BMB 170 Lecture 13 Nucleic Acids, Nov 7th
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1 BMB 170 Lecture 13 Nucleic Acids, Nov 7th Chloroplast Ribosome h"p:// Ban N, Beckmann R, Cate JH, Dinman JD, Dragon F, Ellis SR, Lafontaine DL, Lindahl L, Liljas A, Lipton JM, McAlear MA, Moore PB, Noller HF, Ortega J, Panse VG, Ramakrishnan V, Spahn CM, Steitz TA, Tchorzewski M, Tollervey D, Warren AJ, Williamson JR, Wilson D, Yonath A, Yusupov M. A new system for naming ribosomal proteins. Curr Opin Struct Biol. 2014;24: doi: /j.sbi
2 Tth 70S Structure First high-resolu^on structure of the 70S Contains mrna, AP &E site trnas 1j00 & 1j01 (2 molecules in the asymmetric unit) Ramakrishnan Lab: Selmer et al Science (2006) 313:1935
3 Evolution of Ribosomes Anger..Beckmann Nature (2013) 497:80
4 Eukaryo^c ribosomes Universal Archaea/eukarya Eukarya Klinge..Ban TiBS (2012) h"ps://doi.org/ /j.^bs
5 Eukaryo^c ribosomes Protein connec^vity Universal Archaea/eukarya Eukarya Klinge..Ban TiBS (2012) h"ps://doi.org/ /j.^bs
6
7 Mitochondrial ribosome structures Bacterial Bacterial Extensions Mitochondrial specific Brown, Amunts..Scheres, Ramakrishnan Science (2014) 346:718 See several publications from Ramakrishnan and Ban groups respectively of Yeast and Human mitoribosomes
8 Mitochondrial Ribosomes Human Pig Amunts, Brown..Ramakrishnan Science (2015) DOI: /science.aaa1193 Greber, Bieri, Leibundgut..Ban Science (2015) DOI: /science.aaa3872
9 Features of the mito-ribo DOI: /science.aab1054
10 Ribosome Architecture Review: Schmeing & Ramakrishnan (2009) Nature
11 Gene^c code Stable to muta^ons Wobble hypothesis
12 The gene^c code in prac^ce From Jason Chin (MRC-LMB)
13 Model for decoding 30S structure (1j5e) 30S plus paramomycin (1hg)
14 The main steps of protein synthesis Fig. 8.11
15 Ini^a^on complexes IF1 protects A-site IF1 soaked into 30S crystals Carter..Ramakrishnan (2001) Science 291:498
16 IF3 bound to the ribosome EM structure of bound IF3 Domains of IF3 solved independently Docked into low resolu^on model McCutcheon..Ramakrishnan (1999) PNAS 96:4301
17 Reading the minor groove A and P site models Minor groove is measured Ogle et al Science (2001) 292:897 (1ibm)
18 Decoding Review: Schmeing & Ramakrishnan (2009) Nature
19 An^-codon stem loop induced fit From Ramakrishnan lab
20 EF-Tu/EF-Ts Fig. 8.22; EF-Tu (unstable) is a stable complex with EF-Ts in the absence of trna
21 EF-Tu is a G-protein Switch II P-loop Switch I EF-Tu Ras Fig N-terminal domain of EF-Tu compared to Ras
22 Fig.8.21 EF-Tu/aa-tRNA complex
23 8.26 Binding to the A-site
24 EF-Tu/tRNA 70S structure Schmeing, Voorhees..Ramakrishnan (2009) Science Kirromycin bound form
25 GTPase ac^va^on High resolu^on structure of EF-Tu/tRNA/Ribosome His84 acts as base to ac^vate the water for hydrolysis Voorhees, Schmeing..Ramakrishnan (2010) Science 330:835
26 Rebecca Voorhees and Mar^n Schmeing
27 Pep^dyltransferase reac^on Review: Schmeing & Ramakrishnan (2009) Nature
28 EF-G structures Catalyzes transloca^on from P to E site Bacterial Fig Yeast
29 Ribosome recycling factor Fig RRF structure: Selmer..Liljas Science (1999) 286:2349 (1dd5) RRF/ribosome: Weixelbrunner, Selmer..Ramakrishnan NSMB (2007) 14:733 (2V46, 2V47, 2V48 and 2V49)
30 Fig Exit tunnel
31 Bacterial transla^on
32
33 Paromomycin Aminoglycoside family Binds near the A-site Reduces trna dissocia^on
34 Paromomycin Binding Flips Out Bases A1492 and A1493 into the A site
35 Spectinomycin Small subunit antibiotics Pactamycin Streptomycin Tetracycline Hygromycin B Carter..Ramakrishnan (2000) Nature 407:340 Brodersen..Ramakrishnan (2000) Cell 103:1143
36 Large subunit antibiotics H. marismortui has G2099 (A2058 in E. coli) Mutated the native 16S RNA (had to delete two copies) Big money drugs! Tu..Steitz (2005) Cell 121:257-70
37 Mechanism
38 Competing models? Antibiotic (CSD a Erythromycin (NAVTAF) Clindamycin 1 c (SUPBIO) H. marismortui D. radiodurans b (1JZY) (1JZX) Clindamycin Clindamycin Telithromycin (GOPGAT) Virginiamycin S (KEFWUN) (1P9X) (1SM1) Deinococcus radiodurans is a eubacteria that should be sensitive to all the clinical drugs.
39 Ribosome pausing Certain sequences can stall translation, in this case TnaC leader peptide. Seidelt..Schulten, Steitz, Beckmann (2009) Science 326:1412
40 Stalling by disrupting peptidyltransferase
41 Regulating Trp by translational pausing Bischoff, Berninghausen & Beckmann Cell Rep (2014) 9:469
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Bellringer What is the central dogma of biology? A. RNA DNA Protein B. DNA Protein Gene C. DNA Gene RNA D. DNA RNA Protein Review of DNA processes Replication (7.1) Transcription(7.2) Translation(7.3)
ATP. P i. trna. 3 Appropriate trna covalently bonds to amino acid, displacing AMP. Computer model Hydrogen bonds
mino acid attachment site nticodon Hydrogen bonds mino acid T i denosine i i denosine minoacyl-trn synthetase (enzyme) trn 1 ctive site binds the amino acid and T. 2 T loses two groups and bonds to the
Molecular Biology, Genetic Engineering & Biotechnology Operons ???
1 Description of Module Subject Name?? Paper Name Module Name/Title XV- 04: 2 OPERONS OBJECTIVES To understand how gene is expressed and regulated in prokaryotic cell To understand the regulation of Lactose