Friday, November 13, 2009

the oldest photosynthesizing organism

Fig. 1, Origin of life and oxygen evolving organisms based on geological records (from Xiong and Bauer, 2002)

Jacinta: It's probable that photosynthesis evolved slowly, bitsily, growing gradually more sophisticated, more complete - by which I mean growing to be what we recognize it as today. For example, modern organisms use photosynthesis to make oxygen, and starches and sugars, from water, but in earlier environments it's likely that something other than water was used.
Canto: Right, if water can be utilized by some sort of redox reaction, then so can other molecules. But how long has water existed on Earth?

Jacinta: Don't sidetrack me Canto. One of the world's foremost authorities on photosynthesis and its origins is Carl Bauer of Indiana University. In the graphic above, taken from the website of Bauer's lab, he presents an outline of the origin of 'oxygen evolving organisms', by which he presumably means photosynthesizing organisms that generate oxygen.
Canto: Right, so he's taking biological carbon fixation back to 3.8 billion years or so.
Jacinta: At that time, our atmosphere was rich in carbon dioxide. In any case, no matter what molecules were used to produce fuel for metabolism, Bauer has found, through detailed phylogenetic analysis, that Rhodobacter, aka purple bacteria are the oldest lineage of photosynthetic organisms on the planet.
Canto: But they don't 'evolve oxygen' as he puts it?
Jacinta: Right, they're anoxygenic. In fact, there are five known branches of microbes that engage in chlorophyll-based photosynthesis, and only one of them, cyanobacteria, evolve oxygen.
Canto: Can you explain what phylogenetic analysis might be - not for me of course, but for our vast readership out there.
Jacinta: Of course. To examine the phylogeny of an organism, or indeed an organ, is to trace its evolutionary development. The phylogenetic analysis we're talking about here involves molecular phylogenetics. Closely related organisms have similar molecular structures, re their genetic material and their proteins. There's a pattern of similarity to related organisms traceable back in time, revealing a pattern of evolution. There's more to it than that, but it'll do for now.
Canto: So tell me more about these anoxygenic purple bacteria.
Jacinta: Well, Rhodobacter have long been of interest to molecular biologists because of their interesting metabolic processes, and they're the most studied of micro-organisms. They live in water - freshwater or marine environments, and their diverse methods of survival - not just through photosynthesis but through a variety of processes - has made them a favourite for study, due to our own concerns about survival.
Canto: Okay, I'll keep them in mind - but you've pointed out that they're aquatic, which raises the question again - when did water first appear on Earth, and what about non-photosynthesizing organisms that might be older than Rhodobacter?
Jacinta: Yes, all that is interesting, along with the actual origins of these Rhodobacter, and the origins of viruses, which we haven't gotten into as yet. Everybody is obsessed with water as an essential source of life, so that when we look for life elsewhere, we tend to look for signs of water - but it ain't necessarily so.
Canto: Wow, lots to explore there - can't wait for our next little chat!

Wednesday, November 11, 2009

fixation, redox reactions, nucleotides and more

ATP - see the triphosphate bit?

Jacinta: Okay, so since we're both thoroughgoing obsessional types, we'll have to get to the bottom of photosynthesis, at least to clarify some of the cycles and molecules and such that we referred to last time.
Canto: Great, we're talking the same language. So tell me about this fixing, in relation to carbon dioxide. I'm sure I've also heard of nitrogen fixing...
Jacinta: Well let's not get too sidetracked, but fixation, in chemical terms, means transforming a substance, or molecule...
Canto: Or molecular substance?
Jacinta: Yeah, into a more usable form, like ammonia, in the case of atmospheric nitrogen.
Canto: N2 into NH3, I get it.
Jacinta: Right, though of course much more complicated. And carbon fixation is hideously complicated. The Calvin cycle, worked out many decades ago, basically traces the carbon fixation process. All I can competently say at this stage is that the key enzyme in the process has come to be known as rubisco. I won't say anything more about NADPH - it's essential in the photosynthetic process in chloroplasts. I could say more but it wouldn't make much sense to either of us.
Canto: It acts as a reducing agent, doesn't it?
Jacinta: Yes. You know about oxidation-reduction?
Canto: I know of it. If I was a hands-on biochemist or whatever I'm sure I'd know about it.
Jacinta: Actually redox reactions aren't too difficult to understand. They generally involve electron transfer. The reductant, or reducing agent transfers electrons to the oxidant, or oxidizing agent. So the reducing agent gets oxidized, and the oxidizing agent gets reduced.
Canto: Believe it or not, I follow you. So in the Calvin cycle, NADPH is the reduced form of NADP+, and therefore NADP+ is the oxidized form of NADPH.
Jacinta: You read that somewhere mate.
Canto: Yes but it makes sense all the same. So what's ATP? That's a biggie isn't it?
Jacinta: Adenosine triphosphate is indeed a very important wee nucleotide, the key molecule in cellular metabolism.
Canto: Let's do each other's heads in - what's a nucleotide, and what exactly is metabolism?
Jacinta: Come on Canto, metabolism's just what you think it is - it's the breaking down of food to construct proteins, nucleic acids and so forth. Without which not. A nucleotide is a molecule with a particular structure, found in all cells performing various metabolic functions. They also are the bases of polymeric nucleic acids, as well as being the structural units of DNA and RNA.
Canto: Well read Jacinta.
Jacinta: Well digested encore.
Canto: Whatever you say mate. So, getting back to photosynthesis, how did plants, or bacteria, start getting into this?
Jacinta: You could just as well ask how did more complex organisms start using oxygen and other nutrients to sustain themselves, or how did pre-photosynthesizing organisms, or non-photosynthesizing organisms start utilizing whatever they utilized...
Canto: I could just as well, but I asked about photosynthesis.
Jacinta: Okay, it's known that photosynthesis evolved in bacteria and that it's been going on on our planet for at least 2.5 billion years. As to the how, I'll try to answer that in the next post.

Saturday, November 7, 2009

more on photosynthesis

a simplified version of glyceraldehide [C3H6O3], a triose three carbon sugar used in photosynthesis

Canto: So is it to be photosynthesis today?
Jacinta: Maybe. Not all life depends on photosynthesis, you realize.
Canto: Uhh, yes of course, but tell me what photosynthesis is, then I can be clear about what it is that life doesn't entirely depend on.
Jacinta: Well, most people know that the oxygen around us, the oxygen we breathe, that we depend upon, has been produced by microbial and planktonic life, in the oceans mainly. Now this oxygen is a kind of waste product of a process that transforms oxides into sugars by means of sunlight. What's really important about photosynthesis, apart from its obvious importance for us, is that it's a process that creates 'food' from the most ordinary, inanimate chemicals around - carbon dioxide and water. Did you know that water was an oxide?
Canto: No. I knew that it contained oxygen, though.
Jacinta: Well there you go. Would you like a glass of dihydrogen monoxide?
Canto: You can't get rid of me that easily. Okay, so your plankton or whatever takes a ray of sunlight, or a photon or whatever, and synthesizes sugars out of carbon dioxide or water. That's as clear as mud.
Jacinta: Well, I seem to remember that the exact mechanisms were worked out only quite recently. Let's take plant photosynthesis. Light energy is absorbed by proteins containing chlorophyll...
Canto: Hang on, hang on - absorbed? What's this absorbed? Is that where a miracle occurs?
Jacinta: A miracle is just something we haven't examined sufficiently.
Canto: Oh how prosaic, how materialist.
Jacinta: Okay I'm not sure if absorption is a technical term but sunlight excites molecules, and I presume that's the key. The excitation results in electron transfer reactions. Chlorophyll is involved, absorbing the light due to its pigmentation, and promoting electrons to higher energy levels, creating free energy.
Canto: The electrons then release energy in returning to their stable or ground state.
Jacinta: Too right. When an electron goes into a higher energy state, the molecule it inhabits is said to have a higher reduction potential, so that it tends to donate electrons. That's how light energy becomes chemical energy, apparently.
Canto: How?
Jacinta: Get an education Canto.
Canto: No I think I understand.
Jacinta: Well what follows is very complex and I can't say I fully understand it myself. Electrons are donated to electron acceptors in an electron transfer chain. There's a whole heap of them, and what results at the end of this chain is a reduced molecule called NADPH. This molecule, along with ATP [which is also produced through this process], is involved in the Calvin cycle which fixes carbon dioxide into triose sugars.
Canto: What? Do you really know what you're talking about Jass? What's this thing called 'fixing' I've heard so much about? What are these molecules? What's a triose sugar?
Jacinta: Okay, you’re right, I’ve not got my head around those details, but there’s so much to explore in this universe, mate. I’ll answer your questions, but I’m also interested in pre-photosynthetic life, and much else besides.
Canto: I can’t wait.

Monday, November 2, 2009

cyanobacteria, meteorites, fossils and photosynthesis

Canto: I'm still wondering about life.
Jacinta: There's a lot to wonder about.
Canto: Well, bearing in mind those rough and ready rules, what is the earliest form of life we know of?
Jacinta: Nobody knows. There are big arguments about the status of viruses, but the earliest candidate we know of, I mean the earliest fossil, was some sort of prokaryote, something like a modern cyanobacterium.
Canto: But it's unlikely that the earliest fossil was the earliest life form. I mean, I know very little about cyanobacteria, and obviously prokaryotes are much less complex than eukaryotes, but even one of those things couldn't have just - spontaneously generated. There must've been precursors.
Jacinta: Surely, but it's worth thinking about timelines here. The earliest prokaryotic fossil - the oldest know fossil of any kind - dates to 3.8 billion years ago. The earth was formed 4.6 billion years ago, and clearly it would've taken some time for it to be ready to sustain life.
Canto: Not so fast about that. We always think of life as we know it,we of little imagination. Look at the archaea so recently discovered. If life can thrive in hot volcanic springs, that certainly extends the range of possibilities.
Jacinta: Good point, but there's another interesting thing about this 3.8 billion date. Have you heard of the Late Heavy Bombardment?
Canto: Come on, forget about Armageddon, this is getting interesting.
Jacinta: No, really, what astronomers call the LHB took place just about 3.8 billion years ago - a heavy shower of meteorites in this region. All our evidence is from the Moon, which as you know is almost as pock-marked as Manuel Noriega's mug. Being a more or less dead rock, the Moon still bears the scars, whereas Earth's surface is shifting and spewing and subducting all over the place, so there's no direct terrestrial evidence of this shower, but it's a reasonable assumption...
Canto: Aha! Life from outer space.
Jacinta: Yes, well, that's one of many hypotheses. It's all very speculative.
Canto: Okay, I won't get carried away. Tell me about this cyanobacteria.
Jacinta: Uhh - do you mean the earliest fossils or cyanobacteria in general?
Canto: Dunno.
Jacinta: Well, cyanobacteria are mainly associated with marine environments, and they're also known as blue green algae. 'Cyano' comes from the Greek for 'blue'.
Canto: Right, as in Cyano de Bergerac, the guy with the big blue nose.
Jacinta: They've been around for a long time, engaging in what's called oxygenating photosynthesis to help transform our planet's atmosphere into something habitable for big beasties like ourselves.
Canto: Wow, photosynthesis, tell me about photosynthesis. But first, you mentioned blue green algae. Now, I would've thought algae were eukaryotic. 
Jacinta: Ah yes, nomenclature and taxonomy, always fraught. The term 'blue green algae' came in long before those distinctions were made and so it has stuck. As to photosynthesis, that's one of those key and fateful processes that link the organic to the inorganic and make our fragile biosphere such an astonishing place.
Canto: You're astonished eyes delight me Jacinta, let's shore up our fragile relationship for a while before you reveal all.
Jacinta: Okay, let me reveal all before we begin. Symbiosis here we come.

Frank Ryan, Darwin's blind spot: evolution beyond natural selection. Thomson Texere, 2003