The citric acid cycle (CAC) is the final common pathway for the oxidation of nutrients. It occurs in the mitochondria of cells. Acetyl-CoA from various sources enters the CAC and is oxidized to CO2, producing reduced cofactors that drive ATP synthesis. The 8-step cycle produces ATP, GTP, and reduced cofactors NADH and FADH2. Key enzymes and cofactors regulate the cycle in response to energy demands and product inhibition. Anaplerotic reactions maintain CAC intermediate levels.

1. Citric acid cycle Synthesis of heme. Hemoproteins © Department of Biochemistry (J.D.) 2011

2. Recommended intake of nutrients SAFA  5 % MUFA  20 % PUFA  5 % Essential FA: linoleic, α -linolenic Semiessential FA: arachidonic Essential AA: Phe, Trp, Val, Leu, Ile, Met, Thr, Lys, His Semiessential AK: Arg (childhood), Ala, Gln (metab . stress) 60 % 30 % 10 % Starch Lipids Proteins Percentage of energy intake/day Nutrient

3. ATP ATP ATP Phases of catabolism I II III Resp. ch. Acetyl-CoA Pyruvate Reduced cofactors NADH + H + , FADH 2 C O 2 Glucose Fatty acids Amino acids Saccharides Lipids Proteins Citric acid cycle

6. Compare different ways of pyruvate de c arboxyla tion pyruvate simple decarboxylation acetaldehyde acetic acid oxidative decarboxylation in vitro oxidative decarboxylation in vivo

8. (1) Decarboxylation of pyruvate thiazolium ring

10. (3) Transfer of acetyl to coenzyme A dihydrogen lipoate

11. (4) Transfer of 2H to NAD + via FAD

12. Balance reaction Pyruvate dehydrogenase is allosterically inhibited by end products: ac etyl-CoA + NADH CH 3 -CO-COOH + CoA-SH + NAD +  CO 2 + CH 3 -CO-S-CoA + NADH+H +

15. (2) Citrate  Isocitrate Reaction type: isomeration Enzyme: aconitase Cofactor: Fe-S Note: two-step-reaction, intermediate is cis -aconitate C C H 2 C O O H C O O H C H 2 H O C O O H C H C H 2 C O O H C H C O O H H O C O O H tertiary hydroxyl group secondary hydroxyl group citrate isocitrate

16. (2a) Dehydration of citrate citrate C C H 2 C O O H C O O H C H O C O O H H H H 2 O C C C O O H H C H 2 C O O H H O O C cis -aconitate

17. (2b) Hydratation of cis-aconitate stereospecific rea ction C H C H 2 C O O H C H C O O H H O C O O H C C C O O H H C H 2 C O O H H O O C cis -aconitate H 2 O isocitrate

18. Aconitase is inhibited by f luor o acet ate Dichapetalum cymosum ( see also Med. Chem. II, p . 65 ) FCH 2 COOH reacts with oxaloacetate to give fluorocitrate CAC is stopped LD 50 for human is 1 mg/kg rat poison

19. (3) Isocitrate  2-oxoglutarate Reaction type: dehydrogenation + decarboxylation Enzyme: isocitrate dehydrogenase Cofactor: NAD + Note: irreversible isocitrate 2-oxoglutarate

20. (4) 2-Oxoglutarate  succinyl-CoA Reaction type: oxidative decarboxylation Enzyme: 2-oxoglutarate dehydrogenase complex Cofactors: TDP, lipoate, CoA-SH, FAD, NAD + Note: irreversible , similar to pyruvate dehydrogenase reaction (five coenzymes) C H 2 C H 2 C O O H C C O O H O + N A D H + H + N A D + - C H 2 C H 2 C O O H C O S C o A + C O 2 2-oxoglutarate succinyl-coenzyme A thioester macroergic intermediate H S C o A

21. (5) Succinyl-CoA + GDP + P i Reaction type: substrate phosphorylation Enzyme: succinyl-CoA synthetase (succinate thiokinase) Cofactor: coenzyme A + C H 2 C H 2 C O O H C O S C o A + + G D P P i C H 2 C H 2 C O O H C O O H G T P succinyl-coenzyme A succinate origin of oxygen ? - coenzyme A

23. (5a) Addition of phosphate to succinyl-CoA mixed anhydride four oxygen atoms in phosphate P O O O O H C O O C H 2 C H 2 C O S C o A H S C o A C O O C H 2 C H 2 C O O P O O O succinyl-CoA succinylphosphate

24. (5b) Phosforylation of His in the active site of enzyme substituted phosphoamide N N H E n z y me C O O C H 2 C H 2 C O O P O O O C O O C H 2 C H 2 C O O succinylphosphate succinate phospho-His N N E n z y me P O O O H +

25. (5c) Phosforylation of GDP N N N N O H 2 N H O O H O H O P O O O P O O O N N E n z y me P O O O N N N N O H 2 N H O O H O H O P O O O P O O O P O O O guanosine diphosphate guanosine triphosphate N N H E n z y me H +

26. Distinguish -PO 3 2- HPO 4 2- (P i ) phosphate inorganic P O O O P O O O O H phosphoryl phosphate

27. GTP is quickly converted to ATP GTP + ADP ATP + GDP nucleoside-diphosphate kinase

28. (6) Succinate  fumarate Reaction type: dehydrogenation (-CH 2 -CH 2 - bond) Enzyme: succinate dehydrogenase Cofactor: FAD C O O H C H 2 C H 2 C O O H + FAD C C C O O H H H O O C H - II - II - I - I + F A D H 2 succinate fumarate

29. M alonate is c ompetitiv e inhibitor of succinate dehydrogenase Do not confuse : malon ate × mal ate C O O C H 2 C H 2 C O O C O O C H 2 C O O succinate malonate

30. (7) Fumarate  L-malate Reaction type: hydration Enzyme: fumarase Cofactor: none Notes: 1) addition of water on double bond is stereospecific 2) hydration is not redox reaction - II + H 2 O C O O H C H C H 2 H O C O O H 0 fumarate L-malate  = -II  = -II C C C O O H H H O O C H - I - I

31. Distinguish : hydrol ysis × hydrat ion substr a t e + H 2 O  substr ate + H 2 O  + Hydrol ysis = decomposition of substrate by the action of water ( typical in ester s , amid es , peptid es , gly c osid es , anhydrid es ) Hydrat ion = a d di tion of water ( to unsaturated substrates) produ c t 2 OH produ c t 1 H produ c t OH H

32. Compare : Hydration of fumarate in vivo and in vitro in vivo : ( enzymatic reaction) : only one enantiomer is formed (L-malate) in vitro: formation of racemate C C C O O H H H O O C H H H O H H O C C O O H C H 2 C O O H O H H C C O O H C H 2 C O O H H H O L-malate D-malate C C C O O H H H H O O C H O H Enzyme Substrate

33. (8) L-malate  oxalacetate Reaction type: dehydrogenation Enzyme: malate dehydrogenase Cofactor: NAD + C O O H C H C H 2 H O C O O H + N A D + C O O H C C H 2 C O O H O + N A D H H + + L-malate oxaloacetate

37. Key enzymes for regulation of citrate cycle a allosteric inhibitor b feed-back inhibito r (inhibition by a product) c allosteric a c tiv a tor  succinyl-CoA b  2-OG dehydrogenase  ADP c   Isocitrate dehydrogenase  citrate b  Citrate synthase  acetyl-CoA b   Pyruvate dehydrogenase Other effect NADH a ATP a Enzyme

39. Carboxylation of pyruvate (biotin) B i o t i n C O O H H 3 C C O C O O H B i o t i n H C H 2 C O C O O H H O O C pyruvate oxaloacetate pyruvate carboxylase

40. Reductive carboxylation of pyruvate Reaction is more important for production of NADPH for reductive synthesis ( FA , cholesterol) malic enzyme (malate dehydrogenase decarboxylating) C O O H C C H 3 O C O O NADP H + H C O O H C C H 2 H O H C O O H L-malate NADP

42. Catabolic processes - entries into the cycle Leu, Ile Phe, Tyr, Lys, Trp oxaloacetate fumarate succinyl-CoA 2-oxoglutarate CC acetyl-CoA Phe, Tyr ureosynthesis purine synthesis Ile, Val, Met, Thr Arg, Glu, Gln, His, Pro Asp, Asn pyruvate Ala, Cys, Gly, Ser, Thr, Trp fatty acids glucose

43. Anabolic processes – intermediates for syntheses citrate Fatty acids, steroids Intermediates drawn off for biosyntheses are replenished by anaplerotic reactions oxaloacetate succinyl-CoA 2-oxoglutarate CC malate porphyrines, heme (collector of amino groups) pyruvate + NADPH aspartate purine pyrimidine phosphoenolpyruvate g l u co se glutamate

44. CAC a nd the synt hesis of lipid s ATP TAG malate FA synthesis CAC mitochondria citrate cytosol citrate oxaloacetate acetyl-CoA malic enzyme C O 2 N A D P H H + + + + pyruvate

45. CAC and t ransamination oxaloacetate 2-oxoglutarate CAC aspartate glutamate

46. Vitamins necessary for CAC Try to complete Pantothenic acid Thiamin Niacin Riboflavin Reaction in citrate cycle Vitamin

47. Relationships among the major energy metabolism pathways GLYCOGEN Glucose FAT STORES TRIACYLGLYCEROLS FATTY ACIDS PROTEINS Gluco genic AA ( non-essent .) Gluco genic AA ( essentia l) Keto genic AA ( essentia l) KETONE BODIES Glycerol × Pyruvate × × × × ACETYL-CoA Citrate cycle OXIDATIVE PHOSPHORYLATION ATP

48. Interconversions between nutrients × × pyruvate dehydrogenase reaction is irreversible ketogenic AA and most mixed AA are essential Lipids  amino acids in excess of proteins Amino acids  lipids pyruvate and CAC intermediate provide arbon skeleton for some amino acids Glucose intermediates  AA most AA are glucogenic Amino acids  glucose not possible, pyruvate dehydrogenase reaction is irreversible Lipids  glucose very easy and quickly Sugars  lipids Commentary Interconversion

49. Saccharides are the most universal nutrients – the overdose is transformed in the fat stores, carbon skelet of non-essential amino acids may originate from saccharides. Triacylglycerols exhibit the highest energetic yield – but fatty acids cannot convert into saccharides or the skelet of amino acids. Amino acids represent the unique source of nitrogen for proteosynthesis that serves as fuel rather when the organism is lacking in other nutrients - glucogenic amino acids can convert into glucose, a overdose of diet protein may be transformes in fat stores. The metabolism of nutrients is sophistically controlled with different mechanisms in the well-fed state (absorptive phase), short fasting (post-absorptive phase), and in prolonged starvation . It also depends on energy expenditure (predominantly muscular work) – either of maximal intensity (anaerobic, of short duration only) or aerobic work of much lower intensity (long duration).

50. The tissues differ in their enzyme equipment and metabolic pathways * K B = keto ne bodies - - - + - +++ Gluconeogenesis +++ + +++ + +++ + Glycolysis - + +++ + + - KB oxidation * - - - - - + Ketogenesis - +++ ± ± ± +++ FA synthesis - - ++ + - ++ FA β -oxidation - + + + + + CAC Ery Adipocyte Muscles Kidneys CNS Liver Pathway

51. Cellular compartmentation of major metabolic pathways Proteosynthesis on ribosomes (translation of mRNA) Rough ER Glycolysis, gluconeogenesis, gly c ogen  , pentose c ycle, transamination, synt hesis of FA / urea / urate / heme ; ethanol oxidation Cytosol Formation and decomposition of H 2 O 2 and peroxides Peroxisomes Glycosylation of proteins, sorting and export of protein s Golgi apparat. transport of molecules/ions/information = transporters/channels/ receptor s Cell membrane Non-specific hydrolysis of various substrates Lysosomes Synthesis of TAG / chol., FA desaturation, hydroxylations of xenob ioti cs Smooth ER Oxidative decarboxylation of pyruvate, CAC, RCh, FA β - oxidation, synthesis of KB / urea / heme / Gln , AST rea ction Mitochondria DNA replication, RNA synthesis (= DNA transcription) Nucleus

52. Metabolic effects of insulin  Pentose phosphate cycle  Synthesis of fatty acids  Glycogenolysis  Synthesis of glycogen  Gluconeogenesis  Glycolysis  Glucose phosphorylation Liver  Lipolysis  Synthesis of TG  Hydrolysis of TG in lipoproteins  Ox. decarboxylation of pyruvate  Pentose phosphate pathway  Glycolysis  Glucose uptake (GLUT 4) Adipose tissue  Synthesis of proteins  Glycogenolysis  Synthesis of glycogen  Glycolysis  Glucose uptake (GLUT 4) Muscle

53. Metabolic effects of glucagon (not on muscles)  Lipolysis (HSL, hormone sensitive lipase) Adipocytes  Oxidation of fatty acids  Synthesis of fatty acids  Glycogenolysis  Synthesis of glycogen  Gluconeogenesis  Glycolysis Liver

54. Biosynthesis of heme ~ Hemoproteins

55. Heme Prostetic group of many proteins (hemoglobin, myoglobin, cytochromes) Synthesis in the body: 70-80 % in erythroid cells in bone marow - hemoglobin 15 % liver – cytochroms P450 and other hemoproteins Heme consists of porphyrin ring coordinated with iron cation

57. Synthesis of  -aminolevulinate (ALA) ALA-synthase C H 2 N H 2 C O O H H O O C C H 2 C H 2 C S O C o A glycin succinyl-CoA H O O C C H 2 C H 2 C O C H 2 N H 2 H O O C C H 2 C H 2 C O C H N H 2 C O O H 2-amino-3-oxoadipate H S C o A - CO 2  -aminolevulinate (5-amino-4-oxobutanoic acid) pyridoxalphosphate is cofactor mitochondria

58. ALA-synthase is the rate-controlling enzyme of porphyrine biosynthesis ALA-synthase - is inhibited by heme (allosteric inhibition) - synthesis of enzyme is repressed by heme - is induced by some drugs (barbiturates, phenytoin, griseofulvin) Half-life about 1 hour

59. Why some drugs increase activity of ALA-synthase? For biotransformation (hydroxylation) of xenobiotics is necessary cytochrome P-450 Indu ction of enzyme synthesis

60. Condensation to substituted pyrrole δ -aminolevulinate cytosol C O O H N O H H H H O N H 2 C O O H H H - 2 H 2 O porphobilinogen N N H 2 C O O H C O O H H

61. Condensation of porphobilinogen Under physiological circumstances , due to the presence of a protein modifier called co-synthase, uroporphyrinogen III with an asymmetrical arrangement of side chains of the ring D is formed. Only traces of symmetrical uroporphyrinogen I are produced Porphobilinogen uroporphyrinogen I (minor product) uroporphyrinogen III (main product)

62. Condensation of porphobilinogen cytosol N N H 2 C O O H C O O H H porphobilinogen 4 N H 3 4 H N H N N N C O O H H O O C C O O H H O O C H O O C H O O C C O O H C O O H H H uroporphyrinogen III methylene bridge A B C D

63. Decarboxylation of four acetates – formation of methyl groups cytosol H N H N N N C O O H H O O C C O O H H O O C H O O C H O O C C O O H C O O H H H H N H N N N C H 3 H 3 C C O O H H O O C H 3 C H O O C C H 3 C O O H H H 4 CO 2 uroporphyrinogen III coproporphyrinogen III

64. Formation of vinyl groups from two propionates mitochondria H N H N N N C H 3 H 3 C C O O H H O O C H 3 C H O O C C H 3 C O O H H H coproporphyrinogen III - 4H - 2 CO 2 H N H N N N C H 3 H 3 C C O O H H O O C H 3 C C H 3 H H protoporphyrinogen IX

65. Formation of conjugated system colourless red mitochondria H N H N N N C H 3 H 3 C C O O H H O O C H 3 C C H 3 H H protoporphyrinogen IX - 6 H N N N N C H 3 H 3 C C H 3 H 3 C C O O H H O O C H protoporphyrin IX H methyne (methenyl) bridge

66. Heme is coloured chelate with Fe 2+ protoporphyrin IX F e heme H N N N N C H 3 H 3 C C H 3 H 3 C C O O H H O O C H ascorbate F e 3+ - 2H + N N N N C H 3 H 3 C C H 3 H 3 C C O O H H O O C F e 2+

67. CO and bilirubin are formed by the degradation of heme oxidative cleavage (heme oxygenase) CO + biliverdin bilirubin carbonyl-hemoglobin 3 O 2 3 NADPH+H + more details in the 4 th semest e r

69. Hemoproteins Transport of O 2 in blood Store of O 2 muscle Decomposition of H 2 O 2 Decomposition of peroxides Components of resp. chain H ydroxyla tion Desatur ation of FA Fe 2+ Fe 2+ Fe 2+  Fe 3+ Fe 2+  Fe 3+ Fe 2+  Fe 3+ Fe 2+  Fe 3+ Fe 2+  Fe 3+ Hemoglobin Myoglobin Catalase Peroxidase Cytochroms Cytochrom P-450 Desaturas es of FA Function Redox state of Fe Protein

72. Quaternary structure of hemoglobin 4 O 2 α 1 α 2 β 1 β 2 deoxygenated hemoglobin (2,3-bisphosphoglycerate) T-conformation 4 O 2 2 H + 2 H + α 2 α 1 β 2 β 1 oxyhemoglobin R-conformation α 1 O 2 α 2 O 2 β 1 O 2 β 2 O 2

75. Language note : How to express two redox states of iron -i -o Infix iron(III) chloride iron(II) chloride New English example ferr i c chloride ferr o us chloride Old English example ferr i chloridum ferr o si chloridum Latin example hem i globin (methemoglobin) hem o globin English example Fe 3+ Fe 2+

76. Heme as cofactor of oxidoreductases transfers one ele c tron Examples of hem e enzym es C atalas e : H 2 O 2  ½ O 2 + H 2 O Myeloperoxidas e : H 2 O 2 + Cl - + H +  HClO + H 2 O

80. Desaturation of fatty acids ∆ 9 desaturas e H 3 C C O O H C O O H H 3 C C O O H C H 3 9-10 desaturation (humans) 12-13 desaturation (plants) stearic acid 18:0 oleic acid 18:1 (9) linoleic acid 18:2 (9,12)

81. Desaturation of FA requires cytochrome b 5 h ydroxylation at C-10 dehydrat ion