XII
Contents
3
3.1
3.1.1
3.1.2
3.1.3
3.1.4
3.1.5
3.2
3.2.1
3.2.2
3.2.3
3.3
3.3.1
3.3.2
3.3.3
3.3.4
3.3.5
3.4
3.4.1
3.4.2
3.4.3
4
4.1
4.2
4.2.1
4.2.2
4.2.3
4.2.4
4.2.5
4.2.6
4.2.7
4.2.8
4.2.9
4.3
4.3.1
The Structural Variety
and Metabolism of Proteins. . . .. 70
Structural Variety. . . . . . . . . . . .. 70
Protein Constituents. . . . . . . . . .. 70
Phosphorylation
and Dephosphorylation. . . . . . . .. 73
Analysis and Comparison
of Protein Sequences . . . . . . . . .. 76
Folding of the Polypeptide Chain .. 77
Multiple Forms of Proteins .. . . .. 78
Protein Synthesis . . . . . . . . . . . .. 80
Aminoacyl-tRNA Synthetases .. .. 81
Initiation, Elongation
and Termination . . . . . . . . . . . .. 81
Transport of Newly Synthesized
Proteins to Their Correct
Destinations in the Cell. . . . . . . .. 83
Proteolysis . . . . . . . . . . . . . . . .. 86
Exopeptidases. . . . . . . . . . . . . .. 89
Serine Proteinases . . . . . . . . . . .. 90
Cysteine Proteinases. . . . . . . . . .. 94
Aspartate Proteinases. . . . . . . . .. 95
Metalloproteinases. . . . . . . . . . .. 96
Proteinase Inhibitors ... . . . . . .. 97
Serine-Proteinase Inhibitors. . . . .. 97
Cysteine-Proteinase Inhibitors .... 101
uz-Macroglobulins ............ 102
References . . . . . . . . . . . . . . . . . 103
Molecular Evolution . . . . . . . . . 111
The Determination of Homology
Between Protein or DNA
Sequences ................. 114
The Mechanisms
of Molecular Evolution. . . . . . . . . 117
Nucleotide Substitution. . . . . . . . . 118
Deletion, Insertion and Duplication
of DNA Sequences. . . . . . . . . . . . 121
Gene Fusion and Exon Shuffling. . . 122
Transposition of DNA Sequences .. 122
The Evolution of Multi-Gene
Families. . . . . . . . . . . . . . . . . . . 123
Polyploidization. . . . . . . . . . . . . . 125
Gene Transfer Between Species
and "Molecular Lamarckism". . . . . 127
Adaptive and Innovative Protein
Evolution. . . . . . . . . . . . . . . . . . 127
Molecular Mechanisms in the
Evolution of Complex Characters . . 129
Protein and Nucleic Acid
Polymorphism. . . . . . . . . . . . . . . 130
Definitions and Concepts ........ 131
4.3.2
4.3.3
4.3.4
4.3.5
4.3.6
4.3.7
4.4
4.4.1
4.4.2
4.4.3
4.5
4.5.1
4.5.2
4.5.3
4.5.4
4.5.5
4.5.6
4.5.7
4.6
4.6.1
4.6.2
4.6.3
4.7
4.7.1
4.7.2
4.7.3
4.7.4
Methodological Problems
in the Determination of Protein
Polymorphism. . . . . . . . . . . . . . . 133
Dependence of Protein
Polymorphism on Protein Type . . . . 134
Differences in Protein
Polymorphism Between
Different Animal Groups
and Habitats. . . . . . . . . . . . . . . . 135
Dependence of Protein
Polymorphism on the Size
and History of a Population . . . . . . 136
Quantitative Genetic Variability . . . 136
DNA Polymorphism. . . . . . . . . . . 137
The Causes
of Genetic Polymorphism ....... 140
Neutral Theories
of Molecular Evolution ......... 140
Selection Theories
of Polymorphism ............. 142
The Controversy Between
Neutralism and Selectionism
143
Methods and Problems
in the Molecular Approach
to Evolutionary Relationships ..... 147
The Evolutionary Distance
Between Amino Acid or Nucleotide
Sequences ................. 148
Determination of Evolutionary
Distance from the Amino Acid
Composition of Proteins . . . . . . . . 150
Immunological Distance
Between Proteins. . . . . . . . . . . . . 151
Genetic Distance Given
by Electrophoretic Data . . . . . . . . 152.
Comparison of DNA Sequences
from the Thermostability
of Heteroduplices . . . . . . . . . . . . 153
DNA Restriction Analysis ....... 154
Construction of Phylogenetic Trees
from Molecular Data . . . . . . . . . . 155
The Rate of Molecular Evolution . . 160
The Rate of Protein Evolution . . . . 160
The Rate of Evolution
of the Nucleic Acids . . . . . . . . . . . 162
Is There a Molecular Clock?
163
Some Results of Molecular
Research into Evolutionary
Relationships . . . . . . . . . . . . . . . 164
Molecular Phylogenetic Trees . . . . . 165
Species Systematics . . . . . . . . . . . 165
Molecular Taxonomy Above
the Species Level. . . . . . . . . . . . . 168
Molecular Data and the Large-Scale
Classification of Organisms ...... 170
Contents
3
3.1
3.1.1
3.1.2
3.1.3
3.1.4
3.1.5
3.2
3.2.1
3.2.2
3.2.3
3.3
3.3.1
3.3.2
3.3.3
3.3.4
3.3.5
3.4
3.4.1
3.4.2
3.4.3
4
4.1
4.2
4.2.1
4.2.2
4.2.3
4.2.4
4.2.5
4.2.6
4.2.7
4.2.8
4.2.9
4.3
4.3.1
The Structural Variety
and Metabolism of Proteins. . . .. 70
Structural Variety. . . . . . . . . . . .. 70
Protein Constituents. . . . . . . . . .. 70
Phosphorylation
and Dephosphorylation. . . . . . . .. 73
Analysis and Comparison
of Protein Sequences . . . . . . . . .. 76
Folding of the Polypeptide Chain .. 77
Multiple Forms of Proteins .. . . .. 78
Protein Synthesis . . . . . . . . . . . .. 80
Aminoacyl-tRNA Synthetases .. .. 81
Initiation, Elongation
and Termination . . . . . . . . . . . .. 81
Transport of Newly Synthesized
Proteins to Their Correct
Destinations in the Cell. . . . . . . .. 83
Proteolysis . . . . . . . . . . . . . . . .. 86
Exopeptidases. . . . . . . . . . . . . .. 89
Serine Proteinases . . . . . . . . . . .. 90
Cysteine Proteinases. . . . . . . . . .. 94
Aspartate Proteinases. . . . . . . . .. 95
Metalloproteinases. . . . . . . . . . .. 96
Proteinase Inhibitors ... . . . . . .. 97
Serine-Proteinase Inhibitors. . . . .. 97
Cysteine-Proteinase Inhibitors .... 101
uz-Macroglobulins ............ 102
References . . . . . . . . . . . . . . . . . 103
Molecular Evolution . . . . . . . . . 111
The Determination of Homology
Between Protein or DNA
Sequences ................. 114
The Mechanisms
of Molecular Evolution. . . . . . . . . 117
Nucleotide Substitution. . . . . . . . . 118
Deletion, Insertion and Duplication
of DNA Sequences. . . . . . . . . . . . 121
Gene Fusion and Exon Shuffling. . . 122
Transposition of DNA Sequences .. 122
The Evolution of Multi-Gene
Families. . . . . . . . . . . . . . . . . . . 123
Polyploidization. . . . . . . . . . . . . . 125
Gene Transfer Between Species
and "Molecular Lamarckism". . . . . 127
Adaptive and Innovative Protein
Evolution. . . . . . . . . . . . . . . . . . 127
Molecular Mechanisms in the
Evolution of Complex Characters . . 129
Protein and Nucleic Acid
Polymorphism. . . . . . . . . . . . . . . 130
Definitions and Concepts ........ 131
4.3.2
4.3.3
4.3.4
4.3.5
4.3.6
4.3.7
4.4
4.4.1
4.4.2
4.4.3
4.5
4.5.1
4.5.2
4.5.3
4.5.4
4.5.5
4.5.6
4.5.7
4.6
4.6.1
4.6.2
4.6.3
4.7
4.7.1
4.7.2
4.7.3
4.7.4
Methodological Problems
in the Determination of Protein
Polymorphism. . . . . . . . . . . . . . . 133
Dependence of Protein
Polymorphism on Protein Type . . . . 134
Differences in Protein
Polymorphism Between
Different Animal Groups
and Habitats. . . . . . . . . . . . . . . . 135
Dependence of Protein
Polymorphism on the Size
and History of a Population . . . . . . 136
Quantitative Genetic Variability . . . 136
DNA Polymorphism. . . . . . . . . . . 137
The Causes
of Genetic Polymorphism ....... 140
Neutral Theories
of Molecular Evolution ......... 140
Selection Theories
of Polymorphism ............. 142
The Controversy Between
Neutralism and Selectionism
143
Methods and Problems
in the Molecular Approach
to Evolutionary Relationships ..... 147
The Evolutionary Distance
Between Amino Acid or Nucleotide
Sequences ................. 148
Determination of Evolutionary
Distance from the Amino Acid
Composition of Proteins . . . . . . . . 150
Immunological Distance
Between Proteins. . . . . . . . . . . . . 151
Genetic Distance Given
by Electrophoretic Data . . . . . . . . 152.
Comparison of DNA Sequences
from the Thermostability
of Heteroduplices . . . . . . . . . . . . 153
DNA Restriction Analysis ....... 154
Construction of Phylogenetic Trees
from Molecular Data . . . . . . . . . . 155
The Rate of Molecular Evolution . . 160
The Rate of Protein Evolution . . . . 160
The Rate of Evolution
of the Nucleic Acids . . . . . . . . . . . 162
Is There a Molecular Clock?
163
Some Results of Molecular
Research into Evolutionary
Relationships . . . . . . . . . . . . . . . 164
Molecular Phylogenetic Trees . . . . . 165
Species Systematics . . . . . . . . . . . 165
Molecular Taxonomy Above
the Species Level. . . . . . . . . . . . . 168
Molecular Data and the Large-Scale
Classification of Organisms ...... 170