Chapter
Useful internet resources
pp.：
31 – 34
2.2 The amino acids
pp.：
34 – 39
2.1 The polypeptide backbone
pp.：
34 – 34
Chapter 2: Protein structure
pp.：
34 – 34
2.3.1 Enzymatic modifications
pp.：
39 – 43
2.3 Covalent modifications of amino acid side chains
pp.：
39 – 39
2.3.2 Nonenzymatic chemical modifications
pp.：
43 – 44
2.4.1 Noncovalent interactions
pp.：
44 – 45
2.4 Interactions that govern protein folding and stability
pp.：
44 – 44
2.4.2 The hydrophobic interaction
pp.：
45 – 46
2.5 Secondary structural elements
pp.：
46 – 46
2.5.1 The α α -helix
pp.：
46 – 47
2.5.2 β β -sheets
pp.：
47 – 48
2.5.3 Reverse turns
pp.：
48 – 48
2.6 Supersecondary structures
pp.：
48 – 49
2.7 Tertiary structures of proteins
pp.：
49 – 49
2.7.1 Globular proteins
pp.：
49 – 51
2.7.2 Fibrous proteins
pp.：
51 – 52
2.7.3 Unusual structures of internally repeated proteins
pp.：
52 – 53
2.7.4 Secreted proteins and membrane proteins
pp.：
53 – 56
2.7.5 Intrinsically disordered proteins
pp.：
56 – 56
2.8 Multidomain proteins
pp.：
56 – 56
2.9 Multisubunit proteins
pp.：
56 – 57
Useful internet resources
pp.：
57 – 61
3.1 Types of mutations
pp.：
61 – 61
3.1.1 Substitutions
pp.：
61 – 64
Chapter 3: Mutations
pp.：
61 – 61
3.1.2 Deletion, duplication, insertion and fusion
pp.：
64 – 66
3.2 Factors affecting rates of mutation
pp.：
66 – 68
3.3 The fate of mutations
pp.：
68 – 75
3.4 The molecular clock
pp.：
75 – 77
Useful internet resources
pp.：
78 – 79
Chapter 4: Evolution of protein-coding genes
pp.：
79 – 79
4.1 Alignment of nucleotide and amino acid sequences
pp.：
79 – 81
4.2 Estimating the number of nucleotide substitutions
pp.：
81 – 83
4.2.1 Substitutions in translated regions
pp.：
83 – 84
4.3 Rates and patterns of nucleotide substitution
pp.：
84 – 85
4.2.2 Substitutions in untranslated regions, introns and 5and 3flanking regions of protein-coding genes
pp.：
84 – 84
4.3.1 Rates of nucleotide substitution
pp.：
85 – 87
4.4 Variation in substitution rates
pp.：
87 – 88
4.4.1 Variation among different sites of the translated region
pp.：
88 – 90
4.4.2 Variation among genes
pp.：
90 – 91
4.4.3 Constancy and variation in substitution rates of orthologous genes
pp.：
91 – 92
4.4.4 Nonrandom substitutions at synonymous positions
pp.：
92 – 94
4.5.1 Phylogenetic trees
pp.：
94 – 95
4.5 Molecular phylogeny
pp.：
94 – 94
4.5.2 Tree reconstruction
pp.：
95 – 97
4.5.3 Tree-making methods
pp.：
97 – 101
References
pp.：
101 – 103
4.5.4 Estimation of species-divergence times
pp.：
101 – 101
Useful internet resources
pp.：
103 – 105
Chapter 5: Evolution of orthologous proteins
pp.：
105 – 107
5.1 Orthologous proteins with the same function in different species
pp.：
107 – 110
5.2 Orthologous proteins with modified function in different species
pp.：
110 – 114
5.4 Orthologous proteins that have lost their function
pp.：
114 – 115
5.3 Orthologous proteins with major modification of function
pp.：
114 – 114
5.6 Prediction of the function of orthologous proteins
pp.：
115 – 116
5.5 Orthologous proteins that have gained additional functions
pp.：
115 – 115
5.7 The three-dimensional structure of orthologous proteins
pp.：
116 – 116
5.7.1 Prediction of secondary structure of proteins
pp.：
116 – 118
5.7.2 Prediction of the three-dimensional structure of proteins
pp.：
118 – 119
5.8 Detecting sequence homology of protein-coding genes
pp.：
119 – 120
References
pp.：
120 – 121
Useful internet resources
pp.：
121 – 124
6.1 De novo formation of novel protein-coding genes
pp.：
124 – 126
Chapter 6: Formation of novel protein-coding genes
pp.：
124 – 124
6.2 Gene duplications
pp.：
126 – 127
6.2.1 Mechanisms of gene duplication
pp.：
127 – 133
6.2.2 Fate of duplicated genes
pp.：
133 – 137
6.2.3 Fate of genes acquired by lateral gene transfer
pp.：
137 – 137
6.2.4 Dating gene duplications
pp.：
137 – 140
References
pp.：
140 – 141
Useful internet resources
pp.：
141 – 142
Chapter 7: Evolution of paralogous proteins
pp.：
142 – 143
7.1.2 Processed genes
pp.：
143 – 146
7.1 Advantageous duplications
pp.：
143 – 143
7.1.1 Unprocessed genes
pp.：
143 – 143
7.2 Neutral duplications
pp.：
146 – 148
7.2.1 Modification of function by point mutations
pp.：
148 – 156
7.2.2 Major change of function by point mutations
pp.：
156 – 159
7.2.3 Major change of function by domain acquisitions
pp.：
159 – 163
7.3 Similarities and differences in the evolution of paralogous and orthologous proteins
pp.：
163 – 166
7.4 Predicting the function of proteins by homology
pp.：
166 – 167
7.5 Nonhomology-based methods for the prediction of the function of proteins
pp.：
167 – 168
7.6 Detecting distant homology of protein-coding genes
pp.：
168 – 168
7.6.1 Detecting distant homology by consensus approaches
pp.：
168 – 177
7.6.2 Detecting distant homology by comparing three-dimensional structures
pp.：
177 – 178
7.6.3 Detecting distant homology by comparing exon–intron structures
pp.：
178 – 179
References
pp.：
179 – 182
Useful internet resources
pp.：
182 – 186
Chapter 8: Protein evolution by assembly from modules
pp.：
186 – 187
8.1 Modular assembly by intronic recombination
pp.：
187 – 189
8.1.1 Introns
pp.：
189 – 198
8.1.2 Internal gene duplications/deletions via recombination in introns
pp.：
198 – 199
8.1.4 Exon shuffling via recombination in introns
pp.：
199 – 208
8.1.3 Fusion of genes via recombination in introns
pp.：
199 – 199
8.1.5 Factors affecting acceptance of mutants created by intronic recombination
pp.：
208 – 215
8.1.6 Classification of modules and mosaic proteins produced by exon shuffling
pp.：
215 – 223
8.1.7 Genome evolution and the evolution of exon shuffling
pp.：
223 – 225
8.1.8 Evolutionary significance of exon shuffling
pp.：
225 – 227
8.2 Modular assembly by exonic recombination
pp.：
227 – 229
8.1.9 Genome evolution and the evolution of alternative splicing
pp.：
227 – 227
References
pp.：
229 – 232
Useful internet resources
pp.：
232 – 234
Chapter 9: Genome evolution and protein evolution
pp.：
234 – 234
9.1 Evolution of genome size
pp.：
234 – 237
9.2 The role and survival of nongenic DNA
pp.：
237 – 237
9.3 Repetitiveness of genomic DNA
pp.：
237 – 239
9.4 Mechanisms responsible for increases in genome size
pp.：
239 – 240
9.5 Compositional organization of eukaryotic genomes
pp.：
240 – 241
9.6 Genomes of model organisms
pp.：
241 – 242
9.6.1 Viral genomes
pp.：
242 – 246
9.6.2 Cellular genomes
pp.：
246 – 247
9.6.2.1 Eubacterial genomes
pp.：
247 – 254
9.6.2.2 Archaeal genomes
pp.：
254 – 257
9.6.2.3 Organelle genomes
pp.：
257 – 260
9.6.2.4 Eukaryotic genomes
pp.：
260 – 287
9.6.2.5 Genome duplications in the evolution of early vertebrates
pp.：
287 – 292
9.6.3 Value of comparative genomics for the identification of functional elements
pp.：
292 – 293
9.6.4 Finding protein-coding genes in genome sequences
pp.：
293 – 296
9.8 Changes in gene number and gene density in different evolutionary lineages
pp.：
296 – 298
9.7 The genome of the cenancestor
pp.：
296 – 296
9.9 Proteome evolution
pp.：
298 – 298
9.9.1 Proteome evolution – classification of proteins by structural features
pp.：
298 – 299
9.9.2 Proteome evolution – classification of proteins by homology
pp.：
299 – 299
9.9.3 Proteome evolution – classification of proteins by function
pp.：
299 – 303
9.9.4 Proteome evolution – evolution of proteome complexity
pp.：
303 – 307
9.9.5 Proteome evolution and organismic complexity
pp.：
307 – 309
References
pp.：
309 – 318
Useful internet resources
pp.：
318 – 325
Protein Evolution
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