Enzymes

1. Enzymes

2. REFERENSI Harper’s Illustrated Biochemistry. Murray, R.K; D.K. Granner; P.A; Mayes. V.W. Rodwell. 2003. Twenty-Seventh Edition. International Edition. Mcgraw-Hill Companies inc. Lange Medical Publication

3. Digested in the digestive tract Metabolized In cells diet INTRODUCTION Metabolism • Catabolism (biodegradation): larger molecules (nutrients and cell constituents) are broken down (often via exergonic reactions) to salvage (reuse) their components or/and to generate energy. • Anabolism (biosynthesis): The generation of biomolecules from simpler components (often via endergonic reactions).

4. Cells Tissues Organism Composed by molecules Chemical reaction

5. Concepts CHEMICAL REACTION common in laboratory accelerate the reaction NEED WARMING NEED catalyst

6. Organisms Relative Constant Temperature need catalyst Enzyme Biocatalyst

7. Catalyst • Catalyst accelerate the reaction • participate in chemical reactions and speed up chemical reactions but at the end of the reaction will come back as an enzyme in the early • needed in small amounts

8. In-organic catalyst H+, OH-, Pt Activation energy  Organic catalyst PROTEIN  biocatalyst Activation energy  Specific reaction No heat resistant

9. Organisms cell moleculel enzyme Endoplasmic reticulum ribosome cytoskeleton mitochondrial core app.gol lysozyme cytosol peroxisome Eucaryota Cells

10. Location of enzymes in the Cells associated with cell organelles concerned function • Mitochondrial enzymes:Reaction of energy supply, the oxidation reactions that produce energy • Ribosomal enzymes:The reaction of protein biosynthesis • Core enzymes:Associated with the genetic • Lysozyme enzymes:In connection with the digestive process intrasellular,Hydrolytic destruction of materials that are not needed cell • Microsomal enzymes:Hydroxylation reactions in steroid hormone synthesisMetabolism and inactivation of drug

11. Biochemistry To learn chemical composition and chemical process In organisms (virus, bacteria, fungi, plant, animal, human etc) Enzymes protein biocatalyst

12. E3 E5 E1 E2 E4 E6 E7 D F A B C E G P • METABOLIC FLOW • A = substrat awal • P = produk akhir • B,C,D,E,F,G = intermediates compounds

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

14. 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)

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

16. 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

17. Transition state Uncatalyzed G = Ea E. level Inorganic catalyzed Free energy Ea' enzyme Ea'' Initial state D G of reaction products A+B C+D ΔG = 0  balanced ΔG < 0  Rx to the right (exergonic) ΔG > 0  Rx to the left (endorgonic)

18. Ea = activation energy amount of energy needed to bring all molecule in a mole on a temperature of a material particular circumstances from event beginning to transition • energy barrier • ΔG: FREE ENERGY CHANGES (not influenced by the catalyst) • Example : - Lactosa Glucose + Galactose - Heksokinase : - Glucose - other hexose : Fructose (power binding/affinity) different Km lactase

19. 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

20. Catalysis Enzyme Mechanisms + + E S P MOLEKUL BESAR MOLEKUL KECIL Kompleks ES • ACTIVE SITE (BENTUK CELAH) = CATALYTIC SITE = SUBSTRATE BINDING SITE  GUGUS2 PENGIKAT ‘S’ GUGUS2 KATALITIK  GUGUS REAKTIF ASAM2 AMINO DI DAERAH TSB.

21. 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)

22. H | R – C – COOH | NH3+ H | R – C – COO– | NH3+ H | R – C – COO– | NH2 +OH– +H+ iep muatan=0 pH>iep pKa COOH < NH3+ pH < iep Primer Structure PEPTIDA BOND

23. H H O | | || – N – C – C – | CH2 | S | S | CH2 | – N – C – C – | | || H H O R | C – C – N – || | | O H H : : : : : : : : H H O | | || – N – C – C | R Hydrogen bond disulfide bond * Helix Cys – SH Cys – SH Secondary structure * Lain2 : *=  - PLEATED * = RANDOM COIL

24. Active site E Tertiary Structure Polypetida monomer • Hydrogen bond • Van der Walls bond

25. Quaternary Structure subunit subunit Tertiary structure Monomer Protomer Dimer Tetramer Quaternary structure Oligomer Polimer • Hydrogen bond • Electrostatic bond

26. DENATURATION • damage to the structure of the protein but not to damage the primary structure (peptide bond) • Can damage caused : - Extreme pH - heavy metal (Hg ++ binding -SH groups) Peptida bond no damage Disulfide

27. 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)

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

29. Enzymes Mechanisms ENZYMES Protein composed of amino acids amino acids form ions in solution always depends on the pH of the solution catalytic activity of an enzyme closely related to the structure of the enzyme (protein)

30. R - C - COOH R - C - COO I I NH3+ NH3+ _ R -C -COO I NH2

31. S E E A S I LIGAND A E I LIGAND small molecules that can bind to large molecules S=SUBSTRATE I=INHIBITOR A=ACTIVATOR E=ENZYME

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

33. 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)

34. Co-factor • Enzyme : - simple protein - complex protein + co-factor • Co-factor : - metal - organic compounds of non-specific protein (coenzyme) • Enzyme-Cofactor binding - strong bond (covalent) - weak bond (hydrogen or van der walls)

35. enzyme cofactors necessary cofactor must bind first before doing the process of catalysis • Example : hexokinase • GLUCOSE + ATP GLUCOSE–6P + ADP Mg2+

36. Metal Cofactor • Strong bond (covalent) : Metallo-enzyme • Weak bond Function : • participate directly in the catalytic process (catalytic groups) • stabilizers where catalysis • Bonding with 'S' and 'E' • Example : - Zn++  CARBOXYPEPTIDASE - Mg++  HEXOKINASE - Fe++ / Fe+++ CYTOCROME SYSTEM

37. Coenzyme + Apoenzyme Holoenzyme Protein (in active) Active catalyst cofactor in the form of organic compounds of non-specific protein COENZYME • Strong bond : prosthetic gorups • example : H2O2 + H2O2 2H2O + O2 • weak bond : co-substrate • Example : catalase Lactate dehydrogenase PIRUVAT + NADH + H+ LAKTAT + NAD+ Co-substrate S

38. Function of coenzyme • carrier group, a specific atom or electron ex : • NADP+ • FMN • FAD • KoQ • NAD+ • Electron : Heme • Other gorups :  ATP  FOSFAT  PIRIDOKSAL FOSFAT –NH2

39. B vitamins including coenzyme • TPP  THIAMIN • NAD  NIASIN • NADP  NIASIN • FAD  RIBOFLAVIN • KoA  PANTOTENAT ACID

40. PEPSINOGEN PEPSIN H+ / PEPSIN PROENZYME = ZYMOGEN • Enzyme produced in the form of inactive • Function : - protect organs - provide semi-finished material

41. 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)

42. 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)

43. 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)

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

45. chain gen    a.a chain    Isozymes catalyzes the same reaction Isozymes Hb :22 LDH : M4 H4 M3H M2H2 MH3

46. 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)

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

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

49. 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

50. 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