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Enzymes

Enzymes. Vladimíra Kvasnicová. Enzyme is a biocatalyst :. the reaction. The figure is found at: http://fig.cox.miami.edu/~cmallery/255/255enz/enzymology.htm (December 2006).

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Enzymes

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  1. Enzymes Vladimíra Kvasnicová

  2. Enzyme is a biocatalyst: the reaction The figure is found at: http://fig.cox.miami.edu/~cmallery/255/255enz/enzymology.htm (December 2006)

  3. The figure is found at:http://stallion.abac.peachnet.edu/sm/kmccrae/BIOL2050/Ch1-13/JpegArt1-13/05jpeg/05_jpeg_HTML/index.htm (December 2006)

  4. The figure is found at: http://fig.cox.miami.edu/~cmallery/255/255enz/enzymology.htm (December 2006)

  5. The figure is adopted from the book: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, 1997. ISBN 0‑471‑15451‑2

  6. Enzymes • lower an energy of activation (EA) • reduce the time to reach the reaction equilibrium • are not consumed or changed by the reaction • help the reaction proceed under a body´s T, p and pH • are specific • can be regulated • don´tchange the G of the reaction • don´tchange the equilibrium position of the reaction self study

  7. Structure and properties - most of enzymes are proteins The figure is found at: http://fig.cox.miami.edu/~cmallery/255/255enz/enzymology.htm (December 2006)

  8. The figure is found at: http://fig.cox.miami.edu/~cmallery/255/255enz/enzymology.htm (December 2006)

  9. The figure is found at:http://stallion.abac.peachnet.edu/sm/kmccrae/BIOL2050/Ch1-13/JpegArt1-13/05jpeg/05_jpeg_HTML/index.htm (December 2006)

  10. Each enzyme has temperature optimum pH optimum affinity to its substrate The figure is found at:http://stallion.abac.peachnet.edu/sm/kmccrae/BIOL2050/Ch1-13/JpegArt1-13/05jpeg/05_jpeg_HTML/index.htm (December 2006)

  11. The figure is found at:http://www.carleton.ca/biology/2200/schedule.html(December 2006)

  12. Some enzymes are produced as precursors (= PROENZYMES or ZYMOGENS) The figure is found at:http://wine1.sb.fsu.edu/bch4053/Lecture26/zymogen.jpg (December 2006)

  13. or must be activated to be active (e.g. by phosphorylation): The figure is found at:http://fig.cox.miami.edu/~cmallery/150/memb/c11x11enzyme-cascade.jpg (December 2006)

  14. Isoenzymes (isozymes) are enzymes which catalyze the same reaction but differ in their primary structure and phyzico chemical properties • Isoenzymes are • produced by different genes(= true isozymes) • or produced by different posttranslational modification(= isoforms) • found in different compartments of a cell • found in different tissues of an organism • can be oligomers of various subunits(monomers)

  15. example: 5 isozymes (various monomer ratio) The figure is found at:http://wine1.sb.fsu.edu/bch4053/Lecture26/isozymes.jpg(December 2006)

  16. multienzyme complexes separate enzymes of a mtb pathway This is Figure 17.6 from Garrett, R.H.; Grisham, C.M. Biochemistry; Saunders: Orlando,1995; page 553, found at http://www.uwsp.edu/chemistry/tzamis/enzyme_complex.html (December 2006)

  17. example: 2-oxoacid dehydrogenase multienzyme complex The figure is found at:http://faculty.uca.edu/~johnc/pdhrxns.gif(December 2006)

  18. example: 2-oxoacid dehydrogenase multienzyme complex The figure is found at:http://faculty.uca.edu/~johnc/pdhrxns.gif(December 2006)

  19. Allosteric enzyme: a) monomeric, b) oligomeric The figure is adopted from the book: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, 1997. ISBN 0‑471‑15451‑2

  20. Allosteric enzyme in T and R conformations: modulators shift the equilibrium activators and substrates have a greater affinity for R-state inhibitors have a greater affinity forT-state The figure is adopted from the book: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, 1997. ISBN 0‑471‑15451‑2

  21. Enzymes in a medicine • determination of enzyme activity in blood • enzymatic analytical methods • enzyme therapy

  22. Determination of enzyme activity for diagnostic purposes most often blood is investigated (serum, plasma)  evaluation of presence and seriousness of a tissue damage units: kat/L (= catalytical concentration of enzyme) kat = katal 1 katal = 1 mole of a substrate transformed per 1 sec 1 kat = 10-6 kat

  23. Enzymes found in plasma: a) plasma-specific enzymes (e.g. clotting factors) b) secretory enzymes (e.g. digestive enzymes) c) cellular enzymes Important knowledge: 1) intracellular localization of enzymes 2) organ and tissue distribution of enzymes 3) sources of enzymes found in plasma 4) way of enzyme elimination from blood

  24. „ Cardiac enzymes“ The figure is adopted from the book: Devlin, T. M. (editor): Textbook of Biochemistry with Clinical Correlations, 4th ed. Wiley‑Liss, Inc., New York, 1997. ISBN 0‑471‑15451‑2

  25. ENZYMES Laboratory order form from http://spch.cz/kliniky/kbi/laboratorni_prirucka/zadanka_biochemie.pdf (December 2006)

  26. Naming enzymes • -ase / -in • enzyme nomenclature • common names

  27. Enzyme nomenclature EC nomenclature * each enzyme is classified by EC number (Enzyme Commission of IUBMB) – 6 classes: • EC 1.x.x.x oxidoreductases • EC 2.x.x.x transferases • EC 3.x.x.x hydrolases • EC 4.x.x.x lyases • EC 5.x.x.x isomerases • EC 6.x.x.x ligases (synthetases) → classification by a reaction catalyzed by the enzyme

  28. systematic names * are made according to a special rules, they specify a reaction catalyzed by the enzyme example: ATP : D-glucose phosphotransferase (EC 2.7.1.2) transfers (2)phosphate (7) to an alcohol group (1) ATP + D-Glc  ADP + D-Glc-6-phosphate (Glc-6-P)

  29. common names(= accepted names) * easier than the systematic names, widely used * very important! example: EC 2.7.1.2. = glucokinase(see above)

  30. old trivial names * no relationship to the catalyzed reaction * suffixed by -in (pepsin, trypsin) * used for long time known enzymes abbreviations of enzymes * used in medicine e.g. LD, ALT, ALP

  31. Specific suffix of enzyme names: -ase a) substrate name + -ase (e.g. amylase) b) reaction type + -ase (e.g. dehydrogenase) = group name, not individual enzyme

  32. IUBMB Enzyme Nomenclature EC 2.7.1.1 Accepted name: hexokinase Reaction: ATP + D-hexose = ADP + D-hexose 6-phosphate Other name(s): hexokinase type IV glucokinase; hexokinase D; hexokinase type IV; hexokinase (phosphorylating); ATP-dependent hexokinase; glucose ATP phosphotransferase Systematic name: ATP:D-hexose 6-phosphotransferase Comments: D-Glucose, D-mannose, D-fructose, sorbitol and D-glucosamine can act as acceptors; ITP and dATP can act as donors. The liver isoenzyme has sometimes been called glucokinase. The reference is found athttp://www.chem.qmul.ac.uk/iubmb/enzyme/EC2/7/1/2.html

  33. Common names of enzymes(used in biochemistry) 1) oxidoreductases:Aox + Bred Ared +Box * dehydrogenase (H- or H) * reductase * oxidase * peroxidase (various peroxides) * oxygenase (O2) * hydroxylase (= monoxygenase; -OH) * desaturase (-CH2CH2-  -CHCH-)

  34. 2) transferases: A-x + B  A + B-x * grouptransferase (e.g.aminotransferase) * kinase(= phosphotransferase) * phosphorylase * transketolase * transaldolase

  35. 3) hydrolases: A-B + H2O  A-H + B-OH * esterase (R1-CO-O-R2) * phosphatase (phosphate-O-R) Pi !!! * phosphodiesterase (R1-O-phosphate-O-R2) * nuclease, peptidase, glycosidase, lipase

  36. 4) lyases: A-x  B + x * decarboxylase ( CO2) * dehydratase ( H2O) * hydratase (-CHCH- + H2O  -CH(OH)CH2-) * synthase

  37. 5) isomerases: A  iso-A * epimerase (monosacharide  its epimer) * mutase (rearangement of a phosphate group)

  38. 6) ligases: A + B + ATP A-B + ADP + Pi * synthetase * carboxylase

  39. ENZYMES Laboratory order form from http://spch.cz/kliniky/kbi/laboratorni_prirucka/zadanka_biochemie.pdf (December 2006)

  40. Add class to which each enzyme belongs AST aspartate aminotransferase ALT alanine aminotransferase GMT gamma-glutamyl transpeptidase ALP alkaline phosphatase ACP acid phosphatase AMS -amylase LPS lipase CK creatine kinase CHE cholinesterase LD lactate dehydrogenase

  41. Cofactors of oxidoreductases: NAD+nicotinamide adenine dinucleotide NADP+nicotinamide aden. dinucl. phosphate (precursor: niacin = nicotinic acid)H- FAD flavin adenine dinucleotide FMN flavin mononucleotide (precurzor: riboflavin = vitamin B2)2 H heme Fe3+ + e- Fe2+e-

  42. transferases: ATP adenosine triphosphate / phosphate GTP guanosine triphosphate / phosphate TDP thiamine diphosphate / C-fragment (prekurzor: thiamine = vitamin B1) PALP pyridoxalphosphate / -NH2 (prekurzor: pyridoxine = vitamin B6) THF tetrahydrofolate / C1-fragment (prekurzor: folic acid) CoA coenzyme A (HS-Co-A) / acyl PAPS phosphoadenosine phosphosulfate/ sulfate

  43. lyases: PALP pyridoxalphosphate (decarboxylases) ligases: ATP adenosine triphosphate acyl-CoA-synthetases aminoacyl-tRNA-synthetases biotin = vitamin H (carboxylases)

  44. 3´-phosphoadenosine-5´-phosphosulfate (PAPS) transfers sulfate group to a substrate (sulfatation) http://web.indstate.edu/thcme/mwking/amino-acid-metabolism.html (Jan 2007)

  45. Coenzyme A = CoA-SH http://lxyang.myweb.uga.edu/bcmb8010/pic/NAD+.gif and http://oregonstate.edu/instruct/bb450/stryer/ch14/Slide26.jpg (Jan 2008)

  46. Derivates of tetrahydrofolate http://www.dentistry.leeds.ac.uk/biochem/postgrad/thftypes.gif (Jan 2008)

  47. Enzyme kinetics • activity, units • 1 katal = 1 mole of a substrate transformed per 1 sec • 1 IU = 1 μmole of a substrate transformed per 1 minute 1 katal = 1 mole / 1 sec = 106μmole/ 1 sec = 60 x 106μmole/ 1 min (= 60 sec) 1 katal = 6 x 107 IU

  48. The activity is related to aconstant concentration of an enzyme: [E] = constant The figure is found at: http://www.steve.gb.com/science/enzymes.html (December 2006)

  49. ! REMEMBER ! The figure is found at: http://fig.cox.miami.edu/~cmallery/255/255enz/gk3x15.gif (December 2006)

  50. Michaelis-Menten kinetics • the curve can be described by the equation: The figure is found at: http://www.steve.gb.com/science/enzymes.html (December 2006)

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