Protein synthesis by ribosomes:
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Abschlussarbeit Buch |
| Sprache: | English |
| Veröffentlicht: |
2014
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| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | XII, 145 S. Ill., graph. Darst. |
Internformat
MARC
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| 245 | 1 | 0 | |a Protein synthesis by ribosomes |c von Sophia Rudorf |
| 264 | 1 | |c 2014 | |
| 300 | |a XII, 145 S. |b Ill., graph. Darst. | ||
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Datensatz im Suchindex
| _version_ | 1804153330184749056 |
|---|---|
| adam_text | CONTENTS
1 INTRODUCTION 1
1.1 TRANSLATION: FROM MRNA TO PROTEIN 2
1.2 AMINO ACIDS, TRNAS AND TERNARY COMPLEXES 3
1.3 STRUCTURE AND DYNAMICS OF RIBOSOMES 7
1.4 TOWARDS A COMPREHENSIVE MODEL OF TRANSLATION ELONGATION 8
1.5 LIST OF PUBLICATIONS 11
2 BRIEF REVIEW OF CONTINUOUS-TIME MARKOV PROCESSES 13
2.1 MARKOV PROCESS DESCRIPTION OF BIOCHEMICAL SYSTEMS 13
2.2 INFINITESIMAL PROBABILITIES AND MASTER EQUATIONS 15
2.3 ABSORBING STATES 16
2.3.1 ABSORPTION PROBABILITIES 17
2.3.2 MEAN FIRST PASSAGE TIMES 17
3 THEORETICAL FRAMEWORK FOR TRANSLATION ELONGATION 19
3.1 CODONS AND TRNAS 19
3.2 THEORETICAL DESCRIPTION OF THE ELONGATION CYCLE 21
3.3 BINDING RATES AND INTERNAL TRANSITION RATES 22
3.4 CODON-SPECIFIC ELONGATION RATES AND DWELL TIMES 25
3.5 CODON USAGES AND OVERALL ELONGATION RATE 28
3.6 PROBABILITIES TO ATTAIN RIBOSOMAL STATES 28
3.7 RIBOSOMAL AND TRNA SUBPOPULATIONS 32
3.7.1 TIME DEPENDENT CONCENTRATIONS OF RIBOSOMAL AND TRNA SUBPOP
ULATIONS 32
3.7.2 STEADY STATE CONCENTRATIONS OF TRNA SUBPOPULATIONS 35
3.7.3 STEADY STATE CONCENTRATIONS OF FREE TERNARY COMPLEXES 36
4 SPECIFICATION OF ELONGATION PARAMETERS AND IN VITRO MEASUREMENTS 39
4.1 TOTAL TRNA, RIBOSOME AND EF-TU CONCENTRATIONS 39
4.2 CODON USAGES 41
4.3 RIBOSOMAL TRANSITION RATES AND OVERALL ELONGATION RATE 41
4.4 TRNA RECHARGING AND TERNARY COMPLEX FORMATION 44
V
HTTP://D-NB.INFO/1070689475
CONTENTS
4.5 EXPERIMENTAL METHODS 46
4.5.1 IN VITRO TRANSITION RATES WGO
AND WQ.IO
AT 20C 46
4.5.2 IN VITRO OVERALL ELONGATION RATE UI
E
0
AT 20 C AND 37 C 47
5 FROM IN VITRO TO IN VIVO 49
5.1 FUNDAMENTAL DIFFERENCES OF TRANSLATION IN VIVO AND IN VITRO 50
5.2 IN VIVO BINDING RATES 50
5.3 IN VIVO TRANSITION RATES 51
5.3.1 KINETIC DISTANCE 52
5.3.2 CONSTRAINED MINIMIZATION OF THE KINETIC DISTANCE 54
5.4 VALIDATION OF IN VIVO RATES 56
5.5 ESTIMATION OF UNCERTAINTIES 62
5.6 CONCLUSIONS * 63
6 DEPENDENCE OF OVERALL ELONGATION RATE ON TRNA CONCENTRATIONS 65
6.1 THREE DISTINCT REGIMES OF TRANSLATION 65
6.1.1 QUALITATIVE FEATURES OF THE OVERALL ELONGATION RATE 68
6.1.2 QUANTITATIVE ANALYSIS OF THE OVERALL ELONGATION RATE 72
6.2 PHASE TRANSITION AT THE THRESHOLD CONCENTRATION 76
6.2.1 ASYMPTOTIC BEHAVIOR OF THE OVERALL ELONGATION RATE 77
6.2.2 RIBOSOMAL CONCENTRATIONS AT THE THRESHOLD 78
6.2.3 CONCENTRATIONS OF TRNA SUBPOPULATIONS AT THE THRESHOLD 79
6.2.4 REDUNDANT TRNA SPECIES 80
6.3 CONCLUSIONS 81
7 DEPENDENCE OF TOTAL ELONGATION FLUX ON RIBOSOME CONCENTRATION 83
7.1 TOTAL ELONGATION FLUX 83
7.1.1 ANALYSIS OF TOTAL ELONGATION FLUX 86
7.1.2 IN VIVO ELONGATION FLUX IS SEEMINGLY SUBMAXIMAL 90
7.1.3 CONCLUSIONS 93
8 DEPENDENCE OF CODON-SPECIFIC ELONGATION ON CODON USAGE 95
9 SUMMARY, CONCLUSIONS AND OUTLOOK 101
A PAUSES IN PROTEIN SYNTHESIS - ANALYSIS OF TRANSLATION INTERMEDIATES
105
A.L BRIEF INTRODUCTION 105
A.2 DATA PROCESSING 106
A.3 DATA ANALYSIS 107
A.4 CONCLUSIONS 108
B COMPUTER SIMULATIONS 113
VI
ABBREVIATIONS AND SYMBOLS
C ADDITIONAL FIGURES 115
D ADDITIONAL TABLES 123
VII
|
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| indexdate | 2024-07-10T01:24:53Z |
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| language | English |
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| physical | XII, 145 S. Ill., graph. Darst. |
| publishDate | 2014 |
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| spelling | Rudorf, Sophia 1985- Verfasser (DE-588)1070483281 aut Protein synthesis by ribosomes von Sophia Rudorf 2014 XII, 145 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Potsdam, Univ., Diss., 2014 Ribosom (DE-588)4127731-4 gnd rswk-swf Proteinbiosynthese (DE-588)4175987-4 gnd rswk-swf (DE-588)4113937-9 Hochschulschrift gnd-content Ribosom (DE-588)4127731-4 s Proteinbiosynthese (DE-588)4175987-4 s DE-188 DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=027991779&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Rudorf, Sophia 1985- Protein synthesis by ribosomes Ribosom (DE-588)4127731-4 gnd Proteinbiosynthese (DE-588)4175987-4 gnd |
| subject_GND | (DE-588)4127731-4 (DE-588)4175987-4 (DE-588)4113937-9 |
| title | Protein synthesis by ribosomes |
| title_auth | Protein synthesis by ribosomes |
| title_exact_search | Protein synthesis by ribosomes |
| title_full | Protein synthesis by ribosomes von Sophia Rudorf |
| title_fullStr | Protein synthesis by ribosomes von Sophia Rudorf |
| title_full_unstemmed | Protein synthesis by ribosomes von Sophia Rudorf |
| title_short | Protein synthesis by ribosomes |
| title_sort | protein synthesis by ribosomes |
| topic | Ribosom (DE-588)4127731-4 gnd Proteinbiosynthese (DE-588)4175987-4 gnd |
| topic_facet | Ribosom Proteinbiosynthese Hochschulschrift |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=027991779&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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