expelled from the plant into the atmosphere.

That process repeats three times. At each step, the length of the carbon chain extends by two. At the end of this process we have a compound with a relatively long straight chain. This compound has the same number of carbons as Quercetin. The skeleton just need to be rearranged into the shape of the final structure.

That rearrangement involves some really interesting chemistry, and I’d love to wax lyrical about it, but I need to run, that ‘Settlers of Catan’ expansion isn’t going to buy itself.


  1. A little known but interesting fact, is that before 2002, ‘To Steven a Bradbury’ referred to the  alluring practice of adding blond tips to brown hair. This usage is now considered archaic.
  2. OK, maybe that’s a little harsh. I guess if you were to design a rocket that used Quercetin as a fuel, and then strapped yourself to it, it would kind of be ‘synergystically fueling your body’. Let’s assume that’s what the friendly folk at Liftmode.com mean.