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Welcome to CHEM BIO 3OA3!Bio-organic Chemistry

[OLD CHEM 3FF3]Sept. 11, 2009

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• 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

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

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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

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EvaluationAssignments 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)

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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

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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

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BIOLOGY CHEMISTRY

Simple organics

eg HCN, H2C=O

(mono-functional)

Cf 20A3/B3Biologically 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?

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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)

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Key Processes of 1° MetabolismBases + 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?

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Properties of Biological Molecules that Inspire Chemists

1) Large → challenges: for synthesisfor 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

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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

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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:

HCN + NH3 bases

H2C=O sugars

nucleosides

phosphate

nucleotides

RNA

"RNA world"

catalysismore RNA, other molecules

CH4, NH3

H2Oamino acids

peptidesRNA

(ribozyme)

"pre-RNA world"

"pre-protein world"

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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

DNA

transcriptionRNA protein

translation

requiresprotein

requires RNA+ protein

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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?

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Relevance of Labs to the CourseLabs 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)

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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

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Two Views of DNA

1) Biochemist’s view: shows overall shape, ignores atoms & bonds

2) Chemist’s view: atom-by-atomstructure, functional groups; illustrates concepts from 2OA3/2OB3

GOAL: to think as both a chemist and a biochemist: i.e. a chemical biologist!

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Biochemist’s View of the DNA Double Helix

Major groove

Minor groove

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N

NH

O

O

O

H

OH

H

OH

HH

OP OOO

HH

OP

O

OO

2o alcohol(FG's)

alkene

bonds

resonance

Ringconformationax/eq

H-bonds

nucleophilic

electrophilic

substitution rxn

chirality

+

diastereotopic

Chemist’s View

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BASES

N NH

pyridine pyrrole

• 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)

ArN: H+ ArNH+

pKa?

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N H

N

H

H

+

+

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

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• 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

N HO

H:

e- donor e- acceptor

H-bond acceptor

H-bonddonor

acidbase

What about pyrrole?

• Is it soluble in water?

Other groups form H-bonds

• Electronegative atoms, e.g. carbonyl group:• Acetone is soluble in water, but propane is not:

• Again, non-specific interactions

O OH

OH.. ..

Bifunctional compounds

N OH NH

O

N O

mp 105-107oCbp 280-281oC

mp -42oCbp 115oC

mp -47oCbp 155oC

Bifunctional compounds

NH

O

N OH

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Contrast with Nucleic Acid Bases (A, T, C, G, U) – Specific!

N N

NN

NH2

H

N N

NNH

O

NH2

H

N

NH

O

O

H

N

NH

O

O

HN

N

O

NH2

HThymine (T)

Guanine (G)Adenine (A)

Uracil (U)Cytosine (C)

* *

*

*

*

Pyrimidines (like pyridine):

Purines

(DNA only) (RNA only)

* link to sugar

• Evidence for specificity?• Why are these interactions specific? e.g. G-C & A-T

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• 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!

NH N

NN

O

N

H

H

HNHN

O

N

H

H

G C

2 lone pairs inplane at 120o toC=O bond

e.g. Guanine-Cytosine:

• Why?– In G-C duplex, 3 complementary H-bonds can form: donors &

acceptors = molecular recognition

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• 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

G + CKa

G C

get equilibrium constant,

G = -RT ln K = H-TS

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• 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

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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

NH N

NN

NH2

NH3 + HCN

Adenine

Polymerization of HCN

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Mechanism?CN NH

H+

NHN

H

NH

NN

H

H NH

C N

N

H

HNH

NH

N

H+

NH

N

N NH

N

H

NH H+

NN

NN

H

NH2

NH3

H+

NN

NN

NH2

H

H

HH

+

NN

NH

N

NH2

H

H+

tautomerization

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N

NH3

N N

N H

HC

G, U, T and C

(cyanogen)

(cyanoacetylene)

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!

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

N R X N+

R

NX

O

N

O

+SN2

+ +

N

O

NH2

PhN

O

NH2

PhN

O

NH2

Ph

HH

++

aromatic, but +ve charge

electron acceptor:electrophile

"H-"

reduction

(like NaBH4)

non-aromatic,but neutral

[O]

oxidation

e.g. exp 2: benzyl dihydronicotinamide: R = PhCH2

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• Balance between aromaticity & charged vs non-aromatic & neutral!

can undergo REDOX reaction reversibly:

NAD-H NAD+ + "H-"

reductant oxidant

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• Interestingly, nicotinamide may have been present in the pre-biotic world:

• NAD or related structure may have controlled redox chemistry long before enzymes involved!

NH

CN

NH

CN

N

NH2

O

Diels-Alder

[O],hydrolysis of CN

1% yield

electrical discharge

CH4 + N2 + H2

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Another example of N-Alkylation of Pyridines

NHN

NNH

O

O NN

NN

O

O

CH3

CH3

CH3

Caffeine

This is an SN2 reaction: stereospecific with INVERSION

R

NH

RCH3

S+

Met

Ad R

N

R

CH3 SMet

Ad+ +

S-adenosyl-methionine(SAM, important co-factor)

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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