User:J G Campbell/sandbox

=Random Carbon fixation stuff=
 * Tar baby
 * Carbon fixation
 * Fructose-bisphosphate aldolase
 * List of EC numbers
 * Enzyme infobox
 * User:BogBot/logs/Task 01/2009-08-09a

Calvin cycle
The Calvin cycle has thirteen reactions catalyzed by eleven enzymes. It shares five enzymes with gluconeogenesis and three with the pentose phosphate pathway. The remaining three enzymes are largely exclusive to the Calvin cycle. The characteristic enzyme of the Calvin cycle, rubisco, catalyzes the carboxylation of ribulose 1,5-bisphosphate (RuBP). Rubisco also catalyzes a fourteenth reaction, the oxygenation of RuBP, initiating photorespiration which bleeds carbon and energy from the cycle and reduces its efficiency. The Calvin cycle maintains a hexose phosphate pool, a pentose phosphate pool, and a triose phosphate pool.

The Calvin cycle is autocatalytic because it can bootstrap itself from just triose phosphate, carbon dioxide, NADPH, and ATP. Autocatalysis typical of autotrophic carbon fixation pathways. The Calvin cycle can be divided, for convenience, into three phases.

Carboxylation phase
1, 1a. rubisco (EC 4.1.1.39)
 * RuBP + CO2 + H2O --> 2(3-PGA)
 * RuBP + O2 --> 3-PGA + 2-phosphoglycolate

Reduction phase
The reduction phase reduces 3-PGA to GAP, contributes GAP and DHAP to the triose phosphate pool, and contributes fructose 6-phosphate to the hexose phosphate pool. The reduction phase is just gluconeogenesis.

2. phosphoglycerate kinase (EC 2.7.2.3)
 * 3-PGA + ATP <-> 1,3-bisphosphoglycerate + ADP

3. glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.13) and (EC 1.2.1.59)
 * 1,3-bisphosphoglycerate + NADPH + H(+) <-> GAP + NADP(+) + Pi

3a. glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12)
 * 1,3-bisphosphoglycerate + NADH + H(+) <-> GAP + NAD(+) + Pi

4. triose-phosphate isomerase (EC 5.3.1.1)
 * GAP <-> DHAP

5. fructose-bisphosphate aldolase (EC 4.1.2.13)
 * DHAP + GAP <-> fructose 1,6-bisphosphate

6. fructose 1,6-bisphosphatase (EC 3.1.3.11)
 * fructose 1,6-bisphosphate + H2O --> fructose 6-phosphate + Pi

Regeneration phase
The regeneration phase uses fructose 6-phosphate and triose phosphate to regenerate RuBP, and contributes xylulose 5-phosphate, ribose 5-phosphate, and ribulose 5-phosphate to the pentose phosphate pool.

7. transketolase (EC 2.2.1.1)
 * GAP + fructose 6-phosphate <-> xylulose 5-phosphate + erythrose 4-phosphate

8. fructose-bisphosphate aldolase (EC 4.1.2.13)
 * DHAP + erythrose 4-phosphate <-> sedoheptulose 1,7-bisphosphate

9. sedoheptulose-bisphosphatase (EC 3.1.3.37)
 * sedoheptulose 1,7-bisphosphate + H2O --> sedoheptulose 7-phosphate + Pi

10. transketolase (EC 2.2.1.1)
 * GAP + sedoheptulose 7-phosphate <-> xylulose 5-phosphate + ribose 5-phosphate

11. ribulose-phosphate 3-epimerase (EC 5.1.3.1)
 * xylulose 5-phosphate <-> ribulose 5-phosphate

12. ribose-5-phosphate isomerase (EC 5.3.1.6)
 * ribose 5-phosphate <-> ribulose 5-phosphate

13. phosphoribulokinase (EC 2.7.1.19)
 * ribulose 5-phosphate + ATP --> RuBP + ADP

Intermediates

 * 1) RuBP
 * 2) 3-PGA
 * 3) 2-phosphoglycolate
 * 4) 1,3-bisphosphoglycerate
 * 5) GAP
 * 6) DHAP
 * 7) fructose 1,6-bisphosphate
 * 8) fructose 6-phosphate
 * 9) xylulose 5-phosphate
 * 10) erythrose 4-phosphate
 * 11) sedoheptulose 1,7-bisphosphate
 * 12) sedoheptulose 7-phosphate
 * 13) ribose 5-phosphate
 * 14) ribulose 5-phosphate

Sugars
Calvin cycle sugars in linear form
 * 1) D-glyceraldehyde: (2R)-2,3-dihydroxypropanal
 * 2) dihydroxyacetone: 1,3-dihydroxypropan-2-one
 * 3) D-erythrose: (2R,3R)-2,3,4-trihydroxybutanal
 * 4) D-ribose: (2R,3R,4R)-2,3,4,5-tetrahydroxypentanal
 * 5) D-ribulose: (3R,4R)-1,3,4,5-tetrahydroxypentan-2-one
 * 6) D-xylulose: (3S,4R)-1,3,4,5-tetrahydroxypentan-2-one
 * 7) D-fructose: (3S,4R,5R)-1,3,4,5,6-pentahydroxyhexan-2-one
 * 8) D-sedoheptulose: (3S,4R,5R,6R)-1,3,4,5,6,7-hexahydroxyheptan-2-one

Cyclic forms of fructose
 * alpha-D-fructofuranose: (2S,3S,4S,5R)-2,5-bis(hydroxymethyl)oxolane-2,3,4-triol
 * beta-D-fructofuranose: (2R,3S,4S,5R)-2,5-bis(hydroxymethyl)oxolane-2,3,4-triol
 * alpha-D-fructopyranose: (2S,3S,4R,5R)-2-(hydroxymethyl)oxane-2,3,4,5-tetrol
 * beta-D-fructopyranose: (2R,3S,4R,5R)-2-(hydroxymethyl)oxane-2,3,4,5-tetrol

Glucose
 * D-glucose: (2R,3S,4R,5R)-2,3,4,5,6-pentahydroxyhexanal
 * alpha-D-glucopyranose: (2S,3R,4S,5S,6R)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol
 * beta-D-glucopyranose: (2R,3R,4S,5S,6R)-6-(hydroxymethyl)oxane-2,3,4,5-tetrol

GAPDH articles
Willow
 * glyceraldehyde-3-phosphate dehydrogenase (phosphorylating) (EC 1.2.1.12) phosphorylating; glycolysis/gluconeogenesis in eukaryotes, bacteria; Calvin cycle in purple bacteria
 * glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) (EC 1.2.1.13) Calvin cycle
 * glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (EC 1.2.1.59) phosphorylating; Calvin cycle in cyanobacteria; glycolysis/gluconeogenesis in cyanobacteria, archaea
 * glyceraldehyde-3-phosphate dehydrogenase (ferredoxin) (EC 1.2.7.6) non-phosphorylating

New redirect
 * glyceraldehyde-3-phosphate dehydrogenase (NAD(P)+) (phosphorylating) (EC 1.2.1.59)

Not Willow
 * glyceraldehyde-3-phosphate dehydrogenase (NADP+) non-phosphorylating; glycolysis only, in plants, algae, bacteria
 * glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12)
 * GAPDHS (EC 1.2.1.12)

Plastid related articles

 * Chloroplast
 * Chloroplast membrane
 * Plastid
 * Stroma (fluid)
 * Thylakoid

=Fructose-bisphosphate aldolase=
 * See article.

=Aldolase (disambiguation)=
 * See article.

=Glyceraldehyde-3-phosphate dehydrogenase (NADP+)=
 * See article.

=Glyceraldehyde-3-phosphate dehydrogenase (disambiguation)=
 * See article.

=Glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating)=
 * See article.

Reactions
Glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) catalyzes
 * GAP + NADP+ + Pi 1,3-bisphosphoglycerate + NADPH + H+

In the Calvin cycle
 * RuBP + CO2 + H2O → 2(3-PG)
 * 3-PG + ATP 1,3-bisphosphoglycerate + ADP
 * 1,3-bisphosphoglycerate + NADPH + H+ GAP + NADP+ + Pi

Triose-phosphate isomerase maintains DHAP and GAP in near equilibrium, producing the mixture called triose phosphate (TP)
 * GAP DHAP

=Scratch= weird URL