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.
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.
The accession numbers of the coordinates related to the ribosome are 1GIX , 1GIY, and 1jgo. (1,2).
The particular files used here are modified versions of 1GIX and 1GIY and 1jgo.
This presentation temlate was developed
Eric Martz for use in his class
Macromolecular Visualization Laboratory. He hopes to soon make it publicly available.
Development of the
template used to construct this presentation
was supported by a
from the Division of Undergraduate Education of the
National Science Foundation. When released, the template will
be available as part of the
The original impetus for designing chime-based images of the ribosome was to accompany a series of presentations given in the Fall 2000 Molecular Biology Journal Club at the University of Massachusetts at Amherst. The journal club was run by Professor Maurille 'Skip' Fournier. Positive feedback on those first ones encouraged me to incorporate other structures such as the complete ribosome at 5.5 angstroms used here, as they became available.
The complex nature of the data used here made it impossible to strictly adhere to the DRuMS color scheme proposed by Tim Driscoll, Freida Reichsman, and Eric Martz, but much of that scheme was used in some manner.