The “Dark” Reaction: Carbon Fixation

The “Dark” Reaction: Carbon Fixation Requires Rubisco: Ribulose-1,5-bisphosphate carboxylase RuBPi + CO2 6 2 x 3PG MW = 550, 000 g/mol Subunits eight small (14,000 g/mol) eight large (53,000 g/mol) 4 mM in stroma (250 mg/mL) “dark” means light-indendent! Mg2+ required in active and allosteric sites Allosteric site lysine is bound 2+to CO2 Mg lysine-NH2 + CO2 à lysine-NH-CO2 - + H+ (carbamate – nonsubstrate CO2 ) Mechanism of CO 2 Fixation: Rubisco Step 1 Ribulose 1,5-Bisphosphate Carboxylase “rubisco” Fig. 20-23 First Step: CO2 adds to enediol form of RuBPi (not HCO 2- or lysine-NH-CO2-!) 1 Mechanism of CO 2 Fixation: Rubisco Step 2 H2O adds to β -keto intermediate Fig. 20-23 Mechanism of CO 2 Fixation: Rubisco Step 3 Hydrated intermediate breaks down to 2 x 3PG Fig. 20-23 **C3 plants** (nontropical) All steps catalyzed by rubisco! Enzyme makes up ~50% by wt total chloroplast protein Most abundant protein in biosphere 10 11 tons CO2 fixed per year! 2 Why is rubisco reaction energetically favorable? 1 2 3 Fig. 20-23 RuBPi + CO2 6 2 x 3PG ∆ Go’ = -35 kJ/mol Step 1: highly unfavorable Step 3: highly favorable Regulation of Enzymatic Activity of Rubisco (stroma) Rubisco pHmax ~ 8 (H+ pumped into lumen from stroma) With hv, as H+ pumped into lumen, Mg2+ pumped out into stroma As hv 8 , NADPH 8 , ATP 8 , [Mg2+ 8 H+ 9 ], Rubisco activity 8 CO2 fixation does not take place in the dark! At night, glycolysis and oxidative phosphorylation meet energy needs of the plant. Rubisco activity is controlled by a redox system that is dependent upon [NADPH] 3 Fig. 20-36 Redox regulation of Rubisco active Rubisco (red) ox NADPH NADP+ red Where is this protein found? SUMMA RY OF ELECTRON TRA NSF ER IN PS I TO NADP+ 4 Cu+ plastocyanin +2 4 Cu Chla+. Chla -. 4 hνν Chla Chla RXN 4 Chla Ao 4 PQ A1 4 Fe 2+ 4 Fe 3+ Fe4S4 Fd 4 Fe 3+ 4 Fe 2+ CTR 2 NADPH 2 NADP + + H + inactive Rubisco (ox) What controls reduction of Fd? hv + PSI What glycolytic enzymes must be activated? deactivated? FBPi phosphatase 8 , PFK9 Allosteric regulation of Rubisco At high CO2 , no ATP or activase is required. allosteric subunit RuBPi At low CO2 , ATP required to help displace a RuBPi which blocks the lys and prevents carbamylation + RuBPi allosteric subunit RuBPi binds in both the active site and the allosteric site? Fig. 20-33 4 From where comes the ribulose 1,5-bisphosphate (RuBPi)? Understanding of C5 sugar synthesis requires a knowledge of how the pentose phosphate pathway works for carbon fixation! Pentose-Pi pathway: Pentose Pi “Shunt” Functions: oxidative portion Produces NADPH for biosynthesis (fatty acids, steroids). Produces Ribose (C5) for RNA and cofactors (ATP, NAD, FAD, etc.). Provides a breakdown pathway for C 5 sugars. Provides a pathway to regenerate Ru-5-Pi (C 5) for carbon fixation. regenerative (nonoxidative) portions Ribulose 5-phosphate is produced in 3 steps! Ribulose 1,5-bisphosphate is synthesized how? Ru-5-Pi + ATP º Ru-1,5-BPi + ADP 5 Pentose-Pi pathway (oxidative): Step 1 glucos e-6-Pi-de hydrogenase NADPH + H+ NADP+ PiO PiO O O H OH HO O OH 1 HO OH OH OH 6-Pi- glucono- δ -lactone C6 glucos e-6-Pi C6 Typical hydride transfer mechanism to NADP+ What “H-” is transferred? What is the source of G-6-Pi? Comes from phosphorylation of glucose and from G-1-Pi from glycogen phosphorylase breakdown of glycogen using Pi Pentose-Pi pathway (oxidative): Step 2 lactonase PiO H+ H2O O PiO O OH OH O- 2 HO OH O HO OH OH 6-Pi-glucono- δ -lactone C6 6-Pi-gluconate C6 Typical hydrolysis of an ester bond. Where is the ester? 6 Pentose-Pi pathway (oxidative): Step 3 6-phosphogluconate dehydrogenase PiO NADP + PiO 3 OH O HO O HO O OH H 6-Pi-gluconate C6 unstable Typical hydride transfer mechanism to NADP+ In what other pathway was a β -keto acid formed? Name of enzyme? CAC: isocitrate dehydrogenase! isocit + º α -KG 3 OH ββ -keto acid NADPH + H+ H+ What “H-” is transferred? NAD+ O- OH OH O - CO2 PiO OH OH HO O + CO2 + NADH ketose ribulose-5-Pi C5 Phosphorylation of Ribulose-5-Pi to Bisphosphate PiO ribulose-5-Pi kinase OH OH + ATP HO O ribulose-5-Pi C5 PiO OH OPi + ADP HO O ribulose-1,5-BPi C5 7 A review of C 6 synthesis: Start with ? Using “Cx” notation, summarize the rubisco reaction: C5 + C1 à 2 C3 How is C6 made from 2C3? Reverse of glycolysis starting from 3-phosphoglycerate! O C O- H 2,5C OH 3,4 1,6 CH2OPi 3-phosphoglycerate (3PG) A review of C 6 synthesis: Continue with ? O 3,4 CH 2 ,5 H C OH 1,6 CH O Pi 2 glyce r alde hyde- 3 -ph os pha t e ( GAP ) P i + NADP+ 6 - glyceraldehyde-3-phosphate dehydrogenase 6 NADPH + H O O C O P 3, 4 H 2 ,5 1 ,6 + ∆∆ G BB NN = + 6.3 kJ/mol O- C OH O CH2O Pi 1,3 - bi sph os p hogly ce rat e (1 ,3-B PG) ADP 7 7 - phosphoglycerate kinase ∆∆ G BB NN = - 18.5 kJ/mol ATP 1st e nergy conse rv ation st ep O 3,4 H C 2,5 1,6 C OOH 7 Start here CH2OPi 3 -phosphoglyc erate (3PG ) 8 A review of C 6 synthesis: End with ? C6 O 6 PiO OH 5 Yeah! OPi 1 4 2 4 - aldolase OH ∆∆ G 3 OH fr uctose-1,6-bisphosphate (F6P) BB NN = + 24.0 kJ/m ol Cleavage of C6 into 2 x C3 fragments 4 5 - triosephosphate isomerase PiO OH 6 1 5 OH 5 4 ∆∆ G OPi BB NN = - 7.6 kJ/mol 2 OH Isomerization of C3 to interconver t forms 3 O gl yceraldehyde-3-phosphate (GAP) + dihydroxyacetone phosphate (DHAP) For 2 C 3 à C6, how many ATP required? NADPH? Note: 1 ATP and 1 NADPH 3PG (C 3 ) How is C5 regenerated? Rubisco reaction: C5 + C1 à 2 C3 C6 Oops! C5 consumed Multiply by 6 6 C5 + 6 C1 à 12 C3 30 6 36 10 ? 10 C3 30 2 2 C3 6 C5 regenerated using: 1) C2 transfers (transketolase) 2) Condensations (transaldolase)! C6 9 CO2 Fixation is called “Calvin Cycle” 6 C5 + 6 C1 à 12 C3 30 6 36 10 2 10 C3 2 C3 30 6 C6 http://www.nobel.se/chemistry/laureates/1961/calvin-bio.html Photorespiration: Oxygenase Activity of Rubisco O2 competes with CO2 for enol form of RuBPi Km O2 350 µ M Km CO2 9 µ M Only 1 x 3PG formed Other product, Pi-glycolate, is salvaged through a complex series of reactions involving both peroxizomes and mitochondria! Fig. 20-38 10 Salvage Pathway of Pi-glycolate Photorespiration is a wasteful process, and is especially problematic at higher temperatures (above 28°C) At 25°C, the carboxylase activity is four times the oxygenase activity) Fig. 20-39 Function of Photorespiration? Oxygenase Activity of Rubisco? Km CO2 9 µ M Km O2 350 µ M Rubisco… …most likely evolved before atmosphere had O2 ! …retains ability to react with O2 ? Why? Photorespiration… …dominates if light levels are high à high O2 production …scavenges O2 to help prevent oxidative damage to cells under intense light conditions 11 CO2 Fixation by C4 Plants (Tropical) Tropical grasses such as sugar cane use a different pathway for CO2 fixation Short-time CO2 fixation with 14 CO2 leds to 14 C in C4 intermediates CO2 is fixed as follows: PEP + CO2 à OXAL (PEP carboxylase) Good summaries: http://methanogens .pdx.edu/boone/courses/BI336/BI336Lectures/200201/BI336Lec16.html See also Fig 20-40 http://138.192.68.68/bio/Courses/biochem2 /Photosynthesis/Photosynthesis2.html Advantage of C4 Plants CO2 fixation: photorespiration Depends upon CO2 :O2 ratio Air has ~ 3 x 10-4 atm (300 ppm) of CO2 biotin http://138.192.68.68/bio/Courses/biochem2/Photosynthesis/Photosynthesis2.html C4 plants use CO2 at PCO2 down to 1 to 2 x 10-6 atm (1 to 2 ppm). In C3 plants, CO2 fixation stops when PCO2 is 5 x 10 -5 atm (50 ppm). At 5 x 10 -5 atm, CO2 fixation rate = photorespiration rate. However, plants living in hot climates need to conserve water, which requires them to use low CO2 concentration (water is used in rubisco reaction!) The disadvantage of C4 plants is extra ATP used and a more complex pathway http://methanogens .pdx.edu/boone/courses/BI336/BI336Lectures/200201/BI336Lec16.html 12 Photoinhibition Photoinhibition: Too much light can cause problems for photosynthetic cells Destruction of RXN CTR occurs by side reactions of the Chla+. The P680+. (reaction center of photosystem II) is strongly oxidizing RXN CTR proteins are oxidatively damaged by Chla +. At high hv intensity, RXN CTR proteins turn over rapidly 13