RIBULOSE-1,5-BISPHOSPHATE (RUBP): CHARACTERISTICS, CARBOLIXATION - CHEMISTRY - 2025

The ribulose 1,5-diphosphate, commonly abbreviated RuBP, is a biological molecule that acts as a substrate in the Calvin cycle of photosynthesis, being the molecule upon which is fixed the CO ₂.

In this process, RuBP can be oxygenated or carboxylated, giving way to the synthesis of hexoses and undergoing various reactions until its own regeneration (recycling). The carboxylation and oxidation of RuBP is carried out by the same enzyme: ribulose-1,5-bisphosphate carboxylase / oxygenase (RuBisCO or Rubisco). In the regeneration of this molecule, the phosphorylation of ribulose-5-phosphate occurs by the enzyme phosphoribulokinase.

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characteristics

RuBP is a ketopentose-like molecule. These monosaccharides are characterized, as their name indicates, by presenting five carbons with a ketone group, that is, a carbonyl group in one of the central carbons.

As in most ketoses, the carbonyl group is found at C2, while hydroxyl groups are found at C3 and C4 carbons. RuBP is a derivative of ribulose, where the C1 and C5 carbons also have hydroxyl groups. In RuBP these carbons (C1 and C5) are activated by two phosphate groups located at the respective sites.

Carboxylation of RuBP

In the first stage of the Calvin cycle, an enzyme called phosphoribulokinase causes the phosphorylation of ribulose-5-phosphate to generate RuBP. Subsequently, carboxylation occurs, due to the action of the Rubisco enzyme.

In the carboxylation of RuBP, it acts as a CO ₂ acceptor, binding to said molecule to form two molecules of 3-phosphoglycerate (3PG). During this reaction an endiolate intermediate is formed by taking up the proton from the C3 carbon of RuBP.

Endiolate generates a nucleophilic attack on CO _2, forming a β-oxoacid that is rapidly attacked by H ₂ O at its C3 carbon. The product of this attack undergoes a reaction very similar to an aldol breakdown, generating two 3PG molecules, one of which carries the carbon from CO ₂.

The Rubisco enzyme that carries out this reaction is a large enzyme, made up of eight equal subunits. This enzyme is considered one of the most abundant proteins on earth, representing approximately 15% of the total proteins within chloroplasts.

As its name indicates (Ribulose bisphosphate carboxylase / oxygenase), Rubisco can catalyze both the carboxylation and the oxidation of RuBP, being able to react with both CO ₂ and O ₂.

RuBP in the formation of glucose

In green plants, photosynthesis produces ATP and NADPH in the light phase. These molecules are used to carry out the reduction of CO ₂ and form reduced products such as carbohydrates, mostly starch and cellulose.

As mentioned, in the dark phase of photosynthesis, the cleavage of RuBP occurs by the action of Rubisco, with a ratio of two 3PG molecules formed by each RuBP. At the completion of six rounds of the Calvin cycle, the formation of a hexose (eg glucose) occurs.

In the six rounds of this cycle, six molecules of CO ₂ react with six of RuBP to form 12 molecules of 3PG. These molecules are transformed into 12 BPG (1,3-bisphosphoglycerate) and then into 12 GAP.

Of these 12 GAP molecules, five are isomerized to DHAP of which three react with three more GAP molecules to form three fructose-1,6-bisphosphate. The latter are dephosphorylated to fructose-6-phosphate (F6P) by the action of the enzyme hexosadiphosphatase.

Finally, a glucose phosphate isomerase converts one of the three F6P molecules into glucose-6-phosphate, which is dephosphorylated by its respective phosphatase to glucose, thus completing the path of the formation of a hexose from CO ₂.

RuBP regeneration

In the previously described pathway, the GAP molecules formed can be directed towards the formation of a hexose or towards the regeneration of RuBP. For each turn of the dark phase of photosynthesis, a molecule of RuBP reacts with one of CO ₂ to finally regenerate a RuBP.

As described in the previous section, for every six turns of the Calvin cycle 12 GAP molecules are formed, of which eight are involved in the formation of a hexose, with four remaining available for the regeneration of RuBP.

Two of these four GAPs react with two F6Ps through the action of a transketolase to form two xyluloses and two erythrocytes. The latter bind to two DHAP molecules to produce two seven-carbon carbohydrates, sedoheptulose-1,7-bisphosphate.

The sedoheptulose-1,7-bisphosphate are dephosphorylated and then react with the last two GAPs to form two xyluloses and two ribose-5-phosphate. The latter are isomerized to ribulose-5-phosphate. On the other hand, xyluloses, by the action of an epimerase, are transformed into four more ribuloses.

Finally, the six ribuloses-5-phosphate formed are phosphorylated by phosphoribulokinase to give rise to six RuBPs.

RuBP can be oxygenated

Photorespiration is a "light" respiration process that occurs together with photosynthesis, being very active in C3 type plants and almost absent in C4 plants. During this process, the RuBP molecules are not reduced, so hexose biosynthesis does not occur, since the reducing power is diverted towards oxygen reduction.

Rubisco exerts its oxygenase activity in this process. This enzyme has a low affinity towards CO ₂, in addition to being inhibited by the molecular oxygen present in cells.

Because of this, when cellular concentrations of oxygen are higher than those of CO ₂, the process of photorespiration can overcome the carboxylation of RuBP by CO ₂. In the mid-20th century this was demonstrated by observing that illuminated plants fixed O ₂ and released CO ₂.

In photorespiration, RuBP reacts with O ₂ through the action of Rubisco, forming an endiolate intermediate that produces 3PG and phosphoglycollate. The latter is hydrolyzed by the action of a phosphatase, giving rise to glycolate that is subsequently oxidized by a series of reactions that occur in peroxisomes and mitochondria, finally yielding CO ₂.

Mechanisms to avoid oxygenation of RuBP

Photorespiration is a mechanism that interferes with the photosynthesis process, undoing part of its work, by releasing CO ₂ and using the substrates necessary for the production of hexoses, thus slowing down the growth rate of plants.

Some plants have managed to avoid the negative effects of the oxygenation of RuBP. In C4 plants for example, the previous fixation of CO ₂ occurs, concentrating it in photosynthetic cells.

In this type of plants, CO ₂ is fixed in mesophilic cells that lack Rubisco, by condensation with phosphoenolpyruvate (PEP), producing oxaloacetate that is transformed into malate and passes to the surrounding cells of the bundle, where it releases the CO ₂ that finally enters the Calvin cycle.

CAM plants, on the other hand, separate the fixation of CO ₂ and the Calvin cycle in time, that is, they carry out the uptake of CO ₂ at night, through the opening of their stromata, storing it through the Crassulacean acid (CAM) metabolism through malate synthesis.

As in C4 plants, malate passes into the sheath cells of the bundle to release CO ₂.

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