Biopolymers, Natural Polymers

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Chapter 8: Biopolymers
Examples of biopolymers are:
Starch
Cellulose
Proteins
Nucleic Acids
Polymer
Nylon 6
PS
PBI
Modulus
1.5 GPa
3 GPa
6 GPa
Strength
36 MPa
45 MPa
186 MPa
Biopolymers’ locations
Animal Cell
Plant Cell
RNA
Nucleus
Cytoplasm1
Nucleus
Cytoplasm
DNA
Nucleus
Organelles
(e.g.
Mitochondrion)
Nucleus
Organelles (e.g.
Chloroplast)
Starch
-
Chloroplasts
Cellulose
-
Cell Walls
Fish Red Blood Cell
Note: Not an exhaustive list, these are a few representative examples
~ 15m
1 Cytoplasm: the organic and inorganic material inside the cell but outside its nucleus.
Deoxyribonucleic Acid
DNA
Tensile 476±84 pN
isolated during war in 1860’s in
puss from wounds
3.14 x 10-18m2 and 4.76 x 10-10 N
1.5 x 108 Pa
2 nm
The Human genome (all the nuclear DNA) has approximately 3
x 109 nucleotide monomers in the shape of a double helix with a
radius of ~ 1 nm.
Chromatin packing of DNA
A
B
2 nm
2 nm
1111
nmnm
D
300300
nm nm
E
700 nm
700 nm
F
C
3030
nmnm
1400
1400
nmnm
Upon “melting”
DNA strands can
be replicated
RNA is less stable &
is never found in old
bones
Photocrosslinking leads to a helix that won’t un-zip!!
DNA Melting
Proteins
O
H2N
R
Insulin crystal
Strong inter- and intra-molecular effects
beta sheets
alpha helices
N
H
OH
O
O
H2N
Proteins by Function
R
N
H
OH
O
O
H2N
R
N
H
OH
O
O
H2N
R
N
H
OH
O
O
H2N
R
N
H
OH
O
O
H2N
R
N
H
OH
O
Proteins
O
H2N
R
N
H
OH
O
• The control of protein structure builds information into
the molecule that translates into function
• Proteins are the most common biological
macromolecules in the extra cellular matrix
• Perform structural and functional tasks
– Collagen (triple helix – gly-X-Y) where proline and hydroxy
proline is often present is the basic stuctural protein
– Enzymes perform specific catalytic tasks
– Adhesive proteins are bind cells to substrates – fibronectin,
integrin, etc.
– Provide signal transduction between cells and ECM
Protein
Structure
O
Primary - identitiy and order of amino acids
HN
N
R H
-determines all other levels of structure
-covalent bonding
Secondary - helices % sheets, turns, random coils
-driven & stabilized by hydrogen bonding
-sterics
Tertiary - 3-D Folded structures
-hydrophobic interactions
-often direct determinant of function
Quaternary - multiple peptides aggregating
-multiple bonding interactions
OH
2
O
Structure is a consequence of sequence
Function is a consequence of structure
Primary Structure: Amino Acid Sequence
•20 amino acids •
O
H2N
R1
Alanine
Arginine
O
H2N CHC OH
CH3
Asparagine
O
H2N CHC OH
H2C
H 2C
H2C
HN
C NH
NH2
Glycine
O
H2N CHC OH
CH2
C O
NH2
Histidine
O
H2N CHC OH
H
N
NH
Proline
H
N
C O
OH
O
H2N CHC OH
CHCH3
H2C
CH3
Serine
O
H2N CHC OH
CH2
OH
N
H
Aspartic Acid
O
H2N CHC OH
H2C
C O
OH
Isoleucine
O
H2N CHC OH
CH2
R2
Leucine
O
H2N CHC OH
CH2
CHCH3
CH3
Threonine
O
H2N CHC OH
CHOH
CH3
O
H
N
O
R3
R4
N
H
O
H
N
O
OH
R5
Cysteine
Glutamic acid
O
H2N CHC OH
CH2
SH
O
H2N CHC OH
H2C
H2 C
C O
OH
Lysine
O
H2N CHC OH
H2C
H 2C
H2C
H 2C
NH2
Methionine
Phenylalanine
O
H2N CHC OH
CH2
CH2
S
CH3
O
H2N CHC OH
H2 C
Tryptophan
O
H2N CHC OH
CH2
Tyrosine
O
H2N CHC OH
CH2
HN
OH
Glutamine
O
H2N CHC OH
CH2
CH2
C O
NH2
Valine
O
H2N CHC OH
CHCH3
CH3
Primary Structure: Amino Acid Sequence
•20 amino acids •
O
H2N
R1
R2
N
H
O
O
H
N
R3
R4
N
H
O
H
N
O
OH
R5
Average protein 300-400 amino acids = 30-45K Daltons
Protein with 300 mers based on 20 amino acids:
P =20300 or 10390 different possible sequences
Estimated:
100,000 human proteins (coded by 30,000 genes)
Identified:
10,000 human proteins
O
H2N
H
N
H
H
O
H2N
Me
O
Me
N
H
O
H
N
O
N
H
H
H
N
H
O
Me
O
H
N
O
Me
N
H
H
HN
H
O
O
H
N
O
O
N
H
H
N
O
N
H
O
H
N
HN
Me
H
H
Me
O
H3N
O
H
N
Me
N
H
N
H
meta-enkephalin
O
H
N
O
H
N
Polyglycine
H
OH
Me
O
O
O
S
HO
OH
O
Me
O
O
H
N
Me
Polyalanine
Primary Structure: Amino Acid Sequence
•20 amino acids • All one stereoconfiguration
Two configurations possible
Only (S)-isomers of amino acids used in life on Earth
Mirror images
Secondary Structure:  Helix
Pauling 1954
Nobel Prize
3.6 aa per turn
Alanine
Methionine
Glutamate
 Sheet
Valine
Leucine
Tyrosine
Beta- or Hair-Pin Turn
two to five residues, of which one is
frequently a glycine or a proline
Secondary Structure: Random Coiling
Secondary Structures:
Tertiary Structure: Folding
Quaternary Structure: Aggregation
Tetramers
haemoglobin
Quaternary Structure: Coils
Eg. Collagen
Quaternary Structure: Dimers
Eg. Collagen
Catabolic activator protein
Quaternary Structure: Complex
Eg. Collagen
Catabolic activator protein
Prostaglandin H2 synthase-1
Protein Structure Overview
Prions
normal
abnormal
Denaturation
loss of 3-D conformation by heat, pH, organic solvents, detergents
Spiders spin 6 different fibers
Flagelliform
Large diameter egg
Case fiber (Tubuliform)
Aggregate Tubuliform
Minor ampullate
Capture Spiral
(Flagelliform)
Pyriform
Major
ampullate
Aciniform
Glue coating
(Aggregate silk) (?)
Wrapping and egg case fiber
(aciniform)
Web reinforcement
(Minor ampullate
1 and 2)
Dragline (major
ampullate 1 and 2)
Vollrath, F. J. Biotechnol. 2000, 74, 67-83.
Hu, X. et al. Cell. Mol. Life Sci. 2006, 63, 1986-1999.
Pyriform silk (?)
The classic strong synthetic fiber
Kevlar®:
Dupont (1960s)
Uses
- Bulletproof vests and helmets
- Automobile brake pads
- Ropes and cables
- Aerospace components
Material
Dragline Silk
Kevlar
Rubber
Nylon, type 6
Fiber
axis
Strength (GPa) Elasticity (%) Energy to break (J/kg)
1.1
3.6
0.001
0.07
35
5
600
200
5
4 x 10
4
3 x 10
4
8 x 104
6 x 10
Lewis, R. Chem. Rev. 2006, 106, 3762-3774. Vollrath, F.; Knight, D.P. Nature 2001, 410, 541-548.
Tanner, D.; Fitzgerald, J.A.; Phillips, B.R. Angew. Chem. Int. Ed. Engl. Adv. Mater. 1989, 5, 649-654.
Kubik, S. Angew. Chem. Int. Ed. 2002, 41, 2721-2723.
Spider silks have potential in many applications
Biomedical applications
Surgical sutures
Scaffolds for tissue engineering
Technical and industrial applications
High strength
ropes/cables
Ballistics
Parachutes
Fishing line
Forced silking to obtain silk fibers
Spiders are anesthetized with CO2
and secured ventral side up
Silk is pulled from the spinneret,
attached to a reel, and drawn at a
specified speed
Work, R. W.; Emerson, P. D. J. Arachnol. 1982, 10, 1-10.
Elices, M.; Perez-Rigueiro, J.; Plaza, G. R.; Guinea, G. V. JOM 2005, 57.
Proposed secondary structure and mode of elasticity
• Poly(Ala) modules form anti-parallel β-sheets (~30-40%)
• Glycine-rich, amorphous regions are thought to be helical
Crystalline region with
-sheet structure
Strain
Disordered
chain region
Kubik, S. Angew. Chem. Int. Ed. 2002, 41, 2721-2723.
Van Beek, J. D.; Hess, S.; Vollrath, F. Meier, B. H. Proc. Nat. Acad. Sci. 2002, 99, 10266-10271.
Primary structure of spider dragline silk
Fibrous protein composed of Spidroin 1 (MaSp1) and Spidroin 2 (MaSp2)
- Sequences highly conserved
- Repetitive stretches of poly(Ala) and (GlyGlyXaa)n sequences
(Xaa = Tyr, Leu, Gln)
- MW of MaSp1 ~ 275-320 kDa; Sp1+Sp2 ~ 700-750 kDa
Repeating sequence of MaSp1
QGAGAAAAAAGGAGQGGYGGLGGQGAGQGGYGGLGGQGAGQGAGAAAAAAAGGAGQGGYGGLG
GLGGYGGQGAGGAAAAAAGAGQGGRGAGQS
SQGAGRGGLGGQGAGAAAAAAAGGAGQGGYGGLG
GLGGYGGQGAGGAAAAAAGQGGRGAGQN
SQGAGRGGLGGQAGAAAAAAGGAGQGGYGGLGGQGAGQGGYGGLG
GLGGYGGQGAGGAAAASAGAGQGAGQGGLGGQGAGGAAAAAAAGAGQGGLGGRGAGQS
SQGAGRGGEGAGAAAAAAGGAGQGGYGGLGGQGAGQGGYGGLG
GLGGYGGQGAGGAAAAAAGAGQGAGQGGLGGQGAGGAAAAGAGQGGLGGRGAGQS
SQGAGRGGLGGQGAGAVAAAAGGAGQGGYGGLG
GLGGYGRQGAGGAAAAAAGAGQGGRGAGQS
NQGAGRGGLGGQGAGAAAAAAAGGAGQGGYGGLG
GLGGYGGQGAGGAAAAAGQGGRGAGQN
SQGAGRGGQGAGAAAAAAVGAGQEGIRGQGAGQGGYGGLG
GAGGYGGQRVGGAAAAAAGAGQGAGQGGLGGQGAGGAAAAAAGAGQGGLGGRGSGQS
SQGAGRGGQGAGAAAAAAGGAGQGGYGGLGGQGVGRGGLGGQGAGAAAAGGAGQGGYGGVG
SSLRSAAAAASAASAGS
Hinman, M.B.; Jones, J. A.; Lewis, R. TIBTECH 2000, 18, 374-379. Vollrath, F.; Knight, D. P. Nature 2001, 410, 541-548.
Simmons, A. H.; Michal, C. A.; Jelinski, L. W. Science 1996, 271, 84-87.
BioSteel®
- Genetically modified goats produce silk in mammary glands
- Silk is spun from the goats’ milk
Extrusion through “spinnerets” produces fibers
Aqueous spinning process is environmentally friendly
- Anticipated uses:
Surgical sutures
Adhesives
Fishing line
Body armor/military applications
Lazaris, A. et al. Science 2002, 295, 472-476.
Karatzas, C. N.; Turcotte, C. 2003, PCT Int. Appl. WO03057727.
Karatzas, C. 2001, PCT Int. Appl. WO0156626.
Islam, S. et al. 2004, U.S. Pat. 20040102614.
Proline & Glycine
Tensile Strength 1-7 MPa
Modulus 10 MPa
Carbohydrate Polymers
amylopectin
•Constituent in starch
•Plants store energy
•Animals use glycogen
(106 glucose)
~10,000 glucose units
Polysaccharides
• Polymers composed of sugars
• Similar to synthetic polymers in that
primary structure, DP not as fixed as
proteins
• Uses include energy storage,
component of extra cellular matrix
(hyaluronan)
Cellulose
Animal enzymes ineffective
Tensile Strength: 800 MPa
•Structural plant material
Modulus 75-100 GPa
•Cotton = >95% cellulose, wood = 50%
•MW of cellulose in 400,000 g/mol, corresponding to about 2200 D-glucose units
per molecule
•Stiff rods Conformation
•Well-organized water-insoluble fibers (20 nm diameter, 40,000 nm long)
•The -OH groups form numerous intermolecular hydrogen bonds adding strength
to the network.
•70% crystalline structure
•Tg = 227 °C, TB = 298 °C
Cellulose: Fibrous structure
Strong hydrogen bonding interactions ( 35 kJ/mole)
from 3 hydroxyl groups per sugar monomer
Acidic Polysaccharides
Acidic polysaccharides are a group of poly saccharides that
contain carboxyl groups and/or sulfonic esters.
These compounds play an important roles in structure and function
of connective tissues. These tissues form the matrix between
organs and cells that provides mechanical strength as well filtering
the flow of molecular information between cells.
Many connective tissues are made up of collagen, a structural
protein, in combination with an assortment of acidic
polysaccharides that interact with collagen to form loose or tight
networks.
OSO3-
*
O
HO
D-glucuronic acid
O
O
HN
O
OH
O
O
CH3
O
HO
N-acetyl-D-glucosamine
OH
O
O
-O
L-iduronic acid
O
3S
HN
O
O
SO3O HO
HO
OSO3
D-glucosamine
-OOC
OSO3O
NH
O
SO3-
D-glucosamine
Pentasaccharide unit of heparin responsible for binding to
antithrombin III.
*
Hyaluronic acid
D-glucuronic acid
N-acetyl-D-glucosamine
O
OH
O
O
*
HO
HO
O
1
OH
2
3
O
1
O
NH
O
*
CH3
Hyaluronic acid is the simplest acidic polysaccharide
present in connective tissue
MW of ~ 105 and 107 g/mol and contains 30.000 to
100,000
Found in embryonic tissues and specialized connective
tissues such as synovial fluid, the lubricant of joints in the
body, and the vitreous humor of the eye where it provides
a clear, elastic gel that maintains the retina in proper
position.
Cellulose pulp
Enzymes
Alkalies
Enzymatic processing
Alkali cellulose
CS2
NaOH
ksantogenation
Cellulose xanthate
Dissolving
Ripening
Spinning acidic bath
Fibre
Other products
Similar in both
processes
Waste
Na2SO4 / OH2O
Spinning acidic bath
Fibre
Other products
acetate rayon
O
OH
O
HO
O
O
O
OH
+
O
3
H3C
O
H3C
CH3
O
O
acetic anhydride
glucose unit in
cellulose fiber
O
O
O
CH3
O
O
H3C
O
A fully acetylated glucose unit
Tensile 10-250 Mpa
Modulus 2 GPa
Viscose rayon
S C S
NaOH
Cellulose OH
Cellulose O-Na+
S
Cellulose O C S-Na+
Na+ salt of a xanthate ester
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