1. Pathways & Molecules M.A. Ott (CMBI)

2. Contents Pathways and Molecules M.A. Ott Enzymes and Metabolites Metabolic Pathways: Cholesterol Biosynthesis Metabolic Disorders BioMeta Database

3. Metabolite and Pathway Databases Pathways and Molecules M.A. Ott http://www.genome.ad.jp/kegg/ http://www.brenda.uni-koeln.de/ http://www.expasy.org/tools/pathways/ http://www.empproject.com/ http://metacyc.org/ http://ecocyc.org/ http://www.ncgr.org/pathdb/ http://medicago.vbi.vt.edu/B-Net/ http://www.mol-net.de/biopath/ http://www.ergo-light.com/ERGO/ http://www.reactome.org/ http://www.chem.qmul.ac.uk/iubmb/enzyme/ Kyoto Encyclopedia of Genes and Genomes BRENDA enzyme database ExPASy biochemical pathway EMP enzymology and metabolism data MetaCyc metabolic pathways EcoCyc E. coli genome and metabolism PathDB biological pathways and networks B-NET - Biochemical Network BioPath C@ROL database ERGO comprehensive genome analysis Reactome biological processes IUBMB enzymes

4. Metabolism and Friends Pathways and Molecules M.A. Ott Metabolism: The reactions in organisms Anabolism: Synthesis of larger biomolecules from smaller ones » Usually requires energy input Catabolism: Break down of larger molecules into smaller ones » Usually releases energy

5. Enzymes Pathways and Molecules M.A. Ott Virtually all metabolic reactions require enzymatic catalysis Rate enhancement factor can be up to 10 15 Enzymes are highly reaction-specific, catalyzing only one conversion Enzymes are substrate-specific, limiting their action to only one compound or to related compounds

6. The Metabolic Network Pathways and Molecules M.A. Ott

7. Some Metabolites Pathways and Molecules M.A. Ott “Common” metabolites: Water, NADH, ATP, Phosphate, … End products of pathways: Vitamin B 12, Urea, Penicillin, Ecdysone, … Intermediates in pathways: Glucose-6-P, Lanosterol, Precorrins, Shikimate, …

8. Common Metabolites: ATP / ADP Pathways and Molecules M.A. Ott Full structures: Shorthand:

9. Common Metabolites: NADH / NAD + Pathways and Molecules M.A. Ott Full structures: Shorthand:

10. Common Metabolites Pathways and Molecules M.A. Ott Water Ammonia Phosphate ATP, ADP NADH, NAD + NADPH, NADP + FAD, FADH2 FMN, FMNH2 SAM, SAH Coenzyme A Glutamate/2-Oxoglutarate Phosphorylation Reduction/oxidation Methyl group transfer Acyl group transfer Amino/ketone group exchange

11. Cholesterol Biosynthesis: Outline Pathways and Molecules M.A. Ott

12. Cholesterol Biosynthesis from Squalene Pathways and Molecules M.A. Ott

13. Metabolic Disorders Pathways and Molecules M.A. Ott Inability to synthesize compounds: Absence of important compounds Inability to degrade compounds: Accumulation of undesired waste products E.g., in phenylketonuria

14. Phenylketonuria (Error in Phenylalanine Catabolism) Pathways and Molecules M.A. Ott

15. The BioMeta Database Pathways and Molecules M.A. Ott

16. BioMeta Database Structure Pathways and Molecules M.A. Ott

17. BioMeta Database Structure Pathways and Molecules M.A. Ott Molecules Reaction 1: Mol_1 + Mol_2 Mol_3 + Mol_4 Reaction 2: Mol_2 + Mol_3 --> Mol_5 + Mol_6 Reaction 3: 2 Mol_6 --> Mol_7 R-M Links Reactions

18. Sample Database Query Pathways and Molecules M.A. Ott ec_nr | enzyme_name | rxn_id |rev| role |stoich| name --------+-----------------+----------+---+------+------+------------ 1.2.3.4 | oxalate oxidase | MR000247 | i | s | 1 | Oxalic acid 1.2.3.4 | oxalate oxidase | MR000247 | i | s | 1 | O2 1.2.3.4 | oxalate oxidase | MR000247 | i | p | 1 | H2O2 1.2.3.4 | oxalate oxidase | MR000247 | i | p | 2 | CO2

19. Molecular Structures and Reactions Pathways and Molecules M.A. Ott Reactions:balancing atoms & charges adding direction/reversibility Molecules:adding stereochemical configurations “canonicalizing” tautomeric form

20. Alternative Pathways Pathways and Molecules M.A. Ott

21. BioMeta Database Pathways and Molecules M.A. Ott Based on freely available data (KEGG Ligand database) Augmentation, completion and correction of small-molecule information: - Adding missing stereochemistry to structures - Balancing atoms and charges in reactions - Establishing the reversibility and direction of reactions Search for alternative pathways between metabolites Search for “missing” enzymes

22. BioMeta: Things Being Done Pathways and Molecules M.A. Ott Enhancing compound/reaction structures Establishing directionality/reversibility of reactions Distinguishing cofactors/“current”/“external”/ “common” metabolites from “real” metabolites Adding more compound data, e.g. pK a (curve) Building WWW interface

23. BioMeta: Things To Do Pathways and Molecules M.A. Ott Atom-to-atom correspondence (reaction mapping) Pathway search & generation Cellular localization Enzyme – species relations

24. Acknowledgements Pathways and Molecules M.A. Ott Felix van Diggelen Gert Vriend CMBI