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Enzimologija

Enzimologija

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Enzimologija

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  1. Enzimologija Nastavnik: Tanja Ćirković Veličković

  2. Pregled • Opšte informacie o predmetu i načinu ocenjivanja • Literatura • Opšti pojmovi • Nomenklatura enzima • Uvodna znanja

  3. Program i organizacija vežbi • Teorijske vezbe – izračunavanja u enzimologiji • Laboratorijske vežbe: osnovna odredjivanja u enzimologiji • Laboratorijske vežbe: Razni aspekti primene enzima Fond časova predavanja i vežbi: 3 + 3 (teorijske vežbe) Asistent: Marija Stojadinovic i Dragana Stanic

  4. Način ocenjivanja • Predavanja: 10 bodova • Kolokvijum 1: 20 bodova • Kolokvijum 2: 20 bodova • Seminarski rad: 5 bodova • Problemski zadatak: 20 bodova • Usmeni deo ispita: 25 bodova

  5. Literatura • Structure and mechanism in protein science, Alan Fersht • Enzimologija: Laboratorijski priručnik, Radivoje Prodanović i Tanja Ćirković Veličković • Zbirka zadataka iz enzimologije, Ivanka Karadžić

  6. Enzyme catalysis, not different, just better! • Katalizator je supstanca koja dovodi do ubrzanja hemijske reakcije, tako da se pri tom promena G ne menja (IUPAC, 1981.) • Biološki katalizatori: Proteini (enzimi, abzimi) RNK (ribozimi) Mimetici enzima - Šta enzim radi? Struktura proteina – enzima Hemijska kinetika – enzimska kinetika

  7. Sukcinat dehidrogenaza sa vezanim hemom (prostetičnom grupom) • Enzim • Monomeran • Homo/hetero dimeran, trimeran etc • Oligomeran • Multienzimski kompleksi • Holoenzim (apoenzim + kofaktor/koenzim) • Kofaktor • Koenzim • Prosteticna grupa (čvrsto vezan kofaktor)

  8. Nomenklatura • Trivijalna imena enzima • E.C. nomenklatura

  9. E.C. Nomenklatura enzima • Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes by the Reactions they Catalyse • http://www.chem.qmul.ac.uk/iubmb/enzyme/

  10. EC 1.1 Oksidoreduktaze • Acting on the CH-OH group of donors • ContentsEC 1.1.1 With NAD or NADP as acceptor • EC 1.1.2 With a cytochrome as acceptor • EC 1.1.3 With oxygen as acceptor • EC 1.1.4 With a disulfide as acceptor • EC 1.1.5 With a quinone or similar compound as acceptor • EC 1.1.99 With other acceptors EC 2Transferaze EC 3Hidrolaze EC 4Liaze EC 5Izomeraze EC 6Ligaze

  11. EC 1Oxidoreductases • EC 1.1Acting on the CH-OH group of donors • EC 1.2Acting on the aldehyde or oxo group of donors • EC 1.3Acting on the CH-CH group of donors • EC 1.4Acting on the CH-NH2 group of donors • EC 1.5Acting on the CH-NH group of donors • EC 1.6Acting on NADH or NADPH • EC 1.7Acting on other nitrogenous compounds as donors • EC 1.8Acting on a sulfur group of donors • EC 1.9Acting on a heme group of donors • EC 1.10Acting on diphenols and related substances as donors • EC 1.11Acting on a peroxide as acceptor • EC 1.12Acting on hydrogen as donor • EC 1.13Acting on single donors with incorporation of molecular oxygen (oxygenases) • EC 1.14Acting on paired donors, with incorporation or reduction of molecular oxygen • EC 1.15Acting on superoxide radicals as acceptor • EC 1.16Oxidising metal ions • EC 1.17Acting on CH or CH2 groups • EC 1.18Acting on iron-sulfur proteins as donors • EC 1.19Acting on reduced flavodoxin as donor • EC 1.20Acting on phosphorus or arsenic in donors • EC 1.21Acting on X-H and Y-H to form an X-Y bond • EC 1.97Other oxidoreductases

  12. E.C. vs. Trivijalna nomenklatura • EC 1.1.1.1 alcohol dehydrogenaseEC 1.1.1.2 alcohol dehydrogenase (NADP+)EC 1.1.1.3 homoserine dehydrogenaseEC 1.1.1.4 (R,R)-butanediol dehydrogenaseEC 1.1.1.5 acetoin dehydrogenaseEC 1.1.1.6 glycerol dehydrogenaseEC 1.1.1.7 propanediol-phosphate dehydrogenaseEC 1.1.1.8 glycerol-3-phosphate dehydrogenase (NAD+)EC 1.1.1.9 D-xylulose reductaseEC 1.1.1.10 L-xylulose reductase

  13. http://www.chem.qmul.ac.uk/iubmb/enzyme/search.html

  14. Searching the Enzyme list • This search form looks at IUBMB Enzyme Nomenclature with a URL starting http://www.chem.qmul.ac.uk/iubmb/enzyme/ All recommended Enzymes are listed on the web. This search excludes other biochemical recommendations on enzyme kinetics, biochemical thermodynamics, and recommendations made by IUBMB only. To search these click here or for more chemical recommendations and other IUPAC recommendations click here. • Search: PEPSIN • Some search terms cause problems:For (S)-stylopine use stylopine otherwise all references with S as an initial are included. For germacrene A use "germacrene A"

  15. Web Results 1 - 10 of about 32 for pepsin [definition]. (0.06 seconds)  • EC 3.4.23 • EC 3.4.23. Aspartic endopeptidases. Contents. EC 3.4.23.1 pepsin A EC 3.4.23.2 pepsin B EC 3.4.23.3 gastricsin EC 3.4.23.4 chymosin EC 3.4.23.5 cathepsin D ...www.chem.qmul.ac.uk/iubmb/enzyme/EC3/4/23/ - 5k - Cached - Similar pages • EC 3.4.23.1 • Human pepsin A occurs in five molecular forms. Pig pepsin D [1,2] is ... Lee, D. and Ryle, A.P. Pepsin D. A minor component of commercial pepsin...www.chem.qmul.ac.uk/iubmb/enzyme/EC3/4/23/1.html - 5k - Cached - Similar pages • EC 3.4.23.18 • In peptidase family A1 (pepsin A family). Formerly included in EC 3.4.23.6 ... proteinase of Aspergillus awamori - an analog of penicillopepsin and pepsin. ...www.chem.qmul.ac.uk/iubmb/enzyme/EC3/4/23/18.html - 7k - Cached - Similar pages • EC 3.4.23.3 • Other names: pepsin C; pig parapepsin II; parapepsin II ... In peptidase family A1 (pepsin A family). Formerly EC 3.4.4.22. Links to other databases: BRENDA ...www.chem.qmul.ac.uk/iubmb/enzyme/EC3/4/23/3.html - 4k - Cached - Similar pages

  16. IUBMB Enzyme Nomenclature • EC 3.4.23.1 • Accepted name: pepsin A • Reaction: Preferential cleavage: hydrophobic, preferably aromatic, residues in P1 and P1' positions. Cleaves Phe1 Val, Gln4 His, Glu13 Ala, Ala14 Leu, Leu15 Tyr, Tyr16 Leu, Gly23 Phe, Phe24 Phe and Phe25 Tyr bonds in the B chain of insulin • Other names: pepsin; lactated pepsin; pepsin fortior; fundus-pepsin; elixir lactate of pepsin; P I; lactated pepsin elixir; P II; pepsin R; pepsin D • Comments: The predominant endopeptidase in the gastric juice of vertebrates, formed from pepsinogen A by limited proteolysis. Human pepsin A occurs in five molecular forms. Pig pepsin D [1,2] is unphosphorylated pepsin A. Type example of peptidase family A1. Formerly EC 3.4.4.1 • Links to other databases:BRENDA, EXPASY, GTD, MEROPS, PDB, CAS registry number: 9001-75-6 • References: • 1. Lee, D. and Ryle, A.P. Pepsinogen D. A fourth proteolytic zymogen from pig gastric mucosa. Biochem. J. 104 (1967) 735-741. [PMID: 4167464] • 2. Lee, D. and Ryle, A.P. Pepsin D. A minor component of commercial pepsin preparations. Biochem. J. 104 (1967) 742-748. [PMID: 4860638] • 3. Foltmann, R. Gastric proteinases -structure, function, evolution and mechanism of action. Essays Biochem. 17 (1981) 52-84. [PMID: 6795036] • 4. James, M.N.G. and Sielecki, A.R. Molecular structure of an aspartic proteinase zymogen, porcine pepsinogen, at 1.8 Å resolution. Nature 319 (1986) 33-38. [PMID: 3941737] • 5. Fruton, J.S. Aspartyl proteinases. In New Comprehensive Biochemistry Vol. 16, Hydrolytic Enzymes (Neuberger, A. and Brocklehurst, K., eds), pp. 1-38 (1987) Elsevier, Amsterdam • 6. Tang, J. and Wong, R.N.S. Evolution in the structure and function of aspartic proteases. J. Cell. Biochem. 33 (1987) 53-63. [PMID: 3546346] • 7. Pohl, J. and Dunn, B.M. Secondary enzyme-substrate interactions: kinetic evidence for ionic interactions between substrate side chains and the pepsin active site. Biochemistry 27 (1988) 4827-4834. [PMID: 3139029]

  17. acetyl-L-phenylalanyl-L-diiodotyrosine+H2O =acetyl-L-phenylalanine+L-diiodotyrosine

  18. PDB: x-ray struktura pepsina u kompleksu sa inhibitorom