Welcome to 3FF3!Bio-organic Chemistry

Jan. 7, 2008

• 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!)

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

EvaluationAssignments 2 x 5% 10%

Labs: -write up 15% - practical mark 5%

Midterm 20%Final 50%

Midterm test:

Fri. Feb. 29, 2008 at 7:00 pmMake-up test: TBDAssignments: Feb.6 – Feb.13 Mar.7 – Mar.14 Note: academic dishonesty statement on outline-NO

copying on assignments or labs (exception when sharing results)

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

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

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 cell (focus of 3FF3)

2 ° Metabolism – specific species, eg. Caffeine (focus of 4DD3)

CHEMISTRY:

Round-bottom flask

BIOLOGY:

cell

How different are they?

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)

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:

1) How do chemists synthesize these structures?

2) How are they made in vivo?

3) Improved chemistry through understanding the biology: biomimetic synthesis

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

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

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: HCN + NH3 bases

H2C=O sugars

nucleosides

phosphate

nucleotides

RNA

"RNA world"

catalysismore RNA, other molecules

modern "protein" world

CH4, NH3

H2Oamino acids

proteinsRNA

(ribozyme)

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

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?

Relevance of Labs to the CourseLabs illustrate:

1) Biologically relevant small molecules (e.g. caffeine –Exp 1)

2) Structural principles & characterization(e.g. anomers of glucose, anomeric effect, diastereomers, NMR, Exp 2)

3) Cofactor chemistry – pyridinium ions (e.g. NADH, Exp 3 & 4)

4) Biomimetic chemistry (e.g. simplified model of NADH, Exp 3)

5) Chemical mechanisms relevant to catalysis (e.g. NADH, Exp 3)

6) Application of biology to stereoselective chemical synthesis (e.g. yeast, Exp 4)

7) Synthesis of small molecules (e.g. drugs, dilantin, tylenol, Exp 5,7)

8) 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

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

Biochemist’s View of the DNA Double Helix

Major groove

Minor groove

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

BASES

N N

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?

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

• 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

N HO

H:

e- donor e- acceptor

H-bond acceptor

H-bonddonor

acidbase

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

N N

NN

NH2

H

N N

NN

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

• 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

• 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

• 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

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

NH N

NN

NH2

NH3 + HCN

Adenine

Polymerization of HCN

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

N

NH3

N N

N H

HC

G, U, T and C

(cyanogen)

(cyanoacetylene)

Other Bases?

** Try these mechanisms!

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)

e.g. exp 3: benzyl dihydronicotinamide

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

can undergo REDOX reaction reversibly:

NAD-H NAD+ + "H-"

reductant oxidant

• 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

electical discharge

CH4 + N2 + H2

Another example of N-Alkylation of Pyridines

NHN

NNH

O

O NN

NNH

O

O

CH3

Caffeine

This is an SN2 reaction with stereospecificity

R

NH

RCH3

S+

Met

Ad R

N

R

CH3 SMet

Ad+ +

s-adenosyl methionine

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

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:

OHH

CH2OH

OHOH

O

OHCH2OH

OH

glyceraldehyde (chiral)

dihydroxyacetone(achiral)

Aldose Ketose

glycolaldehyde

Aldose

• Most sugars, i.e., glyceraldehyde are chiral: sp3 hybridized C with 4 different substituents

The last structure is the Fischer projection:1) CHO at the top2) Carbon chain runs downward3) Bonds that are vertical point down from chiral centre4) Bonds that are horizontal point up5) H is not shown: line to LHS is not a methyl group

OH

OH

H

CHOCHO

OH

OHH

CHO

OH

OHH= =

(R)-glyceraldehyde

• 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

• 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)

Reactions of Sugars1) The aldehyde group:

a) Aldehydes can be oxidized

“reducing sugars” – those that have a free aldehyde (most aldehydes) give a positive Tollen’s test (silver mirror)

b) Aldehydes can be reduced

OH OOH

Ag(I) Ag(0)

NH3

Aldose Aldonic acid

OH OHHNaBH4

c) Reaction with a Nucleophile

• Combination of these ideas Killiani-Fischer synthesis: used by Fischer to correate D/L-glyceraldehyde with threose/erythrose configurations:

OH OHMeMgBr

OHOH

CN

OH

CN

OH

CO2H

OH

CO2H

OH

CHO

OH

CHO

-CN +

cyanohydrins(stereoisomers)

H3O+

+

aldonic acids

NaBH4

+

pair of homologousaldoses

Nu, (recallfrom base synthesis)

nitrile hydrolysis

(reduce)

Reactions (of aldehydes) with Internal Nucleophiles

• Glucose forms 6-membered ring b/c all substituents are equatorial, thus avoiding 1,3-diaxial interactions

O

OHOH

OH

OH

OH

OH

OHOH

OH

O

OHH

O

OH

OH

OH

OH

OH

CH2OH D-glucose

H+

a "hemiacetal"D-glucopyranose

Derivative of pyran

1

2

3

4

5

6

12

3

45

6

=

• Can also get furanoses, e.g., ribose:

O

H

OHOH

OHOH

OOH

OHOH

OH

O

ribofuranose

like furan

• Ribose prefers 5-membered ring (as opposed to 6) otherwise there would be an axial OH in the 6-membered ring

OOH

OHOH

Why do we get cyclic acetals of sugars? (Glucose in open form is << 1%)

a) Rearrangement reaction: we exchange a C=O bond for a stronger C-O σ bond ΔH is favored

b) There is little ring strain in 5- or 6- membered rings

c) ΔS: there is some loss of rotational entropy in making a ring, but less than in an intermolecular reaction:1 in, 1 out.

H

O

H

MeO OMe

+ 2 MeOH+ H2O

3 molecules in 2 molecules out

** significant –ve ΔS! ΔG = ΔH - TΔS

Favored for hemiacetal

Not too bad for cyclic acetal

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

O

OHOH

OH

OH

OH

OH

OHOH

OH

O

OHH

OH

OHOH

OH

OOH

HO

OHOH

OH

OHOH

-D-glucopyranose (19o)

-D-glucopyranose (112o)

Mutatrotation

In solution, with acid present (catalytic), get MUTAROTATION: not via the aldehyde, but oxonium ion

OOH

O+ O

OHH+

H2O

oxonium ion

• At equilibrium, ~ 38:62 α:β despite α having an AXIAL OH…WHY? ANOMERIC EFFECT

+112o ()[]D

+19o ()

+52.7o

at equilibrium

time

MUTAROTATION

O

OH

O+

-OH

O lone pair is antiperiplanar to C-O σ bond GOOD orbital overlap (not the case with the β-anomer)

oxonium ion

Anomeric Effect