Molecular Biochemistry II

Translation: Protein Synthesis

Reading:

Textbook Reading: Voet & Voet, Biochemistry, 3rd E., Chapter 32, especially p. 1318-1342.

Some recent articles (optional reading): 
H. F. Noller, M. M. Yusupov, G. Z. Yusupova, A. Baucom & J. H. D. Cate (2002) "Translocation of tRNA during protein synthesis," FEBS Lett. 514: 11-16.
A. Bashan, R. Zarivach, F. Schluenzen, I. Agmon, J. Harms, T. Auerbach, D. Baram, R. Berisio, H. Bartels, H. A. S. Hansen, P. Fucini, D. Wilson, M. Peretz,
T. A. Steitz & P. B. Moore (2003) "RNA, the first macromolecular catalyst: the ribosome is a ribozyme," Trends in Biochem. Sci. 28: 411-418.
G. R. Andersen, P. Nissen & J. Nyborg (2003) "Elongation factors in protein biosynthesis," Trends in Biochem. Sci. 28: 434-441.
S. Jenni & N. Ban (2003) "The chemistry of protein synthesis and voyage through the ribosomal tunnel," Current Opinion in Struct. Biol. 13: 212-219.
A. Bergmann & M. E. Lane (2003) "HIDden targets of microRNAs for growth control," Trends in Biochem. Sci. 28: 461-463.
I Agmon, M. Amit, T. Auerbach, A. Bashan, D. Baram, H. Bartels, R. Berisio, I. Greenberg, J. Harms, H. A. S. Hansen, M. Kessler, E. Pyetan, F. Schluenzen, A. Sittner, A. Yonath & R. Zarivach (2004) "Ribosomal crystallography: a flexible nucleotide anchoring tRNA translocation, facilitates peptide-bond formation, chirality discrimination and antibiotics synergism," FEBS Lett. 567: 20-26.
F. Gebauer & M. W. Hentze (2004) "Molecular mechanisms of translational control," Nature Rev. Molec. Cell Biol. 5: 827-835.
L. D. Kapp & J. R. Lorsch (2004) "The molecular mechanics of eukaryotic translation," Annu. Rev. Biochem. 73: 657-704.
T. Daviter, F. V. Murphy, & V. Ramakrishnan (2005) "A renewed focus on transfer RNA," Science 308: 1123-1124.
L. Cochella & R. Green (2005) "An active role for tRNA in decoding beyond codon:anticodon pairing," Science 308: 1178-1180.
T. Dale & O. C. Uhlenbeck (2005) "Amino acid specificity in translation," Trends in Biochem. Sci. 30: 659-665.
J. M. Ogle & V. Ramakrishnan (2005) "Structural insights into translational fidelity," Annu. Rev. Biochem. 74: 129-177.
A. Yonath (2005) "Antibioitics targeting ribosomes: Resistance, selectivity, synergisn, and cellular regulation," Annu. Rev. Biochem. 74: 649-679.
B. S. Schuwirth, M. A. Borovinskaya, C. W. Hau, W. Zhang, A. Villa-Sanjurjo, J. M. Holton & J. H. D. Cate (2005) "Structures of the bacterial ribosome at 3.5 resolution," Science 310: 827-834.
T. Daviter, K. B. Gromadski & M. V. Rodnina (2006) "The ribosome's response to codon-anticodon mismatches," Biochimie 88: 1001-1011.
K. Mitra & J. Frank (2006) "Ribosome dynamics: Insights from atomic structure modeling into cryo-electron microscopy maps," Annu. Rev. Biophys. Biomol. Struct. 35: 299-317.
F. Le Sourd, S. Boulben, R. Le Bouffant, P. Cormier, J. Morales, R. Belle & O. Mulner-Lorillon (2006) "eEF1B: At the dawn of the 21st century," Biochim. Biophys. Acta 1759: 13-31.
A. G. Hinnebusch (2006) "eIF3: a versatile scaffold for translation initiation complexes," Trends in Biochem. Sci. 31: 553-562.
K. H. Nierhaus (2006) "Decoding errors and the involvement of the E-site," Biochimie 88: 1013-1019.
M. Rodnina, M. Beringer & W. Wintermeyer (2007) "How ribosomes make peptide bonds," Trends in Biochem. Sci. 32: 20-26.
Y. Zhao & D. Srivastava (2007) "A developmental view of microRNA function," Trends in Biochem. Sci. 32: 189-197.
E. A. C. Wiemer (2007) "The role of microRNAs in cancer: No small matter," Eur. J. Cancer 43: 1529-1544.

Potential Test Question

a. Describe the role of EF-Tu (EF1A) in translation. What activity does it exhibit?
Members of the family of small GTP-binding proteins generally require two "helper" proteins, GAP and GEF. Explain the general role of each of these helper proteins and indicate what the initials GAP and GEF stand for.
What constituents of the protein synthesis machinery function as GAP and GEF for EF-Tu?
b. How does the ribosome detect that a correct aminoacyl-tRNA has bound at the A site? What are the consequences of this process in relation to EF-Tu and the conformation of the tRNA?
c. Diagram and describe the reaction of peptide bond formation. Does any ribosomal protein have a role in catalysis?
d. Describe the postulated role of EF-G and its reaction cycle. What does the 3D structure of EF-G resemble? What serves as GAP and GEF for EF-G?

Copyright 1998-2008 by Joyce J. Diwan. All rights reserved.

Lecture Notes on
Protein Synthesis

Interactive Quiz on    
  Protein Synthesis      

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