Polymer Science Term Work Bio Polymers

8/9/2019 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

Polymer Science Term Work Bio Polymers

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