12-04-2014, 11:34 AM
Textile processing with enzymes
Introduction
Enzymes are biological catalysts that mediate virtually all of the biochem-
ical reactions that constitute metabolism in living systems. They accelerate
the rate of chemical reaction without themselves undergoing any per-
manent chemical change, i.e. they are true catalysts. The term ‘enzyme’
was first used by Kühne in 1878, even though Berzelius had published a
theory of chemical catalysis some 40 years before this date, and comes
from the Greek enzumé meaning ‘in (en) yeast (zumé)’. In 1897, Eduard
Büchner reported extraction of functional enzymes from cells. He showed
that a cell-free yeast extract could produce ethanol from glucose, a
biochemical pathway now known to involve 11 enzyme-catalysed steps.
It was not until 1926, however, that the first enzyme (urease from Jack-
bean) was purified and crystallised by James Sumner of Cornell University,
who was awarded the 1947 Nobel Prize. The prize was shared with John
Northrop and Wendell Stanley of the Rockefeller Institute for Medical
Research, who had devised a complex precipitation procedure for isolating
pepsin. The procedure of Northrop and Stanley has been used to crystallise
several enzymes. Subsequent work on purified enzymes, by many
researchers, has provided an understanding of the structure and properties
of enzymes.
In this chapter
This chapter is concerned mainy with the fundamental aspects of enzymes
that determine their properties and catalytic capabilities. It is intended to
provide a sound basis for understanding of many of the applied aspects of
enzymes considered in subsequent chapters in this text. Given the wealth
of fundamental knowledge on enzymes, it is only possible here to provide
a perspective on each of the topics. Some of the topics will be considered
in more detail, or from a different perspective, later on in the text.
Section 1.2 deals with the classification and nomenclature of enzymes. It
considers some of the rules that form the basis of a rational system classi-
fication and naming enzymes, and provides examples of enzymes in each of
the six main classes. Much of the chapter is devoted to protein structure
(Section 1.3) because this ultimately defines the properties of enzymes,
such as substrate specificity, stability, catalysis and response to physical and
chemical factors. Protein structure is considered at all levels of organisa-
tion, from the ‘building blocks’ (amino acids) of proteins, through backbone
conformations and three-dimensional shapes, to enzymes having more than
one sub-unit. Consideration of the forces that stabilise protein molecules
follows (Section 1.4) and the strengths of the various bonds are compared
in relation to level of protein structure.
Classification and nomenclature of enzymes
Organisms – whether animal, plant or microorganism – are both complex
and diverse. In biological systems, thousands of different types of reactions
are known to be catalysed by different enzymes; many more are yet to be
discovered. The diversity of enzymes is, therefore, enormous in terms of
type of reaction(s) they catalyse, and also in terms of structure. Enzymes
range from individual proteins with a relative molecular mass (RMM) of
around 13 000 catalysing a single reaction, to multi-enzyme complexes of
RMM several million catalysing several distinct reactions.
Given such diversity, it is essential to have a rational basis for classifica-
tion and naming of enzymes. Currently, it is the Nomenclature Committee
of the International Union of Biochemistry and Molecular Biology (NC-
IUBMB) that considers these matters and gives recommendations to the
international scientific community.
Primary structure of proteins
Amino acids (monomers) are joined together by peptide bonds to give
proteins. Addition of increasing numbers of amino acids gives peptides
and then polypeptides. If the RMM of the chain is more than 5000, the
molecule is usually referred to as a polypeptide rather than a peptide. The
primary structure of a polypeptide refers to the amino acid sequence,
together with the positioning of any disulfide bonds that may be present.
The peptide (amide) bond that joins amino acids together to form a
polypeptide is formed by elimination of water, i.e. a condensation reaction
(Fig. 1.5). The polypeptide chain formed (the residue) has one free carboxy
and one free amino group at opposite ends of the molecule, known as the
carboxy and amino termini, respectively. Peptide bonds are rigid, being
stabilised by resonance, i.e. the amide nitrogen lone pair of electrons is
delocalised across the peptide linkage.The bond can be thought of as having
an intermediate form between the two extremes (cis and trans forms).
However, in most instances steric interference between the amino acid side
groups and the a-carbon atoms of adjacent amino acid residues means that
the trans form (R-group lies on opposite sites of the polypeptide chain; Fig.
1.5) is around 1000-fold more common than the cis form.
Forces that stabilise protein molecules
The conformation of a protein is ultimately defined by its amino acid
sequence, i.e. its primary structure. Upon biosynthesis of a polypeptide,
folding is thought to occur simultaneously in many places, giving rise to sec-
ondary structure. The folded regions then interact to form structural motifs
and domains and, finally, the domains associate to give rise to the tertiary
structure of the protein, i.e. its native conformation. Whereas regions of
secondary structure are stabilised by interactions between amino acids
close together within the polypeptide chain, tertiary structure is stabilised
by interactions between amino acids that are far apart on the chain but that
are brought into close proximity by protein folding. The main forces
that stabilise tertiary structure are hydrophobic interactions, electrostatic
interactions and covalent linkages. Table 1.2 compares bond strengths of
interactions involved in stabilising protein molecules.