Biopolymers

610 Pages·1973·14.04 MB·English

by  Alen Walton (Auth.)

MOLECULAR BIOLOGY
An International Series of Monographs and Textbooks
Editors: BERNARD HORECKER, NATHAN O. KAPLAN, JULIUS MARMUR, AND
HAROLD A. SCHERAGA
A complete list of titles in this series appears at the end of this volume.
BIOPOLYMERS
Alan G. Walton and John Blackwell
Division of Macromolecular Science
Case Western Reserve University
Cleveland, Ohio
with a contribution by Stephen H. Carr
Department of Materials Science
The Technological Institute
Northwestern University
Evanston, Illinois
®
ACADEMIC PRESS New York and London 1973
A Subsidiary of Harcourt Brace Jovanovich, Publishers
COPYRIGHT © 1973, BY ACADEMIC PRESS, INC.
ALL RIGHTS RESERVED.
NO PART OF THIS PUBLICATION MAY BE REPRODUCED OR
TRANSMITTED IN ANY FORM OR BY ANY MEANS, ELECTRONIC
OR MECHANICAL, INCLUDING PHOTOCOPY, RECORDING, OR ANY
INFORMATION STORAGE AND RETRIEVAL SYSTEM, WITHOUT
PERMISSION IN WRITING FROM THE PUBLISHER.
ACADEMIC PRESS, INC.
Ill Fifth Avenue, New York, New York 10003
United Kingdom Edition published by
ACADEMIC PRESS, INC. (LONDON) LTD.
24/28 Oval Road, London NW1
LIBRARY OF CONGRESS CATALOG CARD NUMBER: 79-182627
PRINTED IN THE UNITED STATES OF AMERICA
PREFACE
The term biopolymer has been defined in a variety of ways by researchers
in different disciplines. In strict analogy with the development of synthetic
commercial polymers we might, for example, require that its use be limited to
synthetic molecules fabricated from biological "monomer" units such as
amino acids and sugars. However, if biological/« vivo synthesis is encompassed
by the definition, the full gambit of biological macromolecules—proteins
nucleic acids, and polysaccharides—is included. We have chosen an inter-
mediate ground in which emphasis is placed on the simpler synthetic (in
vitro) biopolymers and native materials for which the molecular architecture
is most fully understood. In this sense, the objectives of the biopolymer
researcher would be, generally, to characterize the structure of biomolecules
by using physical techniques and, by so doing, gain insight into physiological
function.
The main theme of this book is concentrated on the methods of physical
characterization and the principles which underly them. The contents stress
the more quantitative aspects of sequence, conformation, and structure in both
laboratory-synthesized and native biopolymers. Even in the area of character-
ization of biopolymers, the available techniques, the evaluation of underlying
principles, and the experimental applications have mushroomed to such a
degree in the past few decades that we have been forced to make some arbi-
trary limitations to the scope of the methods and applications discussed. To an
extent, these limitations are imposed both by the nature of the audience to
which this book is directed and the influence of our immediate academic
environment. Thus, some of the newer methods are outlined, such as Raman
spectroscopy, theoretical conformation analysis, and electron microscopy
and morphology of laboratory-synthesized polymers, whereas others of
recent vintage such as spin labeling, fluorescent spectroscopy, and electron
spin resonance are excluded.
The book is directed to those who have relatively little background in the
application of physical methods to the study of biological macromolecules—
the undergraduate who wishes to familiarize himself (herself) with the area
ix
X Preface
or the researcher who is faced with proceeding in a new direction. Thus,
although much of the material is presented at an elementary level, an effort
has been made to reference the more important aspects and to present a
current account of the status of biopolymer research. In addition, the results
and implications of physical characterization of native biopolymers are
presented with emphasis on structure. Where possible, the principles of
molecular conformational analysis are thus projected through model com-
pounds to their native counterparts.
We are pleased to acknowledge the assistance of our colleagues in pro-
viding useful suggestions and material and the many investigators who pro-
vided us with photographs, original figures, and tables, several of which have
not previously been published. We are particularly grateful for the contri-
bution of Chapter 7 by Professor Stephen H. Carr of Northwestern University,
for the diligent efforts of Drs. Elizabeth Simons and Barton Rippon, and for
the unending patience, assistance, and cheerfulness brought to this project
by Peggy Buccieri.
ALAN G. WALTON
JOHN BLACKWELL
I
STRUCTURAL UNITS OF BIOPOLYMERS
Introduction
A polymer is a large molecule comprised of many fundamental units
joined together. If these units, called for present purposes the monomers,
are identical, the result is a " homopolymer " ; if they are of two or more kinds,
the product is a hetero- or copolymer that is either random or sequential.
In the latter case the monomers are present in the primary structure in a
specific sequence. In the following text we shall be concerned with the primary
structure (sequence and chemical structure), secondary structure (conforma-
tion or shape), and tertiary structure (arrangement and ultrastructure) of
biopolymers, and it is well to realize from the onset that all are interrelated,
although often in a manner which is not yet clear. This chapter deals with
primary structure and specifically with the monomer units from which both
synthetic and native biopolymers are generated. Three categories are dealt
with—proteins and polypeptides, polysaccharides, and polynucleotides and
nucleic acids.
Amino Acids
Proteins are broken down by hydrolysis into a mixture of about 20 dif-
ferent monomer units, known as amino acids. These are all α-amino acids,
1
2 1. Structural Units of Biopolymers
i.e., the amino group is attached to the a carbon atom, and with two excep-
tions (proline and hydroxyproline) they are primary amino acids with the
general formula
H
I
R—Ca-COOH
r
NH2
Amino acids fall into seven categories, depending mainly upon the nature
of the functional group R: aliphatic, hydroxylic, carboxylic, basic, aromatic,
sulfur-containing, and imino acids (proline and hydroxyproline). In the
imino acids the R group takes the form of a five membered ring containing
the α-carbon. A list of the naturally occurring amino and imino acids is
given in Table 1.1 (1). With such a large number of available building blocks,
nature is able to promote an extremely large variety of combinations, and can
thus control the subtle functions performed by proteins.
Apart from the simplest amino acid, glycine where R = H, all the amino
acids are optically active because of the asymmetry of the α-carbon atom.
We shall see later that this optical anisotropy is a useful basis for studying
the biopolymers that are comprised of these amino acids. With very few
exceptions the amino acids are found to be in the L configuration, where the
distribution of groups bonded to the α-carbon is as shown in Fig. 1.1. The
CHO CHO COOH
I \
H—C—OH
I
CH2OH CH2OH R
(a) (b) (c)
Fig. 1.1. Alternative representations of L-glyceraldehyde (a and b) and an L-amino
acid (c). Groups are at the corner of a tetrahedron.
exceptions are the occasional D forms which are found in certain bacterial
peptides. (The distinction between proteins, polypeptides, and peptides, is
mainly one of size and will be defined later.)
Polymerization of amino acids, either in the laboratory or in physiological
systems, involves the formation of peptide units,
H R
I I
— N—C—CO —
I
H
by a condensation process, and the properties of the functional R groups
will, to a large extent, control the properties of the polymer. In biological
systems the polypeptide chain is always straight, i.e., there is no branching,
and is almost always made up of a variety of amino acid monomers. An
interesting exception to the latter generalization is poly-y-D-glutamic acid, an
Amino Acids
TABLE LI
Amino Acids That Commonly Occur in Proteins'1
Name Structure ρΚ (Side chain)
Λ
I. Aliphatic amino acids
Glycine (Gly) H2N—CHjf-C02H
ÇH
3
HaN—CH—C02H
Alanine (Ala)
H3C^H/CH3
H2N—CH—C02H
Valine (Val)
H3C^H/CH3
I
ÇH,
HjjN—CH—C02H
Leucine (Leu)
CH3
CH2
CH—CH3
H2N—CH—C02H
Isoleucine (He)
II. Hydroxyamino acids
CH2OH
Serine (Ser) H2N—CH—C02H 9.15
ÇH
3
CH—OH
Threonine (Thr) 1 10.43
NH— CH—C02H
;. Dicarboxylic amino acids and
amides
C02H
Aspartic acid (Asp) CH2 3.86
NHJS—CH—C02H
CONILj
Asparagine (AspNH2 or Asn) CH2
NH2—CH—C02H
^Adapted in part from "Biological Chemistry," second edition; by Henry R. Mahler and
Eugene H. Cordes. Harper and Row, New York, 1971.
4 1. Structural Units of Biopolymers
TABLE 1.1 {continued)
Name Structure pÄ'a (Side chain)
ço H
2
Glutamic acid (Glu) 4.25
ÇHs
NH2—CH—C02H
CONH2
CH2
Glutamine (GluNH2 or Gin) CH2
NH2—CH—C02H
IV. Amino acids having basic functions
(CH2)4—NH2
Lysine (Lys) NH2—CH—C02H 10.53
CH2—NH2
CH—OH
Hydroxylysine (Hylys) (CH2)2 9.67
NH2— CH—C02H
Histidine (His) CH2 6.0
NH2—CH—C02H
H NH
Arginine (Arg) (ÇHjjJa—N-C—NH2 9.04
NH2—CH—C02H
V. Aromatic amino acids
CH,
Phenylalanine (Phe)
NH2—CH—C02H
OH
Tyrosine (Tyr) 10.07
CH2
NH—CH— C02H
Amino Acids 5
TABLE 1.1 (continued)
Name Structure pÄ'a (Side chain)
p
NH
Tryptophan (Try)
CH2
NH — CH—C02H
VI. Sulfur-containing amino acids
CH — SH
Cysteine (CySH) NH— CH—C02H 8.33
v
Cystine (CyS—SCy) ( ' HH2-—CS0 2H/2\ —
\NH— C
(CH2)2— SCH3
Methionine (Met) NH2— CH— C02H
VII. Imino acids
Proline (Pro) ^N C02H
H
ΗΟ^
Hydroxyproline (Hypro)
^Ν^ΧΟ,,Η
H
insect wax that is not only a homopolymer, but consists of D residues linked
through the y- rather than the α-carboxyl group. However, no proteins are
homopolymers and we may accept as a general rule that they are a-linked L-
amino acids. In the laboratory the most straightforward synthetic process is
the formation of a homopolymer, i.e., a poly-a-amino acid. Nevertheless,
recent developments have made possible the preparation of mixed and
sequential polypeptides that are, perhaps, realistic protein models.
As previously mentioned, the properties of the polypeptide are, to an
extent, governed by the (R-)side group or groups, and some general rules
may be pointed out here. Polymers of the aliphatic amino acids are "non-
polar" because of the lack of ionizable side groups and are thus usually
insoluble in aqueous solution. In proteins the apolar side groups interact
unfavorably with the surrounding aqueous medium and tend to fold inside
globular structures. The hydroxylic functional groups of serine and threonine