Ribosomes (eBook)

Preface 6
Contents 8
I Historical and Fundamental Introduction 17
Protein Biosynthesis 18
References 20
Messenger RNA and the Genetic Code 21
2.1. Discovery of mRNA 21
2.2. Deciphering the Code 22
2.3. Some Features of the Code Dictionary 26
2.4. Deviations from the Universal Code 27
2.5. Structure of mRNA 28
2.6. Messenger Ribonucleoproteins of Higher Eukaryotes 33
References 35
Transfer RNA and Aminoacyl-tRNA Synthetases 37
3.1. Discovery 37
3.2. Structure of tRNA 38
3.3. Aminoacyl-tRNA Synthetases 46
3.4. Aminoacylation of tRNA 50
3.5. Specificity of tRNA Aminoacylation 54
References 58
Ribosomes and Translation 60
4.1. First Observations 60
4.2. Localization of Ribosomes in the Cell 61
4.3. Prokaryotic and Eukaryotic Ribosomes 63
4.4. Sequential Readout of mRNA by Ribosomes Polyribosomes
4.5. Stages of Translation: Initiation, Elongation, and Termination 67
4.6. Chemical Reactions and Overall Energy Balance of Protein Biosynthesis 68
4.7. Cell-free Translation Systems 70
References 72
II Structure of the Ribosome 74
Morphology of the Ribosome 75
5.1. Size, Appearance, and Subdivision into Subunits 75
5.2. Small Subunit 77
5.3. Large Subunit 79
5.4. Association of Subunits into the Complete Ribosome 80
5.5. Morphology of the Ribosome at 25-Å Resolution 81
5.6. X-Ray Crystallography of the Ribosome 85
References 85
Ribosomal RNA 86
6.1. Introduction 86
6.2. Types of Ribosomal RNAs and their Primary Structures 86
6.3. Secondary Structure of Ribosomal RNAs 88
6.4. Tertiary Structure and Compact Folding of Ribosomal RNAs 98
References 105
Ribosomal Proteins 107
7.1. Diversity and Nomenclature 107
7.2. Primary Structures 109
7.3. Three-dimensional Structures 112
7.4. Protein Complexes 114
7.5. Interactions with Ribosomal RNA 115
7.6. Disassembly and Reassembly of Ribosomal Subunits 120
References 125
Mutual Arrangement of Ribosomal RNA and Proteins (Quaternary Structure) 127
8.1. Peripheral Localization of Proteins on the RNA Core 127
8.2. Topography of Proteins 129
8.3. Topography of RNA 134
8.4. Quaternary Structure 138
References 138
III Function of the Ribosome 140
Functional Activities and Functional Sites of the Ribosome 141
9.1. Working Cycle of the Ribosome 141
9.2. Methodological Approaches to Localization of Ribosomal Functional Sites 143
9.3. Binding, Retention, and Sliding of the Message (mRNA-Binding Site on the Small Subunit) 144
9.4. Catalysis of Peptide Bond Formation (Peptidyl Transferase on the Large Subunit) 150
9.5. GTP-Dependent Binding of Translation Factors (Factor-Binding Site on the Large Subunit) 154
9.6. Binding of Aminoacyl-tRNA and Retention of Peptidyl-tRNA (tRNA-Binding Sites at the Intersubunit Space) 159
9.7. Ligand Displacements (Translocation) 165
9.8. The Material and Energy Balance of the Elongation Cycle 165
References 167
Elongation Cycle, Step I: Aminoacyl-tRNA Binding 170
10.1. Codon–Anticodon Interaction 170
10.2. Participation of the Elongation Factor 1 (EF-Tu or eEF1A) in Aminoacyl-tRNA Binding 176
10.3. Inhibitors of Aminoacyl-tRNA Binding 184
10.4. Miscoding 189
10.5. Summary: Sequence of Events and Molecular Mechanisms 195
References 199
Elongation Cycle, Step II: Transpeptidation (Peptide Bond Formation) 201
11.1. Chemistry of the Reaction 201
11.2. Energy Balance of the Reaction 204
11.3. Stereochemistry 205
11.4. Movement of Transpeptidation Products 208
11.5. Inhibitors 210
References 217
Elongation Cycle, Step III: Translocation 218
12.1 Definition and Experimental Tests 218
12.2. Participation of the Elongation Factor 2 (EF-G or eEF2) in Translocation 219
12.3. “Nonenzymatic” (Factor-Free) Translocation 226
12.4. Movement of the Template during Translocation 227
12.5. Mechanics and Energetics of Translocation 236
12.6. Inhibitors of Translocation 238
12.7. Summary: Sequence of Events and Molecular Mechanisms 241
References 243
Elongation Rate and its Modulation 245
13.1. Elongation Rates in Prokaryotes and Eukaryotes 245
13.2. Discontinuities in Elongation 248
13.3. Selective Regulation of Elongation on Different mRNAs 253
13.4. Total Regulation of Elongation 254
13.5. Elongation Toxins 257
References 261
Termination of Translation 264
14.1. Termination Codons 264
14.2. Termination Protein Factors 266
14.3. Ribosomal Site for Binding Termination Factors 268
14.4. Hydrolysis of Peptidyl-tRNA 269
14.5. Sequence of Events during Termination 269
References 272
Initiation of Translation 274
15.1. General Principles 274
15.2. Initiation in Prokaryotes 279
15.3. Initiation in Eukaryotes 289
References 309
Translational Control in Prokaryotes 312
16.1. General Considerations 312
16.2. Discrimination of mRNAs 313
16.3. Translational Coupling 315
16.4. Translational Repression 322
16.5. Antisense Blockade 336
References 338
Translational Control in Eukaryotes 342
17.1. Importance of Translational Control in Eukaryotes 342
17.2. Total Translational Regulation 343
17.3. Discrimination of mRNAs 348
17.4. Regulation of Initiation by Upstream Open Reading Frames 353
17.5. Translational Repression 358
17.6. mRNA Masking 364
References 369
Cotranslational Folding and Transmembrane Transport of Proteins 373
18.1. Contribution of Ribosomes to Protein Folding 373
18.2. Ribosome-Associated Molecular Chaperones 377
18.3. Synthesis of Proteins by Free 378
and Membrane-Bound Polyribosomes 378
18.4. Interaction of Translating Ribosomes with Membranes 380
18.5. Cotranslational Transmembrane Translocation 387
of Nascent Polypeptide Chains 387
18.6. Cotranslational Covalent Modifications 394
and Folding of the Nascent Polypeptide 394
Chain in the Endoplasmic Reticulum 394
References 395
Conclusion: General Principles of Ribosome Structure and Function 399
19.1. Introduction 399
19.2. Basic Features of Ribosome Structure 399
19.3. Structural and Biochemical Grounds of Ribosome Function 401
Index 408