Martin A

Think of the most senitive engineering prototype you ever built, one which only worked when conditions were exactly right and which went off tune with even slight variations in temperature or voltage.Enzymes are the biological equivalent. They work brilliantly when conditions are right, but only within a very narrow sweet spot.

An enzyme catalyses a chemical reaction by lowering the activation nergy threshold required.

They do this using an active site which positions the substrates in the optimum positions to encourage the reaction, along with providing an appropriate charge distribution and sometimes stressing bonds intended to be broken.

If this is even slightly away from the optimum configuration you get a big drop in efficiency and reaction rate. Thus a 0.1 unit change in pH can sometimes be enough to cut the reaction rate in half.

The site and shape of electron orbitals varies slightly between isotopes, as does their physical properties. This is enough for one isotope to interact less effectively with the active site, taking longer to react or failing to react at all. Since the enzyme will be optimised for the majority isotope, even a small difference will be enough to depress the frequency of the minority isotope in the product.

Incidentally this is often represented as a bell curve of reaction rate against some environmental variable. Draw curves for the same enzyme for two species and you may get different shapes.

An estuary crab, tolerant to pH changes, will have a wide curve with a low peak. A coral reef crab experiences only small pH variation and will have a narrow curve with a higher peak.

Evolution has optimised each enzyme for the local environment but you can have tolerance of variation or maximum efficiency, not both.

"Abiogenic petroleum"

This may be produced, or it may not. It would be expected to have the same isotope composition as diamonds or meteorites. The problem is that the vast majority of fossil fuels have the biogenic isotope ratios.

Any abiogenic petroleum gets swamped by biogenic petroleum and is effectively undetectable. The existence of abiogenic petroleum cannot be disproved, because it might appear in the next sample, but its existence is extremely difficult to demonstrate.

In science absence of evidence is not necessarily evidence of absence, but experience across many fields of science is that it is a good way to bet.

Inorganic reactions do show rate variations based on atomic mass, but enzymes tend to be much more rate sensitive to such small differences.
Oct 30, 2014 at 2:30 PM Entropic man

Could you give some sort of explanation of how that could be? Why should the reaction rate of reactions involving enzymes depend more on the ratio of CO2 molecular masses than other chemical reactions? I can't see it (unless there is some physical principle that I'm missing).

Oct 30, 2014 at 7:33 PM | Registered CommenterMartin A

Martin, there is no fundamental reason why that should necessarily be the case. Entropic Man is talking out of his fundament, as usual. Mechanistically, enzymes are governed by the same physico-chemical principals that pertain in non-enzymatic chemistry.

Some enzymes may show an isotope effect, some enzymes will not. Just like regular non-catalyzed chemical reactions. No way of knowing in advance.

For a "reaction rate", it depends on whether the heavy/light isotope is involved in the rate determining step(s) and (usually) the bonds formed or broken. There are common theoretical treatments in advanced texts which involve the "reduced mass" of the participating nuclei. As an example, I recall a primary isotope effect involving hydrogen/deuterium often might see up to a seven-fold rate enhancement in some instances, because the ratio of the relative masses of hydrogen and deuterium is relatively large. A rate enhance/reduction between 12C/13C, if observed at all will typically be much lower because the ratio of the masses of the nuclei is much closer to unity.

But, the rate enhancement might be zero. In either biological, or physico/chemical processes. And often is. It depends on the mechanism of the reaction, which is usually not necessarily known a priori. I certainly don't know the chemical reactions/processes and their respective mechanisms that give rise to petroleum deposits, and neither does Entropic Man.

michael hart
Thanks for clarification.
Do you mean Isotopic Mass?

Sandy

This is an interesting discussion, partly fascinating to read because knowledge displayed of processes both on short and long term time scales during geological processes that may affect isotopic compositions is only partial.

There is a very rich literature on isotope fractionation during photosynthesis. This goes back to the early days of isotoep geochemistry when it was observed that C3 photosynthetic pathway plants have a d13C isotopic composition of typically -28 per mille wrt to the VPDB standard. C4 photosynthetic plants are typically about -14 per mille. This discrimination between these two groups has been demonstrated time and time again. The implication is that the different photosynthetic pathways provide for different degrees of isotopic fractionation. Whilst the chemical pathway is complex involving CO2 diffusion through stomata, dissolution and hydrolysis, carboxylation reactions etc. a lot of research has been done on plant physiology, carbon fixing and isotopic fractionation. At a first pass isotopic fractionation during photosynthesis is dominated by reaction kinetics and not an equilibrium isotope fractionation. The rate determining step appears to be carboxylation of Rubisco in C3 plants and stomatal diffusion of CO2 in C4 plants. Taking these reactons/processes as rate limiting doesn't exactly match observed values but are close.

During geological processes of sedimentation, burial, and heating resulting in maturation the temperatures and time scales are such that isotope fractionation is dominated by equilibrium isotope effects and not kinetic effects. The long time scales of geological processes, even at moderate sedimentary basin temperatures of many tens to several hundred degrees C allow equilibrium to be reached. At these temperatures fractionation factors (largely determined by the reduced mass of the molecules involved) tend towards 1 and with chemical equilibrium lying far to the right of many reactions then application of a simple Rayleigh relationship shows the products of maturation must lie close to the isotopic composition of the starting products. Thus we migh expect biogenically derived oils and gases to be close in composition to the organic starting material.

The same applies for abiogenic hydrocarbons (and I'm sure they exist to an extent). Thus we should expect these to have isotopic compositions close to for example mantle derived CO2 which is isotopically very distinct from, and enriched in 13C compared to biogenically derived CO2. I'm working on CO2 from natural CO2 gas reservoirs from the basin and range province in the USA. These are volcanically derived, are of remarkable purity, have volcanic signatures, yet very low amounts of hydrocarbons such as methane.

One should rememember that the whole oil industry is based on an understanding of oil source rocks, likely starting material, sedimentary basin evolution, thermal-time histories, maturation depths, oil separation, migration and trapping. Using this model has led to extraordinary success in the identification of and subsequent exploitation of oil reserves.

We also have very good tracers of deep (abiotic gases) using a range of tracers. These include priiomordial gases from the mantle, recycled volatiles from subduction processes etc. The amount of hydrocarbons associated with such processes don't stack up against our knowledge of biologically derived material.

I'm very much of the opinion that the Thomas Gold ideas are a very interesting hypothesis but the abundant, and different lines of evidence we have for the origin of oils etc., point to the fact that abiotic hydrocarbons are comparatively rare in terms of abundance vis a vis organically derived material.

Paul Dennis

Brilliant. Much clearer than I can manage nowadays. :-)

Martin A

Some enzymes are like tank engines, they run under almost any conditions, but not very fast. Others are like Formula 1 engines, extremely effective but very sensitive to slight changes. In conditions.

Salivary amylase digests starch under almost any liveable conditions and would hardly notice carbon isotopes. Rubisco is more highly tuned and more likely to discriminate.

Martin A

I hope that wasn't sarcasm. :-)

I find it very hard to pitch at the right level here. Patronise an expert or aim over the head of a layman and you get complaints. I usually cant win .The same person may be highly trained in one area and completely naive in others.

I have the same problem myself. In some areas of science I am trained, in others I have read. In politics I am an eight year old.

EM, if you were looking for examples of enzymes operating in 'harsh environments', then human saliva was a poor place to start. Human salivary amylase has its optimal pH at 6.7-7.0, rather close to neutrality, and is actually rapidly inactivated once it reaches the stomach. The amylases present in your washing powder are probably a better bet, as they typically come from bacterial sources.

Also, consistent with what I said earlier about the perils of making armchair pronouncements about kinetic isotope effects, some reported sample 13C kinetic isotope effects for amylases give values both higher and lower than can be found in the literature for Rubisco.

I also see no good reason to think that evolution would have selected these enzymes based on their carbon kinetic isotope effects.

Michael hart

You haven't tried to do enzyme experiments with children! :-)

In most cases, with the possible exception of chlorine, one isotope is much more frequent than the rest. If any selection has taken place, it has tuned enzymes to react optimally with molecules containing the majority isotope.

The ∆C13 effect seen in photosynthesis is more likely to be an example of the Law of Unintended consequences.