Molecular Biochemistry II

tRNA & Ribosomes

Reading:

Textbook Reading: Voet & Voet, Biochemistry, 3rd Edition, p. 1285-1318.

Some recent articles (optional reading): 
B. T. Wimberly, D. E. Brodersen, W. M. Clemons, R. J. Morgan-Warren, A. P. Carter, C. Vonrhein, T; Hartsch & V. Ramakrishnan (2000) "Structure of the 30S ribosomal subunit," Nature 407: 327-339.
J. Frank (2002) "Single-particle imaging of macromolecules by cryo-electron microscopy," Annu. Rev. Biophys. Biomol. Struct. 31: 303-319.
A. Yonath (2002) "The search and its outcome: High-resolution structures of ribosomal particles from mesophilic, thermophilic and halophilic bacteria at various functional states," Annu. Rev. Biophys. Biomol. Struct. 31: 257-273.
P. B. Moore & T. A. Steitz (2003) "The structural basis of large ribosomal subunit function," Annu. Rev. Biochem. 72: 813-850.
T. A. Steitz & P. B. Moore (2003) "RNA, the first macromolecular catalyst: the ribosome is a ribozyme," Trends in Biochem. Sci. 28: 411-418.
M. Ibba & D. Söll (2004) "Aminoacyl-tRNAs: setting the limits of the genetic code," Genes & Development 18: 731-738.
S. W. Lee, B. H. Cho, S. G. Park & S. Kim (2004) "Aminoacyl-tRNA synthetase complexes: beyond translation," J. Cell Science 117: 3725-3734.
X.-L. Yang, P. Schimmel & K. L. Ewalt (2004) "Relationship of two human tRNA synthetases used in cell signaling," Trends in Biochem. Sci. 29: 250-256.
S. W. Lee, B. H. Cho, S. G. Park & S. Kim (2004) "Aminoacyl-tRNA synthetase complexes: beyond translation," J. Cell Sci. 117: 3725-3734.
P. B. Moore & T. A. Steitz (2005) "The ribosome revealed," Trends in Biochem. Sci. 30: 281-283.
H. F. Noller (2005) "RNA structure: reading the ribosome," Science 309: 1508-1514.
D. E. Draper, D. Grilley & A. M. Soto (2005) "Ions and RNA folding," Annu. Rev. Biophys. Biomol. Struct. 34: 221-243.
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.
C. Allmang & A. Krol (2006) "Selenoprotein synthesis: UGA does not end the story," Biochimie 88: 1561-1571.
A. Korostelev & H. F. Noller (2007) "The ribosome in focus: new structures bring new insights," Trends in Biochem. Sci. 32: 434-441.

Potential Test Questions:

1. Diagram the 2-step reaction catalyzed by Aminoacyl-tRNA Synthetases, showing in detail relevant parts of the molecules. What makes the overall reaction spontaneous? How do Class I and Class II Aminoacyl-tRNA Synthetases differ with regard to their interaction with the tRNA and the nature of the linkage formed between the amino acid and the tRNA?

2.a. Describe the structure of tRNA^Gln from E. coli. What types of secondary structure are found in tRNAs? What interactions are responsible for such secondary structure? What is the overall shape of the tRNA (tertiary structure)? What types of interactions stabilize this tertiary structure? Where and by what type of linkage (OK to describe in words) is the amino acid bound. Where in the folded tRNA is the anticodon located?
b. Indicate an example of a region of the E. coli tRNA^Gln that is an identity element recognized by the appropriate Class I Aminoacyl-tRNA Synthetase. Is the interaction of this identity element with the enzyme apparent in the crystal structure that you viewed of the complex of GlnRS with tRNA^Gln?

3.a. Describe in general terms the structure of the large ribosome subunit. What makes up the core of the particle? Where are proteins of the large ribosome subunit located? What is the nature of protein domains that extend into the interior of the ribosomal subunit? Are these proteins likely to maintain their secondary and tertiary structure if isolated from the ribosome? Why? 
  b. What active site residue functions in catalysis during peptide bond formation by the large ribosome subunit? What type(s) of macromolecule are present at the active site? 

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Lecture Notes on tRNA and Ribosomes

Interactive Quiz on         tRNA & Ribosomes