Tuesday, July 10, 2007

Fixing Carbon: the Rubisco Reaction

Life as we know it is based on carbon. All organisms need to have a source of carbon in order to grow and multiply. Animals, such as humans, get their carbon from eating other living things but there are many other species that can assimilate carbon directly from inorganic sources. This process is known as carbon fixation.

In most cases, carbon is derived from carbon dioxide in the atmosphere or dissolved in water. There are dozens of different chemical reactions in which carbon dioxide is taken up and attached to another organic molecule. Humans can do this to limited extent but not enough to support all of our carbon needs. Bacteria, protists, plants and fungi are much better at efficiently incorporating carbon from carbon dioxide.

The reactions of carbon fixation are often expensive because they require an input of energy to drive the assimilation of the newly-fixed carbon into metabolic pathways that are operating inside the cell. Photosynthetic organisms often have an abundant supply of energy so they can take up large amounts of carbon to make organic molecules. In fact, the association between carbon fixation and photosynthesis is so obvious that it's often assumed that the processes are directly coupled.

They aren't. There are many non-photosynthetic species that can efficiently fix carbon from carbon dioxide and there are many organisms that can carry out photosynthesis but they don't fix huge amounts of carbon using the standard pathways.

Nevertheless, there is one major carbon-fixing pathway that is present in most photosynthesizing bacteria, protists, fungi, and especially plants. It's called the Calvin Cycle after its discoverer Melvin Calvin (see photo) [Nobel Laureate 1961]. In modern biochemistry courses we discuss this pathway in the photosynthesis chapter but it's no longer considered to be part of photosynthesis. Photosynthesis ends with the light-driven synthesis of the energy molecules ATP and NADPH.

The first step in this pathway is the most important; it's the step where a carbon dioxide molecule is attached to a five carbon compound and the resulting 6-carbon intermediate is split into two 3-carbon molecules. The 3-carbon molecules then enter various metabolic pathways, including a pathway that recreates the 5-carbon precursor—hence the name "cycle."

The initial reaction is shown in the schematic below where each ball represents a carbon atom. The substrate for the reaction is the 5-carbon compound with the green balls and the blue ball represents the carbon atom in carbon dioxide (CO2). As you can see, the reaction takes place in two steps. The first step is the actual fixation reaction; it creates a 6-carbon molecule with the incorporated carbon atom from CO2. In the second step this 6-carbon molecule is cleaved producing two 3-carbon molecules.

The 5-carbon substrate is called ribulose 1,5-bisphosphate [Monday's Molecule #34]. It's related to the ribose in ribonucleic acid (RNA) except that it's the keto form of ribose and it has two phosphate groups attached to the 1 and 5 positions. The final products are called 3-phosphoglycerate. They are common intermediates in many metabolic pathways.

Here's the complete reaction. The enzyme that catalyzes this reaction is the most abundant enzyme on the entire planet. It's called ribulose 1,5-bisphosphate carboxylase-oxygenase, or Rubisco for short.

Mechanism of Rubisco-catalyzed carboxylation of ribulose 1,5-bisphosphate to form two molecules of 3-phosphoglycerate. A proton is abstracted from C-3 of ribulose 1,5 -bisphosphate to create a 2,3 -enediolate intermediate. The nucleophilic enediolate attacks producing 2-carboxy-3-ketoarabinitol 1,5 -bisphosphate, which is hydrated to an unstable gem diol intermediate. The C-2-C-3 bond of the intermediate is immediately cleaved, generating a carbanion and one molecule of 3-phosphoglycerate. Stereospecific protonation of the carbanion yields a second molecule of 3-phosphoglycerate. This step completes the carbon fixation stage of the Calvin cycle—two molecules of 3-phosphoglycerate are formed from CO2 and the five-carbon sugar ribulose 1,5-bisphosphate.

©Laurence A. Moran and Pearson Prentice Hall 2007


  1. I was just reading about this in Secrets of Life (an old book about biology).

    BTW, you might consider registering your blog on technorati.com; then when people looked at their "Blogs that link here" they'd find that you were linking to them. Just a thoughtl.

  2. Thank you soo much for this article. This post really helped me understand the rubisco reaction. :)

  3. Great article! I especially appreciate the in depth mechanism.