Tour of the Ribosome

by Wayne Decatur,
a research associate in the lab of M. J. Fournier in the department of Biochemistry and Molecular Biology
at the University of Massachusetts, Amherst
  • The tour is designed for users with at least a general familiarity with translation and the ribosome, such as students who have taken general biology classes. It is suitable for self-paced study or lectures.
  • For viewing the tour, you will need a computer capable of using the web browser-based, molecular visualization program called Protein Explorer because this web presentation is a specialized version of Protein Explorer. Protein Explorer requires the free browser plugin, MDL CHIME, available in the company's downloads section. Please, CLICK HERE for more details about Protein Explorer and its computer requirements.
  • For more Chime-based exploration of the ribosome, see my tour that explores the large ribosomal subunit in greater depth using the true atomic resolution structures of Archaeal large ribosomal particles with and without various transition-state analogs. Besides an introductory tour of the large subunit for the general public I have an intensive tour of the large subunit for specialists. These are all indexed on my home page.
  • Introduction

    The ribosome is a large complex made up of two subunits. Each subunit is made of RNA and protein. The large subunit is responsible for the chemistry of peptide bond formation. A peptide bond is found between every amino acid in a protein. When a ribosome is in the process of protein translation, another amino acid is added to the end of a growing polypeptide chain. The amino acid that is to be added to the chain is attached to the end of a transfer RNA. The growing polypeptide chain is bound to the end of a different transfer tRNA. The tranfer RNAs contact the ribosome during translation. The large subunit of the ribosome is about 100 times large than a typical enzyme and sediments at 50S. The identity of the amino acid that is added is controlled by the small subunit of the ribosome. The small subunit of the ribosome guides the interaction between the messenger RNA (mRNA) and anticodon-ends of transfer RNAs. The small subunit therefore controls the reading of the genetic information stored in genes and does it with exquisite fidelity. Despite its name, the small subunit is still rather large consisting of many proteins and an RNA of substantial length.

    In May 2001, Noller and coworkers published a paper in the journal Science detailing the structure of the full ribosome (1). The structural data provided is used here to make a small presentation highlighting the features of the ribosome. The ribosomes used in the crystallization were from a thermophilic eubacteria,Thermus thermophilus. However, due to the high conservation of ribosomal RNA and proteins, the data has immediate value for investigators interested in the machinery that makes proteins in every organism on earth. Though the quality of the crystals used for the structure determination was such that atoms less than 5.5 angstroms apart could not be distinguished, it is being treated as an 'effectively atomic-resolution structure' at this time. This is because it is possible to place most individual components at the proper location in the ribosome due to the availibility of other higher resolution structures (2,3,4,5,6). Work will continue in the hopes of even better full ribosome structures. Even though the ribosome structure was highly enlightening, it also raised many questions as well. In the coming years, better ribosome structures should contribute significantly to understanding translation.

    CLICK HERE to Begin the Tour of the Ribosome
    Tour the Ribosome

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    This and other Chime-based tutorials are indexed at the World Index of Molecular Visualization Resources (linked to the UMass Chime Resources Site). This particular one is under the category Biochemistry Tutorials in Chime.

    If you like this presentation, please let the author know!

    Last updated 1-13-04.