Spirin Ribosomes

1. Auflage 2006
ISBN: 978-0-306-46815-5
Verlag: Springer US
Format: PDF
Kopierschutz: 1 - PDF Watermark

E-Book, Englisch, 422 Seiten

Reihe: Cellular Organelles

Biochemistry, general - Short description currently not available.

Autoren/Hrsg.

Spirin, Alexander S.

Inhaltsverzeichnis

1;Preface;6
2;Contents;8
3;I Historical and Fundamental Introduction;17
3.1;Protein Biosynthesis;18
3.1.1;References;20
3.2;Messenger RNA and the Genetic Code;21
3.2.1;2.1. Discovery of mRNA;21
3.2.2;2.2. Deciphering the Code;22
3.2.3;2.3. Some Features of the Code Dictionary;26
3.2.4;2.4. Deviations from the Universal Code;27
3.2.5;2.5. Structure of mRNA;28
3.2.6;2.6. Messenger Ribonucleoproteins of Higher Eukaryotes;33
3.2.7;References;35
3.3;Transfer RNA and Aminoacyl-tRNA Synthetases;37
3.3.1;3.1. Discovery;37
3.3.2;3.2. Structure of tRNA;38
3.3.3;3.3. Aminoacyl-tRNA Synthetases;46
3.3.4;3.4. Aminoacylation of tRNA;50
3.3.5;3.5. Specificity of tRNA Aminoacylation;54
3.3.6;References;58
3.4;Ribosomes and Translation;60
3.4.1;4.1. First Observations;60
3.4.2;4.2. Localization of Ribosomes in the Cell;61
3.4.3;4.3. Prokaryotic and Eukaryotic Ribosomes;63
3.4.4;4.4. Sequential Readout of mRNA by Ribosomes; Polyribosomes;64
3.4.5;4.5. Stages of Translation: Initiation, Elongation, and Termination;67
3.4.6;4.6. Chemical Reactions and Overall Energy Balance of Protein Biosynthesis;68
3.4.7;4.7. Cell-free Translation Systems;70
3.4.8;References;72
4;II Structure of the Ribosome;74
4.1;Morphology of the Ribosome;75
4.1.1;5.1. Size, Appearance, and Subdivision into Subunits;75
4.1.2;5.2. Small Subunit;77
4.1.3;5.3. Large Subunit;79
4.1.4;5.4. Association of Subunits into the Complete Ribosome;80
4.1.5;5.5. Morphology of the Ribosome at 25-Å Resolution;81
4.1.6;5.6. X-Ray Crystallography of the Ribosome;85
4.1.7;References;85
4.2;Ribosomal RNA;86
4.2.1;6.1. Introduction;86
4.2.2;6.2. Types of Ribosomal RNAs and their Primary Structures;86
4.2.3;6.3. Secondary Structure of Ribosomal RNAs;88
4.2.4;6.4. Tertiary Structure and Compact Folding of Ribosomal RNAs;98
4.2.5;References;105
4.3;Ribosomal Proteins;107
4.3.1;7.1. Diversity and Nomenclature;107
4.3.2;7.2. Primary Structures;109
4.3.3;7.3. Three-dimensional Structures;112
4.3.4;7.4. Protein Complexes;114
4.3.5;7.5. Interactions with Ribosomal RNA;115
4.3.6;7.6. Disassembly and Reassembly of Ribosomal Subunits;120
4.3.7;References;125
4.4;Mutual Arrangement of Ribosomal RNA and Proteins (Quaternary Structure);127
4.4.1;8.1. Peripheral Localization of Proteins on the RNA Core;127
4.4.2;8.2. Topography of Proteins;129
4.4.3;8.3. Topography of RNA;134
4.4.4;8.4. Quaternary Structure;138
4.4.5;References;138
5;III Function of the Ribosome;140
5.1;Functional Activities and Functional Sites of the Ribosome;141
5.1.1;9.1. Working Cycle of the Ribosome;141
5.1.2;9.2. Methodological Approaches to Localization of Ribosomal Functional Sites;143
5.1.3;9.3. Binding, Retention, and Sliding of the Message (mRNA-Binding Site on the Small Subunit);144
5.1.4;9.4. Catalysis of Peptide Bond Formation (Peptidyl Transferase on the Large Subunit);150
5.1.5;9.5. GTP-Dependent Binding of Translation Factors (Factor-Binding Site on the Large Subunit);154
5.1.6;9.6. Binding of Aminoacyl-tRNA and Retention of Peptidyl-tRNA (tRNA-Binding Sites at the Intersubunit Space);159
5.1.7;9.7. Ligand Displacements (Translocation);165
5.1.8;9.8. The Material and Energy Balance of the Elongation Cycle;165
5.1.9;References;167
5.2;Elongation Cycle, Step I: Aminoacyl-tRNA Binding;170
5.2.1;10.1. Codon–Anticodon Interaction;170
5.2.2;10.2. Participation of the Elongation Factor 1 (EF-Tu or eEF1A) in Aminoacyl-tRNA Binding;176
5.2.3;10.3. Inhibitors of Aminoacyl-tRNA Binding;184
5.2.4;10.4. Miscoding;189
5.2.5;10.5. Summary: Sequence of Events and Molecular Mechanisms;195
5.2.6;References;199
5.3;Elongation Cycle, Step II: Transpeptidation (Peptide Bond Formation);201
5.3.1;11.1. Chemistry of the Reaction;201
5.3.2;11.2. Energy Balance of the Reaction;204
5.3.3;11.3. Stereochemistry;205
5.3.4;11.4. Movement of Transpeptidation Products;208
5.3.5;11.5. Inhibitors;210
5.3.6;References;217
5.4;Elongation Cycle, Step III: Translocation;218
5.4.1;12.1 Definition and Experimental Tests;218
5.4.2;12.2. Participation of the Elongation Factor 2 (EF-G or eEF2) in Translocation;219
5.4.3;12.3. “Nonenzymatic” (Factor-Free) Translocation;226
5.4.4;12.4. Movement of the Template during Translocation;227
5.4.5;12.5. Mechanics and Energetics of Translocation;236
5.4.6;12.6. Inhibitors of Translocation;238
5.4.7;12.7. Summary: Sequence of Events and Molecular Mechanisms;241
5.4.8;References;243
5.5;Elongation Rate and its Modulation;245
5.5.1;13.1. Elongation Rates in Prokaryotes and Eukaryotes;245
5.5.2;13.2. Discontinuities in Elongation;248
5.5.3;13.3. Selective Regulation of Elongation on Different mRNAs;253
5.5.4;13.4. Total Regulation of Elongation;254
5.5.5;13.5. Elongation Toxins;257
5.5.6;References;261
5.6;Termination of Translation;264
5.6.1;14.1. Termination Codons;264
5.6.2;14.2. Termination Protein Factors;266
5.6.3;14.3. Ribosomal Site for Binding Termination Factors;268
5.6.4;14.4. Hydrolysis of Peptidyl-tRNA;269
5.6.5;14.5. Sequence of Events during Termination;269
5.6.6;References;272
5.7;Initiation of Translation;274
5.7.1;15.1. General Principles;274
5.7.2;15.2. Initiation in Prokaryotes;279
5.7.3;15.3. Initiation in Eukaryotes;289
5.7.4;References;309
5.8;Translational Control in Prokaryotes;312
5.8.1;16.1. General Considerations;312
5.8.2;16.2. Discrimination of mRNAs;313
5.8.3;16.3. Translational Coupling;315
5.8.4;16.4. Translational Repression;322
5.8.5;16.5. Antisense Blockade;336
5.8.6;References;338
5.9;Translational Control in Eukaryotes;342
5.9.1;17.1. Importance of Translational Control in Eukaryotes;342
5.9.2;17.2. Total Translational Regulation;343
5.9.3;17.3. Discrimination of mRNAs;348
5.9.4;17.4. Regulation of Initiation by Upstream Open Reading Frames;353
5.9.5;17.5. Translational Repression;358
5.9.6;17.6. mRNA Masking;364
5.9.7;References;369
5.10;Cotranslational Folding and Transmembrane Transport of Proteins;373
5.10.1;18.1. Contribution of Ribosomes to Protein Folding;373
5.10.2;18.2. Ribosome-Associated Molecular Chaperones;377
5.10.3;18.3. Synthesis of Proteins by Free;378
5.10.4;and Membrane-Bound Polyribosomes;378
5.10.5;18.4. Interaction of Translating Ribosomes with Membranes;380
5.10.6;18.5. Cotranslational Transmembrane Translocation;387
5.10.7;of Nascent Polypeptide Chains;387
5.10.8;18.6. Cotranslational Covalent Modifications;394
5.10.9;and Folding of the Nascent Polypeptide;394
5.10.10;Chain in the Endoplasmic Reticulum;394
5.10.11;References;395
5.11;Conclusion: General Principles of Ribosome Structure and Function;399
5.11.1;19.1. Introduction;399
5.11.2;19.2. Basic Features of Ribosome Structure;399
5.11.3;19.3. Structural and Biochemical Grounds of Ribosome Function;401
6;Index;408