Welcome to CHEM BIO 3OA3! Bio-organic Chemistry [OLD CHEM 3FF3]

1. Welcome to CHEM BIO 3OA3!Bio-organic Chemistry[OLD CHEM 3FF3] Sept. 11, 2009

2. Instructor: Paul Harrison • ABB 418, ext. 27290 • Email: pharriso@mcmaster.ca • Course website:http://www.elm.mcmaster.ca/ Lectures: MW 08:30, F 10:30 (ABB/106) • Office Hours: M 12:30-2:30 or by appointment • Labs: 2:30-5:30 R or F (ABB 217) • Every week • Labs start next Fri. Sept. 17, 2009

3. Web site update • ELM page: • Lectures 1: includes everything for today, and approx. 1 week of material: intro and bases • Course outline • Detailed course description: lecture-by-lecture • Calendar

4. For Thursday 11th & Friday 12th • Check-in, meet TA, safety and Lab 1 (Isolation of Caffeine from Tea) • Lab manuals: Available on web; MUST bring printed copy • BEFORE the lab, read lab manual intro, safety and exp. 1 • Also need: • Duplicate lab book (20B3 book is ok) • Goggles (mandatory) • Lab coats (recommended) • No shorts or sandals • Obey safety rules; marks will be deducted for poor safety • Work at own pace—some labs are 2 or 3 wk labs. In some cases more than 1 exp. can be worked in a lab period—your TA will provide instruction

5. Evaluation Assignments 2 x 5% 10% Labs: -write up 15% - practical mark 5% Midterm 20% Final 50% Midterm test: Fri. Oct. 30, 2009 at 7:00 pm Assignments: Oct. 9 – Oct. 19 Nov. 13 – Nov. 23 Note: academic dishonesty statement on outline-NO copying on assignments or labs (exception when sharing results)

6. Texts: • Dobson “Foundations of Chemical Biology,” (Optional- bookstore) Background & “Refreshers” • An organic chemistry textbook (e.g. Solomons) • A biochemistry textbook (e.g. Garrett) • 2OA3/2OB3 old exam on web This course has selected examples from a variety of sources, including Dobson &: • Buckberry “Essentials of Biological Chemistry” • Dugas, H. "Bio-organic Chemistry" • Waldman, H. & Janning, P. “Chemical Biology” • Also see my slides on the website

7. What is bio-organic chemistry? Biological chem? Chemical bio? Chemical Biology: “Development & use of chemistry techniques for the study of biological phenomena” (Stuart Schreiber) Biological Chemistry: “Understanding how biological processes are controlled by underlying chemical principles” (Buckberry & Teasdale) Bio-organic Chemistry: “Application of the tools of chemistry to the understanding of biochemical processes” (Dugas) What’s the difference between these??? Deal with interface of biology & chemistry

8. Simple organics eg HCN, H2C=O (mono-functional) Cf 20A3/B3 BIOLOGY CHEMISTRY Life large macromolecules; cells—contain ~ 100, 000 different compounds interacting Biologically relevant organics: polyfunctional 1 ° Metabolism – present in all cells (focus of 3OA3) 2 ° Metabolism – specific species, eg. Caffeine (focus of 4DD3) How different are they? CHEMISTRY: Round-bottom flask BIOLOGY: cell

9. Exchange of ideas: Biology Chemistry • Chemistry • Explains events of biology: mechanisms, rationalization • Biology • Provides challenges to chemistry: synthesis, structure determination • Inspires chemists: biomimetics → improved chemistry by understanding of biology (e.g. enzymes)

10. Key Processes of 1° Metabolism Bases + sugars → nucleosides nucleic acids Sugars (monosaccharides) polysaccharides Amino acids proteins Polymerization reactions; cell also needs the reverse process We will look at each of these processes, forwards and backwards, in 4 parts, comparing and contrasting the reactions: • How do chemists synthesize these structures? • How might these structures have formed in the pre-biotic world, and have led to life on earth? • How are they made in vivo? • Can we design improved chemistry by understanding the biology: biomimetic synthesis?

11. Properties of Biological Molecules that Inspire Chemists • Large → challenges: for synthesis for structural prediction (e.g. protein folding) 2) Size → multiple FG’s (active site) ALIGNED to achieve a goal (e.g. enzyme active site, bases in NAs) 3) Multiple non-covalent weak interactions → sum to strong, stable binding non-covalent complexes (e.g. substrate, inhibitor, DNA) 4) Specificity → specific interactions between 2 molecules in an ensemble within the cell

12. 5) Regulated → switchable, allows control of cell → activation/inhibition 6) Catalysis → groups work in concert 7) Replication → turnover e.g. an enzyme has many turnovers, nucleic acids replicate

13. Evolution of Life • Life did not suddenly crop up in its current form of complex structures (DNA, proteins) in one sudden reaction from mono-functional simple molecules • In this course, we will follow some of the ideas of how life may have evolved:

14. RNA World • Catalysis by ribozymes occurred before protein catalysis • Explains current central dogma: Which came first: nucleic acids or protein? RNA world hypothesis suggests RNA was first molecule to act as both template & catalyst: catalysis & replication

15. How did these reactions occur in the pre-RNA world? In the RNA world? & in modern organisms? CATALYSIS & SPECIFICITY How are these achieved? (Role of NON-COVALENT forces– BINDING) a) in chemical synthesis b) in the pre-biotic world c) in vivo – how is the cell CONTROLLED? d) in chemical models – can we design better chemistry through understanding biochemical mechanisms?

16. Relevance of Labs to the Course Labs illustrate: • Biologically relevant small molecules (e.g. caffeine –Exp 1, related to bases) • Cofactor chemistry – pyridinium ions (e.g. NADH, Exp 2 & 4) • Biomimetic chemistry (e.g. simplified model of NADH, Exp 2) • Chemical mechanisms relevant to catalysis (e.g. NADH, Exp 2) • Structural principles & characterization (e.g. sugars: anomers of glucose, anomeric effect, diastereomers, NMR, Exp 3)

17. Application of biologyto stereoselective chemical synthesis (e.g. yeast, Exp 4) • Synthesis of small molecules (e.g. peptides, drugs, dilantin, esters, Exp 5,6,7) • Chemical catalysis (e.g. protection & activation strategies relevant to peptide synthesis in vivo and in vitro, Exp 5) • Comparison of organic and biological reactions (Exp. 6) • Enzyme mechanisms and active sites (Exp. 7) All of these demonstrate inter-disciplinary area between chemistry & biology

18. Two Views of DNA • Biochemist’s view: shows overall shape, ignores atoms & bonds • Chemist’s view: atom-by-atom structure, functional groups; illustrates concepts from 2OA3/2OB3 GOAL: to think as both a chemist and a biochemist: i.e. a chemical biologist!

19. Biochemist’s View of the DNA Double Helix Minor groove Major groove

20. Chemist’s View

21. BASES • Aromatic structures: • all sp2 hybridized atoms (6 p orbitals, 6 π e-) • planar (like benzene) • N has lone pair in both pyridine & pyrrole  basic (H+ acceptor or e- donor)

22. 6 π electrons, stable cation  weaker acid, higher pKa (~ 5) & strong conj. base sp3 hybridized N, NOT aromatic  strong acid, low pKa (~ -4) & weak conj. base • Pyrrole uses lone pair in aromatic sextet → protonation means loss of aromaticity (BAD!) • Pyridine’s N has free lone pair to accept H+ •  pyridine is often used as a base in organic chemistry, since it is soluble in many common organic solvents

23. The lone pair also makes pyridine a H-bond acceptor e.g. benzene is insoluble in H2O but pyridine is soluble: • This is a NON-specific interaction, i.e., any H-bond donor will work

24. What about pyrrole? • Is it soluble in water?

25. Other groups form H-bonds • Electronegative atoms, e.g. carbonyl group: • Acetone is soluble in water, but propane is not: • Again, non-specific interactions

26. Bifunctional compounds

27. Bifunctional compounds

28. Contrast with Nucleic Acid Bases (A, T, C, G, U) – Specific! • Evidence for specificity? • Why are these interactions specific? e.g. G-C & A-T

29. Evidence? • If mix G & C together → exothermic reaction occurs; change in 1H chemical shift in NMR; other changes  reaction occurring • Also occurs with A & T • Other combinations → no change! e.g. Guanine-Cytosine: • Why? • In G-C duplex, 3 complementary H-bonds can form: donors & acceptors = molecular recognition

30. Can use NMR to do a titration curve: • Favorable reaction because ΔH for complex formation = -3 x H-bond energy • ΔS is unfavorable → complex is organized  3 H-bonds overcome the entropy of complex formation • **Note: In synthetic DNAs other interactions can occur

31. Molecular recognition not limited to natural bases: Forms supramolecular structure: 6 molecules in a ring  Create new architecture by thinking about biology i.e., biologically inspired chemistry!

32. Synthesis of the Bases in Nucleic Acids Thousands of methods in heterocyclic chemistry– we’ll do 1 example: Juan Or (1961) May be the first step in the origin of life… Interesting because H-CN/CN- is probably the simplest molecule that can be both a nucleophile & electrophile, and also form C-C bonds 32

33. Mechanism? 33

34. Other Bases? ** All these species are found in interstellar space: observed by e.g. absorption of IR radiation: a natural example of IR spectroscopy! Try these mechanisms! 34

35. Properties of Pyridine We’ve seen it as an acid & an H-bond acceptor Lone pair can act as a nucleophile: 35

36. Balance between aromaticity & charged vs non-aromatic & neutral!  can undergo REDOX reaction reversibly: 36

37. Interestingly, nicotinamide may have been present in the pre-biotic world: NAD or related structure may have controlled redox chemistry long before enzymes involved! electrical discharge CH4 + N2 + H2 37

38. Another example of N-Alkylation of Pyridines This is an SN2 reaction: stereospecific with INVERSION 38

39. References Solomons Amines: basicity ch.20 Pyridine & pyrrole pp 644-5 NAD+/NADH pp 645-6, 537-8, 544-6 Bases in nucleic acids ch. 25 Also see Dobson, ch.9 Topics in Current Chemistry, v 259, p 29-68 39