Thread: Rubisco (RuBisCo)

Was bored so I Googled the most important enzyme on Earth and rubisco was the overwhelming choice of the biology community.

Excerpt:

RuBisCO is important biologically because it catalyzes the primary chemical reaction by which inorganic carbon enters the organic biosphere.

Bio-chemistry is out of my league but.....It's this part about entering the organic biosphere that intrigued me somewhat. Like what is the difference between inorganic carbon and I would assume organic carbon? Isn't it still carbon except now it's living? or part of something alive? Not quite sure how to approach this but if this enzyme was an evolutionary adaptation, what preceded it? Or has it always been present? I mean if rubisco was absent during the formation of life on the planet was some other catalyst at work? Could one enzyme be the difference between the organic and inorganic? I wonder since the enzyme is so important to life that those trying to recreate life in the lab have looked at this.

Originally Posted by zinjanthropos

Was bored so I Googled the most important enzyme on Earth and rubisco was the overwhelming choice of the biology community.

Excerpt:

RuBisCO is important biologically because it catalyzes the primary chemical reaction by which inorganic carbon enters the organic biosphere.

Bio-chemistry is out of my league but.....It's this part about entering the organic biosphere that intrigued me somewhat. Like what is the difference between inorganic carbon and I would assume organic carbon? Isn't it still carbon except now it's living? or part of something alive? Not quite sure how to approach this but if this enzyme was an evolutionary adaptation, what preceded it? Or has it always been present? I mean if rubisco was absent during the formation of life on the planet was some other catalyst at work? Could one enzyme be the difference between the organic and inorganic? I wonder since the enzyme is so important to life that those trying to recreate life in the lab have looked at this.

What is meant I think is that CO2 is incorporated into a carbon chain by this process. In other words carbon-carbon bonds are formed. It is effectively a form of reduction, as a carbon-oxygen bond becomes a carbon-carbon bond, but the important thing is that the products of reaction can be further combined, to make longer biochemical molecules, once the initial C-C link has been formed to bind the incoming carbon atom onto the end of a carbon chain.

There seem to be three carbon fixation routes in use by plants today, C3 , C4 and CAM: https://en.wikipedia.org/wiki/C3_carbon_fixation RuBisCO seems to be implicated in them all.

Concerning when RuBisCO evolved, I found this: Phylogenetic and evolutionary relationships of RubisCO and the RubisCO-like proteins and the functional lessons provided by diverse molecular forms | Philosophical Transactions of the Royal Society B: Biological Sciences which attributes it to a methanogenic archaeon, so certainly very ancient, but by no means implicated right back to the very start of life. As for what preceded it, I can't quickly find anything. Maybe we do not know, just as we do not know a lot of the biochemistry right back at the start.

From exchemist link:

(rubisco)arguably catalyses the most important biochemical reaction in biology and is responsible for the vast majority of all the organic carbon found in the biosphere. The enzyme, found in phototrophic and chemoautotrophic organisms, basically functions to catalyse the removal and sequestration of carbon dioxide from the environment by reducing this oxidized gas to the level of organic carbon, in the process providing the organic building blocks needed to sustain life.

In the context of the quote, what would be the level of organic carbon? Is it different than non organic carbon?

Seems we don't know a lot about what preceded rubisco in plant evolution. What about animal life, is rubisco proof that all other life evolved from plants?

Just a thought: Makes me wonder if this particular enzyme can be synthesized or used in its natural form to combat CO2 emissions. (ie carbon capture)

In chemistry organic generally means "contains carbon", historically it meant the chemistry in living organisms. By convention today the simple oxides and ions containing carbon are classed as inorganic. All the article is saying is that the enzyme is involved in converting CO2 to biological molecules such as sugars.

As for the carbon capture idea, enzymes just catalyse (make faster) chemical reactions. They can't be used in isolation to remove CO2.

Originally Posted by zinjanthropos

In the context of the quote, what would be the level of organic carbon? Is it different than non organic carbon?

I've always regarded the distinction between organic compounds and inorganic carbon compounds to be rather artificial. The quoted article seems to be suggesting a distinction based on oxidation state, with carbon dioxide and carbonates, regarded as inorganic, having their carbon atoms in the highest oxidation state, whereas the products of reduction such as formic acid, formaldehyde, methanol, and methane are regarded as organic. However, urea is regarded as organic, and hydrogen cyanide is regarded as inorganic, both of which are inconsistent with a distinction based on oxidation state as the carbon in urea has the same oxidation state as carbon dioxide, and the carbon in hydrogen cyanide has the same oxidation state as formic acid.

The significance of RuBisCo is that fixing carbon is rather difficult to carry out in the laboratory, requiring powerful reducing agents or reactive organometallics. By contrast, plants fix carbon under mild aqueous conditions (in which the laboratory reagents would not survive due to their reactivity).

Originally Posted by zinjanthropos

...what preceded it? Or has it always been present? .

Various lines of reasoning suggest that the earliest life, thought to be chemoautotrophic*, also obtained carbon from CO2. One hypothesis suggests something like the Wood–Ljungdahl pathway to be the likely process. How it all started originally is anyone's guess.


* plants, in contrast, are phototrophic.

Originally Posted by PhDemon

In chemistry organic generally means "contains carbon", historically it meant the chemistry in living organisms. By convention today the simple oxides and ions containing carbon are classed as inorganic. All the article is saying is that the enzyme is involved in converting CO2 to biological molecules such as sugars.

As for the carbon capture idea, enzymes just catalyse (make faster) chemical reactions. They can't be used in isolation to remove CO2.

What about a carbonic anhydrase? Can it remove water from CO2 emission and assist in carbon capture?

Dunno, ask a biologist

I always fail to appreciate the "speed" of chemistry. Apparently some carbonic anhydrases can catalyse about 1 million reactions per second. I find it hard to visualize large molecules behaving in that manner.


Some DNA polymerases can incorporate 1,000 nucleotides into an elongating strand of DNA per second. When you consider the 3D architecture and movements of a replication complex, and the diffusion of substrates in the correct orientation, it doesn't seem feasible. But it is nonetheless.

It's all to do with number of collisions and activation energy. At room temperature the number of collisions is massive. If the enzyme/catalyst lowers the activation energy enough you can see huge changes in rate.

Originally Posted by zinjanthropos

Originally Posted by PhDemon

In chemistry organic generally means "contains carbon", historically it meant the chemistry in living organisms. By convention today the simple oxides and ions containing carbon are classed as inorganic. All the article is saying is that the enzyme is involved in converting CO2 to biological molecules such as sugars.

As for the carbon capture idea, enzymes just catalyse (make faster) chemical reactions. They can't be used in isolation to remove CO2.

What about a carbonic anhydrase? Can it remove water from CO2 emission and assist in carbon capture?

In CO2 emissions CO2 and water vapour (if present) are chemically separate species, so the answer must I think be no.

From what I read, carbonic anhydrase catalyses the decomposition of carbonic acid (H2CO3) to CO2 and water. There is a natural equilibrium between dissolved CO2 and carbonic acid (H2CO3 <-> CO2 + H2O) and this enzyme catalyses the interconversion. So it is not relevant to gas phase emissions of CO2 and water.

But, to Zwirko's comments, it seems the catalysis is so effective that the reaction becomes diffusion-limited, i.e. the activation barrier becomes so low that the rate of molecules diffusing to the catalyst surface is what determines the rate, rather than, as with most chemical reactions, the rate at which molecules acquire enough energy (through their constant random statistical collisions) to get over the barrier.

Interesting. I had no idea the H2CO3 <-> CO2 + H2O reaction was so slow that biological processes need to accelerate it. Learn something every day.

Originally Posted by Zwirko

Some DNA polymerases can incorporate 1,000 nucleotides into an elongating strand of DNA per second. When you consider the 3D architecture and movements of a replication complex, and the diffusion of substrates in the correct orientation, it doesn't seem feasible. But it is nonetheless.

I think this animation is quite impressive:



One thing about this that is noteworthy is that because the two strands of DNA are antiparallel, and that DNA polymerases can only extend a DNA strand in a 5′ to 3′ direction, the two strands of DNA have to be treated differently as illustrated above, where one strand is replicated in a straightforward manner while the other strand is replicated in a rather complicated manner.

Cool topic zinjanthropos and thanks all, I learned a lot.

KJW.. From my armchair I find the animation an incredibly spectacular look into the chemistry of the universe and life. Fascinating and I can understand why someone might bypass the science and philosophically ask "WTF is going on?"