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.

Download (PDF, 819KB)

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.


The Moss After Tomorrow

Last weekend I found myself in the black forest, in the south west corner of Germany. I spent much of Saturday afternoon wandering through the woods surrounding a beautiful lake named ‘Titisee’.

There was so much to see here that choosing something to focus on for this month’s blog entry was nigh on impossible, the grand old pine trees,

the creepy stump fungus…

The tacky tourist shops,

But none of them were exciting enough, they lacked pizazz, they lacked charm. No, what I needed was a muse to set the pulse racing, what I needed…. was moss.

If you need to take a moment to calm yourself before reading on, I completely understand. You might try watching this, or this, or maybe for the more adventurous, this.1

Moss is frequently overshadowed by it’s larger and more boisterous cousin, the tree. But after a couple of beers, it likes to spin a yarn where as a younger genus, on a dare from some cyanobacteria, it sent earth into a million year long ice age.

If you haven’t had the pleasure of spending an hour or two with some moss down at your local, I’ll tell the story later. But first… some science. Mosses don’t take up nutrients from the soil like grasses or bushes, instead they get their nutrients from the air and the surface of the ground.

You might not think that the surface of a rock would have much nutritional value, but there is actually a whole stack of biologically useful stuff locked up in rocks. Most living things don’t bother trying to access them, but moss is no ordinary organism.

Some mosses can secrete ‘organic acids’ that are able to dissolve rock. The nutrients in the dissolved rock can then be taken up by the moss to help it grow. Sadly, I don’t have space here to talk about all the organic acids that mosses can make, so I’m just going to discuss the one, malic acid. Below is my attempt to show one of the ways that mosses can make this compound.

Download (PDF, 607KB)

The compound at the top of this month’s biosynthesis doesn’t have anything added to it in the first step. You might notice that Greg does remove two hydrogens (the green circles), but this isn’t the most obvious change. The two carbons in the middle of the compound are simply connected differently.

On the face of it, that looks like a completely pointless exercise. Two bricks side to side are no closer to making a house than two bricks one on top of the other.2 If you only have two tires, it doesn’t matter which wheels you arrange them on, you’re no closer to having a functioning helicopter destroyer. If you have ten thousand spoons, none of the ways that you can arrange them will have you any closer to holding a knife.

But the new arrangement of our compound is just a little bit special. Imagine a high jumper preparing to clear a bar. She needs to crouch slightly on her last step to give her the energy to get over that bar. That second arrangement of carbons is a bit like the crouch position, an energetically more explosive arrangement that can help the compound do difficult things. And it’s this new energy richness that allows Phil to take the compound and react it with some water. The building blocks of water get split between those two middle carbons to give malic acid.

An academic group out of the UK, argue that the secretion of organic acids by an ancient ancestor of moss, might have helped to cause an ice age around 445 million years ago.

Moss is a part of a family of plants called bryophytes, who were the first plants to establish themselves on dry land around 460 million years ago. The theory goes, that when these plants started growing over rocks and dissolving their nutrients for the first time, the surplus nutrients washed into the oceans and made a feast for algae. The amount of algae around boomed, sucking carbon dioxide out of the atmosphere to a point where the planet cooled and entered a million year long ice age.

As a theory, it’s all well and good. But it’s got to be the least cinematic cataclysm imaginable.

No-one is paying money to watch Will Smith wander the planet burning moss wherever he finds it to stop the coming Armageddon.

Although, if you’re reading this Mr Smith, I have a wicked idea for a musical based on the Krebs cycle – call me.


1: If you’ve never spent an hour of your life listening to someone delicately flick the bristles of a hairbrush, you’ve made better life choices me.

2: Source required

Beet this for a first post

On a Sunday morning wander through the fields of Sulzbach, I couldn’t help but notice these things,

Ok, I thought to myself, those plants look to be doing OK, but surely showing that much root is frowned on by the more conservative members of the plant community.

Armed with nothing more than burning desire to know more about these confidently bulbous plants, I interrogated the internet. After hours of ethically borderline questioning, it told me that what I had in front of me was some kind of beet.

The beet it turns out (or at least one of its varieties) is grown in Germany thanks to my own personal favourite short statured, horse riding Frenchman – Napoleon. In response to the English refusing to share their sweet sweet Caribbean cane sugar with him, he supported research into of a cheaper sugar producing plant. His scientists presented him with bread made from beet sugar rather than cane sugar, and he was so impressed that he ordered that 32 000 hectares of the stuff be planted in France. The crop proved so popular that two centuries later, a third of Europe’s sugar comes from the beet.

The sugar is stored in the bulbous root thing that makes the plant look so awkward. I understand why humans might want to grow a plant with a desert for a root, but what on earth is in it for the beet? and how is it making sugar from the things it has access to? – it’s not like the farmers are feeding it jelly beans and toffee.

In order to understand this, first I need to be more precise with my language, sugar, unfortunately isn’t an accurate enough word to describe what the beet is storing. It is hoarding a compound called sucrose. And it’s doing this for the same reason that humans want to eat the stuff. Sucrose is a fantastic way to store energy, energy that the beet can use to grow leaves, keep photosynthesis running and ice skate1.

I’m an organic chemist, and while all that biology is interesting to me, what I really want to know, is how does the little chemical factory that is the beet, make sucrose from the building blocks it has access to. The pdf below shows my attempt to visualise the first couple of steps of this process. I’m using simple shapes here to represent atoms, and lego men to represent enzymes. If you’d like to know more about these things, there are more educational tools on the web than you can poke a stick at, but you might start here, or here or even here.

Download (PDF, 674KB)

The first thing that happens is that the plant takes in water and carbon dioxide from the environment. Lego man one adds the carbon dioxide to the pre-prepared compound at the top of the graphic. I truly wish there was a simple explanation for where that top compound comes from. The way I’m telling this story is a bit like if I told you that Statue of Liberty was built in two stages – first, aliens teleported a giant metallic woman to earth, and then some industrious lego men thought she looked weird with her hand outstretched for no reason, so they built her a torch to hold from things they found lying about.

The Happening has a more satisfying narrative than that.

Unlike The Happening, this story is going to have many many sequels, and hopefully one day, I’ll be able to show you that that top compound is also made from simple building blocks.

Anyway, back to sucrose, the new compound is quite unstable. With the help of some water, and a second lego man, the compound splits in two. This gives two new compounds, which could embark on the epic journey to become sucrose.

I don’t use epic lightly here, these compounds face the kind of insurmountable odds that would make Frodo turn around and head for Bag End. Much like Frodo, at some point on their journey the compounds will probably be burnt alive by Daenerys’ dragons in the sands of Dune.2

As the months and years go by, I hope to show you the more death defying parts of this journey, but there’s every chance I’ll get distracted by some other shiny biochemical pathway….

Is that a lysine over there?

  1. Sure, be skeptical about the beets on skates thing, but let’s just remember which of us is writing the authoritative blog post here.
  2. OK, I didn’t actually read past the Tom Bombadil section, I figured the books couldn’t possibly get any better, so why spoil the memory of a perfect story.