Biopolymers

Istanbul, 2009
 Biopolymers vs. Polymers
• Structure: • Structure:
– Primary, secondary, etc. – Subunits of Polymers: monomers
– Complex (Repeating units)
– Molecular mass distribution – Simpler and more random
cannot be done – Molecular mass distribution can be
– Monodisperse detected
– Polydisperse
• Subunit:
– Biomass • Subunit:
– Usually petroleum stock
• Removal:
– Biodegradable • Removal:
– Often last for very long
 Types of Natural Biopolymers
1. Polysaccharides
2. Proteins and polypeptides
3. Polynucleotides
 Condensation and hydrolysis
reactions

Reactions of polysaccharides. (a) Condensation, (b) Hydrolysis [people.ifm.liu.se/~fenzh/Biopolymers%20Lecture.pdf].

 Polysaccharides

http://employees.csbsju.edu/hjakubowski/classes/ch331/cho/glcfrccycliz.gif

• chains of monosaccharides
• condensation of sugars forms the “cyclolinear
polyethers”
 Polysaccharides
• Homopolymers of glucose: OH
O
– Starch O
OH
H
H
HO
– Cellulose H OH
n

– Glycogen
 Starch vs.Glycogen

Newton, T. A. Biopolymers II. http://www.usm.maine.edu/~newton/Chy251_253/Lectures/BiopolymersII/BiopolymersIFS.html

 Biological Synthesis of
Polysaccharides
• Starting material: Glucose-6-phosphate
• The pyrophosphate is lost from the system by hydrolyis:
• NTP + sugar 1-phosphate NDP-sugar + H2O3P—O—PO3H2
• Chain growth: NDP is lost from the 1-position of the glucose unit
enzymatically while that unit is condensed with the 4-position of a
second sugar molecule
• Chain branching: Condensation at Carbon 6 is performed in the
existence of a special “branching enzyme.”

OH OH OH OH

H O H O HP O O
H H - N D
H H
OH H NDP + OH H OH OH H O OH H OH
HO HO HO
H OH H OH H OH H OH
 Reactions of polysaccharides
• Esterification
• Rayon manufacture
• Etherification
• Other reactions (composite material
synthesis, etc.)
 Esterification
• Nitration (rt, 1 hr):
– Cellulose + (HNO3/H2SO4)  Cellulose nitrate
– Plus unreacted OH- groups, and sulfate linkages
– Actual nitrating agent: nitronium ion
• Reacts with both amorphous and crystalline parts of the polymer
– Cellulose nitrates and the amount of nitrogen:
• 12.5 to 13.4 %: explosive! (known as gun cotton)
• 11 to 12 %: lacquers, films, and plastics; but replaced by less flammable,
newer, and synthetic polymers
• Cellulose + CH3COOH (or Acetic anhydride)  Cellulose acetate:
– 1.Pretreatment of cellulose with acetic acid,
– Reaction with acetic anhydride and sulfuric acid
– Product: ~triacetate: high MP, low solubility,
– 2. Instead, partial hydrolysis and replacement of the sulfate ester groups
by aqueous acetic acid
– Product: polymer with broad industrial use.
 Rayon manufacture
S
OR O
OH OH -
S Na
+

O O
O O - H2 O H O
H O + NaOH+ CS H O OR H
H O OH H 2 O OR H
O OH H n
n
HO
H OR H OR
H OH H OH

The treatment of cellulose with caustic soda (NaOH) and carbon disulfide (CS2) yields viscose. S
R=
- +
S Na

• Rayon: Regenerated cellulose made from wood pulp.

• Definition according to US Trade Commission: A manufactured fiber composed of
regenerated cellulose, in which substituents have replaced not more than 15% of the
hydrogens of the hydroxyl groups.
• Initially called “artificial silk”
– Example: Cellophane film
• Production: xanthate (viscose) method, cuprammonium method, acetate method
• Xanthate Method
– Pros: Cheaper (wood can be used whereas other methods require lignin-free cellulose as starting
materials, large scale of production due to low cosr
– Cons: High degree of flammability, (in the past) contamination of water by broken waste rayon.
 Synthetic and Cellulosic Fiber
Formation Technology

Wet spinning Dry spinning

Melt spinning The Spinneret Gel spinning

Wet, dry, melt, and gel spinning processes used in cellulosic fiber technology.
Extrusion: forcing a thick, viscous liquid through the tiny holes of a spinneret
to form continuous filaments of semi-solid polymer
Sources: http://www.fibersource.com/f-tutor/techpag.htm, Cellulose Commun., 13(2), 70-74 (2006)
 Etherification OR O Na
OH OH
O O C 3HC l
O O H H O
H + NaOH O OR H
H O OH H
O O OR H n
- N a C l
O OH H n
HO H OR
H OH H OR
H OH
OR O CH3

O O
H O H O
O OR H OR H
n

H OR H OR
• Alkaline cellulose composition + Alkyl halide  Ether of
cellulose
• Alkyl halides used in the production of
– Methylcellulose: Methyl chloride,
– Ethylcellulose: Ethyl chloride,
– Carboxymethylcellulose: Chloroacetic acid or sodium
chloroacetate.
• Used in: food grade, toothpaste, Building materials,
paper making, drilling fluid, etc.
• Can be used as adhesives
 Proteins
• Proteins: functional terms of polypeptides
• Synthesized by the condensation
reactions of amino acids
• 20 amino acids are very common
• Range of molecular weight from
6,000 to 1,000,000
• Degree of polymerization range from
about 50 to over 8000
 Prosthetic Groups
• Prosthetic group: Non-
proteinaceous
components in a protein
• Can be a metal group
such as ferric hydroxide,
zinc, or copper, an iron
porphyrin in a myoglobin
or a hemoglobin, etc
• Usually found in globular
proteins, materials that
carry out the chemical
work in a living system

© Irving Geis; xMathews C.K.; van Holde, K.E.; and Ahern,

K.G.; Biochemistry, Third edition, Addison - Wesley
 Condensation of amino acids into
proteins

a) The condensation of three amino acids, b) into a three amino-acid protein [Addison Wesley Longman, Inc., 1999]
Biomacromolecular structural
organization
Primary structure: sequence
of a chain of amino acids

Secondary structure:
sequence of amino acids
linked by hydrogen bonds

Tertiary structure (overall shape of

the molecules): certain attractions
exist between alpha helices and
pleated sheets
Quaternary structure: a
protein consisting of more than
one amino acid chain

Source: people.ifm.liu.se/~fenzh/Biopolymers%20Lecture.pdf
 Fibrous and Globular Proteins Fibrous proteins:
•Tough, insoluble materials
•Found in connective tissues of animals, bird
and reptiles
•Types:
•α-keratins, collagens, and β-keratins.
Globular proteins:
•Soluble in aqueous media
•Found in living systems.
•Organize chemical reactions
•To fully understand structures and functions
of globular proteins:
•Sequence of amino acids in each
chain,
•Conformation of the chain and the
location of prosthetic groups
a) Collagen, a fibrous protein, and
b) b) myoglobin, a globular protein. •Attractive and repulsive forces
[http://www.nd.edu/~aseriann/fibglob.gif, Garnt/Grisham, between different amino acid residues
Biochemistry, p. 90, Saunders College Publishing, 1995] on the same chain in secondary and
tertiary structures
•No globular protein present totally analyzed
in this way.
 Fibrous vs. Globular Proteins
Fibrous Proteins Globular Proteins

Sequences of amino acids Regular Irregular

Polypeptide Chains Long Parallel Strands Folded Into Spherical Shape

Length of Chain Varies Identical

Structure Stable Instable

Solubility in water Insoluble Soluble

Function Structural (connective tissues) Metabolic (in the organization of

chemical reactions in the body)
Examples Collagen and keratin Myoglobin, hemoglobin, cytochrome c,
enzymes and hormones insulin

Source: http://www.revision-notes.co.uk/revision/106.html
 Amino acids
• 20 common amino acids
• All zwitterions
• Classification based on side chains (R):
– Aliphatic
– Aromatic
– Non-polar
– Polar
– Charged
– Non-charged
Common amino acids Amino acids

Source:
http://www.microbiologytext.com/index.php?
module=Book&func=displayarticle&art_id=40
Formation of peptide bonds

Source:
people.ifm.liu.se/~fenzh/Biopolymers%20Lecture.pdf
 Can polypeptides be produced
synthetically?
• Homopolymer Synthesis: Homopolypeptides can be synthesized
in laboratory conditions by typical condensation reactions using
simple amino acids like alanine, valine, phenylalanine, etc. Although
these polymers are not proteins due to their
– high crystallanity,
– low solubility in aqueous media,
– disperse MWs, and
– non-folding conformations,
they are considered as providing raw data for conformational energy
changes in proteins and of interest as fibers in surgery.

• Copolymer Synthesis: Copolymer synthesis reactions are done,

but the main problem is preventing the condensation at both
ends of the polymer to only one end. For such a purpose,
protective groups are used.
 Example: Synthesis of PLGA–PEG–PLGA
triblock copolymer (ReGel®)
• Biodegradable drug
delivery system
• Injected as a liquid into
the body, later forms a
PLGA: gel in response to body
poly(lactide-co- temperature.
glycolide), • Solubilizes and stabilizes
PEG: poorly soluble and
Polyethylene sensitive drugs, including
glycol proteins
• Water used as a solvent
• No organic solvents used
in the synthesis,
purification, or
formulation
G.M. Zentner et al. / Journal of Controlled Release 72 (2001) 203 –215,
S. Chen et al. I. Journal of Pharmaceutics 288, (2), 207-218, 20 January 2005
Zhang, F. http://people.ifm.liu.se/~fenzh/Biopolymers%20Lecture.pdf.
Denaturation of Proteins

Accessed: 09 January 2009

 Denaturation of Proteins
• Usually known as the loss of tertiary structures by some
external stress or compound for example, treatment of
proteins with
– strong acids or bases,
– high concentrations of inorganic salts,
– organic solvents (e.g., alcohol or chloroform), or
– heat.
• If proteins in a living cell are denatured  disruption of
cell activity and
possibly cell death.
Quaternary Structure: dissociation of protein sub-units and/or
disruption of the spatial arrangement of protein subunits
Tertiary Structure: disruption of
• covalent interactions between amino acid side chains
(such as disulfide bridges between cysteine groups)
• Noncovalent dipole-dipole interactions between polar
amino acid side chains (and the surrounding solvent)
• Van der Waals (induced dipole) interactions between
nonpolar amino acid side chains
Secondary Structure: loss of all regular repeating patterns
such as alpha-helices and beta-pleated sheets
Primary Structrure: no disruption
 Hydrolysis vs. Denaturation
• Breakdown of • Primary structure is
peptides bonds not affected (no
through the addition hydrolysis of peptide
of water, forming an bonds)
amine and a • Recoiling: Some
carboxylic acid small proteins can re-
gain their active
shape if the
conditions are turned
back (cooled, or salt
removed, etc.)
 Polynucleotides
NH2
N N
O
HO P O N N
O
OH H H nitrogen base
H H
phosphate residues
OH OH
pentose sugar

• Polynucleotides: macromolecules found in the cells of living organisms, that are in charge of
the storage of the genetic information as well as its replication and protein synthesis.
• Nucleotides: phosphate esters of nucleosides, which are components of both:
– DNA: Deoxyribonucleic acid
– RNA: ribonucleic acid
• Nucleotides:
1. a nitrogen base
2. a pentose sugar
3. a phosphate residue
 Nucleotides: building blocks of
nucleic acids
NH2

Pentose sugars N
N
OH HO OH
HO O
O HO N N
O
A typical nucleotide
monomer residue
OH OH O
OH OH
O P O
R i b o s e D e o x y r i b o s e
OH
Nitrogen bases Complementary
Purines Pyrimidines
base pairing A = T
and C = G
NH2 NH2 NH2 O
N H3C
N N N NH
NH N NH O NH O NH O

A d e n i n eG u a n i n Ce y t o s i n Te h y m i n e
A schematic of a nucleic acid
polymer
 DNA vs. RNA
• Sugar: • Sugar:
– Deoxyribose – Ribose
• Bases: • Bases:
– Adenine – Adenine
– Cytosine – Cytosine
– Guanine – Guanine
– Thymine – Uracil
• Double stranded • Single stranded
• Bases attached to • Bases attached to
deoxyribose ribose
 Hydrogen bonds, coiling, and
uncoiling
Hydrogen bonds are broken
through uncoiling
when temperature is
raised, pH is changed, etc.
Recoiling occurs to form the
double helix when the original
conditions are supplied.

(a)Different levels of uncoiling seen in the chromosome [http://cellbio.utmb.edu/ Cellbio/nucchr1.jpg. Accessed: 09

January 2009], (b) Hydrogen bonds between nucleotides [http://tainano.com/Molecular%2520Biology
%2520Glossary.files/image006.gif. Accessed: 09 January 2009
 Mutations
• Mutations: changes in the nucleotide
sequence or in the chemical organization of a
specific mononucleotide
• Reasons that might cause mutations:
– Exposure to UV, or ionizing radiation,
– Chemical reagents,
– Copying errors in the copying process, and
– Viruses.
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hncasNnoi t aci fil p ma A ND ss el - R
okrS
i .M3m3e9h5C
–.23m9A5. Jpp, ) 91( 621, 4002,
 Further Reading
• Biotechnology of Biopolymers : From Synthesi

– by Alexander Steinbüchel (Editor), Yoshiharu

Doi (Editor)
• Structure and Dynamics of Biopolymers
– by C. Nicolini (Editor)