4
1 The Subject Matter and Methods of Comparative Biochemistry
of different species but also within a species, e.g.
between male and female, between consecutive
generations, between the different castes of the
Hymenoptera, between the members of different
races or populations, and between the individuals
of a population.
If one defines the task of comparative biochemistry in general as the scientific analysis of molecular variety, this also covers variety within individuals, i.e. differences between organs, tissues
and cells, between organelles, and between molecules of the same function or origin. Not only are
the differences "in space" between various parts
of an organism the subject of comparative biochemistry, but also the differences with time. The
molecular changes in the course of embryo development are a part of "molecular embryology" [2].
The molecular viewpoint has also entered into
the study of post-embryonic development and
senescence [25]. Rhythmic processes, e.g. diurnal
rhythms and seasonal periodicity, also belong
to these time differences [7]. Only the qualitative aspects of such time differences and not
their quantitative aspects, will be covered in this
book.
1.3.1 Comparison of Low Molecular Weight
Substances
Comparative investigations of small biological
molecules in different species, tissues and developmental stages were particularly prominent during the initial phase of comparative biochemistry,
before the appearance of methods for studying
the nucleic acids and proteins. The expected
quantitative differences between low molecular
weight substances that are the substrates or intermediates of cell metabolism give important information about the physiological state of cells but
lead to no phylogenetic conclusions. The large
number of experiments carried out before the
1960s, for example to interpret the spectrum of
free amino acids, were in this sense unsuccessful.
However, qualitative differences in the low molecular weight products of secondary metabolism,
e.g. pigments, defence molecules or pheromones,
were found to be useful as biochemical markers.
The spectrum of small molecules not produced de
novo by the animal in question is dependent upon
the composition of the food, e.g. the presence of
carotenoids or, in many marine invertebrates, the
sterols. Otherwise, the spectrum of low molecular
weight compounds is both qualitatively and quantitatively determined by the enzymes active in the
cell. Thus, indications of the presence or absence
of specific enzymes or biosynthetic pathways may
also present direct phylogenetic information.
1.3.2 Comparison of Information-Carrying
Macromolecules
Evolution consists primarily of changes in the
genetic information in succeeding generations,
and its course can, therefore, best be read in the
genes themselves or their products.
One can statistically determine whether compared DNA or protein sequences are derived
from a common ancestral sequence. Sequences
originating from a common ancestral gene are termed homologous; it will be necessary to' discuss
whether, and in what way, this concept in molecular evolution departs from the classical concept of
homology (p. 117). The analysis of homologous
DNA and protein sequences has produced much
new knowledge on the mechanisms of evolution;
as an example one can point to the frequency and
outstanding importance of the transposition of
mobile genetic elements. It will be shown that
this new knowledge, rather than placing any
doubt on the Darwinian synthetic theory of
evolution, actually enriches and broadens the
concept. In the near future, the genetically determined quantitative differences in gene expression, i.e. the control of mRNA or protein concentration, will also be available for phylogenetic
assessment, as soon as more comparative data
become available on the as yet only primitively
understood control mechanisms of gene expression.
The molecular data make available completely
new methods for the analysis of phylogenetic
relationships. Proteins with clear homology have
been organized by Dayhoff into "protein superfamilies" [4]. So far more than 200 such families
have been identified, many of them are found in
all organisms from prokaryotes to man; it is likely
that 500-1000 such protein super-families exist.
However, they number far less, for example, than
enzymes with different reaction or substrate specificities, 2477 of which were listed by the International Union of Biochemistry (IUB) Commission in 1984 [17]. Proteins with very different
functions can be found in the same super family,
i.e. they are homologous. On the other hand,
proteins of very different structure can have practically identical enzymic properties and are then
denoted as "isoenzymes". Isoenzymes encoded
by the alleles of a gene are called "alleloenzy-
1 The Subject Matter and Methods of Comparative Biochemistry
of different species but also within a species, e.g.
between male and female, between consecutive
generations, between the different castes of the
Hymenoptera, between the members of different
races or populations, and between the individuals
of a population.
If one defines the task of comparative biochemistry in general as the scientific analysis of molecular variety, this also covers variety within individuals, i.e. differences between organs, tissues
and cells, between organelles, and between molecules of the same function or origin. Not only are
the differences "in space" between various parts
of an organism the subject of comparative biochemistry, but also the differences with time. The
molecular changes in the course of embryo development are a part of "molecular embryology" [2].
The molecular viewpoint has also entered into
the study of post-embryonic development and
senescence [25]. Rhythmic processes, e.g. diurnal
rhythms and seasonal periodicity, also belong
to these time differences [7]. Only the qualitative aspects of such time differences and not
their quantitative aspects, will be covered in this
book.
1.3.1 Comparison of Low Molecular Weight
Substances
Comparative investigations of small biological
molecules in different species, tissues and developmental stages were particularly prominent during the initial phase of comparative biochemistry,
before the appearance of methods for studying
the nucleic acids and proteins. The expected
quantitative differences between low molecular
weight substances that are the substrates or intermediates of cell metabolism give important information about the physiological state of cells but
lead to no phylogenetic conclusions. The large
number of experiments carried out before the
1960s, for example to interpret the spectrum of
free amino acids, were in this sense unsuccessful.
However, qualitative differences in the low molecular weight products of secondary metabolism,
e.g. pigments, defence molecules or pheromones,
were found to be useful as biochemical markers.
The spectrum of small molecules not produced de
novo by the animal in question is dependent upon
the composition of the food, e.g. the presence of
carotenoids or, in many marine invertebrates, the
sterols. Otherwise, the spectrum of low molecular
weight compounds is both qualitatively and quantitatively determined by the enzymes active in the
cell. Thus, indications of the presence or absence
of specific enzymes or biosynthetic pathways may
also present direct phylogenetic information.
1.3.2 Comparison of Information-Carrying
Macromolecules
Evolution consists primarily of changes in the
genetic information in succeeding generations,
and its course can, therefore, best be read in the
genes themselves or their products.
One can statistically determine whether compared DNA or protein sequences are derived
from a common ancestral sequence. Sequences
originating from a common ancestral gene are termed homologous; it will be necessary to' discuss
whether, and in what way, this concept in molecular evolution departs from the classical concept of
homology (p. 117). The analysis of homologous
DNA and protein sequences has produced much
new knowledge on the mechanisms of evolution;
as an example one can point to the frequency and
outstanding importance of the transposition of
mobile genetic elements. It will be shown that
this new knowledge, rather than placing any
doubt on the Darwinian synthetic theory of
evolution, actually enriches and broadens the
concept. In the near future, the genetically determined quantitative differences in gene expression, i.e. the control of mRNA or protein concentration, will also be available for phylogenetic
assessment, as soon as more comparative data
become available on the as yet only primitively
understood control mechanisms of gene expression.
The molecular data make available completely
new methods for the analysis of phylogenetic
relationships. Proteins with clear homology have
been organized by Dayhoff into "protein superfamilies" [4]. So far more than 200 such families
have been identified, many of them are found in
all organisms from prokaryotes to man; it is likely
that 500-1000 such protein super-families exist.
However, they number far less, for example, than
enzymes with different reaction or substrate specificities, 2477 of which were listed by the International Union of Biochemistry (IUB) Commission in 1984 [17]. Proteins with very different
functions can be found in the same super family,
i.e. they are homologous. On the other hand,
proteins of very different structure can have practically identical enzymic properties and are then
denoted as "isoenzymes". Isoenzymes encoded
by the alleles of a gene are called "alleloenzy-