Download Welcome to 3FF3! Bio

Welcome to 3FF3!
Bio-organic Chemistry
Jan. 7, 2008
• Instructor: Adrienne Pedrech
– ABB 417
– Email: [email protected]
-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
Evaluation
Assignments
Labs:
2 x 5%
-write up
- practical mark
10%
15%
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)
Texts:
• Dobson “Foundations of Chemical Biology,” (Optionalbookstore)
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
Simple organics
BIOLOGY
Life
large macromolecules;
cells—contain ~ 100,
000 different
compounds interacting
CHEMISTRY
eg HCN, H2C=O
(mono-functional)
Biologically relevant organics:
polyfunctional
1 ° Metabolism – present in all cell
Cf 20A3/B3
(focus of 3FF3)
2 ° Metabolism – specific species, eg. Caffeine (focus of 4DD3)
How different
are they?
BIOLOGY:
CHEMISTRY:
cell
Round-bottom flask
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)
2)
3)
How do chemists synthesize these structures?
How are they made in vivo?
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 monofunctional simple molecules
In this course, we will follow some of the ideas of how life may
have evolved:
HCN + NH3
bases
nucleosides
H2C=O
sugars
phosphate
nucleotides
more RNA, other
molecules
catalysis
RNA
"RNA world"
modern "protein" world
CH4, NH3
H2O
amino
acids
RNA
(ribozyme)
proteins
RNA World
• Catalysis by ribozymes occurred before protein catalysis
• Explains current central dogma:
transcription
translation
protein
RNA
DNA
requires
protein
requires RNA
+ protein
Which came first: nucleic acids or protein?
RNA world hypothesis suggests RNA was first molecule
to act as both template & catalyst:
catalysis & replication
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 Course
Labs illustrate:
1)
2)
3)
4)
5)
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)
6)
7)
8)
Application of biology to 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
Two Views of DNA
1)
Biochemist’s view:
shows overall shape, ignores atoms & bonds
2)
chemist’s view: atom-by-atom
structure, functional groups; illustrates concepts
from 2OA3/2OB3
Biochemist’s View of the DNA Double Helix
Minor
groove
Major
groove
Chemist’s View
O
alkene
O
O P O
O H
H
diastereotopic
Ring
conformation
ax/eq
H
H-bonds
NH
N
O
H
 OH
resonance
O
 bonds
H
H
OH
chirality
2o alcohol
(FG's)
nucleophilic
O +
substitution rxn
O P O
O electrophilic
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
6 π electrons, stable cation  weaker
acid, higher pKa (~ 5) & strong conj.
base
+ H
N
H
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:
N :
e- donor
base
H-bond
acceptor
O
H
H
e- acceptor
acid
H-bond
donor
• This is a NON-specific interaction, i.e., any H-bond donor
will suffice
Contrast with Nucleic Acid Bases
(A, T, C, G, U) – Specific!
Pyrimidines (like pyridine):
O
NH2
NH
N
H
H
*
NH
O
N
O
N
O
N
*
H *
Uracil (U)
(RNA only)
Thymine (T)
(DNA only)
Cytosine (C)
Purines
O
NH2
N
N
N
N
H*
Adenine (A)
O
N
N
N
H
*
N
NH2
Guanine (G)
* 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!
e.g. Guanine-Cytosine:
H
H
N
O
N
N
H
N
N
N
NH
H
O
N
H
2 lone pairs in
plane at 120o to
C=O bond
H
• Why?
G
C
– In G-C duplex, 3 complementary H-bonds can form: donors &
acceptors = molecular recognition
• Can use NMR to do a titration curve:
G+C
Ka
GC
get equilibrium constant,
G = -RT ln K = H-TS
• 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
• 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!
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…
NH2
N
NH3
+
N
HCN
N
H
N
Adenine
Polymerization of HCN
– Interesting because H-CN/CN- is probably the simplest molecule
that can be both a nucleophile & electrophile, and also form C-C
bonds
Mechanism?
H
+
N C
H
H
N
+
H
HN
H
C N
H
N
N
N
H
N
NH
+
H
H
NH3
N
N
H
H
H
H
N
NH
NH2
H
N
tautomerization
N
H
N
N
H
NH
N
H
NH
+
NH2
N
H
+
NH
N
N
H
N
+
NH2
N
N
H
N
N
H
N
N
Other Bases?
HC N
G, U, T and C
NH3
N
N
N (cyanogen)
H (cyanoacetylene)
** Try these mechanisms!
Properties of Pyridine
• We’ve seen it as an acid & an H-bond acceptor
• Lone pair can act as a nucleophile:
O
O
N
N
+
+
+
N
X
SN2
R X
+
N R
e.g. exp 3: benzyl dihydronicotinamide
O
O
H2N
(like NaBH4)
N
+
aromatic, but
+ve charge
+
Ph
O
"H-"
H2N
H
H
N
Ph
electron acceptor:
electrophile
H2N
reduction
N
Ph
• 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:
CN
CN
DielsAlder
NH
N
H
electical
discharge
[O],
hydrolysis of CN
CH4 + N2 + H2
O
NH2
N
1% yield
• NAD or related structure may have controlled redox
chemistry long before enzymes involved!
Another example of N-Alkylation of Pyridines
Caffeine
O
N
HN
O
O
N
HN
N
N
H
O
N
N
CH3
This is an SN2 reaction with stereospecificity
R
NH
R
R
Ad
+
+
H3C
S
N
Met
R
s-adenosyl methionine
CH3
+
Ad
S
Met
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:
OH
H
H
O
H
OH
O
CH2OH
CH2OH
O
OH
glycolaldehyde
glyceraldehyde
(chiral)
dihydroxyacetone
(achiral)
Aldose
Aldose
Ketose
•
Most sugars, i.e., glyceraldehyde are chiral: sp3
hybridized C with 4 different substituents
HO
CHO
CHO
=
H
OH
H
OH
OH
CHO
=
H
OH
OH
(R)-glyceraldehyde
The last structure is the Fischer projection:
1) CHO at the top
2) Carbon chain runs downward
3) Bonds that are vertical point down from chiral centre
4) Bonds that are horizontal point up
5) H is not shown: line to LHS is not a methyl group
• 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 rightdexter)
 (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 Sugars
1)
The aldehyde group:
a)
Aldehydes can be oxidized
Ag(0)
Ag(I)
H
NH3
O
O
HO
Aldose
Aldonic acid
“reducing sugars” – those that have a free aldehyde (most aldehydes)
give a positive Tollen’s test (silver mirror)
b)
Aldehydes can be reduced
H
H
O
NaBH4
OH
c)
Reaction with a Nucleophile
H
OH
O
MeMgBr
•
Combination of these ideas  Killiani-Fischer
synthesis: used by Fischer to correate D/Lglyceraldehyde with threose/erythrose configurations:
CN
CN
H
O
OH
- CN
Nu, (recall
from base synthesis)
HO
+
cyanohydrins
(stereoisomers)
H3O+ nitrile hydrolysis
OH
+
HO
CO2H
CO2H
CHO
CHO
NaBH4
OH
+
HO
(reduce)
pair of homologous
aldoses
aldonic acids
Reactions (of aldehydes) with Internal Nucleophiles
O
H
1
2
HO
4
OH
5
OH
CH2OH
6
6
=
3
H+
OH
OH
OH
5
4
HO
HO
O
2
3
HO
1
H
D-glucose
OH
O
HO
HO
OH
HO
a "hemiacetal"
D-glucopyranose
Derivative of pyran
O
• Glucose forms 6-membered ring b/c all substituents are
equatorial, thus avoiding 1,3-diaxial interactions
• Can also get furanoses, e.g., ribose:
OH
HO
O
O
OH
HO
H
HO
OH
HO
OH
ribofuranose
O
like furan
• Ribose prefers 5-membered ring (as opposed to 6)
otherwise there would be an axial OH in the 6-membered ring
O
OH
OH
OH
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.
O
MeO
H
+
2 MeOH
+
H2O
H
2 molecules out
3 molecules in
** significant –ve ΔS!
OMe
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
Mutatrotation
OH
OH
O
HO
HO
OH
OH
HO
HO
HO
O
HO
H
-D-glucopyranose (19o)
OH
OH
O
HO
HO
OH
HO
HO
HO
OH
-D-glucopyranose (112o)
H
HO
O
In solution, with acid present (catalytic), get
MUTAROTATION: not via the aldehyde, but oxonium ion
O
O
OH
+
H2O
O
H+

oxonium ion

OH
+112o ()
[]D
+52.7o
at equilibrium
time
MUTAROTATION
+19o ()
• At equilibrium, ~
38:62 α:β despite α
having an AXIAL
OH…WHY?
ANOMERIC EFFECT
Anomeric Effect
+
O

O
-OH
OH
O lone pair is antiperiplanar to
C-O σ bond  GOOD orbital
overlap (not the case with the βanomer)
oxonium ion