Chapter 8: Biopolymers
Examples of biopolymers are:
StarchCelluloseProteinsNucleic Acids
Polymer Modulus StrengthNylon 6 1.5 GPa 36 MPaPS 3 GPa 45 MPaPBI 6 GPa 186 MPa
Animal Cell Plant Cell
RNA NucleusCytoplasm1
NucleusCytoplasm
DNA NucleusOrganelles (e.g. Mitochondrion)
NucleusOrganelles (e.g. Chloroplast)
Starch - Chloroplasts
Cellulose - Cell WallsNote: Not an exhaustive list, these are a few representative examples ~ 15
Fish Red Blood Cell
1 Cytoplasm: the organic and inorganic material inside the cell but outside its nucleus.
Biopolymers’ locations
Deoxyribonucleic AcidDNA
2 nm
isolated during war in 1860’s in puss from wounds
Tensile 476±84 pN
3.14 x 10-18m2 and 4.76 x 10-10 N1.5 x 108 Pa
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.
A
C
D
E
F
B
300 nm
700 nm
11 nm
30 nm
2 nm
1400 nm
2 nm
11 nm
30 nm
300 nm
700 nm
1400 nm
Chromatin packing of DNA
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
Insulin crystal
Strong inter- and intra-molecular effectsbeta sheetsalpha helices
H2N
O
NH
OH
OR
Proteins by Function
H2N
O
NH
OH
OR
H2N
O
NH
OH
OR
H2N
O
NH
OH
OR
H2N
O
NH
OH
OR
H2N
O
NH
OH
OR
Proteins
• 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
H2N
O
NH
OH
OR
Protein Structure
Primary - identitiy and order of amino acids-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
H2N
O
NH
OH
OR
Structure is a consequence of sequence
Function is a consequence of structure
Primary Structure: Amino Acid Sequence
H2N CHC
CH3
OH
O
H2N CHC
H2C
OH
O
H2C
H2C
HN
C
NH2
NH
H2N CHC
CH2
OH
O
C
NH2
O
H2N CHC
H2C
OH
O
C
OH
O
H2N CHC
CH2
OH
O
SH
Alanine Arginine Aspartic Acid Cysteine
H2N CHC
H2C
OH
O
H2C
C
OH
O
H2N CHC
CH2
OH
O
CH2
C
NH2
O
H2N CHC
H
OH
O H2N CHC
CH2
OH
O
NNH
H2N CHC
CH
OH
O
CH3
H2C
CH3
H2N CHC
CH2
OH
O
CHCH3
CH3
H2N CHC
H2COH
O
H2C
H2C
H2C
NH2
H2N CHC
CH2
OH
O
CH2
S
CH3
H2N CHC
H2C
OH
O
HN C
OH
O H2N CHC
CH2
OH
O
OH
H2N CHC
CH
OH
O
OH
CH3
H2N CHC
CH2
OH
O
HN
H2N CHC
CH2
OH
O
OH
H2N CHC
CH
OH
O
CH3
CH3
Glutamic acid
Leucine Phenylalanine
TyrosineTryptophan
Histidine LysineGlycine
Proline
Asparagine Glutamine
Threonine ValineSerine
MethionineIsoleucine
•20 amino acids • H2NNH
HN
O
O
O
NH
HN
O
O
OHR1
R2 R4
R3 R5
Primary Structure: Amino Acid Sequence•20 amino acids • H2N
NH
HN
O
O
O
NH
HN
O
O
OHR1
R2 R4
R3 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
H2NNH
HN
O
O
O
NH
HN
O
O
Me
Me Me
Me MeHN
HN
O
O
NH
HN
O
O
OH
Me Me
Me Me
H2NNH
HN
O
O
O
NH
HN
O
O
H
H H
H HHN
HN
O
O
NH
HN
O
O
OH
H H
H H
Polyglycine
Polyalanine
H3NNH
HN
O
O
O
NH
HN
O
O
O
HOmeta-enkephalin
SMe
Primary Structure: Amino Acid Sequence•20 amino acids • All one stereoconfiguration
Mirror images
Two configurations possible
Only (S)-isomers of amino acids used in life on Earth
Secondary Structure: Helix
3.6 aa per turn
Pauling 1954 Nobel Prize
AlanineMethionineGlutamate
Sheet
ValineLeucineTyrosine
two to five residues, of which one is frequently a glycine or a proline
Beta- or Hair-Pin Turn
Secondary Structure: Random Coiling
Secondary Structures:
Tertiary Structure: Folding
Quaternary Structure: AggregationTetramers
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
Denaturationloss of 3-D conformation by heat, pH, organic solvents, detergents
Vollrath, F. J. Biotechnol. 2000, 74, 67-83.Hu, X. et al. Cell. Mol. Life Sci. 2006, 63, 1986-1999.
Spiders spin 6 different fibers
Web reinforcement (Minor ampullate 1 and 2) Dragline (major
ampullate 1 and 2)
Wrapping and egg case fiber (aciniform)
Pyriform silk (?)
Acini-form
Capture Spiral(Flagelliform)
Glue coating(Aggregate silk) (?)
Large diameter eggCase fiber (Tubuliform)
Aggregate TubuliformFlagelliform
Pyriform
Minor ampullate
Major ampullate
The classic strong synthetic fiber
Material Strength (GPa) Elasticity (%) Energy to break (J/kg)
Dragline Silk 1.1 35 4 x 105
Kevlar 3.6 5 3 x 104
Rubber 0.001 600 8 x 104
Nylon, type 6 0.07 200 6 x 104
Fiber axis
Kevlar®: Dupont (1960s) Uses
- Bulletproof vests and helmets- Automobile brake pads- Ropes and cables- Aerospace components
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
Surgical sutures Scaffolds for tissue engineering
Biomedical applications
Parachutes
High strength ropes/cables
Fishing line
Technical and industrial applications
Ballistics
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
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.
• Poly(Ala) modules form anti-parallel β-sheets (~30-40%)• Glycine-rich, amorphous regions are thought to be helical
Disordered chain region
Strain
Crystalline region with-sheet structure
Primary structure of spider dragline silk
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.
QGAGAAAAAAGGAGQGGYGGLGGQGAGQGGYGGLGGQGAGQGAGAAAAAAAGGAGQGGYGGLGGLGGYGGQGAGGAAAAAAGAGQGGRGAGQS
SQGAGRGGLGGQGAGAAAAAAAGGAGQGGYGGLGGLGGYGGQGAGGAAAAAAGQGGRGAGQNSQGAGRGGLGGQAGAAAAAAGGAGQGGYGGLGGQGAGQGGYGGLG
GLGGYGGQGAGGAAAASAGAGQGAGQGGLGGQGAGGAAAAAAAGAGQGGLGGRGAGQSSQGAGRGGEGAGAAAAAAGGAGQGGYGGLGGQGAGQGGYGGLG
GLGGYGGQGAGGAAAAAAGAGQGAGQGGLGGQGAGGAAAAGAGQGGLGGRGAGQSSQGAGRGGLGGQGAGAVAAAAGGAGQGGYGGLG
GLGGYGRQGAGGAAAAAAGAGQGGRGAGQSNQGAGRGGLGGQGAGAAAAAAAGGAGQGGYGGLG
GLGGYGGQGAGGAAAAAGQGGRGAGQNSQGAGRGGQGAGAAAAAAVGAGQEGIRGQGAGQGGYGGLG
GAGGYGGQRVGGAAAAAAGAGQGAGQGGLGGQGAGGAAAAAAGAGQGGLGGRGSGQSSQGAGRGGQGAGAAAAAAGGAGQGGYGGLGGQGVGRGGLGGQGAGAAAAGGAGQGGYGGVG
SSLRSAAAAASAASAGS
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
BioSteel®
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.
- Genetically modified goats produce silk in mammary glands
- Silk is spun from the goats’ milkExtrusion through “spinnerets” produces fibersAqueous spinning process is environmentally friendly
- Anticipated uses:
Surgical suturesAdhesivesFishing lineBody armor/military applications
Proline & Glycine
Tensile Strength 1-7 MPaModulus 10 MPa
Carbohydrate Polymers
amylopectin
~10,000 glucose units
•Constituent in starch•Plants store energy•Animals use glycogen (106 glucose)
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
•Structural plant material•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
Animal enzymes ineffective
Tensile Strength: 800 MPaModulus 75-100 GPa
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.
-OOC
OOHO
OHN
OSO3-
O
HO
ONH
OSO3-
O
HOOH
O
O
O
O
OHN
OH
O
HOOSO3
-O
*
*
SO3-
D-glucosamine
L-iduronic acid
SO3-
-O3S
O
D-glucuronic acid
O CH3
N-acetyl-D-glucosamine
D-glucosamine
Pentasaccharide unit of heparin responsible for binding to antithrombin III.
O
HOOH
O
O
OHO
NH
O
OH
1 3
12
*
*
O
O CH3
D-glucuronic acidN-acetyl-D-glucosamine
Hyaluronic acid is the simplest acidic polysaccharide present in connective tissueMW of ~ 105 and 107 g/mol and contains 30.000 to 100,000Found 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.
Hyaluronic acid
Cellulose pulp
Enzymatic processing
Dissolving
Spinning acidic bath
Fibre
Other products
Alkali cellulose
Cellulose xanthate
Ripening
Spinning acidic bath
Fibre
Other products
Similar in both processes
Waste
Na2SO4 / OH2O
NaOH
Enzymes Alkalies
CS2 ksantogenation
OOHO
OHO
OH
+ 3 O CH3H3C
O O
OO
OO
O
O
OH3CCH3
O
O
H3C
A fully acetylated glucose unit
glucose unit incellulose fiber
acetic anhydride
acetate rayon
Cellulose OHNaOH
Cellulose O-Na+
S C SCellulose O C S-Na+
S
Na+ salt of a xanthate ester
Viscose rayon
Tensile 10-250 MpaModulus 2 GPa