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

2. 2 Instructor: Paul Harrison –ABB 418, ext. 27290 –Email: pharriso@mcmaster.capharriso@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. 4 For Thursday 11 th & Friday 12 th 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. 5 Evaluation Assignments2 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. 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. 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. 8 BIOLOGYCHEMISTRY Simple organics eg HCN, H 2 C=O (mono-functional) Cf 20A3/B3 Biologically relevant organics: polyfunctional Life large macromolecules; cells—contain ~ 100, 000 different compounds interacting 1 ° Metabolism – present in all cells (focus of 3OA3) 2 ° Metabolism – specific species, eg. Caffeine (focus of 4DD3) CHEMISTRY: Round-bottom flask BIOLOGY: cell How different are they?

9. 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. 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: 1)How do chemists synthesize these structures? 2)How might these structures have formed in the pre-biotic world, and have led to life on earth? 3)How are they made in vivo? 4)Can we design improved chemistry by understanding the biology: biomimetic synthesis?

11. 11 Properties of Biological Molecules that Inspire Chemists 1)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. 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. 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. 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. 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. 16 Relevance of Labs to the Course Labs illustrate: 1)Biologically relevant small molecules (e.g. caffeine – Exp 1, related to bases) 2)Cofactor chemistry – pyridinium ions (e.g. NADH, Exp 2 & 4) 3)Biomimetic chemistry (e.g. simplified model of NADH, Exp 2) 4)Chemical mechanisms relevant to catalysis (e.g. NADH, Exp 2) 5)Structural principles & characterization (e.g. sugars: anomers of glucose, anomeric effect, diastereomers, NMR, Exp 3)

17. 17 6)Application of biology to stereoselective chemical synthesis (e.g. yeast, Exp 4) 7)Synthesis of small molecules (e.g. peptides, drugs, dilantin, esters, Exp 5,6,7) 8)Chemical catalysis (e.g. protection & activation strategies relevant to peptide synthesis in vivo and in vitro, Exp 5) 9)Comparison of organic and biological reactions (Exp. 6) 10)Enzyme mechanisms and active sites (Exp. 7) All of these demonstrate inter-disciplinary area between chemistry & biology

18. 18 Two Views of DNA 1)Biochemist’s view: shows overall shape, ignores atoms & bonds 2)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. 19 Biochemist’s View of the DNA Double Helix Major groove Minor groove

20. 20 Chemist’s View

21. 21 BASES Aromatic structures: –all sp 2 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. 22 6 π electrons, stable cation  weaker acid, higher pKa (~ 5) & strong conj. base sp 3 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. 23 The lone pair also makes pyridine a H-bond acceptor e.g. benzene is insoluble in H 2 O 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

28. 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. 29 Evidence? –If mix G & C together → exothermic reaction occurs; change in 1 H 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. 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. 31 Molecular recognition not limited to natural bases:  Create new architecture by thinking about biology i.e., biologically inspired chemistry! Forms supramolecular structure: 6 molecules in a ring

32. 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

33. 33 Mechanism?

34. 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!

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

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

37. 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 CH 4 + N 2 + H 2

38. 38 Another example of N-Alkylation of Pyridines This is an S N 2 reaction: stereospecific with INVERSION

39. 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