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History of polymer science and the
determination of DNA structure
• Books on reserve:
“Inventing Polymer Science” by Yasu Furukawa
“The Path to the Double Helix” by Robert Olby
Biopolymers:
The ultimate “block” copolymers
• Three main biopolymers
¬ Peptides/proteins: monomer units: α-amino acids, linked
by amide bonds (20 or more units)
¬ Nucleic acids: monomer units: nucleotides, linked by
phosphate esters of sugar-phosphate backbone (4 units)
¬ Polysaccharides: sugars linked by acetal linkages between
anomeric center of sugar and alcohols of next sugar: can be
branched and stereochemistry of linkage matters
• Nucleic acids and peptides are made naturally with a
particular order of “mers” which determines in part
both 3-D structure and function.
Peptides
• Inherently chiral
R
L-amino acids make • Two distinct ends: amino (N)
OH up proteins and
terminus and carboxyl (C)
H2N
peptides from
terminus
mammalian sources
O
• Primary structure: sequence
of the “blocks”
Rn-1
O
Rn+1
H
N
OH • Secondary structure: folding
H2N
N
H
of short segments into
O
Rn
O
helices, turns, and sheets
R group (side-chain) can be
• Tertiary structure: overall
aromatic,polar, acidic, basic,
folding of 2° structural
aliphatic,cyclic
elements into larger domains
“φ/ψ Space” of Peptides and Proteins
O
H
C
O
N
φ
C
C
ω
ψ C
N
C
H
H(C)
C
α-Helix
φ = -57°, ψ = -47°
3.6 residues/turn
1.5 Å rise/res.
310-Helix
β-Sheet/extended
φ = -49°, ψ = -26° φ = -135 – 180°
3 residues/turn
ψ = 113 – 180°
2.0 Å rise/res.
2 residues/repeat
3.4 Å rise/res.
α-Helical Secondary Structure
β-Sheet secondary structure
Transmission electron micrograph
(TEM) of amyloid β protein (10-35
fragment). Fibrils are 50-100 nm wide
and several microns long. This is a selfassembly mediated by predominantly βsheet interactions.
Tertiary structure
Carboxypeptidase
HIV protease symmetrical dimer
First high-resolution X-ray structure of HIV protease was done using a
fully synthetic protein (made by chemical synthesis; Stephen Kent) and
synthetic inhibitor (Dan Rich).
NUCLEIC ACIDS: Polymers of nucleotides
O
"bases"
pyrimidines
and purines
R
NH
sugar:
D-ribose or
2-deoxy-ribose
furanoside
O
O
O X
O P O
O
Ribonucleic Acid
X = OH, R = H
N
O
NH2
N
N
O
N
N
NH2
N
O X
O P O
O
O
N
O
O
NH
N
Deoxyribonucleic Acid
X = H, R = CH3
O X
O P O
O
phosphodiester
linked via 3',5'
of sugar
N
O
O X
N
NH2
β-linked
bases
Pyrimidines, Purines, Nucleosides and Nucleotides
6
8
2
N
1
C
NH2
N
N
H
O
N
N
H
HO
N
HO
O
O
HO
HO
1-(2'-deoxy-D-ribofuranosyl)thymine
= (deoxy) thymidine
N
O
HO OH
uridine-5'-(mono)phosphate
or uridylic acid or 5'-UMP
O
O P
O
O
O P
O
O
N
O
HO
HO
OH
X
pyranose
Why not pyranosyl DNA or RNA??
N
HO
O
O
N
N
HO
9-(D-ribofuranosyl)guanine 9-(2'-deoxy-D-ribofuranosyl)adenine
= deoxyadenosine
= guanosine
O
N
O
b
N
NH2
N
N
NH2
NH
path
NH2
HO OH
1-(2'-deoxy-D-ribofuranosyl)cytosine
= deoxycytidine
O
CH3
O
N
HO X
NH
N
OH
furanose
O
N
O
b
X = OH, D-ribose
X = H, 2-deoxy-D-ribose
NH2
N
O
a
path
H
X
OH a
O H
CH2OH
NH2
guanine
adenine
NH
O
N
N
H
HO
O
O P
O
O
NH
N
O
CH3
H
H
H
O
N
O
cytosine
R = CH3, thymine
R = H, uracil
O
purine
NH2
NH
N
H
HO
2
N 4 N
9 H
3
pyrimidine
O
R
N 1
O
O
deoxycytidine-3',5'-bisphosphate
O
O P
O
O
O P
O
O
NH2
NH
N
N
N
O
HO OH
guanosine-5'-diphosphate
or (5')GDP
NH2
O
O
O P
O P
O
O
O
O P
O
N
N
O
O
N
N
HO
deoxy-adenosine-5'-triphosphate
or (5')dATP
Nucleotides
7 N 5
N 3
+ purine
or pyrimidine
"bases"
6
Nucleosides
4
5
natural
nucleoside
Sugars
Heteroaromatic "bases"
DNA Double Helix: Factors that
control formation and stability
• Hydrogen bonding of
the bases
• Ionic nature of
backbone (repulsion)
• Base stacking of
purine and pyrimidine
bases in the duplex:
main contributor to
stability
How can DNA/RNA be a repetitive
double helix with different units?
D
A
H
A
N H D
C
D H N
N A
N
R
O
D
O A
C-G
N
D
H N
H
N H
N
G
A
H
A
C
N
R
N
H N
H N
N
G
A
N(Pu)
θ1
55.7°
57.4°
θ2
54.4°
56.2°
X
10.72 Å
10.44 Å
N(Py)
θ2
θ1
C1'
X
C1'
N H D
O
A
T-A
A
N
R
ove
r gro
mino
D
O
T
R
H
D
A
A
R
N
N
O
D
A
O
N
R
major groove
major groove
D
A
D
A
H
H N
A
N
A
R
N
A
N
A
O
T
N
R
A
H
H N
N H
N
N
N
N
A
R
N
O
R
A
A
A
ove
r gro
mino
Ability to form repetitive hydrogen bonding
structures in DNA and RNA is due to the
isostructural (isomorphic) nature of the C-G
and A-T(U) basepairs. That is, the fact that
a C-G, G-C, A-T, and T-A basepairs have
same geometries provides the template to
make a polymeric duplex structure with
different bases. The only caveat is that the
bases must occur pairwise(A w/ T(U), G w/ C)
to get the repetitive structure.
Polysaccharides made from Sugars
Sugars form diastereomeric cyclic
forms: furanoses and pyranoses
Sugars form diastereomeric cyclic
forms: pyranoses α and β anomers
Polysaccharides of even on sugar type
“homopolymer” can vary in structure
• Units linked via acetal
bond at the anomeric
carbon: α or β
• For hexopyranoses can
have 4 possible links
to hydroxyl group
• Branching can occur
as in amylopectin
Polysaccharides of even on sugar type
“homopolymer” can vary in structure
• Cellulose is a
structural polymer
• Insoluble in water
Amylose (Starch) α-linked gives
a helical structure
Polymers for Biopolymers
• Polyacrylamide gel electrophoresis for
analysis of size of DNA, RNA, and protein
• Agarose gels for double-stranded DNA and
RNA size analysis
• Solid-phase or polymer-supported synthesis:
Peptide Synthesis
Because amino acids have two functional groups, a
problem arises when one attempts to make a particular
peptide
Strategy for Making a Specific Peptide Bond
Amino acids can be added to the growing C-terminal end
by repeating these two steps
When the desired number of amino acids has been
added to the chain, the protecting group can be
removed
An Improved Peptide Synthesis Strategy