polymer science term work bio polymers
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Biopolymers
Istanbul, 2009
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Biopolymers vs. Polymers
Structure:
Primary, secondary, etc.
Complex
Molecular mass distribution
cannot be done
Monodisperse
Subunit:
Biomass
Removal: Biodegradable
Structure:
Subunits of Polymers: monomers
(Repeating units)
Simpler and more random
Molecular mass distribution can bedetected
Polydisperse
Subunit:
Usually petroleum stock Removal:
Often last for very long
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Types of Natural Biopolymers
1. Polysaccharides
2. Proteins and polypeptides
3. Polynucleotides
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Condensation and hydrolysis
reactions
Reactions of polysaccharides. (a) Condensation, (b) Hydrolysis [people.ifm.liu.se/~fenzh/Biopolymers%20Lecture.pdf].
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Polysaccharides
chains of monosaccharides
condensation of sugars forms the cyclolinear
polyethers
http://employees.csbsju.edu/hjakubowski/classes/ch331/cho/glcfrccycliz.gif
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Polysaccharides
Homopolymers of glucose:
Starch
Cellulose
Glycogen
O
HH
OH
OH
H OH
OH
O
n
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Starch vs.Glycogen
Newton, T. A. Biopolymers II. http://www.usm.maine.edu/~newton/Chy251_253/Lectures/BiopolymersII/BiopolymersIFS.html
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Biological Synthesis of
Polysaccharides Starting material: Glucose-6-phosphate
The pyrophosphate is lost from the system by hydrolyis:
NTP + sugar 1-phosphate NDP-sugar + H2O
3POPO
3H
2
Chain growth: NDP is lost from the 1-position of the glucose unit
enzymatically while that unit is condensed with the 4-position of asecond sugar molecule
Chain branching: Condensation at Carbon 6 is performed in the
existence of a special branching enzyme.
O
HH
H
OHOH
H OH
OH
NDP +O
HH
H
OHOH
H OH
OH
OH- N D P
O
HH
OH
H OH
OH
OH
O
HH
H
OHOH
H OH
OH
O
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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.
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Rayon manufacture
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 thehydrogens 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 startingmaterials, large scale of production due to low cosr
Cons: High degree of flammability, (in the past) contamination of water by broken waste rayon.
O
HH
OHOH
H OH
OH
OO
HH
OH
H OH
OH
OOn
+ NaOH+ CS2
O
HH
OR
H OR
O
OO
HH
OR
H OR
OR
OO
S
S-Na
+
n
S
S-Na+
R=
- H2 O
The treatment of cellulose with caustic soda (NaOH) and carbon disulfide (CS2) yields viscose.
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Synthetic and Cellulosic Fiber
Formation Technology
Wet 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
Dry spinning
Sources: http://www.fibersource.com/f-tutor/techpag.htm, Cellulose Commun., 13(2), 70-74 (2006)
Melt spinning The Spinneret Gel spinning
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Etherification
Alkaline cellulose composition + Alkyl halide Ether ofcellulose
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
O
HH
OH
OH
H OH
OH
OO
HH
OH
H OH
OH
OOn
+ NaOH
O
HHOR
H OR
O
OOH
HOR
H OR
OR
OO
Na
n
C H3
C l
- N a C l
O
HH
OR
H OR
O
O
HH
OR
H OR
OR
OO
CH3
O
n
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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
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Prosthetic Groups
Prosthetic group: Non-proteinaceouscomponents in a protein
Can be a metal groupsuch as ferric hydroxide,
zinc, or copper, an ironporphyrin in a myoglobinor a hemoglobin, etc
Usually found in globularproteins, materials that
carry out the chemicalwork in a living system
Irving Geis; xMathews C.K.; van Holde, K.E.; and Ahern,
K.G.; Biochemistry, Third edition, Addison - Wesley
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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]
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Biomacromolecular structural
organization
Source: people.ifm.liu.se/~fenzh/Biopolymers%20Lecture.pdf
Primary structure: sequenceof 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
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Fibrous and Globular Proteins
a) Collagen, a fibrous protein, and
b) b) myoglobin, a globular protein.
[http://www.nd.edu/~aseriann/fibglob.gif, Garnt/Grisham,
Biochemistry, p. 90, Saunders College Publishing, 1995]
Fibrous proteins:
Tough, insoluble materials
Found in connective tissues of animals, bird
and reptiles
Types:
-keratins, collagens, and -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
Attractive and repulsive forces
between different amino acid residues
on the same chain in secondary and
tertiary structures
No globular protein present totally analyzed
in this way.
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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
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Amino acids
20 common amino acids
All zwitterions
Classification based on side chains (R):
Aliphatic Aromatic
Non-polar
Polar
Charged
Non-charged
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Amino acids
Sour
ce:
http://www. m
icrobiologytext.com
/index.php?
module=Bo
ok&func=d
isplayarticle&art_id=4
0
Com
monam
ino a
cid
s
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Formation of peptide bonds
Source:people.ifm.liu.se/~fenzh/Biopolymers%20Lecture.pdf
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Can polypeptides be produced
synthetically? Homopolymer Synthesis: Homopolypeptides can be synthesized
in laboratory conditions by typical condensation reactions usingsimple amino acids like alanine, valine, phenylalanine, etc. Althoughthese 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 energychanges 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 bothends of the polymer to only one end. For such a purpose,protective groups are used.
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Example: Synthesis of PLGAPEGPLGA
triblock copolymer (ReGel)
Biodegradable drugdelivery system
Injected as a liquid intothe body, later forms agel in response to body
temperature. Solubilizes and stabilizes
poorly soluble andsensitive drugs, includingproteins
Water used as a solvent
No organic solvents usedin the synthesis,purification, orformulation
PLGA:
poly(lactide-co-glycolide),
PEG:
Polyethylene
glycol
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
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Denaturation of Proteins
Zhang,F.h
ttp://people.ifm.liu.se
/~fenzh/Bio
polymers%20Lecture
.pdf.
Accessed:09January
2009
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Denaturation of Proteins Usually known as the loss oftertiary 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 ofcell activity and
possibly cell death.
Quaternary Structure: dissociation ofprotein sub-units and/ordisruption 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 polaramino acid side chains (and the surrounding solvent)
Van der Waals (induced dipole) interactions betweennonpolar amino acid side chains
Secondary Structure: loss of all regular repeating patternssuch as alpha-helices and beta-pleated sheets
Primary Structrure: no disruption
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Hydrolysis vs. Denaturation
Breakdown ofpeptides bondsthrough the additionof water, forming anamine and acarboxylic acid
Primary structure isnot affected (nohydrolysis of peptidebonds)
Recoiling: Somesmall proteins can re-gain their activeshape if theconditions are turnedback (cooled, or saltremoved, etc.)
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Polynucleotides
N
N
NH2
N
N
OO
OH
OH
OH
O
P
OH
HH
H H
phosphate residues
pentose sugar
nitrogen base
Polynucleotides: macromolecules found in the cells of living organisms, that are in charge ofthe 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
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Nucleotides: building blocks of
nucleic acids
R i b o s e
OHO
OH
OHOH
OHO
OH
OHOH
D e o x y r i b o s e
N
N
NH
N
NH2
A d e n i n e
N
NH
NH2
O
G u a n i n e
N
NH
NH2
O
C y t o s i n e
NH
NH
O
O
CH3
T h y m i n e
NO
OH
OPO
OH
N
NN
NH2
O
A typical nucleotidemonomer residue
Pentose sugars
Nitrogen bases
Purines Pyrimidines
Complementary
base pairing A = T
and C = G
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A schematic of a nucleic acid
polymer
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DNA vs. RNA
Sugar: Deoxyribose
Bases:
Adenine Cytosine
Guanine
Thymine
Double stranded Bases attached to
deoxyribose
Sugar: Ribose
Bases:
Adenine Cytosine
Guanine
Uracil
Single stranded Bases attached to
ribose
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Hydrogen bonds, coiling, and
uncoiling
(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
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.
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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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ADN
(a)Nanop
articlean
dma
Nano
R-lessDN
Aamplificatio
nsch
Mirki
J.Am.
Che
m.So
,2004
,126(19),p
p59325933
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Further Reading
Biotechnology of Biopolymers : From Synthes
by Alexander Steinbchel (Editor), Yoshiharu
Doi (Editor)
Structure and Dynamics of Biopolymers
by C. Nicolini (Editor)
http://www.amazon.com/exec/obidos/external-search?tag=iscid-20&keyword=Biotechnology%20of%20Biopolymers%20:%20From%20Synthesis%20to%20Patents&mode=bookshttp://www.amazon.com/exec/obidos/external-search?tag=iscid-20&keyword=Structure%20and%20Dynamics%20of%20Biopolymers%20&mode=bookshttp://www.amazon.com/exec/obidos/external-search?tag=iscid-20&keyword=Structure%20and%20Dynamics%20of%20Biopolymers%20&mode=bookshttp://www.amazon.com/exec/obidos/external-search?tag=iscid-20&keyword=Biotechnology%20of%20Biopolymers%20:%20From%20Synthesis%20to%20Patents&mode=books
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