Protein synthesis and ribosome structure: translating the genome
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| Format: | Buch |
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Wiley-VCH
2004
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| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XVIII, 579 S. Ill., graph. Darst. |
| ISBN: | 3527306382 |
Internformat
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| 245 | 1 | 0 | |a Protein synthesis and ribosome structure |b translating the genome |c ed. by Knud H. Nierhaus ... |
| 264 | 1 | |a Weinheim |b Wiley-VCH |c 2004 | |
| 300 | |a XVIII, 579 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 650 | 4 | |a Ribosom - Proteinbiosynthese | |
| 650 | 4 | |a Proteins |x Synthesis | |
| 650 | 4 | |a Ribosomes | |
| 650 | 4 | |a Ribosomes |x Structure | |
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| 689 | 0 | 1 | |a Proteinbiosynthese |0 (DE-588)4175987-4 |D s |
| 689 | 0 | |5 DE-604 | |
| 700 | 1 | |a Nierhaus, Knud H. |d 1941-2016 |e Sonstige |0 (DE-588)114779686 |4 oth | |
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Datensatz im Suchindex
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| adam_text | V
Contents
Preface XV
1 A History of Protein Biosynthesis and Ribosome Research 1
Hans Jorg Rheinberger
1.1 Introduction 1
1.2 The Archaeology of Protein Synthesis The 1940s:
Forgotten Paradigms 2
1.3 Basic Mechanisms The 1950s 5
1.3.1 Steps toward an in vitro Protein Synthesis System 5
1.3.2 Amino Acid Activation and the Emergence of Soluble RNA 7
1.3.3 From Microsomes to Ribosomes 13
1.3.4 Models 17
1.4 The Golden Age of Translation The 1960s 21
1.4.1 From Enzymatic Adaptation to Gene Regulation: Messenger RNA 21
1.4.2 A Bacterial in vitro System of Protein Synthesis and the Cracking
of the Genetic Code 25
1.4.3 The Functional Dissection of Translation 28
1.4.4 The Structural Dissection of the Ribosome 33
1.5 1970 1990s: A Brief Synopsis 35
References 38
2 Structure of the Ribosome 53
Cregor Blaha
2.1 General Features of the Ribosome and Ribosomal Subunits 53
2.2 A Special Feature of the 50S Subunit: The Tunnel 54
2.3 Features of the Ribosomal Subunits at Atomic Resolution 59
2.4 The Domain Structure of the Ribosomal Subunits 62
2.5 Interactions of RNA with RNA or Struts and Bolts in the Three
dimensional Fold of rRNA: Coaxial Stacking and A minor Motifs 65
2.5.1 Coaxial Stacking 66
2.5.2 A minor Motifs 69
2.5.3 Ribose Zippers and Patches of A minor Motifs 71
2.5.3.1 Canonical Ribose Zipper 71
2.5.3.2 Single base Ribose Zipper 71
VI Contents
2.6 Progress and New Developments in Understanding
rRNA Structures 72
2.6.1 K turn 73
2.6.2 Lonepair Triloop 73
2.6.2.1 Classification of Lonepair Triloops 75
2.6.3 Systemizing Base Pairs 76
2.6.4 Systemizing RNA Structural Elements 78
2.7 RNA protein Interactions 79
2.7.1 Problem of RNA Recognition 79
2.7.2 Chemistry of RNA protein Interactions 80
2.7.3 rRNA protein Interaction 81
References 82
3 Ribosome Assembly 85
3.1 Assembly Of The Prokaryotic Ribosome 85
Knud H. Nierhaus
3.1.1 Introduction 85
3.1.2 Processing of rRNAs 86
3.1.3 Precursor Particles and Reconstitution Intermediates 90
3.1.4 Assembly initiator Proteins 91
3.1.5 Proteins Essential for the Early Assembly: The Assembly Gradient 95
3.1.6 Late assembly Components 96
3.1.7 Proteins Solely Involved in Assembly 97
3.1.8 Assembly Maps 99
References 204
3.2 Eukaryotic Ribosome Synthesis 107
Denis LJ. Lafontaine
3.2.1 Introduction 107
3.1.1 Prelude 107
3.2.2 Why so many RRPs? 109
3.2.3 (Pre )ribosome Assembly, the Proteomic Era 110
3.2.4 Ribosomal RNA Processing, Getting there... 113
3.2.5 Ribosomal RNA Modification: A Solved Issue? 118
3.2.5.1 Ribose Methylation, Pseudouridines formation and the snoRNAs 119
3.2.5.2 The Emergence of the snoRNAs 121
3.2.5.3 Non ribosomal RNA Substrates for the snoRNAs 122
3.2.5.4 Possible function(s) of RNA modifications 123
3.2.5.5 Base methylation 123
3.2.5.6 U3 snoRNP, the SSU Processome , and the Central Pseudoknot 124
3.2.6 SnoRNA Synthesis and Intranuclear Trafficking 125
3.2.6.1 SnoRNAs Synthesis 125
Contents VII
3.2.6.2 Non core snoRNP Proteins required for snoRNA Accumulation 126
3.2.6.3 Interactions between Cleavage Factors and Core snoRNP Proteins 128
3.2.6.4 SnoRNAs Trafficking 128
3.2.6.5 CB/NB are Conserved Sites of Small RNP Synthesis 130
3.2.7 Ribosome Intranuclear Movements and Ribosome Export 130
3.2.8 The Cytoplasmic Phase of Ribosome Maturation 132
3.2.9 Regulatory Mechanisms, all along 134
3.2.10 And Now ... What s Next? 134
3.2.11 Epilogue 135
3.3.12 Useful WWW links 135
References 136
4 tRNA and Synthetases 145
4.1 tRNA: Structure and Function 145
Viter Marquez and Knud H. Nierhaus
4.1.1 Introduction 145
4.1.2 Secondary Structure 146
4.1.3 Tertiary Structure 149
4.1.4 tRNA Modifications 154
4.1.5 Recognition of tRNA by tRNA synthetase: Identity Elements 154
4.1.6 Is the tRNA Cloverleaf Structure a Pre requisite for the L shape? 160
4.1.7 Other Functions of tRNA outside the Ribosomal Elongation Cycle 161
4.1.8 Human Neurodegenerative Disorders Associated with
Mitochondrial tRNAs 162
References 166
4.2 Aminoacylations of tRNAs: Record keepers for the Genetic Code 369
Liu s Ribas de Pouplana and Paul Schimmel
4.2.1 Introduction 169
4.2.2 The Operational RNA Code 170
4.2.3 Extant Aminoacyl tRNA Synthetases 172
4.2.4 The Origin of Aminoacyl tRNA Synthetase Classes: Two Proteins
bound to one tRNA 174
4.2.5 A Common Genetic Origin for all Aminoacyl tRNA Synthetases ? 177
4.2.5.1 Evolution of Extant Enzymes prior to LUCA 179
4.2.5.2 Changes in Acceptor Stem Identity Elements Correlate with
Changes in the Code 280
References 183
5 mRNA Decay and RNA degrading Machines in Prokaryotes
and Eukaryotes 185
Agamemnon J. Carpousis and Marc Dreyfus
5.1 Summary 185
VIII Contents
5.2 Introduction 385
5.3 mRNA Decay in E. coli 186
5.4 mRNA Decay in S. cerevisiae 188
5.5 A Comparison of mRNA Decay in E. coli and S. cerevisiae 188
5.6 RNase E Specificity: A Role in Translation Arrest? 289
5.7 The E. coli RNA degradosome 292
5.8 The Autoregulation of RNase E and PNPase Synthesis: A Link
between Bulk Translation and mRNA Stability 395
5.9 RNA degrading Machines in other Organisms 197
5.10 DEAD box ATPases 201
5.11 Perspective 202
References 204
6 tRNA Locations on the Ribosome 207
Knud H. Nierhaus
6.1 tRNAs Move through Functional Sites on the Ribosome 207
6.2 Visualization of tRNAs on the Ribosome 209
6.3 tRNA ribosome Contacts 225
References 236
7 Initiation of Protein Synthesis 219
7.1 Initiation of Protein Synthesis in Eubacteria 219
Daniel N. Wilson
7.1.1 Overview of Initiation in Eubacteria 229
7.1.2 Specialized initiation events: translational coupling, 70S initiation
and leaderless mRNAs 222
7.1.3 Initiation Factor 1 Binds to the Ribosomal A site 224
7.1.4 The Domain Structure of Bacterial IF2 227
7.1.5 Interaction Partners of IF2 230
7.1.6 The Role of the IF2 dependent GTPase Activity 232
7.1.7 The Mystery of the IF3 binding Site on the 30S Subunit 233
References 236
7.2 Mechanism and Regulation of Protein Synthesis Initiation
in Eukaryotes 242
Alan C. Hinnebusch, Thomas E. Dever, and Nabum Sonenberg
7.2.1 Introduction 242
7.2.1.1 Overview of Translation initiation Pathways in Eukaryotes
and Prokaryotes 242
7.2.1.2 Conservation and diversity of translation initiation factors among
bacteria, archaea and eukaryotes 244
1.2. .T Genetic assays for in vivo functions of eIF2 248
7.2.2 Generation of Free 40S Subunits and 40S Binding of Met tRNA 252
Contents I IX
7.2.2.1 Dissociation of Idle 80S Ribosomes 251
7.2.2.2 Components of the eIF2/GTP/Met tRNA Ternary Complex 252
7.2.2.3 The GEF eIF2B regulates ternary complex formation 263
7.2.2.4 Binding of Ternary Complex and mRNA to the 40S Ribosome
is Stimulated by el F3 269
7.2.2.5 elFIA Stimulates Ternary Complex Binding to 40S Subunits and
Participates in AUG Selection During Scanning 275
7.2.3 Binding of Ribosomes to mRNA 279
7.23.1 The Ends of Eukaryotic mRNAs Contain Distinctive
Conserved Structures 279
7.2.3.2 Ribosome Binding to mRNA is Stimulated by the eIF4 Factors 279
7.2.3.3 Circularization of mRNA via eIF4G PABP Interaction 290
7.2.4 Translational Control by mRNA Circularization 291
7.2.5 Regulation of el F4 Function by Phosphorylation 292
7.2.5.1 eIF4E Phosphorylation 292
7.2.5.2 eIF4E 4E BPs 292
7.2.5.3 eIF4G Phosphorylation 294
7.2.5.4 eIF4B Phosphorylation 295
7.2.6 Translational Control by Paips PABP Interacting Proteins 295
7.2.7 AUG Recognition during Scanning 296
1.2.1 A AUG is the Predominant Signal for Initiation and is Selected by
Proximity to the 59 end by the Scanning Mechanism 296
7.2.7.2 The Anticodon of tRNA, eIF2 Subunits, elFl, and eIF5 are
Determinants of AUG Selection during Scanning 299
7.2.7.3 elFl plays a role in TC binding, scanning, and AUG selection 299
7.2.7A eIF5 Functions as a GTPase Activating Protein for eIF2 in
AUG Selection and Subunit Joining 300
7.2.8 Joining of 60S Subunits to 40S Ribosomal Complexes 302
7.2.8.1 eIF5B Catalyzes a Second GTP dependent Step in
Translation Initiation 303
7.2.8.2 GTPase Switch Regulates Ribosome Affinity of eIF5B and
Governs Translational Efficiency 304
7.2.9 IRES mediated Translation Initiation 308
7.2.10 Future Prospects 310
References 313
8 The Elongation Cycle 323
Knud H. Nierhaus
8.1 Models of the Elongation Cycle 326
8.1.1 The Hybrid site Model for Elongation 326
8.1.2 The Allosteric Three site Model (a e Model; Reciprocal Coupling
between the A and E sites) 329
X Contents
8.2 Decoding and A site Occupation 333
8.2.1 Some General Remarks about Proofreading 333
8.2.2 Discrimination against Noncognate aa tRNAs 333
8.2.3 Decoding of an aa tRNA (Cognate versus Near cognate aa tRNAs) 337
8.2.4 Roles of EF Tu 341
8.2.5 Mimicry at the Ribosomal A site 341
8.2.5 Translational Errors 342
8.3 The PTF Reaction 345
8.3.1 A Short Intermission: Two Enzymatic Principles of PTF Activity 348
8.3.1.1 Chemical Concept: A Transient Covalent Bond between
Active Center and Substrate(s) 348
8.3.1.2 Physical Concept: The Template Model 350
8.3.2 Data from the Crystal Structures 352
8.3.3 Why both the Physical and Chemical Concepts for
Peptide bond Formation? 355
8.4 The Translocation Reaction 355
8.4.1 Conservation in the Elongation Factor G Binding Site 356
8.4.2 Dynamics within the Ribosome 359
References 363
9 Termination and Ribosome Recycling 367
Daniel N. Wilson
9.1 Introduction 367
9.2 Stop Codon Recognition and Release of the Nascent
Polypeptide Chain 368
9.3 The Bacterial Class I Decoding Release Factors 369
9.3.1 The Structure of RF2 and Translational Mimicry 369
9.3.2 The Two domain Functional Model for RF2 371
9.3.3 Identifying Functional Important Regions within the
Decoding RFs 371
9.3.4 Codon Recognition Domain of Bacterial RFs: the
Termination Signal 374
9.3.5 Codon Recognition Domain of Bacterial RFs: the
Tripeptide Motif 375
9.3.6 Peptidyl tRNA hydrolase function of bacterial RFs: domain III
and the GGQ motif 376
9.3.7 Large Conformational Changes Associated with RF2 Binding
to the Ribosome 379
9.3.8 The Trigger for RF mediated Release of the Nascent Chain
and the Outcome 383
9.4 Eukaryotic Class I Termination Factors 384
9.4.1 Stop codon Recognition is Associated with Domain I of eRFl 386
Contents XI
9.4.2 eRFl mediated Polypeptide Release 388
9.5 Dissociation of the Post termination Complex 388
9.5.1 Eubacterial RF3 Dissociates the Class I Termination Factors 388
9.5.2 Eukaryotic RF3: Dissociation versus Delivery of eRFl 390
9.6 Ribosome Recycling 391
9.6.1 RRF Mediates Ribosome Recycling in Eubacteria 391
References 392
10 The Mechanism of Recoding in Pro and Eukaryotes 397
Elizabeth S. Poole, Louise L Major, Andrew C. Cridge, and Warren P. Tate
10.1 Introduction 397
10.2 Maintaining Decoding Accuracy and the Reading Frame 398
10.3 The Use of a Stop Signal for both Elongation and Termination
of Protein Synthesis 399
10.4 The Mechanism for Sec Incorporation at UGA Sites
in Bacterial mRNAs 399
10.4.1 The Gene Products 400
10.4.2 The Mechanism of Sec Incorporation 401
10.4.3 The Competition between Sec Incorporation and
Canonical Decoding of UGA by RF2 401
10.5 Mechanism for Sec Incorporation at UGA Sites in Eukaryotic
and Archaeal mRNAs 403
10.5.1 The Gene Products 403
10.5.2 The Mechanism of Sec Incorporation at Specific UGA
Stop Codons 404
10.6 Why does Recoding Occur at Stop Signals? 404
10.6.1 The Stop Signal of Prokaryotic Genomes Engineered for
High Efficiency Decoding? 406
10.6.2 The Stop Signal of Eukaryotic Genomes Diversity Contributes
to Recoding 411
10.7 Readthrough of a Stop Signal: Decoding Stop as Sense 413
10.8 Bypassing of a Stop Codon: Free wheeling on the mRNA 415
10.9 Frameshifting Around Stop or Sense Codons 417
10.9.1 Forward Frameshifting: the +1 Event 418
10.9.2 Programed 1 Frameshifting: A Common Mechanism used by
Many Viruses During Gene Expression 420
10.10 Conclusion 424
References 426
11 Regulation of Ribosome Biosynthesis in Escherichia coli 429
Madina Iskakova, Sean R. Connell, and Knud H. Nierhaus
Overview of Ribosome Biosynthesis Regulation 429
XII Contents
11.1 Regulation of rRNA Synthesis 430
11.1.1 Organization of rRNA Operons and Elements of rRNA Promoters 430
11.1.2 Models for rRNA Regulation 434
11.1.3 Stringent Response 435
11.2 Regulation of r protein Synthesis 438
11.2.1 Some General Remarks 438
11.2.2 Various Models for r protein Regulation 441
11.2.2.1 spc operon 441
11.2.2.2 S10 operon 441
11.2.2.3 a operon 443
11.2.2.4 str operon 443
11.2.2.5 IF3 operon 444
11.3 Conclusion 445
References 446
12 Antibiotics and the Inhibition of Ribosome Function 449
Daniel N. Wilson
12.1 Introduction 449
12.1.1 The Inhibition of Protein Synthesis in Bacteria 449
12.2 Inhibitors of Initiation 453
12.2.1 Kasugamycin 456
12.2.2 Edeine 457
12.2.3 Pactamycin 459
12.2.4 Evernimicin and Avilamycin 460
12.2.5 Antibiotic Inhibitors of Ribosome Assembly 462
12.3 Inhibitors of the Elongation Cycle 464
12.3.1 Antibiotic Action and A site Occupation 465
12.3.1.1 Tetracycline: An Inhibitor of A site Occupation 465
12.3.1.2 Antibiotics Affecting the Fidelity of Translation 468
12.3.1.3 Inhibitors of EF Tu mediated Reactions 475
12.3.2 Inhibitors of Peptide bond Formation and Nascent
Chain Progression 480
12.3.2.1 Puromycin and Blasticidin S mimic the CCA end of tRNAs 480
12.3.2.2 Sparsomycin Prevents A site Binding and Stimulates
P site Binding 483
12.3.2.3 Antibiotic Overlap in the PTF Center: chloramphenicol,
Anisomycin and the Lincosamides 484
12.3.2.4 Blocking the Progression of the Nascent Chain by the
Macrolide Antibiotics 488
12.3.2.5 Streptogramins 494
12.3.2.6 New Classes of Translation Inhibitors; the Oxazolidinones and
Novel Ribosome Inhibitors 496
Contents XIII
12.3.3 Translocation Inhibitors 499
12.3.3.1 Thiostrepton and Micrococcin 499
12.3.3.2 Viomycin Blocks Coupled GTPase Activity 502
12.3.3.3 Spectinomycin Interferes with EF G Binding 503
12.3.3.4 Fusidic Acid is the Counterpart of Kirromycin 504
12.4 Inhibitors of Termination, Recycling and trans Translation 506
12.4.1 Termination 507
12.4.2 Recycling 507
12.4.3 Trans translation 508
12.5 Mechanisms Causing Drug Resistance 508
12.5.1 Modification of the Antibiotic 509
12.5.2 Blockage of Transport (without Modification of the Drug) 509
12.5.3 Overproduction of the Inhibited Substrate (Target Dilution) 509
12.5.4 Bypassing or Replacement of the Inhibited Reaction 510
12.5.5 Alteration of the Target Site 510
12.5.6 Active Protection of the Target by a Third Component 511
12.6 Future Perspectives 512
References 513
13 The Work of Chaperones 529
Jean Herv6 Alix
13.1 From The Levinthal Paradox To The Anfinsen Cage 529
13.2 The Folding Machines 532
13.2.1 The Trigger Factor (TF) 532
13.2.2 The DnaK/DnaJ/GrpE System 532
13.2.3 The GroEL/GroES System 535
13.2.4 Other Chaperones 539
13.2.4.1 HSP90 539
13.2.4.2 Clp/HSPlOO Family 539
13.2.4.3 DegP 540
13.2.4.4 Periplasmic Chaperones 540
13.2.4.5 Pili Chaperones 541
13.2.4.6 Small HSPs 541
13.2.4.7 Endoplasmic Reticulum (ER) Chaperones 543
13.2.4.8 Intramolecular Chaperones 543
13.3 Chaperone Networks 543
13.3.1 De novo Protein Folding 543
13.3.2 Protein Disaggregation 545
13.3.3 Posttranslational Quality Control 545
13.4 Chaperones and Stress 547
13.4.1 The Heat shock Response and its Regulation 547
XIV Contents
13.4.2 Thermotolerance 548
13.4.3 Who Detects Stress? 548
13.5 Assembly and Disassembly of Macromolecular Complexes 549
13.6 Protein Translocation Across Membranes 550
13.7 New Horizons in Chaperone Research 551
13.7.1 HSP90 and the Pandora s Box of Hidden Mutations 551
13.7.2 Chaperones and Prions 551
13.7.3 Chaperones and Ribosome Biogenesis 552
13.7.4 RNA Chaperones 553
13.7.5 Chemical Chaperones 553
13.7.6 Medical implications 553
13.7.7 Chaperoning the chaperones 553
References 554
Index 563
|
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| id | DE-604.BV017687430 |
| illustrated | Illustrated |
| indexdate | 2024-07-09T19:20:46Z |
| institution | BVB |
| isbn | 3527306382 |
| language | English |
| oai_aleph_id | oai:aleph.bib-bvb.de:BVB01-010634854 |
| oclc_num | 249259868 |
| open_access_boolean | |
| owner | DE-355 DE-BY-UBR DE-91G DE-BY-TUM DE-M49 DE-BY-TUM DE-703 DE-20 DE-19 DE-BY-UBM DE-11 DE-B768 |
| owner_facet | DE-355 DE-BY-UBR DE-91G DE-BY-TUM DE-M49 DE-BY-TUM DE-703 DE-20 DE-19 DE-BY-UBM DE-11 DE-B768 |
| physical | XVIII, 579 S. Ill., graph. Darst. |
| publishDate | 2004 |
| publishDateSearch | 2004 |
| publishDateSort | 2004 |
| publisher | Wiley-VCH |
| record_format | marc |
| spelling | Protein synthesis and ribosome structure translating the genome ed. by Knud H. Nierhaus ... Weinheim Wiley-VCH 2004 XVIII, 579 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Ribosom - Proteinbiosynthese Proteins Synthesis Ribosomes Ribosomes Structure Proteinbiosynthese (DE-588)4175987-4 gnd rswk-swf Ribosom (DE-588)4127731-4 gnd rswk-swf Ribosom (DE-588)4127731-4 s Proteinbiosynthese (DE-588)4175987-4 s DE-604 Nierhaus, Knud H. 1941-2016 Sonstige (DE-588)114779686 oth HBZ Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=010634854&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Protein synthesis and ribosome structure translating the genome Ribosom - Proteinbiosynthese Proteins Synthesis Ribosomes Ribosomes Structure Proteinbiosynthese (DE-588)4175987-4 gnd Ribosom (DE-588)4127731-4 gnd |
| subject_GND | (DE-588)4175987-4 (DE-588)4127731-4 |
| title | Protein synthesis and ribosome structure translating the genome |
| title_auth | Protein synthesis and ribosome structure translating the genome |
| title_exact_search | Protein synthesis and ribosome structure translating the genome |
| title_full | Protein synthesis and ribosome structure translating the genome ed. by Knud H. Nierhaus ... |
| title_fullStr | Protein synthesis and ribosome structure translating the genome ed. by Knud H. Nierhaus ... |
| title_full_unstemmed | Protein synthesis and ribosome structure translating the genome ed. by Knud H. Nierhaus ... |
| title_short | Protein synthesis and ribosome structure |
| title_sort | protein synthesis and ribosome structure translating the genome |
| title_sub | translating the genome |
| topic | Ribosom - Proteinbiosynthese Proteins Synthesis Ribosomes Ribosomes Structure Proteinbiosynthese (DE-588)4175987-4 gnd Ribosom (DE-588)4127731-4 gnd |
| topic_facet | Ribosom - Proteinbiosynthese Proteins Synthesis Ribosomes Ribosomes Structure Proteinbiosynthese Ribosom |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=010634854&sequence=000002&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT nierhausknudh proteinsynthesisandribosomestructuretranslatingthegenome |