Chemistry Department University of Southern Maine
Links To Files Used In Biochemistry Class (CHY 361-363)
Be sure to read the Introduction to the Biochemistry Graphics Gallery to learn how to view these files.
Topic: Ribosomal Protein Synthesis
For graphics from other topics, see Topics List.
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Molecules to Explore
tRNAPhe To study the structure of a transfer RNA that carries phenylalanine, obtain the file 4TNA from the Protein Data Bank.
For SwissPdbViewer users, click here for a prepared view of the 4TNA model, color coded as follows:
·Amino-acid arm, backbone red in the single-strand region, green in the double-strand region
·T-Psi-C arm, backbone cyan
·DHU arm, backbone yellow
·Anticodon arm, backbone magenta, with anticodon bases green
Glutaminyl-tRNA Synthetase
To study the structure of an aminoacyl-tRNA synthetase, obtain the file 1QRT from the Protein Data Bank. This model shows glutaminyl-tRNA synthetase bound to glutaminyl-tRNA. In addition, ATP is bound to the putative binding site for the aminoacyl adenylate.
Click here for a Medline abstract concerning 1QRT.
For SwissPdbViewer users, click here for a prepared view of the 1QRT model. The model is color coded as follows:
·tRNA is shown in cyan, with the anticodon region in magenta backbone with green bases (doesn't look as bad as it sounds -- but now you know why I ask my wife's approval of my clothing before I leave the house).
·ATP is shown with a dotted surface, in CPK colors.
· Synthetase: Only residues within 4 angstroms Å of the t-RNA or ATP are shown fully, CPK colored. Other residues are in ribbon, with helices red and beta strands yellow.
Compute H-bonds and explore the anticodon region of the t-RNA. Note that recognition of t-RNA by synthetase involves the anticodon region (residues 34-36, 5'-CUG-3'), but that there are also other regions of enzyme-tRNA contact (wherever you see enzyme residues fully displayed (not just ribbon), the enzyme and t-RNA are in contact).
Also look at the ATP binding region. Measure the distance from the 2'-hydroxyl oxygen of t-RNA residue A76 (the 3'-terminal nucleotide, which carries the amino acid) to the phosphorus atom of the middle phosphate of ATP. This phosphorus is at approximately the position of the aminoacyl carbonyl carbon in the aminoacyl adenylate that would normally occupy the ATP position during catalysis.
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