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