Welcome to 3FF3! Bio-organic Chemistry

1. Welcome to 3FF3!Bio-organic Chemistry Jan. 7, 2008

2. Instructor: Adrienne Pedrech • ABB 417 • Email: adriennepedrech@hotmail.com -Course website: http://www.chemistry.mcmaster.ca/courses/3f03/index.html Lectures: MW 8:30 F 10:30 (CNH/B107) • Office Hours: T 10:00-12:30 & F 1:00-2:30 or by appointment • Labs: 2:30-5:30 M (ABB 302,306) **Note: course timetable says ABB217 2:30-5:30 F (ABB 306) • Every week except reading week (Feb. 18-22) & Good Friday (Mar. 21) • Labs start Jan. 7, 2008 (TODAY!)

3. For Monday 7th & Friday 11th • Check-in, meet TA, safety and Lab 1 (Isolation of Caffeine from Tea) • Lab manuals: Buy today! • 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

4. Evaluation Assignments 2 x 5% 10% Labs: -write up 15% - practical mark 5% Midterm 20% Final 50% Midterm test: Fri. Feb. 29, 2008 at 7:00 pm Make-up test: TBD Assignments: Feb.6 – Feb.13 Mar.7 – Mar.14 Note: academic dishonesty statement on outline-NO copying on assignments or labs (exception when sharing results)

5. 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 notes on the website

6. 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

7. 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 cell (focus of 3FF3) 2 ° Metabolism – specific species, eg. Caffeine (focus of 4DD3) How different are they? CHEMISTRY: Round-bottom flask BIOLOGY: cell

8. 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)

9. 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 3 parts: • How do chemists synthesize these structures? • How are they made in vivo? • Improved chemistry through understanding the biology: biomimetic synthesis

10. 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

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

12. Evolution of Life • Life did not suddenly crop up in its element 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:

13. 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

14. 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 vivo – how is the cell CONTROLLED? c) in chemical models – can we design better chemistry through understanding biochemical mechanisms?

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

16. Application of biologyto stereoselective chemical synthesis (e.g. yeast, Exp 4) • Synthesis of small molecules (e.g. drugs, dilantin, tylenol, Exp 5,7) • Chemical catalysis (e.g. protection & activation strategies relevant to peptide synthesis in vivo and in vitro, Exp 6) All of these demonstrate inter-disciplinary area between chemistry & biology

17. 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

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

19. Chemist’s View

20. 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)

21. 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

22. 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 suffice

23. 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

24. 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

25. 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

26. 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!

27. Synthesis of Bases (Nucleic) • Thousands of methods in heterocyclic chemistry– we’ll do 1 example: • 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

28. Mechanism?

29. Other Bases? ** Try these mechanisms!

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

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

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

33. Another example of N-Alkylation of Pyridines This is an SN2 reaction with stereospecificity

34. 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

35. Sugar Chemistry & Glycobiology • In Solomons, ch.22 (pp 1073-1084, 1095-1100) • Sugars are poly-hydroxy aldehydes or ketones • Examples of simple sugars that may have existed in the pre-biotic world:

36. Most sugars, i.e., glyceraldehyde are chiral: sp3 hybridized C with 4 different substituents The last structure is the Fischer projection: • CHO at the top • Carbon chain runs downward • Bonds that are vertical point down from chiral centre • Bonds that are horizontal point up • H is not shown: line to LHS is not a methyl group

37. In (R) glyceraldehyde, H is to the left, OH to the right  D configuration; if OH is on the left, then it is L • D/L does NOT correlate with R/S • Most naturally occurring sugars are D, e.g. D-glucose • (R)-glyceraldehyde is optically active: rotates plane polarized light (def. of chirality) • (R)-D-glyceraldehyde rotates clockwise,  it is the (+) enantiomer, and also d-, dextro-rotatory (rotates to the right-dexter)  (R)-D-(+)-d-glyceraldehyde & its enantiomer is: (S)-L-(-)-l-glyderaldehyde (+)/d & (-)/l do NOT correlate

38. Glyceraldehyde is an aldo-triose (3 carbons) • Tetroses → 4 C’s – have 2 chiral centres • 4 stereoisomers: D/L erythrose – pair of enantiomers D/L threose - pair of enantiomers • Erythrose & threose are diastereomers: stereoisomers that are NOT enantiomers • D-threose & D-erythrose: • D refers to the chiral centre furthest down the chain (penultimate carbon) • Both are (-) even though glyceraldehyde is (+) → they differ in stereochemistry at top chiral centre • Pentoses – D-ribose in DNA • Hexoses – D-glucose (most common sugar)

40. Reactions of Sugars • The aldehyde group: • Aldehydes can be oxidized “reducing sugars” – those that have a free aldehyde (most aldehydes) give a positive Tollen’s test (silver mirror) • Aldehydes can be reduced

41. Reaction with a Nucleophile • Combination of these ideas  Killiani-Fischer synthesis: used by Fischer to correate D/L-glyceraldehyde with threose/erythrose configurations:

43. Reactions (of aldehydes) with Internal Nucleophiles • Glucose forms 6-membered ring b/c all substituents are equatorial, thus avoiding 1,3-diaxial interactions

44. Can also get furanoses, e.g., ribose: • Ribose prefers 5-membered ring (as opposed to 6) otherwise there would be an axial OH in the 6-membered ring

45. Why do we get cyclic acetals of sugars? (Glucose in open form is << 1%) • Rearrangement reaction: we exchange a C=O bond for a stronger C-O σ bond  ΔH is favored • There is little ring strain in 5- or 6- membered rings • ΔS: there is some loss of rotational entropy in making a ring, but less than in an intermolecular reaction:1 in, 1 out. ** significant –ve ΔS! ΔG = ΔH - TΔS Favored for hemiacetal Not too bad for cyclic acetal

46. Anomers • Generate a new chiral centre during hemiacetal formation (see overhead) • These are called ANOMERS • β-OH up • α-OH down • Stereoisomers at C1 diastereomers • α- and β- anomers of glucose can be crystallized in both pure forms • In solution, MUTAROTATION occurs

47. Mutatrotation

48. In solution, with acid present (catalytic), get MUTAROTATION: not via the aldehyde, but oxonium ion • At equilibrium, ~ 38:62 α:β despite α having an AXIAL OH…WHY? ANOMERIC EFFECT

49. Anomeric Effect oxonium ion O lone pair is antiperiplanar to C-O σ bond  GOOD orbital overlap (not the case with the β-anomer)