Carbon fixation

Carbon fixation
n., plural: carbon fixations
[ˈkɑɹbən fɪkˈseɪʃən]
Definition: a biological process wherein carbon dioxide from the atmosphere is converted into an organic compound

Carbon Fixation Definition

We know that the earth contains many elements. The periodic table shows us just how many elements exist right now, some in their natural states and others scientifically made. Often, some elements go through processes to change from one state or form to another. This can be seen in compounds like water, with the water cycle, nitrogen in the nitrogen cycle, and carbon in the carbon cycle. Within the carbon cycle, plants play a crucial role as they undergo photosynthesis. Photosynthesis is the process by which plants use energy from the sun to create their own source of energy while synthesizing the by-products of carbon dioxide (CO₂) and water. In photosynthesis, carbon fixation occurs.

What is carbon fixation? To define carbon fixation, we must look at what fixation means.  In general, fixation means making something stable. Thus, in biology, carbon fixation involves the addition of carbon dioxide to organic molecules (usually carbohydrates) to prevent it from remaining in the atmosphere in that free state. And in doing so, energy is created. Carbon dioxide fixation is also known as CO₂ assimilation.

The Calvin Cycle is the process by which organisms – specifically plants and algae – create energy and food from the carbon dioxide in the air. It is usually part of photosynthesis and the main source of food for autotrophs. The Calvin cycle occurs in four main steps, the first being carbon fixation. This can be seen above in Figure 1. The other steps include the reduction phase, carbohydrate formation, and regeneration phase.

In that first step of carbon fixation, the enzyme rubisco captures carbon dioxide from the atmosphere in order for it to be able to be fixed. The Calvin cycle and carbon fixation are very important because all organisms depend on them in order for the environment to run smoothly. The Calvin cycle not only helps provide the main source of food and energy for most organisms but also helps maintain the CO₂ levels in the atmosphere.

Net vs. Gross CO₂ fixation

As previously stated above, the carbon fixation reaction usually takes place with the carbon source CO₂. The net amount of carbon dioxide that is fixed is much less than the gross as it is thought that the majority of CO₂ is used in respiration following photosynthesis. In fact, every year over billions of tons of carbon dioxide is averaged to be converted by photosynthesis. Most of the time that the carbon fixation cycle occurs, it takes place during photosynthesis in terrestrial environments.

Overview of Pathways

Carbon can be fixed by either autotrophic or non-autotropic pathways. In terms of autotropic pathways, there are six (6) main pathways that the carbon can decide to follow that have been discovered. Carbon fixation pathways that are autotropic include carbon fixation that occurs in the chloroplasts of plants and in the cells of cyanobacteria. The other five pathways occur in 2 bacteria, 2 archaea, and one in both bacteria and archaea.

Oxygenic Photosynthesis

Photosynthesis is the process by which green plants make their own energy or food. Oxygenic photosynthesis occurs when this process uses oxygen as one of its main reactants in order for it to proceed. The organisms that undergo oxygenic photosynthesis all contain chlorophyll, a pigment that contains stroma. This can be seen in Figure 2 above. It is within this stroma where the Calvin cycle occurs and the carbon dioxide is fixed. This particular type of photosynthesis occurs in plants, algae, and cyanobacteria. The chemical process for oxygenic photosynthesis will look like this:

2H₂O → 4e⁻ + 4H+ + O₂
CO₂ + 4e⁻ + 4H⁺ → CH₂O + H₂O

The light-dependent stage of oxygenic photosynthesis deals with the use of adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide phosphate (NADP). Then begins the second stage- the light-independent one – where ATP and NADP combine with water (H₂O) to reduce carbon dioxide. This reduced CO₂ will eventually form part of a carbohydrate, usually glucose by the end of the process. The entire process will look like this chemical equation:

12 NADPH + 18 ATP + 6 CO₂ → C6H₁₂O₆ (glucose) + 12 NADP+ + 18 ADP + 18 Pi + 6 H₂O

Evolutionary considerations

There was a giant change in the evolutionary process of how cyanobacteria feed. The ancestors of the cyanobacteria began to use water to catalyze the ATP synthesis process over 2.3 billion years ago. This allowed for the cyanobacteria to begin to use carbon fixation and water to make their own source of energy and food. Though this happened billions of years ago, autotrophy already existed and plants were already undergoing oxygenic photosynthesis.

CO₂ concentrating mechanisms

CCM or the CO₂ concentrating mechanism can be defined as the method by which the way carbon is acquired and stored allows microalgae to continue to thrive and multiply even when there are low amounts in the atmosphere. This means that the organisms process carbon in such a way that they are able to carry out photosynthesis even when CO₂ concentrations are in limited demand.

This makes the organisms stronger as they become more tolerant to difficult situations such as heat stress and water stress. They are able to cope with intense situations. This is needed as sometimes during the Calvin cycle, the rubisco (which has the job of fixing carbon) grabs oxygen instead of carbon dioxide from the atmosphere. This is photorespiration and produces none of the true Calvin cycle products in the long run. It is more like to happen during the heat and water stress periods and wastes carbon, water, and energy of the plant.

CAM plants

Plants that can adapt to water-scarce and desert-like terrains like many succulents use the crassulacean acid metabolism (CAM) to avoid accidentally undergoing the photorespiration pathway. Some examples of CAM plants can be seen in Figure 3 below. Instead of allowing the sunlight to access their stomata during the day, they open their stomata at night and allow the carbon dioxide to diffuse in them. When the CO₂ gets in, since there is no light to begin the Calvin cycle steps, the CO₂ combines with an acid in the leaf so that it can be stored in the vacuoles until daytime. The stored CO₂ is transported and broken down in the day so that the plant can photosynthesize and create its own food without losing too much water and not letting too much oxygen in.

C4 plants

The C4 plants have separated the areas where the light-dependent and the l Calvin cycle take place in the plant. While the Calvin cycle steps take place closer to the cells near the veins of the leaf (bundle sheath), where there are fewer stomata, the light-independent stages take place in the mesophyll. The mesophyll cells are those that make up the general, spongy area of the lead and contain numerous stomata. The mesophyll cells with greater access to the atmosphere, pick up CO₂ and continue to constantly pump CO₂ to the bundle sheaths. This aids in avoiding photorespiration since the bundle sheaths don’t need to obtain the carbon dioxide themselves.

C3 plants

C3 photosynthesis does not contain any special adaptations to prevent photorespiration. This is why C3 plants are known as the “normal” plants. C3 plant examples include trees, rice, wheat, and about 85% of all plant species on the planet. These plants regularly use rubisco in the first step of the Calvin cycle to fix carbon and complete photosynthesis. No other method is used. Have a look at this video to compare CAM, C3 and C4 Plants.

Bacteria and cyanobacteria

There are protein shells that contain rubisco and a special enzyme. These shells are called carboxysomes. Some special bacteria and the majority of cyanobacteria chose to use carboxysomes in order to keep carbon dioxides in concentrations. The special enzyme – carbonic anhydrase – helps CO₂ to be produced in a bicarbonate form so it is able to get into the carboxysome through diffusion. The shell surrounding all these products doubles as both a container and a protector to prevent CO₂ from being lost and helping its concentration to remain high around rubisco.

Other autotrophic pathways

The five other autotrophic pathways include the reverse Krebs cycle, reductive acetyl CoA pathway, 3-Hydroxpropionate bicycle, and two other cycles related to the 3-Hydroxpropionate bicycle.

The reverse Krebs Cycle

This pathway becomes useful for organisms that live in anaerobic environments. This is because the reverse Krebs cycle does not use oxygen in its pathway in order to complete carbon fixation. The reverse Krebs cycle becomes most useful to microorganisms such as microaerobic bacteria and anaerobic archaea as well as microbes that live in the oceans.

Reductive acetyl CoA pathway

Also known as the Wood-Ljungdahl pathways, this pathway is unique in the way it used CO₂ to build up the acetyl group of acetyl-CoA. Through the reduction and condensation of two molecules. This allows for carbon fixation to occur as a side process of the process. It is in this pathway that only one molecule of ATP is required for carbon fixation to occur. This makes it an ideal pathway for organisms that are chemolithoautotrophs as they generally tend to live in anaerobic conditions and so have restricted energy and energy sources.

3-Hydroxypropionate bicycle

This pathway of carbon fixation is used by non-sulfur and green phototrophs. It is called a bicycle because it uses a combination of 19 processes to undergo two main steps or cycles in order for it to be completed. It is within these processes that the bicycle contains 13 multifunctional enzymes, out of which three allow the fixation of some bicarbonate molecules.

Other two cycles related to the 3- Hydroxypropionate bicycle

There are two variants of the 3-Hydroxypropionate bicycle pathways. One of them is known to be used among anaerobic archaea and is called the dicarboxylate/4-hydroxybutyrate cycle. Whereas the other was used in a thermoacidophile archaeon which resides in an extremely aerobic environment. That pathway is the 3-hydroxypropionate/4-hydroxybutyrate cycle.

Chemosynthesis

As the name itself implies, chemosynthesis is the creation or process of creating organic compounds. This is done through the utilization of energy by bacteria or other organisms which they obtained from reactions with inorganic chemicals. This process does not require energy to occur and includes organic and dehydration synthesis.

Non-autotrophic pathways

Most heterotrophs directly consume their energy through other sources and would not need to have carbon dioxide anywhere in their diet or metabolism. However, a few like pyruvate carboxylase and 6-phosphogluconate dehydrogenase will consume or use CO₂ in catalyzed reactions and through this carbon, fixation will occur. Notably, E.coli, which is in the gut of most if not all mammals, also store high levels of carbon dioxide — a form of carbon fixation.

Carbon isotope discrimination

It is funny to think that plants and other organisms that photosynthesize can be picky about what kind of carbon it wants to use. Despite this, the case is often that rubisco prefers the carbon-12 over its isotope carbon-13 because of its stability and lightweight. This carbon isotope discrimination affects the ratio of carbon-12 to carbon -13 in the atmosphere as carbon-13 tends to be in higher concentrations. It also affects how the plants use water as the highest water use efficiency will occur as a combination of biomass accumulation and water consumption. Of course, biomass accumulation will not be as high if the lighter carbon isotope is preferred.

Try to answer the quiz below to check what you have learned so far about carbon fixation.

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References

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