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Table of Contents
(Subject Area: Polymers)
Pages in the
Article Authors
Encyclopedia
Biopolymers E. Ann MacGregor Pages 207-245
Macromolecules, Peter A. Mirau, Lynn W.
Pages 857-901
Structure Jelinski and Frank A. Bovey
Plastics Engineering R. J. Crawford Pages 457-474
Polymer Processing Donald G. Baird Pages 611-643
Polymers, Electronic
J. Mort Pages 645-657
Properties
Polymers, T. C. Mike Chung and A.
Pages 659-674
Ferroelectric Petchsuk
Polymers, Inorganic
Martel Zeldin Pages 675-695
and Organometallic
Polymers,
Garth L. Wilkes Pages 697-722
Mechanical Behavior
Polymers, Elsa Reichmanis, Omkaram
Pages 723-744
Photoresponsive (in Nalamasu and Francis
Polymers, Recycling Richard S. Stein Pages 745-750
Timothy E. Long, James E.
Polymers, Synthesis Pages 751-774
McGrath and S. Richard
Polymers, Thermally
J. P. Critchley Pages 775-807
Stable
Rheology of
Chang Dae Han Pages 237-252
Polymeric Liquids
Rubber, Natural Stephen T. Semegen Pages 381-394
Rubber, Synthetic Stephen T. Semegen Pages 395-405
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Biopolymers
E. Ann MacGregor
UniversityofManitoba
I. GeneralCharacteristicsofPolymers
II. Biopolymers
GLOSSARY Tertiary structure Overall folding of a polymer chain,
includingrelativeorientationsofsecondarystructures.
α-Amino acid Chemical compound containing a car-
boxylicacidgroup(COOH)andanaminogroup(NH )
2
attachedtoonecarbonatom. A POLYMERisachemicalsubstancewhosemolecules
Anomers Carbohydrates differing only in configuration arelargeandconsistofmanysmallrepeatingunitscova-
ofsubstituentgroupsatcarbon1ofanaldosesugar. lentlybondedtogether.Innature,awidevarietyofpoly-
Configuration Arrangement of atoms in a molecule mers, the biopolymers, are synthesized by living organ-
in space.One configuration cannot be changed to isms. Among such biopolymers are the proteins which
another without breaking interatomic bonds in the perform many different functions, such as acting as cat-
molecule. alysts or regulators, the polysaccharides—important in
Conformation Arrangementoftheatomsofamolecule structuresandasenergyreserves—andthenucleicacids
inspace,whichcanbechangedbyrotationofchemical which carry genetic information from one generation to
groupingsaroundsinglebondsinthemolecule. the next. In addition, rubber, a plant polymer, is an in-
Covalentbond Bondbetweentwoatomsinwhicheach dustrially important elastomer, while little direct com-
atomcontributesoneelectrontothebonding. mercialusehasyetbeenfoundforlignin,anotherabun-
Dalton Unitofatomicmass,equalto1.66053×10−27kg. dantplantpolymer.Themicrobialpolyesters,polyhydrox-
Gel Semisolidjellyofsoliddispersedinliquid. yalkanoates, are, in contrast, growing in importance as
Hydrogen bond Weak bond formed when a hydrogen biodegradableplasticsmadefromrenewableresources.
atomissharedbetweentwoelectron-attractingatoms
suchasoxygenornitrogen.
Primarystructure Sequenceofmonomerresiduesina I. GENERAL CHARACTERISTICS
polymerchain. OF POLYMERS
Quaternary structure Arrangement of subunits of a
polymer molecule in space (especially for pro- Polymermolecules,ormacromolecules,arecomposedof
teins).Eachsubunitmustitselfbeapolymerchain. largenumbersoflinked,smallrepeatunits.Theunitsfrom
Secondarystructure Regularfoldingofapolymerchain, which polymers are synthesized are called monomers.
stabilizedbyhydrogenbonding. Polymersmaybemadefromonekindofmonomer,giving
207
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208 Biopolymers
homopolymers,orfromseveralkindsofmonomers,giv- B-B-B-. Examples of all these kinds of biopolymer ar-
ingcopolymers.Formanybiopolymerstherepeatunitsof rangementsareknown.
the macromolecule are not identical in structure to the Apolymersamplemayconsistofacollectionofiden-
monomers, because a small molecule such as water is ticalmolecules(i.e.,withthesamesequenceofmonomer
eliminatedfromthemonomersduringincorporationinto residues,thesamepositionandlengthofbranches[where
thepolymer.Thisleavesmonomerresiduesorrepeatunits present]andthesamedegreeofpolymerization).Onthe
smaller than the original monomers (e.g., consider three other hand, polymers are known where the molecules
hypothetical monomers becoming linked at the start of are heterogeneous with respect to number and sequence
synthesisofapolymer,asinI). of monomer residues and distribution of branches. Pro-
teinsandnucleicacids,forexample,fallinthefirstcate-
HO R OH (cid:2) HO R OH (cid:2) HO R OH gory,whilepolysaccharidesandlignincomeinthesecond
category.
One of the characteristics of polymers, apart from
molecularsize,whichdistinguishesthemfromsubstances
HO R O R O R OH (cid:2) 2H2O made of small molecules is the importance of nonco-
valent bonding between two parts of the same polymer
monomer residue
or molecule or between two separate molecules. This non-
repeat unit covalentbondingcanbeofvariouskinds.Hydrogenbond-
ingariseswhenhydrogenatomsaresharedbetweentwo
I atomssuchasoxygenornitrogenwhichcarrypartialneg-
ative charges. Hydrogen bonds are particularly common
The monomer is HOROH, while the repeat unit is inbiopolymers,buttheycanbedisruptedeasilybyheator
R O .Moleculesconsistingofasmallnumber(<20) changesinacidity(orpH)oftheenvironmentofthepoly-
ofrepeatunitsarecalledoligomers,butthereisnogener- mer. Many groups attached to polymer main chains can
allyacceptedvalueforthenumberofrepeatunitswhich ionize,andelectrostaticattractions,orionicbonding,can
distinguishes a large oligomer from a small polymer. In occur between positively and negatively charged group-
thisarticlethemoleculesofthepolymersdiscussedgener- ings.Conversely,groupscarryinglikechargesrepeleach
allyhaveadegreeofpolymerization(thenumberofrepeat other.Ionicbondingisimportantinmanyproteinsandin-
unitsinthepolymermolecule)ofmorethan30. organicpolymersbutagaincanbelessenedbychangesin
Wherepolymersaresynthesizedfrommonomerscon- pHoftheenvironment.Inproteins,itisoftenfoundthat
tainingtwochemicallyreactive,orfunctional,groups,the hydrocarbon groups associate with each other. This hy-
resultantpolymermoleculesarelinear.Ifmonomershave drophobicinteractionexcludeswaterfromthevicinityof
more than two functional groups, however, branched or thehydrocarbongroupings.Infact,itisthisexclusionof
even network polymers may be formed (Fig. 1). waterwhichprovidesthedrivingforcefortheassociation.
Carbonatomsareanimportantconstituentofabiopoly- In addition to these kinds of bonding, all atoms in close
merchain.Suchatomsareusuallybondedtofouratoms contactattracteachotherweakly.Suchforcesarecalled
or chemical groupings arranged tetrahedrally in space. vanderWaalsforcesandcanbeimportantintheinteriors
When the four groups attached to one carbon atom are ofhighlyfoldedandcompactpolymermolecules.
different,twopossiblearrangementsinspace,orconfig-
urations, are possible (Fig. 2). Biosynthesis of polymers
isunderstrictstereochemicalcontrol,however,andusu- II. BIOPOLYMERS
ally only one possible configuration is incorporated into
a biopolymer. Thus, proteins, which are polymers of α- Alargenumberofpolymers,differingwidelyinstructure
aminoacids,aresynthesizedfromL-α-aminoacidsonly, and function, are synthesized in living organisms. It is
and not from D-α-amino acids (see Fig. 2). convenient, therefore, to discuss biopolymers in groups,
Incopolymers,wheremorethanonemonomerresidue ratherthanasawhole.Thepolymersdescribedbelowhave
(sayAandB)ispresent,theseresiduescanbearranged been assigned to groups on the basis of structure, but at
alongthepolymerchainindifferentways,givingforex- bestthisdivisionisapproximate.
ample an apparently random sequence A–B-A-A-B-A- Although individual polymers are important, in living
B-B-B-A-A-, or an alternating sequence A-B-A-B-A-B- organismsitisoftentheinteractionsbetweenbiopolymers
A-B-,orasequenceconsistingofablockofoneresidue whichconferonatissueitsformandfunction.Muchwork
followedbyablockoftheotherA–A-A-A-A-A-A-B-B- isnowbeingcarriedouttoelucidatetheseinteractions.
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Biopolymers 209
FIGURE1 (a)FormationofalinearpolymerfrommonomerAwithtwofunctionalgroupsand(b)formationofnonlinear
polymersfrommonomerBwiththreefunctionalgroups:(i)branchedpolymer,(ii)branch-on-branchpolymer,and(iii)
networkpolymer.
A. Proteins increased, so also has our understanding of the relation-
shipbetweenstructureandfunction.
Allproteinsarepolymersofα-aminoacids,buttheydiffer
inthree-dimensionalmolecularstructureandinthefunc-
1. Structure
tionstheyperforminlivingorganisms.Proteinmolecules
can,forexample,havestructural,transporting,orregula- As mentioned earlier, the monomers of proteins are α-
toryroles;inaddition,asantibodiestheyprotectmammals amino acids. Such acids can exist in two configurations
fromdiseaseandasenzymesactasthemostefficientcat- (see Fig. 2), but the strict stereochemical requirements
alystsknown.Asourknowledgeofproteinstructurehas of the processes involved in protein biosynthesis result
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210 Biopolymers
in only L-α-amino acids becoming incorporated into the
polymers.Nineteendifferentaminoacidsofgeneralfor-
mulaH N-CHR-COOHcanbeusedasmonomersinpro-
2
tein synthesis, and these vary only in the nature of the
side group R. A list of possible side groups is shown in
Table I. In addition an imino acid, proline, with a cyclic
sidechainandhavingan NHgroupinsteadofthe NH
2
oftheaminoacids,canactasaproteinmonomer.Some
side chains (R groups) can be chemically modified after
incorporationoftheaminoacidintoaprotein,andthree
of these modifications are also shown in Table I. Thus, hy-
FIGURE2 Twopossibleconfigurationsofα-aminoacidsofstruc-
droxyl groups can be introduced onto lysine and proline
tureH2N CHR COOH.
residues to give hydroxylysine and hydroxyproline, re-
spectively.Oxidation,asinII,oftwocysteinesidechains Proteinbiosynthesisisacomplexprocessdirectedbyother
closetoeachotherintheproteinmoleculegivescystine, biopolymers,thenucleicacids,andthisisdescribedlater
containinganewdisulfidebondwhichhelpstostabilize in Section II.C.2. X-ray studies of peptides have shown
proteinstructure: that the atoms involved in the peptide bond are almost
coplanar,andthatadjacentsidegroups(Rgroups)project
oxidation
CH2 SH (cid:2) HS CH2 on opposite sides of the polypeptide chain (see Fig. 3).
Thisimposesrestrictionsonthewayapolypeptidechain
CH S S CH (cid:2) H O
2 2 2 canfoldupinthreedimensions.
disulfide Allproteinshavecertainstructuralfeaturesincommon.
bond
Each protein molecule consists of at least one polypep-
II tide chain. Most polypeptide chains have a free amino
group (NH ) at one end—this is the N-terminal end of
2
Duringproteinbiosynthesis,aminoacidsbecomelinked the chain—and a carboxylic acid group (COOH) at the
togethereffectivelybytheeliminationofwater: other or the C-terminal end of the chain. By conven-
H N CHR COOH (cid:2) H N CHR COOH tion, polypeptide chain formulas are written with the N-
2 x 2 y
terminalendattheleftandtheC-terminalendattheright.
Theaminoandcarboxylgroupsatchainendsandonthe
sidegroupsoftheaminoacids,lysine,arginine,aspartic,
andglutamicacidscanionizetogive NH+and COO−
3
groups,respectively.Thus,polypeptidechainsarecharged
H N CHR CO HN CHR COOH
2 x y
in solution, but the magnitude of the charge depends on
peptide the pH. For each protein there is a pH at which the net
bond chargeonthemoleculesiszero.ThispHisknownasthe
isoelectricpointoftheprotein.
III
Proteins differ from one another in the number, mod-
Thenewbondformediscalledapeptidebond;twoamino ification, and sequence of amino acid residues in the
acidslinkedbysuchabondconstituteadipeptide;three polypeptide chains and in the number of chains making
aminoacidsjoinedbytwopeptidebondsformatripeptide. uptheproteinmolecule.Hence,proteinsdifferwidelyin
Achainofseveral(e.g.,ten)aminoacidssolinkedgivesan molecularweight.Inaddition,someproteins,theconju-
oligopeptide,whilealongchainofuptoseveralthousand gated proteins, contain nonamino acid material such as
amino acids as in IV is called a polypeptide. A protein complex organic molecules or simple metal ions. These
issimplyasubstancewhosemoleculesconsistofoneor are called prosthetic groups, and they alter the physical
morepolypeptidechains: andchemicalpropertiesofproteins.
H N CHR CO NH CHR CO NH CHR CO
2 a b c
NH CHR COOH
x
IV
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Biopolymers 211
TABLEI TheCommonAminoAcidsFoundinProteins
Common
Name abbreviation Sidegroup,R
Glycine Gly H
Alanine Ala CH
3
CH
3
Valine Val CH CH
3
CH
3
Leucine Leu CH CH CH
3 2
CH
3
Isoleucine Ile CH CH CH
3 2
Serine Ser HO CH
2
OH
Threonine Thr CH CH
3
Asparticacid Asp HOOC CH
2
Asparagine Asn H NOC CH
2 2
Glutamicacid Glu HOOC CH CH
2 2
Glutamine Gln H NOC CH CH
2 2 2
NH
Arginine Arg H N C NH CH CH CH
2 2 2 2
Lysine Lys H N CH CH CH CH
2 2 2 2 2
OH
Hydroxylysinea Hyl H N CH CH CH CH
2 2 2 2
Methionine Met CH3 S CH2 CH2
Cysteine Cys HS CH
2
Cystinea (Cys)2 CH2 S S CH2
N
N CH
2
Histidine His H
N CH
2
Tryptophan Trp H
CH
2
Phenylalanine Phe
HO CH
2
Tyrosine Tyr
completestructure
CH NH
2
H C
2
Proline Pro CH2 CH COOH
CH NH
2
HOHC
4-Hydroxyprolinea Hyp CH2 CH COOH
aProducedfromprecedingacidbychemicalreactionafterincorporationintoprotein.
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212 Biopolymers
The α-helix structure of proteins was first proposed
by Pauling and Corey and was confirmed later by X-ray
diffraction studies. For L-α-amino acids a right-handed
helix, as shown in Fig. 5a, is energetically more favorable
than a left-handed helix. The helix is stabilized by hydro-
gen bonds from a backbone NH group to oxygen of a
C O group of the fourth amino acid residue further back
on the chain. The side groups of amino acids project out-
ward from the helix. Proline residues (see Table I) in a
polypeptide chain lack the hydrogen necessary for hydro-
gen bonding; a helix-stabilizing hydrogen bond cannot
form, and so the presence of proline tends to disrupt
α-helices.
FIGURE 3 Arrangement in space of atoms of an extended poly-
peptide. Atoms 1–6 are almost coplanar, as are atoms 6–11, but N CHR C Nl C
1 2
in a different plane from 1–6.
H O H O
Hydrogen
At first sight, the amino acid sequence, or primaryluc- bonds
O H O H
ture, of a polypeptide chain appears to be random (Fig. 4),
yet it is this sequence that determines how the chain will C CHR N C CHR N
3 4
fold up. Thus, different sequences give protein molecules
with a variety of three-dimensional shapes. V
Although different proteins have different primary
structures, there is sufficient similarity in the backbone β-Structures, which involve highly extended polypeptide
of all polypeptide chains so that certain regular types of chains, are favored particularly where amino acid side
chain folding are found in many proteins. Chain folding chains are small. The chains appear to be pleated, as in
can be stabilized by hydrogen bonds, formed between Fig. 5b, and hydrogen bonds can form between several
the NH and C O groups of the chain backbone as parts of a polypeptide chain to give sheet formations. In
in V. Such structures are called the secondary structure of these the chains may run in the same direction (Fig. 5c)
proteins, and two main types occur—the α-helix and the to give a parallpleated sheet, or in opposite directions
β-structure. (Fig. 5d) to give an antiparallel pleated sheet. In the sheets
FIGURE 4 Amino acid sequence of porcine insulin.
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Biopolymers 213
FIGURE 5 Secondary structures of proteins: (a) α-helix, (b) “pleated” extended polypeptide chain, (c) parallel pleated
sheet, and (d) antiparallel pleated sheet. The arrow indicates chain direction from N-terminal to C-terminal.
the R groups project above or below the plane of the orientations of regular structures in a protein molecule are
sheets, and frequently the sheets are not flat, but are bent determined by the amino acid sequences of the polypep-
or twisted. In some proteins, however, the polypeptide tide chains.
chain containing the β-strands may coil like a helix, The overall folditf a polypeptide chain (i.e., the rel-
giving a so-called β-helix. ativeorientationsofhelices,β-strands,andthefoldingof
Proteins do not have structures which are entirely heli- segmentsbetweenthem)constitutesthetertiarystructure
cal or β-sheet. In general, a protein molecule made of one of a proteilln (Fig. 6). This folding can be stabilized by addi-
polypeptide chain consists of short stretches of helix and tionalhydrogenbondsbetween,forexample,aminoacid
β-structure connected by apparently randomly folded seg- sidegroupsbroughtclosetogetherbythefolding,byionic
ments of chain. Some proteins contain no helices, while bonds if side chains carrying opposite electrical charges
others contain no β-structure. The proportion and relative arebroughtintocloseproximity,byvanderWaalsforces
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214 Biopolymers
thefoldingofmoreandmoreproteinsisstudied,were-
alize that most proteins can be described in terms of a
smallnumberofregularpackingarrangementsofhelices
and/or β-structures. Thus, proteins can be considered to
beconstructedofmodules,eachmodulebeingastructural
domainofmainlyα-helicesand/orβ-structure.Onepro-
tein differs from another, then, in the number, type, and
relativearrangementofdomainswithinthemolecule,and
inthedetailedarrangementofaminoacidsidegroups,R
groups,onthemolecularsurface.
The tertiary structure of a protein molecule encom-
passes the overall folding of polypeptide chains, where,
if more than one chain is present, the chains are linked
bycovalentbonds—mostoftendisulfidebonds(asinII).
However,someproteinsexistwherethemoleculesconsist
ofseveralseparatepolypeptidechains;suchchainswould
beheldtogetherinthemoleculebyweakerbondssuchas
hydrogenandionicbonds,hydrophobicinteractions,and
vanderWaalsforcesandeachchaincanactasaseparate
subunitoftheproteinmolecule.Theseproteinsaresaidto
possess quaternary structure (i.e., specific arrangements
FIGURE6 Tertiarystructureofahypotheticalprotein.Thecylin-
of subunits within the macromolecule). Changes in sub-
dersrepresenthelices,whilethearrowsrepresentpleatedsheet
strands. The five strands of β-structure form a twisted parallel unit arrangement and even, to a small degree, in tertiary
pleatedsheet. structureofeachsubunitcantakeplacewhiletheprotein
carriesoutitsbiologicalfunction.Proteinsinwhichsuch
changestakeplacearesaidtobeallosteric.
if side chains are packed closely together, by hydropho- Insummary,anyoneproteinhasauniqueprimarystruc-
bicinteractionswherehydrocarbonsidechainscometo- ture which in turn specifies the secondary and tertiary
gether,andbythedisulfidebondsofcystine(asinII). structure (i.e., folding of the polypeptide chains). Rel-
Polypeptidechainsofoneproteinusuallyadoptapre- atively minor changes in tertiary structure are possible
ferredtertiarystructurethatisessentialforbiologicalac- as the protein functions in a living organism. Some pro-
tivity.Thenoncovalentbonding,whichstabilizestertiary teinsalsopossessquaternarystructurewhichmayundergo
structure,caneasilybeweakenedbyheatorchangesinpH changesassociatedwithbiologicalactivity.
and salt concentration. When this happens, the polypep-
tidechainsunwindandbecomerandomlycoiled.Biolog-
2. Function
icalactivityislostandtheproteinissaidtobedenatured.
For some proteins, removal of the denaturing agent per- Thefunctionsofproteinsaremanyandvaried.Hererep-
mitsareturnofthepreferredtertiarystructureandofbi- resentativesofsomeofthemajorfunctionsaregiven,with
ologicalactivity.Theproteinisthensaidtoberenatured, adescriptionwherepossible,oftherelationshipbetween
anditisthisabilitytorecoverfromunfoldingwhichhas structureandactivity.
ledustobelievethattheinformationrequiredtospecify Enzymes are an extremely important group of
thecorrectfoldingforbiologicalactivityisencodedinthe proteins—theproteinsthatactascatalysts.Theseincrease
aminoacidsequencesofpolypeptidechains. the rates of reactions by factors of from 108 up to 1020,
Thetertiarystructureofmanyproteinscanbedescribed andsoarethemostefficientcatalystsknown.Unlikemost
intermsof“domains”ratherthanpolypeptidechains.A man-madecatalysts,enzymesareextremelyspecific;each
domain is a polypeptide chain, or section thereof, often enzymecatalyzesonereactionoragroupofcloselyrelated
ofmolecularweightaround20,000andwhichconstitutes reactions.Thespecificityextendsnotonlytothechemical
a geometrically separate entity (i.e., a region of regular natureofthereactantsandproductsofareactionbutalsoto
and irregular folding separated from other such regions thestereochemistry(i.e.,arrangementofatomsinspace)
byalongerstretchofirregularfolding).Comparisonsof ofthesubstancesinvolved.Thustheenzymesofprotein
many proteins have shown that the same structural do- biosynthesis can distinguish between D- and L-α-amino
main,characterizedbyitsownfoldingpattern,mayoccur acidsandensurethatonlyL-aminoacidsareincorporated
in different proteins or several times in one protein. As into a growing polypeptide chain. In a living organism,
