Enzymes 1


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Enzymes 1

  1. 1. Enzymes I  Department of Biochemistry, FM MU, 2011 (J.D.) General features , c ofa ctors
  2. 2. Literatur e for Biochemi stry I <ul><li>Lecture files on is.muni.cz. </li></ul><ul><li>Tomandl J., Táborská E.: Biochemistry I – Semin ars . MU, 200 8. </li></ul><ul><li>Harvey R.A., Ferrier D.R.: Biochemistry . 5th ed., Lippincott Williams & Wilkins, 2011. </li></ul>
  3. 3. General features of enzymes <ul><li>bio catalysts </li></ul><ul><li>different types of proteins / also RNA (ribozyme) </li></ul><ul><li>with covalently attached prosthetic group and/or metal cation, </li></ul><ul><li>oligomeric / multienzyme complexes / associated with membranes etc. </li></ul><ul><li>different distribu tion in cell and in the body, make i s oform s (i s oenzym es ) </li></ul><ul><li>s pecific ( towards substr ate and reaction ) , highly effective </li></ul><ul><li>work under mild conditions </li></ul><ul><li>in vivo - can be regulated in two ways </li></ul><ul><li>in vitro - sensitive to many factors </li></ul>CAUTION: peptidyltransferase is ribozyme (AK) n -tRNA 1 + AK-tRNA 2  tRNA 1 + (AK) n+1 -tRNA 2 rRNA
  4. 4. Enzymes are highly efficient catalysts <ul><li>decrease activation energy  increase the reaction rate </li></ul><ul><li>much more efficient than other (inorganic) catalysts </li></ul><ul><li>remain unchanged after reaction </li></ul><ul><li>do not alter equilibrium constant K </li></ul><ul><li>in vitro sensitive to many factors </li></ul>
  5. 5. Enzymes work under mild conditions <ul><li>narrow temperature range around 37 °C </li></ul><ul><li>over 50 °C become denaturated = inactivated </li></ul><ul><li>narrow pH range  pH optimum </li></ul><ul><li>most intracellular enzymes have pH optima around 7 </li></ul><ul><li>digestion enzymes function in rather stronger acidic / alkaline environment (pepsin 1-2, trypsin ~ 8) </li></ul>
  6. 6. Enzymes can be regulated (see the lecture Enzym es II ) <ul><li>Activity of enzyme </li></ul><ul><li>a ctivators </li></ul><ul><li>inhibitors </li></ul><ul><li>covalent modification (phosphorylation ) </li></ul><ul><li>Quantity of enzym e </li></ul><ul><li>regula tion of proteosynt hesis a nd proteol ysis of enzyme </li></ul><ul><li>some hormones act as indu cers × repres s or s </li></ul>
  7. 7. Dual specifity of enzymes towards: <ul><li>Reaction </li></ul><ul><li>catalyze just </li></ul><ul><li>one type of reaction </li></ul><ul><li>Substrate </li></ul><ul><li>work with one substrate </li></ul><ul><li>(or group of similar substrates) </li></ul><ul><li>often stereospecific </li></ul>
  8. 8. Enzymes are stereospecific catalysts <ul><li>there are two types of stereospecific conversions: </li></ul><ul><li>non-chiral substrate  chiral product (one enantiomer) pyruvate  L-lactate fumarate  L-malate </li></ul><ul><li>chiral substrate (one enantiomer)  product </li></ul><ul><li>L-alanine  pyruvate (D-alanine does not react) </li></ul><ul><li>D-glucose   pyruvate (L-glucose does not react) </li></ul><ul><li>chiral signal molecule  complex with receptor  biological response </li></ul><ul><li>chiral drug (ant)agonist  complex with receptor  pharmacological response </li></ul>
  9. 9. Hydrogenation of pyruvate When pyruvate is hydrogenated without enzyme ( in vitro ), the reaction product is the racemic mixture of D-lactate and L-lactate : In the same reaction catalyzed by lactate dehydrogenase (in the presence of NADH +H + ), pyruvate is reduced stereospecifically to L-lactate only: 1. non-chiral substrate  chiral product L-Lactate C COOH CH 3 H H O H C C CH 3 O O HO Enzyme L-Lactate D-Lactate
  10. 10. Non- enzym atic hydration of fumarate in vitro reaction proceeds to racemic D,L-malate fumarate L-malate D-malate addition from one side addition from another side 1. non-chiral substrate  chiral product
  11. 11. Enzymatic hydration of fumarate (citrate cycle) in vivo just one enantiomer (L-malate) is produced reagent substrate 1. non-chiral substrate  chiral product enzyme
  12. 12. Hydrogenation of D-fructose in vitro gives two epimer s 2 H + D-fructose D-glucitol D-mannitol reaction site is planar i n vivo : enzym atic reaction gives just one product (D-glucitol) 1. non-chiral substrate  chiral product
  13. 13. Chiral substrates /signal molecules are bound to the stereospecific enzymes /receptors at three sites: Enzymes or receptors recognize only one enantiomer If the reactant of an enzymatic reaction is a chiral compound, only one of the two enantiomers is recognized as the specific substrate. 2. chiral substrate  product see also MCH II, p. 13 R R X x p roper enantiomer n ot-fitting enantiomer
  14. 14. Enzyme nomenclature : the ending -ase Systematic names identify the enzymes fully with the EC code number , contain information about substrate and type of reaction, not very convenient for everyday use. Recommended (accepted) names are shorter than systematic names , include also some historical names (pepsin, amylase) EC (abbr. Enzyme Commission) of International Union of Biochemistry (IUB) major class number . subclass number . sub-subclass number . enzyme serial number http://www.chem.qmul.ac.uk/iubmb/enzyme/
  15. 15. Examples <ul><li>Recommended name: alcohol dehydrogenase </li></ul><ul><li>Systematic name: EC ethanol:NAD + -oxidoreductase </li></ul><ul><li>Rea ction : ethanol + NAD +  acetaldehyde + NADH + H + </li></ul>Recommended name: alanine aminotransferase (ALT) Systematic name: EC L-alanine:2-oxoglutarate-aminotransferase Rea ction : L-alanine + 2-oxoglutarate  pyruvate + L-glutamate
  16. 16. Classification of enzymes: six classes according to reaction type (Each class comprises other subclasses) General scheme of reaction Enzyme class A + B + ATP  A-B + ADP + P i 6. Ligases (synthetases) A-B-C  A-C-B 5. Isomerases A-B  A + B (reverse reaction: synthases) 4. Lyases A-B + H 2 O  A-H + B-OH 3. Hydrolases A-B + C  A + C-B 2. Transferases A red + B ox  A ox + B red 1. Oxidoreductases
  17. 17. 1 Oxidoreductases <ul><li>catalyze the oxidation or reduction of substrate </li></ul><ul><li>s ubclasses: </li></ul><ul><li>dehydrogenases catalyze transfers of two hydrogen atoms </li></ul><ul><li>oxygenases catalyze the incorporation of one / two O atoms into the substrate (monooxygenases, dioxygenases) </li></ul><ul><li>oxidases catalyze transfers of electrons between substrates </li></ul><ul><li>(e.g. cytochrome c oxidase, ferroxidase) </li></ul><ul><li>peroxidases catalyze the breakdown of peroxides </li></ul>Example: lactate + NAD +  pyruvate + NADH + H + Recommended name : lactate dehydrogenase Systematic name : ( S )-lactate :NAD + oxidoreductase
  18. 18. 2 Transferases <ul><li>catalyze the transfer of a group from one to another substrate </li></ul><ul><li>s ubclasses: </li></ul><ul><li>aminotransferases, methyltransferases, glucosyltransferases </li></ul><ul><li>phosphomutases – the transfer of the group PO 3 2– within molecule </li></ul><ul><li>kinases phosphorylat e substrate by the transfer </li></ul><ul><li>of phosphoryl group PO 3 2– from ATP (e.g. hexokinases, proteinkinases) </li></ul>Example: glucose + ATP  glucose 6- P + ADP Recommended name : glucokinase Systematic name : ATP:D-glucose phosphotransferase
  19. 19. Example: P hosphor ylation of glucose glucose glucose 6-phosphate gluco kinase
  20. 20. 3 Hydrolases Example: glucose 6- P + H 2 O  glucose + P i Recommended name of the enzyme : glucose 6-phosphatase Systematic name : glucose 6-phosphate phosphohydrolase <ul><li>catalyze the hydrolytic splitting of esters, glycosides, amides , peptides etc. </li></ul><ul><li>s ubclasses: </li></ul><ul><li>esterases (lipases, phospholipases, ribonucleases, phosphatases ) </li></ul><ul><li>glycosidases (e.g. s ucrase , maltase, lactase, amylase) </li></ul><ul><li>proteinases and peptidases (pepsin, trypsin, cathepsins, dipeptidases, carboxypeptidases , aminopeptidases) </li></ul><ul><li>amidases (glutaminase, asparaginase) </li></ul><ul><li>ATPases ( split anhydride bonds of ATP ) </li></ul>
  21. 21. Example: Glucose 6-phosphatase Glc 6-P Glc
  22. 22. Compare two antagonistic enzymes kinase phosphatase
  23. 23. Glutaminase is amidase which catalyzes the deamidation of glutamine glutam ate glutamin e glutamin ase
  24. 24. ATPase catalyzes the exergonic hydrolysis of phosphoanhydride bond in ATP ATP + H 2 O  ADP + P i + energ y Example: muscle contraction myosine head exhibits ATPase activity, chemical energy of ATP is transformed into mechanical work (= actin-myosin contraction)
  25. 25. Examples of lysosomal h ydrolas es gly c oside gly c oside gly c oside sulfoester gly c oside peptide peptide peptide phosphodiester ester phosphoester amide Glu c osidas e Gala c tosidas e Hyaluronidas e Arylsulfatas e Lysozym e C athepsin Collagenase Elastase Ribonuclease Lipase Phosphatase Ceramidase Bond hydrolyzed Hydrolas e
  26. 26. Distinguish : lysozym e × ly s osom e <ul><li>Lyso zym e is en zym e </li></ul><ul><li>compound word , lyso ( Greek lysis ) + zym e ( from enzym e ) </li></ul><ul><li>hydrolas e , gly c osidas e , cleaves β -1,4-gly c osid e bond in ba c teri al hetero polysa c charide s, antiseptic defense </li></ul><ul><li>occurs in saliva, tears, and other body fluids </li></ul><ul><li>Lysosom e is intracellular digestion organelle </li></ul><ul><li>Greek compound word from lysis (to lyse) and soma (body) </li></ul><ul><li>typic al for animal cells </li></ul><ul><li>acidic pH, contains many acidic hydrolas es </li></ul>
  27. 27. 4 Lyases <ul><li>catalyze non-hydrolytic splitting or forming bonds C–C, C–O, C–N, C–S through removing or adding , respectively, a small mole c ule ( H 2 O, CO 2 , NH 3 ) </li></ul><ul><li>Some frequent recommended names: </li></ul><ul><li>ammonia lyases (e.g. histidine ammonia lyas e: histidine  urocanate + NH 3 ) </li></ul><ul><li>decarboxylases ( amino acid  amine + CO 2 ) </li></ul><ul><li>aldolases (catalyz e aldol cleavage and formation) </li></ul><ul><li>( de ) hydratases (carbonate dehydratase : CO 2 + H 2 O  H 2 CO 3 ) </li></ul>Example: fumarate + H 2 O  L-malate Recommended name : fumarate hydratase Systematic name: ( S )-malate hydro-lyase (fumarate-forming)
  28. 28. 5 Isomerases <ul><li>catalyze intramolecular rearrangements of atoms </li></ul><ul><li>examples : </li></ul><ul><li>epimerases </li></ul><ul><li>racemases </li></ul><ul><li>mutases </li></ul>Example: UDP-glucose  UDP-galactose Recommended name : UDP-glucose 4-epimerase Systematic name: UDP-glucose 4-epimerase
  29. 29. 6 Ligases <ul><li>catalyze formation of high-energy bonds C–C, C–O, C–N </li></ul><ul><li>in the reaction s coupled with hydrolysis of ATP </li></ul><ul><li>Frequent recommended names : </li></ul><ul><li>carboxylases </li></ul><ul><li>synthetases </li></ul><ul><li>(e.g. glutamine synt h etase : glutamate + ATP + NH 3  glutamine + ADP + P i ) </li></ul>Example: p yruvate + CO 2 + ATP + H 2 O  oxaloacetate + ADP + P i Recommended name : pyruvate carboxylase Systematic name: pyruvate:carbon-dioxide ligase (ADP-forming)
  30. 30. T hree enzym es have something to do with ph os phate ! (gly c ogen) n + P i  (gly c ogen) n-1 + glu c os e 1 -P inosine + P i  hypoxanthine + ribose 1-P ph os ph orol ysis = the splitting of gly c osid e bond by ph os phate = transfer of glu c osyl to in organic ph os phate Ph os ph orylas e (Transferas e ) substr ate -O-P + H 2 O  substr ate -OH + P i the h ydrol ysis of ph os ph oester bond Ph os ph atas e (Hydrolas e ) substr ate -OH + ATP  substr ate -O-P + ADP ph os ph oryla tion = transfer of ph os ph oryl PO 3 2– from ATP to substr ate Kinas e (Transferas e ) Reaction s ch eme / Reaction type Enzym e ( Class )
  31. 31. Distinguish : Three types of lysis (decomposition of substrate) ! the cleavage of C-C bond by s ulfur atom of coenzyme A in β -oxida tion of FA or keto ne bodies catabolism RCH 2 COCH 2 CO-SCoA + CoA-SH  RCH 2 CO-SCoA + CH 3 CO-SCoA Thiol ysis the cleavage of O / N -gly c osid e bond by ph os phate : (gly c ogen) n + P i  (gly c ogen) n-1 + glu c os e 1-P Ph os ph orol ysis (see previous page) the decomposition of substr ate by water , frequent in intestine: sucrose + H 2 O  glu c os e + fru c tos e ( starch ) n + H 2 O  maltos e + ( starch ) n-2 Hydrol ysis
  32. 32. Cofactors of enzymes <ul><li>low-molecular non-protein compounds </li></ul><ul><li>many of them are derived from B-complex vitamins </li></ul><ul><li>many of them are nucleotides </li></ul><ul><li>transfer 2 H or e - (cooperate with oxidoreductases) </li></ul><ul><li>transfer groups (cooperate with transferases) </li></ul><ul><li>tightly (covalently) attached – prosthetic groups </li></ul><ul><li>loosely attached – coenzymes (cosubstrates) </li></ul>
  33. 33. T hree different components in enzyme reaction <ul><li>Notes: </li></ul><ul><li>one or two substrates may be involved (dehydrogenation × transamination) </li></ul><ul><li>substrate can be low / high molecular (hexokinase × protein kinase) </li></ul><ul><li>some reactions proceed without cofactor (hydrolysis, isomeration) </li></ul><ul><li>reaction can be reversible or irreversible (dehydrogenation × decarboxylation) </li></ul>enzyme substrate cofactor  product cofactor altered + + <ul><li>substrate(s) </li></ul><ul><li>cofactor </li></ul><ul><li>enzyme catalyzes the whole process </li></ul>react to each other
  34. 34. Cofactors of oxidoreductases NAD + acceptor of 2H NADPH+H + donor of 2H FAD acceptor of 2H BH 4 donor of 2H electron transfer antioxidant / transfer of acyl transfer of 2 electrons + 2 H + transfer of 1 electron transfer of 1 electron 2 GSH donor of 2H The function of cofactor NADH+H + NADPH+H + FADH 2 tetrahydrobiopterin (BH 4 ) molybdopterin red dihydrolipoate (2 -SH) ubiquinol (QH 2 ) heme-Fe 2+ non-heme-S-Fe 2+ glutathione red (GSH) NAD + NADP + FAD Dihydrobiopterin (BH 2 ) Molybdopterin oxid Lipoate (-S-S-) Ubiquinone (Q) Heme-Fe 3+ Non-heme-S-Fe 3+ Glutathione oxid (G-S-S-G) Reduced form Oxidized form
  35. 35. NAD + is the cofactor of dehydrogenas es <ul><li>NAD + is oxidant – takes off 2 H from substr ate </li></ul><ul><li>one H adds as hydrid e ion (H - ) into para- po sition of pyridini um c ation of NAD + </li></ul><ul><li>NAD + + H - = NADH = equivalent of two electrons </li></ul><ul><li>the second H is released as proton (H + ) and binds to enzyme molecule </li></ul>2 H = H – + H +
  36. 36. NAD + ( n icotinamide a denine d inucleotide) ribose diphosphate ribose N-glycosidic linkage N-glycosidic linkage addition of hydride anion anhydride adenine
  37. 37. Redox p air of co fa c tor oxidized form NAD + reduced form NADH aromatic ring aromaticity totally disturbed tetravalent nitrogen trivalent nitrogen positive charge on nitrogen electroneutral species high-energy compound !
  38. 38. Dehydrogenation by NAD + <ul><li>typical substrate groups: </li></ul><ul><li>primary alcohol -CH 2 -OH </li></ul><ul><li>secondary alcohol >CH-OH </li></ul><ul><li>se condary amine >CH-NH 2 </li></ul><ul><li>double bond (C=O, C=N) is produced </li></ul>
  39. 39. NAD + dehydrogena tions form a double bond compare Med. Chem. II Appendix 3 aldehyd e keton e c arboxyl ic acid ester la c ton e o xo acid i mino acid prim ary al c ohol se condary al c ohol a ldehyd e hydr ate hemi acetal cy clic hemiacetal h ydroxy acid a mino acid Produ c t Substr ate
  40. 40. Dehydrogenation of ethanol (alcohol dehydrogenase)
  41. 41. Dehydrogenation of glutamate (glutamate dehydrogenase) glutamate 2-imino glutarate
  42. 42. NAD + -dependent enzym es are called pyridin e dehydrogenas es <ul><li>Citr ate cy cle </li></ul><ul><li>isocitr a t e dehydrogenas e </li></ul><ul><li>2-oxoglutar ate dehydrogenas e </li></ul><ul><li>mal a t e dehydrogenas e </li></ul><ul><li>Gly colysis </li></ul><ul><li>glyceraldehyd e 3-P dehydrogenas e </li></ul><ul><li>la ctate dehydrogenas e </li></ul><ul><li>Oxida tion of ethanol </li></ul><ul><li>al c ohol dehydrogenas e </li></ul><ul><li>acetaldehyd e dehydrogenas e </li></ul>
  43. 43. Redu ced c ofa c tor NADPH+H + is hydroge nation agent <ul><li>donor of 2 H in hydrogenations </li></ul><ul><li>cofactor of reducing syntheses (FA, cholesterol) </li></ul><ul><li>regenera tion of glutathione ( GSH ) in eryt h rocyte s </li></ul><ul><li>cofactor of hydroxylation reactions: </li></ul><ul><li>cholesterol   bile acids </li></ul><ul><li>calciol   calcitriol </li></ul><ul><li>xenobiotic  hydroxylated xenobiotic </li></ul><ul><li>general scheme of hydroxyla tion: </li></ul>R-H + O 2 + NADP H+H +  R- O H + H 2 O + NADP +
  44. 44. FAD is c ofa c tor of flavin dehydrogena ses <ul><li>f lavin a denin e d inu c leotid e </li></ul><ul><li>dehydrogena tion of -CH 2 -CH 2 - group </li></ul><ul><li>two H atom s are attached to two nitrogens of riboflavin (N-1 a nd N-10) </li></ul><ul><li>FAD + 2H  FADH 2 </li></ul>
  45. 45. FAD ( f lavin a denine d inucleotide) vazba 2H adenine ribosa difosfát ribitol dimethylisoalloxazine ribose diphosphate the sites for accepting two H atoms
  46. 46. Redox p air of c ofa ctor oxidized form FAD reduced form FADH 2 aromatic system aromaticity partially disturbed electroneutral species electroneutral species high-energy compound !
  47. 47. Dehydrogenation of succinate to fumar ate (flavin dehydrogenas e )
  48. 48. T etrahydrobiopterin (BH 4 ) is a cofactor of hydroxylations <ul><li>made in the body from GTP </li></ul><ul><li>donor of 2H </li></ul><ul><li>oxid ized to dihydrobiopterin (BH 2 ) </li></ul>guanine
  49. 49. Redox pair of cofactor
  50. 50. Hydroxyla tion of ph enylalanin e phenylalanine tyrosine
  51. 51. Coenzyme Q (ubiquinone) <ul><li>derivative of 1,4-benzoquinone </li></ul><ul><li>cyclic diketone, not aromatic </li></ul><ul><li>component of respiratory chain </li></ul><ul><li>gradually accepts electron and proton (2x) </li></ul><ul><li>reduced to semiubiquinone and ubiquinol </li></ul>
  52. 52. Reversible reduction of ubiquinone R = long polyisoprenoid chain  lipophilic character electron (e - ) and proton (H + ) have different origin: electron comes from red. c ofa c tor s (= nutrients ) , H + from matrix of mitochondrion ( n on-aromatic diketone) ( arom atic ring + radi cal) ( di ph enol ) ubiquinone semiubiquinone ubiquinol Q  • QH  QH 2
  53. 53. Heme of various cytochromes <ul><li>transfers just 1 electron </li></ul><ul><li>cytochromes are hemoprotein s </li></ul><ul><li>components of respiratory chain or other heme enzymes (cyt P-450) </li></ul><ul><li>reversible redox reaction: Fe 2+  Fe 3+ </li></ul>
  54. 54. Non-heme iron (Fe 2 S 2 cluster) transfers electron in R.CH. just one iron cation changes oxidation number oxidized state reduced state
  55. 55. Xanthine oxidase catalyzes the oxygenation of purine bases (catabolism) hypoxanthine  xanthine  uric acid Molybdopterin (formula in Seminars) side product: H 2 O 2
  56. 56. Sulfite oxidase : sulfate is catabolite from cysteine cysteine HSO 3 - + H 2 O  SO 4 2- + 3 H + + 2 e - pla s ma urine acidify plasma urine reduce Mo (see Seminars, p. 46 ) Molybdopterin
  57. 57. Redox pair lipoate/dihydrolipoate is antioxidant system. It is also involved in the acyl transfer (see later) oxidized form – lipoate (cyclic disulfide 1,2-dithiolane) reduced form - dihydrolipoate - 2H one S atom transfers acyl in oxidative decarboxylation of pyruvate / 2-oxoglutarate
  58. 58. Glutathione (GSH) <ul><li>tripeptide </li></ul><ul><li>γ -glutamyl-cysteinyl-glycine </li></ul><ul><li>cofactor of glutathione peroxidase (contains selenocysteine) </li></ul><ul><li>reduces H 2 O 2 to water </li></ul><ul><li>2 G-SH + H-O-O-H  G-S-S-G + 2 H 2 O </li></ul>Remember: The -SH compounds have generally reducing properties.
  59. 59. Dehydrogenation of two GSH molecules
  60. 60. Vitamins and cofactors of transferases -NH 2 (transamination) -PO 3 2- (phosphoryl) -SO 3 2- CO 2 acyl acyl -CH 3 C 1 groups -CH 3 r esidue of oxo acid Transferred group pyridoxal phosphate ATP PAPS carboxybiotin CoA-SH dihydrolipoate SAM tetrahydrofolate methylcobalamin t hiamin diphosphate Pyridoxin (Made in body) (Made in body) Biotin Pantothenic acid (Made in body) ( Methionin e) Folate Cyanocobalamin Thiamin Cofactor Vitamin
  61. 61. Pyridoxal phosphate is the cofactor of transamination and decarboxylation of AA aldimine (Schiff base) - H 2 O transamination decarboxylation
  62. 62. Two phases of transamina tion Schiff base amino acid oxo acid glutamate 2-oxoglutarate blue colour indicates the pathway of nitrogen
  63. 63. ATP is the cofactor of kinases (phosphorylation agent) N-glycoside bond ester anhydride
  64. 64. Phosphorylation of substrate substrate kinase phosphorylated substrate CAUTION: creatine kinase (CK) phosphorylation on nitrogen (the bond N-P)
  65. 65. PAPS is sulfation agent <ul><li>3 ’- ph osfoadenosin e -5’- phosphosulfate </li></ul><ul><li>mixed anhydride of H 2 SO 4 and H 3 PO 4 </li></ul><ul><li>esterification of hydroxyl groups by sulfuric acid = sulfation </li></ul><ul><li>sulfated sphingoglycolipids </li></ul><ul><li>sulfated glycosaminoglycans (heparin, chondroitin sulfate, keratan sulfate) </li></ul>
  66. 66. Carboxybiotin <ul><li>cofactor of carboxylation reactions </li></ul><ul><li>carboxylation of biotin needs ATP </li></ul>carboxybiotin biotin
  67. 67. Carboxybiotin is the cofactor of carboxylation reactions + pyruvate oxaloacetate pyruvate carboxylase
  68. 68. Distinguish: Decarboxylation vs. Carboxylation ! protein-glutamate + O 2 + vit K red + CO 2  protein- γ -carboxyglutamate posttranslational carboxylation of glutamate  hemostasis Phylloquinone (vitamin K) Hb-NH 2 + CO 2  Hb-NH-COOH (unstable Hb-carbamate, spontaneous) None pyruvate + CO 2 + ATP  oxaloacetate acetyl-CoA + CO 2 + ATP  malonyl-CoA propionyl-CoA + CO 2 + ATP  methylmalonyl-CoA  succinyl-CoA carboxylations (ATP) in the catabolism of Val, Leu, Ile Biotin Carboxylation (requires energy) Cofactor acetoacetate  acetone + CO 2 (non-enzymatic, spontaneous) None amino acid  amine + CO 2 Pyridoxal-P pyruvate  acetyl-CoA + CO 2 2-oxoglutarate  succinyl-CoA + CO 2 Thiamin-diP Decarboxylation (does not require energy) Cofactor
  69. 69. Coenzyme A (CoA-SH) <ul><li>transfers acyl </li></ul><ul><li>attached to sulfur atom </li></ul><ul><li>thioester bond </li></ul><ul><li>a cyl -CoA is a c tiv ated acyl </li></ul><ul><li>e.g. acetyl-CoA </li></ul>
  70. 70. Coenzyme A acyl ~ O O H C H 2 O P O O O O P O O O N N N N N H 2 H O P O O O C H 2 C HS C H 2 C H 2 H N O C C H 2 C H 2 H N O C C H C H 3 C H 3 Cysteamine β-Alanine Pantoic acid Pantothenic acid 3´ - PhosphoADP
  71. 71. Lipo ate ( lipoamide ) part of the 2-oxo acid dehydrogenase complex (see the following lectures) it is oxidant of a group carried by thiamine d iphosphate (TDP ), binds the resulting acyl as thioester and transfers the acyl to coenzyme A: S S CO– NH –L ys–Enzyme Lipoamide ( oxidized form) S 6 -Acyldihydrolipoamide (reduced form) S H CO– NH – Lys–Enzyme S H S H CO– NH –L ys–Enzyme S R-CO – 2 H R 1 -C H – TDP O H CoA-S H R-CO–S-CoA Dihydrolipoamide ( reduced form) H –TDP
  72. 72. S -Adenosylmethionine (SAM) <ul><li>„ active methyl“, trivalent sulfur  sulfonium cation </li></ul><ul><li>cofactor of methylation reactions: </li></ul><ul><li>ethanolami n e -> cholin e (3 × methylation) </li></ul><ul><li>guanidine acetate -> creatine </li></ul><ul><li>noradrenaline -> adrenaline ..... and many others </li></ul><ul><li>side product is homocysteine </li></ul><ul><li>remethylation of homocysteine needs methyl-FH 4 + B 12 cofactor (see Seminars, p. 27 and 45) </li></ul>
  73. 73. S -Adenosylmethionine (SAM)
  74. 74. Folic acid is vitamin. In the body, it is hydrogen ated to 5,6,7,8-tetrahydrofol ate . Tetrahydrofol ate (FH 4 ) is c ofa c tor for the transfer of C 1 groups amid 5 6 7 8 p-aminobenzoic acid glutamic acid amide pteridine transfer of 1C groups
  75. 75. C 1 Groups transferred by FH 4 compare scheme Seminars, p. 26 catabolism of histidine formimino -CH=NH +I catabolism of tryptophan  formiate  formyl synthesis of purine bases formyl -CH=O +I deamination of formimino-FH 4 (from histidine) synthesis of purine bases methenyl -CH= -I catabolism of serine, glycine used in synthesis of dTMP  DNA methylene -CH 2 - -II reduction of methylene-FH 4 (from serine, glycine) methyl-FH 4 cooperates with B 12 cofactor in methylation methyl -CH 3 -III Metabolic Origin / Comment Name Formula Oxidation number of C
  76. 76. B 12 vitamin is cyano or hydroxo cobalamin R = CN or OH c o r rin cycle hydroxo c obalamin is used in the treatment of cyanide poisoning - binds cyanide ions to non-toxic cyanocobalamin
  77. 77. B 12 cofactor is methyl or deoxyadenosyl cobalamin, it is needed for two reactions in the body <ul><li>homocysteine  methionine methylation of homocysteine (regeneration of methionine) </li></ul><ul><li>homocysteine   propionyl-CoA  succinyl-CoA </li></ul><ul><li>you can see both reactions in Seminars, p. 45 </li></ul>B 12 FH 4 / B 12
  78. 78. Compare: Four different cofactors of methylations SAM = S -adenosylmethionine, FH 4 = tetrahydrofolate, COMT = catechol O -methyltransferase ! homocysteine  methionine methyl-FH 4 methyl-B 12 dUMP  dTMP serine, glycine methylene-FH 4 homocysteine  methionine methylene-FH 4 methyl-FH 4 <ul><li>ethanolamine  choline </li></ul><ul><li>guanidineacetate  creatine </li></ul><ul><li>noradrenaline  adrenaline </li></ul><ul><li>the methylation of DNA (regulation of gene expression) </li></ul><ul><li>methylation of bases in tRNA / mRNA (guanine-N 7 = cap) </li></ul><ul><li>the inactivation of catecholamines (COMT): </li></ul><ul><li>dopamine  methoxytyramine </li></ul><ul><li>noradrenaline  normetanephrine </li></ul><ul><li>adrenaline  metanephrine </li></ul><ul><li>the methylation of xenobiotics (II. phase - conjugation) </li></ul>methionine SAM Examples of methylation reactions Methyl origin Cofactor -CH 2 -
  79. 79. Thiamin is vitamin B 1 Thiamin diphosphate (TDP) is cofactor <ul><li>Oxidative decarboxylation of some 2-oxo acids </li></ul><ul><li>pyruvate  acetyl-CoA </li></ul><ul><li>2-oxoglutar ate  su c cinyl-CoA ( citrate cycle ) </li></ul><ul><li>2-oxo acids in the catabolism of Val, Leu, Ile </li></ul><ul><li>Transketolase reactions in pentose cycle </li></ul><ul><li>ribose-5-P + xylulose-5-P  glyceraldehyd-3-P + sedoheptulose-7-P </li></ul><ul><li>xylulose-5-P + erythrose-4-P  fructose-6-P + glyceraldehyd-3-P </li></ul>transfer to dihydrolipoate and CoA
  80. 80. Thiamin di phosphate (TDP) is the c ofa c tor of the oxida tive de c arboxyla tion of pyruv ate glu c os e  pyruv ate  acetyl-CoA C A C TDP attachment of pyruv ate and its de c arboxyla tion
  81. 81. In human body, a number of non-enzymatic reactions proceeds <ul><li>decarboxylation of acetoacetate  acetone </li></ul><ul><li>glycation / carbamylation / nitrosylation / nitration of proteins </li></ul><ul><li>the reactions of ROS (reactive oxygen species, e.g. lipoperoxidation) </li></ul><ul><li>spontaneous oxidation of hemoproteins (hemoglobin  methemoglobin) </li></ul><ul><li>spontaneous oxidation of urobilinogens to urobilins (large intestine) </li></ul><ul><li>condensation of amines with carbonyl compounds to heterocyclic derivatives dopamine + pyruvate  salsolinol </li></ul><ul><li>tryptamine + pyruvate  harmane </li></ul><ul><li>dopamine + dihydroxyphenylacetaldehyde  tetrahydropapaveroline </li></ul><ul><li>binding ligands to proteins: </li></ul><ul><li>bilirubin + albumin  bilirubin-albumin complex </li></ul><ul><li>CO + hemoglobin  carbonylhemoglobin </li></ul><ul><li>the interactions of macromolecules: </li></ul><ul><li>antigen + antibody  immuno complex </li></ul>neurotoxins