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Welcome to 3FF3!Bio-organic Chemistry
Jan. 7, 2008
• Instructor: Adrienne Pedrech– ABB 417– Email: [email protected] 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