Examples of asymmetry in (non-biological) nature

[Karl Coryat]

Hello all, I am writing an article on symmetry in the living vs. non-living worlds, and I am looking for inorganic/non-biological examples of asymmetrical structures or relations at the molecular level and higher, similar to the kinds seen in biological systems. For example: The natural occurrence of only one enantiomer of an inorganic compound; substances/structures that react to only one enantiomer of a compound (as certain enzymes do); crystals that exhibit chirality (I don't know if there is such a thing) in a ratio other than 50-50; self-organization that shows any kind of asymmetrical bias, like certain biological structures. Sorry for being vague, but I'm trying to keep it open-ended and not limited to one area such as chirality.

Basically I'm trying to see if there's any support for the idea that all natural structures not derived from biological systems exhibit certain classes of symmetry, such as 50-50 ratios of enantiomers. I'd also be interested in hearing any opinions that examples of this kind of asymmetry do NOT exist in the non-biological world. Thank you very much!

 

[alxm]

Hmm, I'm not really sure I know what you're getting at, because I don't see that there's any fundamental physical/chemical difference between non-biological and biological compounds regarding symmetry.

Much is made of the 'coincidence' that all living things are essentially all made of L-amino acids, and that chemically, you're equally likely to end up with either L or D. I'll get back to the chemical aspect, but the main reason for this isn't chemical but evolutionary. There's an obvious synergy to be had if all organisms use the same form - an organism can then eat another and steal its amino acids! But there are few benefits from changing from one to the other. You could make analogy to human-built things - We use right-handed bolts almost exclusively, even though left-handed bolts are just as good. Or rather, because left-handed bolts are just as good. Changing would just cost you for re-tooling, make you unable to use parts from other manufacturers, etc. So we use right-handed ones except for some niche applications, basically as a result of historic accident.

Similarly, D-amino acids do have some 'niche' uses in biology. The only question then, is how one won out over the other, rather than having two parallel evolutionary threads. The probable answer is that there was some 'bottleneck', where one group evolved and proliferated to some extent that both out-competed the other and blocked any new development. It's not the only time that has happened; life as-a-whole only evolved once. Eukaryotic life only evolved once. And so on. To continue the analogy, Henry Ford might've been able to use left-handed bolts, set the standard at least for cars, and be equally successful, but you couldn't start a auto factory today using non-standard parts. That window of opportunity has passed.

Now, as for the chemistry, it's true that chemical reactions, and in particular chemical synthesis performed by humans, tends to be symmetric, in the sense that it usually creates racemates (equal mixtures of both enantiomers). That's because chemistry is crude. We perform chemical reactions by letting molecules bump into each other. We can control which molecules are present (concentrations, pH, solvent), and we can control their speeds (temperature), but that's about it. We can't control how they bump into each other. In, for instance, a nucleophilic substitution reaction, the nucleophile molecule may often be able to 'attack' from many equivalent angles, giving rise to racemic mixtures, since we can't control where it's coming from. Chemistry's construction methods amount to throwing the parts at each other at random until they fit together.

There's no comparing that to how chemistry is done in biology, because there, reactions aren't occurring between free molecules in solution, and to the extent they are, it's often unwanted (e.g. oxidation). Biology uses enzyme-catalyzed reactions almost exclusively. In a way, it has to: An organism can't change its cellular environment, solvent, pH and temperature for the sake of a single reaction. Life requires an far more fine-grained control over what's going on than conventional chemical synthesis provides. In biology, a substrate molecule binds to a specific site in a specific enzyme in a specific way that catalyzes a specific reaction. Given that level of control, enantioselectivity is relatively simple; the substrate molecule binds in a certain way, and the surrounding enzyme structure only allows the reacting molecule to approach from a single direction. So the difference between symmetric and asymmetric chemistry here is due to the fundamental difference between uncatalyzed and catalyzed reactions. If you're talking about catalytic reactions, then stereoselectivity is entirely possible, and indeed a major topic in catalysis, e.g. the 2001 Nobel Prize in Chemistry was for chirally-selective catalysis.

In general, I see no deep connection though. Biomolecules are more often asymmetric compared to simple organic ones, which are more often asymmetric compared to inorganic ones. But that's a straightforward consequence of their relative sizes. Stereochemistry is less of a big deal in inorganic chemistry because there simply aren't as many compounds with sufficiently complex geometry to have stereoisomerism. But there are many biomolecules which have beautiful symmetry (e.g. http://www.rcsb.org/pdb/explore.do?structureId=1AON" heat-shock chaperone which is essentially C_7v), not to mention that most known protein structures were determined from crystallography, meaning that they do form symmetric crystals (or can be coaxed into doing so). And there are inorganic substances that form large-scale crystals that are entirely amorphous, i.e. glass. There are uncatalyzed reactions that result in asymmetric products, and catalyzed reactions that yield symmetric ones.

I just don't see any deep link between any kind of symmetry property and biochemistry. Stereoselectivity, the only specific example given, is pretty shallow. It amounts to little more than pointing out that biomolecules were produced catalytically, and that's essentially what 'life' is: One big autocatalytic system.

 

[Karl Coryat]

Thank you alxm for the detailed response. I actually got my degree in biology, but I don't remember encountering much about stereochemistry.