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User:UndercoverGeologicalAgent/Ribulose 1,5-bisphosphate

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UndercoverGeologicalAgent/Ribulose 1,5-bisphosphate
Skeletal formula of RuBP
The acid form of the RuBP anion
Ball-and-stick model, based on x-ray diffraction data
Names
IUPAC name
1,5-Di-O-phosphono-D-ribulose
Other names
Ribulose 1,5-diphosphate
Identifiers
3D model (JSmol)
ChEBI
ChemSpider
KEGG
UNII
  • InChI=1S/C5H12O11P2/c6-3(1-15-17(9,10)11)5(8)4(7)2-16-18(12,13)14/h3,5-6,8H,1-2H2,(H2,9,10,11)(H2,12,13,14)/t3-,5-/m1/s1 checkY
    Key: YAHZABJORDUQGO-NQXXGFSBSA-N checkY
  • O=P(O)(OCC(=O)[C@H](O)[C@H](O)COP(=O)(O)O)O
Properties
C5H12O11P2
Molar mass 310.088 g·mol−1
Except where otherwise noted, data are given for materials in their standard state (at 25 °C [77 °F], 100 kPa).
☒N verify (what is checkY☒N ?)

Ribulose 1,5-bisphosphate (RuBP) is an organic substance that is involved in photosynthesis, notably as the principal CO2 acceptor in plants.[1]: 2  It is a colourless anion, a double phosphate ester of the ketopentose (ketone-containing sugar with five carbon atoms) called ribulose. Salts of RuBP can be isolated, but its crucial biological function happens in solution.[2]

History

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RuBP was originally discovered by Andrew Benson in 1951 while working in the lab of Melvin Calvin at UC Berkeley.[3][4] 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".[3][5] 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.[3][4][6]

Role in photosynthesis and the Calvin-Benson Cycle

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See also: Calvin-Benson Cycle

The enzyme ribulose-1,5-bisphosphate carboxylase-oxygenase (rubisco) catalyzes the reaction between RuBP and carbon dioxide. 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).[7] This six-carbon β-ketoacid intermediate hydrates into another six-carbon intermediate in the form of a gem-diol.[8] 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.[9][10]

In the Calvin-Benson cycle, RuBP is a product of the phosphorylation of ribulose-5-phosphate (produced by glyceraldehyde 3-phosphate) by ATP.[10][11]

 
The Calvin cycle showing the role of ribulose-1,5-bisphosphate.

Interactions with rubisco

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RuBP acts as an enzyme inhibitor for the enzyme rubisco, which regulates the net activity of carbon fixation.[12][13][14] When RuBP is bound to an active site of rubisco, the ability to activate via carbamylation with CO2 and MG2+ is blocked. The functionality of rubisco activase involves removing RuBP and other inhibitory bonded molecules to re-enable carbamylation on the active site.[1]: 5 

Role in photorespiration

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See also: Photorespiration

Rubisco also catalyzes RuBP with oxygen (O
2) in an interaction called photorespiration, a process that is more prevalent at high temperatures.[15][16] During photorespiration RuBP combines with O
2 to become 3-PGA and phosphoglycolic acid.[17][18][19] Like the Calvin-Benson Cycle, the photorespiratory pathway has been noted for its enzymatic inefficiency[18][19] although this characterization of the enzymatic kinetics of rubisco have been contested.[20] Due to enhanced RuBP carboxylation and decreased rubisco oxygenation stemming from the increased concentration of CO2 in the bundle sheath, rates of photorespiration are decreased in C4 plants.[1]: 103 

Measurement

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RuBP can be measured isotopically via the conversion of 14CO2 and RuBP into glyceraldehyde 3-phosphate.[21] G3P can then be measured using an enzymatic optical assay.[21][22][a] 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.[23]

References

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  1. ^ a b c Leegood, R.C.; Sharkey, T.D.; von Caemmerer, S., eds. (2000). Photosynthesis: Physiology and Metabolism. Advances in Photosynthesis. Vol. 9. Kluwer Academic Publishers. doi:10.1007/0-306-48137-5. ISBN 978-0-7923-6143-5.
  2. ^ Nelson, D.L.; Cox, M.M. (2000). Lehninger, Principles of Biochemistry (3rd ed.). New York: Worth Publishing. ISBN 1-57259-153-6.
  3. ^ a b c Sharkey, T.D. (2018). "Discovery of the canonical Calvin–Benson cycle" (PDF). Photosynthesis Research. 140: 235–252. doi:10.1007/s11120-018-0600-2.
  4. ^ a b Benson, A.A. (1951). "Identificiation of Ribulose in C14O2 Photosynthesis Products". Journal of the American Chemical Society. 73 (6): 2971–2972. doi:10.1021/ja01150a545.
  5. ^ Benson, A.A. (2005). "Following the path of carbon in photosynthesis: a personal story". In Govindjee; Beatty, J.T.; Gest, H.; Allen, J.F. (eds.). Discoveries in Photosynthesis. Advances in Photosynthesis and Respiration. Vol. 20. pp. 795–813. doi:10.1007/1-4020-3324-9_71. ISBN 978-1-4020-3324-7.
  6. ^ Wildman, S.G. (2002). "Along the trail from Fraction I protein to Rubisco (ribulose bisphosphate carboxylase-oxygenase)" (PDF). Photosynthesis Research. 73: 243–250. doi:10.1023/A:1020467601966. PMID 16245127.
  7. ^ Lorimer, G.H.; Andrews, T.J.; et al. (1986). "2´-carboxy-3-keto-D-arabinitol 1,5-bisphosphate, the six-carbon intermediate of the ribulose bisphosphate carboxylase reaction". Phil. Trans. R. Soc. Lond. B. 313: 397–407. doi:10.1098/rstb.1986.0046.
  8. ^ Mauser, H.; King, W.A.; Gready, J.E.; Andrews, T.J. (2001). "CO2 Fixation by Rubisco: Computational Dissection of the Key Steps of Carboxylation, Hydration, and C−C Bond Cleavage". J. Am. Chem. Soc. 123 (44): 10821–10829. doi:10.1021/ja011362p.
  9. ^ Kaiser, G.E. "Light Independent Reactions". Biol 230: Microbiology. The Community College of Baltimore County, Catonsville Campus. Retrieved 7 May 2021.{{cite web}}: CS1 maint: url-status (link)
  10. ^ a b Hatch, M.D.; Slack, C.R. (1970). "Photosynthetic CO2-Fixation Pathways". Annual Review of Plant Physiology. 21: 141–162. doi:10.1146/annurev.pp.21.060170.001041.
  11. ^ Bartee, L.; Shriner, W.; Creech, C. "The Light Independent Reactions (aka the Calvin Cycle)". Principles of Biology. Open Oregon Educational Resources. ISBN 978-1-63635-041-7.
  12. ^ Jordan, D.B.; Chollet, R. (1983). "Inhibition of ribulose bisphosphate carboxylase by substrate ribulose 1,5-bisphosphate". Journal of Biological Chemistry. 258 (22): 13752–13758. doi:10.1016/S0021-9258(17)43982-2. PMID 6417133.
  13. ^ Spreitzer, R.J.; Salvucci, M.E. (2002). "Rubisco: Structure, Regulatory Interactions, and Possibilities for a Better Enzyme". Annual Review of Plant Biology. 53: 449–475. doi:10.1146/annurev.arplant.53.100301.135233.
  14. ^ Taylor, Thomas C.; Andersson, Inger (1997). "The structure of the complex between rubisco and its natural substrate ribulose 1,5-bisphosphate". Journal of Molecular Biology. 265 (4): 432–444. doi:10.1006/jmbi.1996.0738.
  15. ^ Leegood, R.C.; Edwards, G.E. "Carbon Metabolism and Photorespiration: Temperature Dependence in Relation to Other Environmental Factors". In Baker, N.R. (ed.). Photosynthesis and the Environment. Advances in Photosynthesis and Respiration. Vol. 5. Kluwer Academic Publishers. pp. 191–221. ISBN 978-0-7923-4316-5.
  16. ^ Keys, A.J.; Sampaio, E.V.S.B.; et al. (1977). "Effect of Temperature on Photosynthesis and Photorespiration of Wheat Leaves". Journal of Experimental Botany. 28 (3): 525–533. doi:10.1093/jxb/28.3.525.
  17. ^ Sharkey, T.D. (1988). "Estimating the rate of photorespiration in leaves". Physiologia Plantarum. 73 (1): 147–152. doi:10.1111/j.1399-3054.1988.tb09205.x.
  18. ^ a b Kebeish, R.; Niessen, M.; et al. (2007). "Chloroplastic photorespiratory bypass increases photosynthesis and biomass production in Arabidopsis thaliana". Nature Biotechnology. 25: 593–599. doi:10.1038/nbt1299.
  19. ^ a b Leegood, R.C.; Lea, P.J.; et al. (1995). "The regulation and control of photorespiration". Journal of Experimental Botany. 46: 1397–1414. doi:10.1093/jxb/46.special_issue.1397. JSTOR 23694986.
  20. ^ Bathellier, C.; Tcherkez, G.; et al. "Rubisco is not really so bad". Plant, cell, and environment. 41 (4): 705–716. doi:10.1111/pce.13149.
  21. ^ a b Latzko, E.; Gibbs, M. (1972). "Measurement of the intermediates of the photosynthetic carbon reduction cycle, using enzymatic methods". Photosynthesis and Nitrogen Fixation Part B. Methods in Enzymology. Vol. 24. Academic Press. pp. 261–268. doi:10.1016/0076-6879(72)24073-3. ISBN 9780121818876. ISSN 0076-6879.
  22. ^ Latzko, E.; Gibbs, M. (1969). "Level of Photosynthetic Intermediates in Isolated Spinach Chloroplasts". Plant Physiology. 44 (3): 396–402. doi:10.1104/pp.44.3.396. PMID 16657074.
  23. ^ Sicher, R.C.; Bahr, J.T.; Jensen, R.G. (1979). "Measurement of Ribulose 1,5-Bisphosphate from Spinach Chloroplasts". Plant Physiology. 64: 876–879. doi:10.1104/pp.64.5.876. PMID 16661073.
  1. ^ Note that G3P is a 3-carbon sugar so its abundance should be twice that of the 6-carbon RuBP, after accounting for rates of enzymatic catalysis.

Category:Photosynthesis Category:Organophosphates Category:Monosaccharide derivatives

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