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 pm

Make-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 CHEMISTRYSimple organics

eg HCN, H2C=O

(mono-functional)

Cf 20A3/B3Biologically relevant organics: polyfunctional

Lifelarge 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 flaskBIOLOGY:

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° 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 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 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

5) Regulated → switchable, allows control of cell → activation/inhibiton

6) Catalysis → groups work in concert

7) Replication → turnovere.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" worldCH4, NH3H2O

amino 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

DNAtranscription

RNA proteintranslation

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

OPO

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

NH

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

N N

NH2

H

N N

N N

O

NH2H

N

NH

O

O

HN

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

N N

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

N N

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

ONH2

PhN

ONH2

PhN

ONH2

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