Fire, fuel and futures

There is a fascinating link between photosynthesis, fire, and an the development of our technological and political landscapes. I have been inspired by Iain Stewart's series on BBC "how the earth made us" and strongly recommend that you watch it whilst it still available. Photosynthesis, the conversion of carbon dioxide gas to sugars by plants using energy from light is probably one of the most important chemical reactions on Earth and has shaped the course of evolution on our planet. Between 2.5 and 1.5 billion years ago, the abundance of of algae and related organisms were such that oxygen started to accumulate in the earth's atmosphere, at first the reaction of oxygen with iron led to a global rusting event, which can still be seen in banded iron deposits in the world rocks. Secondly, when about 13% oxygen in the atmosphere was reached, the first fires could burn. It is astonishing to think that for the vast majority of our planet's history, fire did not exist.

The accumulation of oxygen was due to the proliferation of photosynthetic organisms, unfortunately, as anaerobes their waste product - oxygen - was toxic to them. The reaction with iron at first provided a buffer by effectively drawing down excess oxygen from the atmosphere. However, once a majority of reactive compounds had precipitated, free oxygen accumulated in the atmosphere, leading to probably the greatest extinction event, where over 97% of life on earth perished. Thus, the accumulation of oxygen in our atmosphere can be regarded as one of the greatest pollution events ever with catastrophic and planet changing consequences. However, aerobic respiration, using oxygen is essential for the energy demands of multicellular organisms, and their diversity flourished under these new conditions. Eventually leading to all of the wonderful flora and fauna that you and I are aware of and indeed part of.

Oxygen also enabled fire to burn and our ability to use ever more sophisticated sources of fuel has played an essential role in the development of civilisations. Initially our ancestors' ability to use wood fire greatly extended the range of food available, by modifying the chemistry of proteins and other components of our food. Humans may also have had used fire to create and manage grasslands from quite an early stage. Subsequently the ability to burn charcoal ushered in the bronze age, coal the steam age and industrial revolution and oil - well, you know we still dealing with oil. Fire is still central to our energy needs, although its appearance is often hidden within the generation of electricity or combustion engines. And the stuff that burns? Biological carbon atoms reacting with oxygen; both products of photosynthesis.

Much of our energy resources are derived from plant materials bringing us neatly to the photosynthetic reaction and the molecule I would like to introduce, Rubisco, the most abundant protein on earth. So how do plants take light and gas to make sugars and from there wood, charcoal...? Well, energy from light (photons) is converted by chlorophyll, a complex antenna-like pigment, to electrical energy you can think of the impact of a photon 'knocks out' an electron. The rest of the photosynthetic chain can be viewed as a sophisticated game of pass the parcel where an electron moves from molecule to molecule until trapped into the addition of H+ to NADP to give NADPH (the + on H+ signifies that this hydrogen has lost an electron, you can just think of NADP as 'a energy carrier' for now). These reactions are summarised in the image below. I would like to point out that chlorophyll is, quite bizarrely, closely biochemically related to haemoglobin, the red pigment in our blood. And that ATP synthase, the orange molecule on the right hand side of the diagram below, is a most wonderful and impressive rotary generator (I hope to talk about this and other time), one example where a wheel-like mechanism does exist in nature.


Thanks to wiki commons for the image

Rubisco didn't come in to this first stage of photosynthesis, but now it picks up the NADPH and it uses it in the fixation of carbon. By the way, did you notice, in the very first step of photosynthesis, the generation of oxygen (on the bottom left hand corner in the picture above)? No? Ah well, as such is the way with waste products. Rubisco is like a blobby doughnut (round with a small hole in the middle) made out of eight separate protein chains and is unusual in being a soluble enzyme that has only extremely recently been successfully re- folded in a test tube. This tells us that the structure of Rubisco needs to be extremely precise in order for it to work. (Most other soluble enzymes can be treated a lot more roughly and are generally easy to manipulate.)

Rubisco does fiddly task holding three components together; first the sugar (ribulose 1,5-bisphosphate), which can be thought of as a small string of five carbon atoms with a phosphate at each end, then the NADPH produced by the photosynthetic chain and finally carbon dioxide. The sugar is bent awkwardly so that some bonds are under strain, and the NADPH and carbon dioxide are brought into close proximity. These molecules react to create two 3 carbon sugars, each with one phosphate at an end (3-phosphoglycerate) . Et volia! The carbon from carbon dioxide is now trapped in a new smaller sugar molecule. The three carbon sugar can then be used for other things (e.g. to make wood or seeds) or recycled to create a new ribulose 1,5-bisphosphate and fix more carbon (this is known as the Calvin cycle). To be honest when I first learnt this I felt a bit cheated - so how did the cycle get started, where did the first five carbon sugars come from? Now, that's a topic for the origin of life.

Few people can be unaware of carbon dioxide in the current discussion of climate change, and Rubisco is the enzyme at the heart of the carbon cycle, busily adding and stitching new carbons on to old sugars. No matter how far up the food chain you think you are, all of the carbon atoms in your body will have at some point been fixed by Rubisco. Similarly, all of the carbon atoms released by the consumption of fuel to keep you warm and entertained will have passed through the same route. So photosynthesis has built up the immense reservoirs of coal, gas oil that the last century has been so extravagantly dependent upon. And is possible that photosynthesis will have a role to play in averting climate change. Rubisco works very slowly capturing only 2 to 3 molecules of carbon dioxide per second, as the reaction it catalyses is so fiddly . Worse, as Rubisco evolved when there was very little free oxygen in the atmosphere, it is inhibited by a high amounts of oxygen. Oxygen can squeeze into the slot that should be occupied by carbon dioxide, wasting the NADPH and five carbon sugar. Efforts are under way to re-engineer the enzyme for modern times. However I'm a little sceptical about how successful this will be, given the exquisite positioning of sugar, NAHPH and carbon dioxide that is needed. Rubisco is so sensitive that it is biased against naturally occurring radioactive isotopes of carbon (14C). This bias gives us the ability to carbon-date biological materials but does not bode well for our ability to re-engineer something so highly conserved in nearly all photosynthetic organisms over several billion years! Guess we've been playing with fire...

Henrietta Lacks -The first immortal?

Several book reviews this week have covered "The immortal life of Henrietta lacks " such as this one in the New York Times. I was astonished to learn the origin of probably the most famous human cell line, HeLa, through these reviews Even I, a plant scientist, have heard of them and regularly, enviously, read papers based on their research. HeLa stands for Henrietta Lacks, the unfortunate black woman from whom these cancerous cells were taken. Henrietta died in 1951 and her race was an integral part of the circumstances of her death and the immortality of the her cells. As I have not yet read the book I cannot comment on Henrietta's life, but I can describe the impact that her cells have on me.

Cell culture, that is the growth of individual cells in a nutrient broth, are an invaluable research tool. As the cells divide and grow continuously they are known as "immortal". Of course individual cells cannot cover the complexity of an organism with many different cell types and tissues (eyes muscles skin etc.) But as their growth conditions can be tightly controled to suit experiments, for example by adding drugs the all hormones to the growth media, they provide material for testing that cannot be done on the entire organisms. Furthermore, cell cultures have done more than any other technique to replace experiments on animals. Some types of cells do not grow well and only survive for a few weeks but HeLa cells have now survived for decades. This is perhaps an alarming measure of the malignancy of Henrietta's cancer. By the way, plant cells can also be grown in cell culture and a few can survive as long.

HeLa cells were one of the first products of what are now multinational pharmaceutical companies and have been used for research beyond that of human cancer. I first became aware of a HeLa cells through work on signaling pathways (i.e. receptor proteins), in particular those experiments using special forms of amino acids to determine changes that occur after receptor proteins have been elicited (triggered). It is really astounding to consider how far medical research has changed from the 1950s when the cancer cells were taken from Henrietta. Doubtless she would be astounded, and perhaps horrified, to learn of the fate of her cells. But I hope that she would also be amazed at the progress. It is shameful that the debt medical research goes to her, and by extension her family, is as yet unpaid.

The special forms of amino acids, I mentioned above, are made extra heavy at the atomic level through incorporation of stable isotopes (naturally occurring heavy forms of atoms i.e. C13 rather than C12 and N15 rather than N14). I am amazed that we can manipulate atoms and molecules at this level and delighted that one can simply order these custom made molecules from a pharmaceutical company: I feel future-shocked. So, to set up a cutting edge experiment on human cells one can simply order or borrow a HeLa cell line and custom amino acids and make light and have the forms of the cells. One can then treat or not two batches of the cells and go and look for differences. Could Henrietta be a real-life Cold Lazarus?

And as for the effect that HeLa cell research has had on me, well it has been truly inspirational. Plant science lags behind mammalian research on the finer details of signaling pathways, and I would love to obtain the same a level of detail that has been achieved for the egf pathway using HeLa cells. So far I had written two grants to try and achieve this and will shortly be writing my third. So results from human cell line research has played a crucial role in steering the course of my own career.