Appendix A Metabolic Pathways

Appendix A Metabolic Pathways Glycolysis (Embden-Meyerhof Pathway) A-6 Pentose Phosphate Pathway A-8 Entner-Doudoroff Pathway A-9 Krebs Cycle A-10 Calvin-Benson Cycle A-11 A-5 Z02_BAUM7206_05_SE_APPA.indd 5 11/25/16 3:14 PM A-6 Appendix A H Energy Investment Stage H H C O H C OH HO C H H C OH H C OH H C OH 1 Hexokinase ATP ADP OH C O Phosphoglucoisomerase HO C H OH H C OH C OH H C OH C O H C O O H C OH HO C H H C H H H Glucose (6C) C C H 2 P H Glucose 6-phosphate (6C) P H Fructose 6-phosphate (6C) ATP Phosphofructokinase 3 ADP GLYCOLYSIS (Embden-Meyerhof Pathway): H Energy Investment Stage H C O C O Step 1 . Hexokinase transfers phosphate from ATP to carbon 6 of glucose, forming glucose 6-phosphate—a charged molecule. Since the cytoplasmic membrane is impermeable to ions, phosphorylated glucose cannot diffuse out of a cell. HO C H H C OH Step 2 . Phosphoglucoisomerase rearranges the atoms of glucose to form an isomer—fructose 6-phosphate. H C OH H C O Step 3 . Phosphofructokinase invests more energy by adding another phosphate group from ATP to form fructose 1,6-bisphosphate. P P H Fructose 1,6-bisphosphate (6C) Lysis Stage Aldolase 4 Lysis Stage Step 4 . Aldolase (fructose 1,6-bisphosphate aldolase) splits six-carbon fructose 1,6-bisphosphate into three-carbon glyceraldehyde 3-phosphate (G3P) and three-carbon dihydroxyacetone phosphate (DHAP). It is this cleavage that gives glycolysis its name. H H HO C O C O C H P H Dihydroxyacetone phosphate (DHAP) (3C) 5 Step 5 . Triose phosphate isomerase rearranges the atoms of DHAP to form another molecule of glyceraldehyde 3-phosphate. From this point, every step of glycolysis occurs twice—once for each of the three-carbon molecules. H C O H C OH H C O Triose phosphate isomerase P H Glyceraldehyde 3-phosphate (G3P) (3C) to Step 6 1 Z02_BAUM7206_05_SE_APPA.indd 6 11/25/16 3:14 PM Appendix A A-7 Energy Conserving Stage Energy Conserving Stage 2 P Glyceraldehyde6 3-phosphate dehydrogenase 2 NAD+ 2 NADH O C O H C OH H C O Step 6 . Glyceraldehyde-3-phosphate dehydrogenase catalyzes a reaction with two parts: (a) It oxidizes G3P, transferring electrons (and hydrogen) to NAD+ to form NADH and (b) it adds inorganic phosphate from the cytosol to G3P with a high-energy bond to form 1,3-bisphosphoglyceric acid. This two-part reaction is among the more important in glycolysis because it generates a molecule of NADH for each molecule of G3P and because it creates the first high-energy intermediate. P P H 1,3-bisphosphoglyceric acid (3C) (2 molecules) 2 ADP Phosphoglycerate kinase 7 2 ATP Step 7 . Phosphoglycerate kinase conserves the energy in the high-energy bonds in two molecules of ATP, yielding 3-phosphoglyceric acid molecules. O C OH H C OH H C O P H 3-phosphoglyceric acid (3C) (2 molecules) Phosphoglycerate mutase Step 8 . Phosphoglycerate mutase rearranges the atoms to form 2-phosphoglyceric acid. 8 O C OH H C O H C OH P H 2-phosphoglyceric acid (3C) (2 molecules) Enolase 9 H2O O H C OH C O Step 9 . Enolase removes a molecule of water from each substrate, forming a double bond and a high-energy bond with phosphate. Step 10 . Pyruvate kinase ends glycolysis by transferring energy to ATP, forming pyruvic acid. In the final analysis, two molecules of ATP are invested to yield four molecules of ATP—a net gain of two molecules of ATP—and two molecules of NADH. Pyruvic acid then undergoes respiration (when there is an inorganic, or rarely an extracellularly derived organic, final electron acceptor) or fermentation (when the final electron acceptor is an organic molecule from the cell). P NAD+ C H Phosphoenolpyruvic acid (PEP) (3C) (2 molecules) 2 ADP Pyruvate kinase 10 2 H C H Pyruvate dehydrogenase C C O C H Various enzymes H+ + NADH NAD+ H To Krebs cycle O C OH H C OH H C H H OH CoA H Acetyl-CoA (2C) Respiratory Conditions Fermentation Conditions H Pyruvic acid (3C) (2 molecules) Z02_BAUM7206_05_SE_APPA.indd 7 O CO2 CoA ATP O C NADH + H+ H C OH H C H H Ethanol (2C) and CO2 (1C) + CO2 OR Other OR fermentation products H Lactic acid (3C) 11/25/16 3:14 PM A-8 Appendix A H C O H C OH HO C H H C OH H C OH H C O Glucose-6-phosphate dehydrogenase 1 NADP+ P H Glucose 6-phosphate (6C) NADPH C O H C OH HO C H H C OH H C H C COOH Lactonase O 2 H2O O H C OH HO C H H C OH H C OH H C O H+ P H 6-phosphogluconic acid dehydrogenase CH2OH 3 NADP+ P CO2 NADPH C O H C OH H C OH H C O H 6-phosphogluconolactone (6C) P H 6-phosphogluconic acid (6C) Ribulose 5-phosphate (5C) 4 PENTOSE PHOSPHATE PATHWAY 5 Phosphopentose isomerase Phosphopentose epimerase Step 1 . Glucose-6-phosphate dehydrogenase oxidizes glucose 6-phosphate to 6-phosphogluconolactone by transferring hydrogen to NADP+, forming NADPH. CH2OH Step 2 . Lactonase adds hydroxide from a water molecule, forming 6-phosphogluconic acid. Step 3 . 6-phosphogluconic acid dehydrogenase oxidizes this intermediate (transferring hydrogen to another molecule of NADPH) and removes a molecule of carbon dioxide to form ribulose 5-phosphate. This five-carbon phosphorylated sugar is used in the synthesis of nucleotides, certain amino acids, and glucose (via photosynthesis). CHO C O H C OH HO C H H C OH H C OH H C OH H C O H C O P H P H Xylulose 5-phosphate (5C) Ribose 5-phosphate (5C) 6 Step 4 . Phosphopentose epimerase converts some molecules of ribulose 5-phosphate to xylulose 5-phosphate. Transketolase CH2OH Step 5 . Simultaneously, phosphopentose isomerase converts other molecules of ribulose 5-phosphate to ribose 5-phosphate. Step 6 . Transketolase catalyzes a reaction in which a two-carbon fragment from xylulose 5-phosphate is transferred to ribose 5-phosphate, forming seven-carbon sedoheptulose 7-phosphate and three-carbon glyceraldehyde 3-phosphate (G3P). CHO C O H C OH HO C H H C O H C OH H C OH H C OH H C O P H Glyceraldehyde 3-phosphate (3C) P H Sedoheptulose 7-phosphate (7C) 7 Step 7 . Transaldolase then transfers a three-carbon fragment from sedoheptulose 7-phosphate to G3P, yielding four-carbon erythrose 4-phosphate and forming six-carbon fructose 6-phosphate. Transaldolase CHO H C OH H C OH C O P Erythrose 4-phosphate (4C) 8 Step 8 . Transketolase transfers another two-carbon fragment from another molecule of xylulose 5-phosphate to erythrose 4-phosphate, forming another molecule of fructose 6-phosphate and another molecule of G3P. G3P enters glycolysis at step 6; fructose 6-phosphate can enter glycolysis at step 1 or may be converted into glucose 6-phosphate, which reenters the pentose phosphate pathway. CH2OH Transketolase O C H H C OH H C OH H C O HO CHO H C OH H C O P H Glyceraldehyde 3-phosphate (3C) Z02_BAUM7206_05_SE_APPA.indd 8 C P H Fructose 6-phosphate (6C) 11/25/16 3:14 PM Appendix A A-9 H C O H C OH HO C H H C OH H C OH H C O Glucose-6-phosphate dehydrogenase 1 NADP+ P H Glucose 6-phosphate (6C) NADPH C O H C OH HO C H H C OH H C H C COOH Lactonase O 2 H2O O P H+ H C OH HO C H H C OH H C OH H C O H 6-phosphogluconolactone (6C) P H 6-phosphogluconic acid (6C) 3 ENTNER-DOUDOROFF PATHWAY The first two steps of the Entner-Doudoroff pathway are the same as the first two steps of the pentose phosphate pathway: Step 1 . Glucose-6-phosphate dehydrogenase oxidizes glucose 6-phosphate to 6-phosphogluconolactone by transferring hydrogen to NADP+, forming NADPH. Step 2 . As in step 2 of the pentose phosphate pathway, lactonase adds hydroxide from a water molecule, forming 6-phosphogluconic acid. Step 3 . 6-phosphogluconic acid dehydrase removes a molecule of water to form a six-carbon molecule. (The enzyme in this step should not be confused with the similarly named 6-phosphogluconic acid dehydrogenase of the pentose phosphate pathway.) 6-phosphogluconic acid dehydrase H2O COOH C O HO C H H C OH H C OH H C O P H 2-keto-3-deoxy6-phosphogluconic acid (6C) 4 KDPG aldolase Step 4 . Aldolase splits 2-keto-3-deoxy-6-phosphogluconic acid into two three-carbon compounds: pyruvic acid and glyceraldehyde 3-phosphate (G3P). CHO H C OH H C O P H Glyceraldehyde 3-phosphate (3C) via glycolysis Step 5 . G3P is converted to pyruvic acid by steps 6 through 10 of Embden-Meyerhof glycolysis. 5 steps 6–10 COOH H C O C H H Pyruvic acid (3C) (2 molecules) Z02_BAUM7206_05_SE_APPA.indd 9 11/25/16 3:14 PM A-10 Appendix A KREBS CYCLE Pyruvic acid (3C) In a complex reaction with several parts, pyruvate dehydrogenase decarboxylates and oxidizes pyruvic acid (from the Embden-Meyerhof or Entner-Doudoroff pathways) and adds the remaining two-carbon acetic acid to coenzyme A, forming acetyl-CoA. It is this molecule that enters the Krebs cycle. Recall that for every molecule of glucose that enters glycolysis, two molecules of pyruvic acid are produced, necessitating two sets of Krebs cycle reactions. H HO C H CoA C C C C H H H O C C HO OH OH O CoA C C C H OH O 1 Citrate synthase HO C H H2O H Oxaloacetic acid (4C) 8 C C O O NAD C O C H + H H Acetyl-CoA (2C) NADH O Pyruvate dehydrogenase CO2 H+ + NADH O H CoA NAD+ Citric acid (6C) 2 Aconitase Malic acid dehydrogenase H H HO OH C C OH C C OH H Isocitric acid (6C) 7 Fumarase HO C O Malic acid (4C) H2O C O H C O OH O HO H H O O C C C C Krebs cycle Isocitric acid dehydrogenase OH H Fumaric acid (4C) Succinic acid FADH2 H FAD H O C C c-ketoglutaric acid O HO C C H dehydrogenase CoA OH H 2O Succinyl-CoA synthetase 5 H Succinic acid (4C) H O H C C H C H C GTP GDP NADH + CO2 H O H C C H C H OH O CoA + NAD+ 6 dehydrogenase NAD+ 3 4 HO C C c-ketoglutaric O acid (5C) OH NADH + CO2 CoA O Succinyl-CoA (4C) ADP Step 1 . Citrate synthase adds the two carbons of acetic acid from acetyl-CoA to oxaloacetic acid, forming citric acid. This step gives the Krebs cycle its alternate name—the citric acid cycle. Step 2 . Aconitase forms an isomer, isocitric acid, by removing a molecule of water and then adding another molecule of water back. Step 3 . Isocitric acid dehydrogenase oxidizes and decarboxylates six-carbon isocitric acid to five-carbon c-ketoglutaric acid; a molecule of NADH is formed in the process. Step 4 . c-ketoglutaric acid dehydrogenase oxidizes and decarboxylates c-ketoglutaric acid to form a four-carbon fragment that is attached to coenzyme A, forming succinyl-CoA. Z02_BAUM7206_05_SE_APPA.indd 10 ATP Step 5 . Succinyl-CoA synthetase forms four-carbon succinic acid and simultaneously phosphorylates GDP to form GTP. The latter molecule subsequently phosphorylates ADP to ATP. Step 6 . Succinic acid dehydrogenase oxidizes succinic acid to four-carbon fumaric acid, forming a molecule of FADH2. Step 7 . Fumarase rearranges the four carbons to form malic acid. Step 8 . Malic acid dehydrogenase oxidizes malic acid to reform oxaloacetic acid, completing the cycle and forming another molecule of NADH. NADH and FADH2 carry electrons to an electron transport chain. 11/25/16 3:14 PM Appendix A A-11 CALVIN-BENSON CYCLE Fixation of CO2 H H C H2O CO2 O HO C O H C OH H C O C O H C OH 1,5-bisphosphate H C OH H C O Ribulose- 1 carboxylase H C O H C OH H C O ADP P 2 P P Phosphoglyceric H acid kinase 1,3-bisphosphoglyceric acid H 3-phosphoglyceric acid (3C) (2 molecules) P O ATP P Reduction Glyceraldehyde3-phosphate 3 dehydrogenase Ribulose 1,5-bisphosphate (RuBP) (5C) P 14 Glucose synthesis C O H C OH H C O by reverse glycolysis Reduction Step 2 . Phosphoglyceric acid kinase phosphorylates phosphoglyceric acid at the expense of ATP to form 1,3-bisphosphoglyceric acid. NADPH NADP+ H Triose phosphate isomerase P CH2OH H 4 C O C O P H H Glyceraldehyde 3-phosphate (3C) Dihydroxyacetone phosphate Aldolase H CH2OH C ATP 13 Phosphoribulokinase O Phosphatase 6 HO C H H C OH H C OH H C O P H2O P O C O HO C H H C OH H C OH H C O C O C OH H C OH H C O C O C H H C OH H C O Phosphopentose epimerase HO 12 P H H Ribulose 5-phosphate Xylulose 5-phosphate Ribose-5-phosphate isomerase Step 9 . Phosphatase adds water and removes a phosphate group to form sedoheptulose 7-phosphate. H P C O H C OH 8 H C OH Aldolase H C O O H C OH H C OH H C O Step 10 . Transketolase combines this molecule with a molecule of G3P (from step 3) to form five-carbon ribose 5-phosphate and five-carbon xylulose 5-phosphate. P 10 Transketolase P Step 11 . Ribose-5-phosphate isomerase rearranges the atoms of ribose 5-phosphate to form its isomer—ribulose 5-phosphate. Erythrose 4-phosphate H C OH Step 8 . Aldolase rearranges the carbons of erythrose 4-phosphate and of a molecule of DHAP (from step 4), forming sedoheptulose 1,7-bisphosphate. 7 Transketolase H C P Fructose 1,6-bisphosphate (6C) H CH2OH C Step 7 . Transketolase combines fructose 6-phosphate with a molecule of G3P (from step 3) to form five-carbon xylulose 5-phosphate and four-carbon erythrose 4-phosphate. H 11 H Step 6 . Phosphatase adds water and removes a phosphate group, forming fructose 6-phosphate. H Fructose 6-phosphate (6C) CH2OH CH2OH P C H H Step 5 . Aldolase combines a molecule of G3P and a molecule of DHAP to form fructose 1,6-bisphosphate. H ADP O HO C H H C OH H C OH H C OH H C O H 2O P 9 Phosphatase P C O C O HO C H H C OH H C OH H C OH H C O P Step 12 . Phosphatase epimerase similarly rearranges the atoms of xylulose 5-phosphate, forming another molecule of ribulose 5-phosphate. Step 13 . Phosphoribulokinase phosphorylates ribulose 5-phosphate to regenerate ribulose bisphosphate (RuBP). P H H H Ribose 5-phosphate (5C) Sedoheptulose 7-phosphate (7C) Sedoheptulose 1,7-bisphosphate (7C) Z02_BAUM7206_05_SE_APPA.indd 11 Step 3 . Glyceraldehyde-3-phosphate dehydrogenase reduces (using NADPH) and removes one phosphate from 1,3-bisphosphoglyceric acid, forming glyceraldehyde 3-phosphate (G3P). Regeneration of RuBP Step 4 . Triose phosphate isomerase changes some molecules of G3P to dihydroxyacetone phosphate (DHAP). 5 Regeneration of RuBP Fixation of CO2 Step 1 . Ribulose-1,5-bisphosphate carboxylase adds CO2 and H2O to five-carbon ribulose 1,5-bisphosphate (RuBP), forming a six-carbon intermediate (not shown) that is immediately split into two, three-carbon molecules of 3-phosphoglyceric acid. Step 14 . For every three molecules of CO2 that enter the Calvin-Benson cycle (at step 1), one molecule of G3P leaves the cycle to be used for the synthesis of glucose via the reversal of the early reactions of glycolysis. 11/25/16 3:14 PM