Question

QUESTION 5 This question explores the Calvin cycle in plants. A summary of the three stages of CO, assimilation in photosynthetic organisms is shown below (Fig. 20-31 from the text book). All the reactions of the Calvin cycle in detail are shown on the last page. Only the first three reactions are directly involved in carbon-fxation, assimilation and reduction, to Stage 3: ATP3 Regeneration of (3) Stage 1a Ribulose 1.5 e (GAP). The rest of the pathway results in the regeneration of ribulose ,5-bisphosphate (RuBP), the molecule that CO, reacts with at the beginning of the cycle. Stage 21 NADP We should be able to make some reasonable predictions on certain reactions of the Calvin cycle based on what we know of the glycolysis and the T cycle. G) NADPH+* ADP 6) 6 a) Reaction : This first reaction involving CO, is a complicated reaction and is not similar to any reaction we have seen in glycolysis, TCA or the pentose phosphate pathway. Do not wory about the details. b) Reaction 2: Here, ATP is used to phosphorylate a carboxlate group. i. Why is ATP used to donate a phosphoryl group, and not PI? ii. Why is this step of phosphorylating a carboxylate group necessary? BIOL201 2018W2-all rights reserved Problem Set g Page 3 ofs c) Reaction 3: In this reaction, a carbon atom is reduced. i. Which carbon atom is reduced? ii. How can you discern the oxidation/reduction state of a carbon atom in this reaction? ii. Which groups serve as the nucleophile and electrophile in this reaction? d) Reaction 4A and 4B:the to reactions are identical, and they use two of the six GAP molecules generated in Reaction 3. Which Glyco reaction is this reaction similar to? e) Reaction 5,7, 8, 10: All four of these reactions involve the making andor breaking of carbon-carbon bonds. i. Reaction 5 is the reverse of which Glyco reaction? i. Which of these reactions require thiamine pyroposphate (TPP) as a cofactor and which do not? Explain f) Reaction , 12, 13: What types of reactions are these? g) Reaction 14: ATP is used to phosphorylate an alcoholic hydroxyl (OH) group, why is ATP used as the source of h) Several of the reactions in the Calvin cycle are identical to those in glycolysis, yet they proceed in the opposite ) Name the classes of enzymestttalyze reactions 2 through 14 the phosphoryl group here, and not a Pi? direction. How is this possible in the same cell?

Answer 1

a) The reaction of Calvin cycle involves the conversion of ribulose-5-phosphate with carbon-dioxide into 12 molecules of 3-phosphoglycerate and then they are converted to 12 molecules of glyceraldehyde-3-phosphate. It is then converted into 2 molecules of glyceraldehyde-3-phosphate and 6 molecules of ribulose- 5, bisphosphate. It is then converted to ribulose-1,5-bisphosphate after combining with a molecule of carbon dioxide.

b) The difference between a phosphoryl group and a phosphate group is given below as follows like

P-O phosphoryl group phosphate group|

i)The phosphoryl group does not contain an oxygen atom and can be used for the energy derivation in the conversion of 3-phosphoglycerate to glyceraldehyde-3-phosphate with generation of NADP⁺ from NADPH which relieves the inorganic phosphate group later in the reaction.

ii)The reaction step of phosphorylating a carboxyl group is depicted in the form of diagram given below as follows like

Reduction Phase: catalyzed in two steps он OOC-CH-CH2-OPO32 3-phosphoglycerate phosphoglycerate kinase о он ATP 203PO-C-CH-CH2-OPO32 ADP 1,3-bisphosphog ycerate NADPH glyceraldehyde-3-phosphate dehyhdrogenase NADP+ он The main product of the Calvin Cycle O-CH-CH-CH2-OPO32 glyceraldehyde- 3-phosphate

The conversion of 3-phosphoglycerate takes place into 1,3 bisphosphoglycerate which is converted further into glyceraldehyde-3-phosphate. The formation of 1,3 bisphosphoglycerate requires the addition of a phosphate group to the carboxyl functional group and addition of phosphate to the hydroxyl group at the end of the metabolite 3-phosphoglycerate.

c)i) The conversion of 3-phosphoglycerate to glyceraldehyde-3-phosphate involves the reduction of the carboxyl group to aldehyde group in this metabolite molecule.The oxidation of CHOH which is the 3rd carbon atom in the metabolite ribulose-1,5 bisphosphate takes place to form the metabolite 3 phosphoglycerate.

ii) The oxidation and reduction involves the conversion of carboxyl group to the aldehyde group in the metabolite 3-phosphoglycerate to form glyceraldehyde-3-phosphate.

iii)The enolate ion is the nucleophile and the carbonyl ion is the electrophile in the calvin benson cycle. It is given below in the diagram as follows namely:

HO--H

d)The reactions of Calvin-Benson cycle and pentose phosphate pathway are given below in the form of a table as follows:

RuBP Phosphoribulokinase (PRK) Rru_A2404 (cbbP) Ribulose bisphosphate carboxylase/oxygenase Rubisco) Rru_A2400 (cbbM) ADP ATP 3PG ATP Ru5P Ribulose 5-phosphate epimerase (RPE) Rru_A2402 (cbbE) Ribose 5-phosphate isomerase (RPI) RruA1359 (piB), A1334, A1828 ADP Transketolase (TKL) RSP Rru_A2405 (cbbT), A059:s S7P Phosphoglycerate kinase (PGK) Rru_A0221 (cbbK) X5P 1,3-BPG G3P Sedoheptulose-1,7-bisphosphatase (SBPase) Rru_A2409 (glpX)? NADPH SDP NADP+P E4P Fructose-bisphosphate aldolase (FBA) Rru_A0596 (cbbA), A1345, A2509 Transketolase (TKL) Rru_A2405 (cbb), A0595 Triosephosphate isomerase (TPD)Glyceraldehyde-3-phosphate dehydrogenase (GAPDH) Rru A0222 (cbbG) G3P Rru_A1358 (tpiA), A1889 DHAP G3P F6P Fructose-bisphosphate aldolase (FBA) Rru A0596 (cbbA), A1345, A2509 Fructose bisphosphatase (FBPase) Rru_A2403 (cbbF) FBP

Two molecules of glyceraldehyde-3 phosphate are used for the formation of sugar glucose after generating dihydroxyacetone phosphate by the action of enzyme triose phosphate isomerase.

e)i)The conversion of 3-phosphoglycerate to 1, 3 bisphospoglycerate and then the conversion to glyceraldehyde-3-phosphate are the reverse reactions of glycolysis. The reactions of glycolysis are given below as follows namely-

ii)Thiamine pyrophosphate is used in the transketolase reaction which transfers a two carbon unit from a ketose to an aldolase in the pentose phosphate pathway and calvin-benson cycle. The reaction of calvin cycle is depicted below along with pentose phosphate pathway as follows:

H-C-O- HO-C-H Dihydroxyacetone H-C-OH H-C-O- ATP ADP H-C-OH HO-C-H H-C-OH H phosphate c#0 ATP ADP HO-C-H H CH HO-C-H Fructose phosphate H-COHH-OH H-C-OH н-с-он Н-С-ОН H-C-O u Hexokinase Phosphoglucose H-C-OHo kinase но H-C-O-P-O H-C-O-P-O нон H-C-O Glucose 6-phosphate Fructose 6-phosphate Fructose 1, 6-bisphosphate Glyceraldehyde 3-phosphate Glucose H-С-О-Р-О NAD + P Glyceraldehyde 3-phosphate dehydrogenase GLYCOLYSIS NADH H 2X O-P-O ATP ADP O ATP ADP H-C-O-P-O H-C-O H-C Enolase H-C-OHO phosphoglycerateH-C-o ruvate H-C-H H-C-O- mutase Phosphoenolpyruvate (PEP) 2-Phosphoglycerate 3-Phosphoglycerate 1,3-Bisphosphoglycerate Pyruvate

CO2 DHAPPGAPEP Ru5PRuBP PGA BPGA PEP → Trp, Tyr, Phe GAP R5P S7P GAP + DHAP Pyruvate Ala, Val, lle Acetyl-CoA Xu5P GAP FBP SBP E4P F6P Fatty acid synthesis Calvin cycle DHAP G6P-G 1 P ADP-Glc → Starch PLASTID DHAP S6PSucrose GAP F6P CYTOSOL

f)Reactions 11, 12 ad 13 involve the pentose phosphate pathway metabolites which combine with glyceraldehyde-3-phosphate to generate ribulose-5-phosphate in the Calvin -Benson cycle.

g)The phosphoryl group transfer involves the transfer of phosphate without oxygen atom to the CH₂OH functional group present in the 3-phosphoglycerate molecule to form glyceraldehyde-3-phosphate molecule.

h)The reactions in the calvin cycle proceed in the opposite direction due to the action of certain enzymes as compared to the glycolytic pathway.

i)The enzymes are phosphoribulokinase, ribulose-bisphosphate carboxylase, phosphoglycerate kinase, glyceraldehyde-3-phosphate dehydrogenase in the calvin -benson cycle.