It's life, but not as we know it
May 19, 2009 1:05 PM   Subscribe

Alternative-biochemistry-filter

I'm an undergraduate neurobiology student, so first of all, I know my chemistry.

At the same time, I am not in the biochemical field. So I have a query:

There are a handful of different types of 'alternative biochemistries, classifiable into some categories:

1) Opposite chirality. Our DNA goes one way and some molecules are L-chiral or D-chiral and we can only use one of the chiralities. Could there conceivably be life forms that use the mirror images of the molecules we can use? This seems to be the most plausible answer.

2) Slightly more ridiculous, different elements to base life on. A few being bandied around are silicon, arsenic, and nitrogen-phosphorus. Chlorine and sulfur are a bit more ridiculous.

3) In addition, there are a handful of different solvents: ammonia, hydrofluoric acid, formamide, and methanol. The solvent would have to exhibit some polarity to work.

So what's plausible? What's not? Help me navigate the world of speculative biochem, because I think it's intriguing.
posted by kldickson to Science & Nature (7 answers total) 5 users marked this as a favorite
 
It's been years since my biochemistry days, but if I recall correctly the advantage of being carbon based is the bonding potential and energy, such as from photosynthesis. And having 4 potential bonds.
Ditto why we need Oxygen, for energy from the glycolysis and all those fun energy-producing cycles that I knew by rote once upon time.

Anyways, I had considered the same question when I knew what I was actually talking about, and to me this is where evolution comes in use: We don't use C and O and P randomly...rather, it's because in terms of building blocks for life and creating energy, it works the best! You have to consider, in the primordial soup of life, which elements would allow for the lowest energy barrier to creating useful, multiple, connectible bonds needed for life? In addition, these bonds must be able to remain intact in water and until energy produced from breaking said bonds is needed. Ditto for oxygen and it's electron potential to produce energy.
posted by jmd82 at 1:57 PM on May 19, 2009


#1, certainly.

You're overlooking an option between #1 and #2 though (1.5?): still primarily carbon-based, but with different (not merely mirror-image) compounds which perform the functions of storing hereditary information, transferring that information, catalyzing highly specific reactions, providing structural integrity, storing energy, etc., etc. You might take a look at nucleic acid analogues for one such area where there is active research.
posted by DevilsAdvocate at 2:48 PM on May 19, 2009


I can't answer your questions specifically, but I would suggest a great article from Scientific American on alternative biochem by Paul Davies. It touches on many of these points and you should be able to find some more good sources from both of those links.
posted by sophist at 3:15 PM on May 19, 2009


I took an astrobiology course that explored some of these ideas back in undergrad.

I remember the great buildup from my professor of silicon based lifeforms, and the eventual tear down of why it was less feasible than carbon since while silicon was a heavier atom making it more difficult to form double/triple covalent bonds.

The wiki article is actually really fascinating and is jogging some old memories of my class.
posted by liquoredonlife at 5:41 PM on May 19, 2009


As above, I sort of recall that the main reason that carbon-based chemistry (and, more narrowly, the subset of organic chemistry that is biochemistry) is more favorable than similar silicon-based chemistry is that the distance between singly-bonded silicon's p-orbitals are not conducive to double and triple bonds, the formation and breaking of which--essentially, the shuttling of electrons around a molecule's structure--are extremely important in most of those reactions. So, no silicon-based biochemistry.
posted by pullayup at 6:50 PM on May 19, 2009


How about this: Different monomer inventories. There are a couple of non-standard amino acids that some organisms use. I don't class the ones that arise post-translationally as being an 'alternate biochemistry', but where a genetic code actually provides for them directly, sure.

That article also mentions limited earthly use of opposite-chirality amino acids. With a little imagination we could take the 'limited' out of that phrase: Potentially four different biochemistries there, if nucleic acid chirality and amino acid chirality are allowed to vary independently. Protein folding producing the amazing variety of shapes that it does, I rather suspect that proteins could still be found to interact with genetic molecules as needed, even if you changed the chirality of one but not the other.

Another phenomenon in actual use that could be used more widely is non Watson-Crick base pairing.

I also recall reading about a fellow who had gotten a five-nucleotide system going: The fifth base paired with itself via hydrophobic interaction or some such, and it was the proper length to fit into the standard DNA ladder. If I recall, there was a working polymerase for the system and everything. But I've just gone looking for it and couldn't find it. I wish you better Google-fu than mine.

Getting wilder, Schafmeister and Levins have had some decent success reducing the complexities of protein folding by using monomers with two links to each neighbor. Makes me wonder: Could such a system function naturally, or is there an evolutionary advantage to the system we've got, where one changed amino acid may radically alter the final shape?
posted by eritain at 8:47 PM on May 19, 2009


Could there conceivably be life forms that use the mirror images of the molecules we can use? This seems to be the most plausible answer.

There is actually a Z-form of DNA that is left-handed, which may prove to serve a biological purpose, but DNA in most situations is right-handed.

Some of the work my lab does is on nucleosome structure with human DNA and that of other eukaryotes. Nucleosomes are made up of histones — proteins around which DNA wraps itself, to compress the genetic information into larger chromosomes.

These histone complexes are themselves chiral, I believe. Further, the handedness of the DNA molecule itself allows energetically favorable folding around these histones. Most histone mutations undergo strong negative selection: in other words, they are strongly conserved as they are critical to survival.

So, for eukaryotes and Archaea, at least, there seems to be a tight relationship between the chemical structure of the DNA "software" and the makeup of its "hardware" storage medium, such that a change in handedness would be very evolutionarily expensive, requiring other protein machinery switching gears.

The building blocks of DNA are themselves chiral, which is probably the bigger deal from a chemical standpoint. It's not just the shape of DNA, but all the enzymes that need to be able to catalyze reactions of a different chirality. Biologically, it would require a number of neutral- or positively-selected mutations. You may also need feedstock (sugars and fats) that are themselves of a different chirality, to be able to work well with these new chemical reactions.

Bacteria do not have histones, but also share somewhat similar protein and genetic constitution that is also chiral. Sugars that make up the DNA backbone are themselves chiral. If bacteria went with their own "custom" chiral chemistry, they would have less to feed on in nature, which, as one example, would make it difficult to obtain the building blocks they would need in order to synthesize nucleotides and — the ultimate goal of life — be able to reproduce.

Perhaps there was some point in the evolution of life here on earth that ambidextrous chemistries were pushed in a direction that was more energetically favorable than the other.

At this tipping point, perhaps, it was too difficult for other-handed life to continue to survive in the long term, and here we are. With the luck of the draw, on another planet — or here, after a few asteroids or disasters clean the earth of all life and things start anew — perhaps it could go the other way.
posted by Blazecock Pileon at 10:31 PM on May 19, 2009


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