Ribulose 1,5-bisphosphate (RuBP) is an

organic substance Some chemical authorities define an organic compound as a chemical compound that contains a Carbon–hydrogen bond, carbon–hydrogen or carbon–carbon bond; others consider an organic compound to be any chemical compound that contains carbon. F ...

that is involved in

photosynthesis Photosynthesis ( ) is a system of biological processes by which photosynthetic organisms, such as most plants, algae, and cyanobacteria, convert light energy, typically from sunlight, into the chemical energy necessary to fuel their metabo ...

, notably as the principal acceptor in plants. It is a colourless anion, a double phosphate ester of the

ketopentose In chemistry, a pentose is a monosaccharide (simple sugar) with five carbon atoms. The chemical formula of many pentoses is , and their molecular weight is 150.13 g/mol.ketone In organic chemistry, a ketone is an organic compound with the structure , where R and R' can be a variety of carbon-containing substituents. Ketones contain a carbonyl group (a carbon-oxygen double bond C=O). The simplest ketone is acetone ( ...

-containing sugar with five

carbon Carbon () is a chemical element; it has chemical symbol, symbol C and atomic number 6. It is nonmetallic and tetravalence, tetravalent—meaning that its atoms are able to form up to four covalent bonds due to its valence shell exhibiting 4 ...

atoms) called ribulose. Salts of RuBP can be isolated, but its crucial biological function happens in solution. RuBP occurs not only in plants but in all domains of life, including

Archaea Archaea ( ) is a Domain (biology), domain of organisms. Traditionally, Archaea only included its Prokaryote, prokaryotic members, but this has since been found to be paraphyletic, as eukaryotes are known to have evolved from archaea. Even thou ...

Bacteria Bacteria (; : bacterium) are ubiquitous, mostly free-living organisms often consisting of one Cell (biology), biological cell. They constitute a large domain (biology), domain of Prokaryote, prokaryotic microorganisms. Typically a few micr ...

, and

Eukarya The eukaryotes ( ) constitute the domain of Eukaryota or Eukarya, organisms whose cells have a membrane-bound nucleus. All animals, plants, fungi, seaweeds, and many unicellular organisms are eukaryotes. They constitute a major group of l ...

History

RuBP was originally discovered by Andrew Benson in 1951 while working in the lab of

Melvin Calvin Melvin Ellis Calvin (April 8, 1911 – January 8, 1997) was an American biochemist known for discovering the Calvin cycle along with Andrew Benson and James Bassham, for which he was awarded the 1961 Nobel Prize in Chemistry. He spent most of ...

at UC Berkeley. Calvin, who had been away from the lab at the time of discovery and was not listed as a co-author, controversially removed the full molecule name from the title of the initial paper, identifying it solely as "ribulose". At the time, the molecule was known as ''ribulose diphosphate'' (RDP or RuDP) but the prefix di- was changed to bis- to emphasize the nonadjacency of the two phosphate groups.

Role in photosynthesis and the Calvin-Benson Cycle

The enzyme ribulose-1,5-bisphosphate carboxylase-oxygenase (

rubisco Ribulose-1,5-bisphosphate carboxylase/oxygenase, commonly known by the abbreviations RuBisCo, rubisco, RuBPCase, or RuBPco, is an enzyme () involved in the light-independent (or "dark") part of photosynthesis, including the carbon fixation by wh ...

) catalyzes the reaction between RuBP and

carbon dioxide Carbon dioxide is a chemical compound with the chemical formula . It is made up of molecules that each have one carbon atom covalent bond, covalently double bonded to two oxygen atoms. It is found in a gas state at room temperature and at norma ...

. The product is the highly unstable six-carbon intermediate known as 3-keto-2-carboxyarabinitol 1,5-bisphosphate, or 2'-carboxy-3-keto-D-arabinitol 1,5-bisphosphate (CKABP). This six-carbon β-ketoacid intermediate hydrates into another six-carbon intermediate in the form of a gem-diol. This intermediate then cleaves into two molecules of 3-phosphoglycerate (3-PGA) which is used in a number of metabolic pathways and is converted into glucose. In the Calvin-Benson cycle, RuBP is a product of the

phosphorylation In biochemistry, phosphorylation is described as the "transfer of a phosphate group" from a donor to an acceptor. A common phosphorylating agent (phosphate donor) is ATP and a common family of acceptor are alcohols: : This equation can be writ ...

of ribulose-5-phosphate (produced by

glyceraldehyde 3-phosphate Glyceraldehyde 3-phosphate, also known as triose phosphate or 3-phosphoglyceraldehyde and abbreviated as G3P, GA3P, GADP, GAP, TP, GALP or PGAL, is a metabolite that occurs as an intermediate in several central pathways of all organisms.Nelson, D ...

) by ATP. Calvin-cycle4

Interactions with rubisco

RuBP acts as an

enzyme inhibitor An enzyme inhibitor is a molecule that binds to an enzyme and blocks its Enzyme activity, activity. Enzymes are proteins that speed up chemical reactions necessary for life, in which Substrate (biochemistry), substrate molecules are converted ...

for the enzyme rubisco, which regulates the net activity of carbon fixation. When RuBP is bound to an active site of rubisco, the ability to activate via carbamylation with and is blocked. The functionality of rubisco activase involves removing RuBP and other inhibitory bonded molecules to re-enable carbamylation on the active site.

Role in photorespiration

Rubisco also catalyzes RuBP with oxygen () in an interaction called

photorespiration Photorespiration (also known as the oxidative photosynthetic carbon cycle or C2 cycle) refers to a process in plant physiology, plant metabolism where the enzyme RuBisCO oxygenates RuBP, wasting some of the energy produced by photosynthesis. Th ...

, a process that is more prevalent at high temperatures. During photorespiration RuBP combines with to become 3-PGA and phosphoglycolic acid. Like the Calvin-Benson Cycle, the photorespiratory pathway has been noted for its enzymatic inefficiency although this characterization of the enzymatic kinetics of rubisco has been contested. Due to enhanced RuBP carboxylation and decreased rubisco oxygenation stemming from the increased concentration of in the

bundle sheath A vascular bundle is a part of the transport system in vascular plants. The transport itself happens in the Plant stem, stem, which exists in two forms: xylem and phloem. Both these tissues are present in a vascular bundle, which in addition ...

, rates of photorespiration are decreased in plants. Similarly, photorespiration is limited in CAM photosynthesis due to kinetic delays in enzyme activation, again stemming from the ratio of carbon dioxide to oxygen.

Measurement

RuBP can be measured isotopically via the conversion of and RuBP into

. G3P can then be measured using an enzymatic optical assay. Given the abundance of RuBP in biological samples, an added difficulty is distinguishing particular reservoirs of the substrate, such as the RuBP internal to a chloroplast vs external. One approach to resolving this is by subtractive inference, or measuring the total RuBP of a system, removing a reservoir (e.g. by centrifugation), re-measuring the total RuBP, and using the difference to infer the concentration in the given repository.

References