On the right is the structure of yeast phenylalanine tRNA (pdb file 1EHZ.pdb) from Shi H, Moore PB. (2000) RNA 6: 1091-105. (also see 6tna.pdb, Sussman,J.L., Holbrook,S.R., Warrant,R.W., Church,G.M. and Kim,S.-H. (1978) J. Mol. Biol. 123: 607-630. At any time you can reset the model by clicking this button .
To turn spinning on or off click this button: (Note: spinning starts with a stutter!)

To manipulate the model press and hold the left hand mouse button and drag to obtain the desired view. To zoom press the shift key and left mouse button while moving the mouse. To alter the presentation of the image click with the right hand mouse button and select one of the options. The original view shows the tRNA with the atoms coloured as follows; Carbon - grey, Oxygen - red, Nitrogen - light blue, Hydrogen - white and phosphorous - orange. The model is displayed in the stick form to show the bonds between atoms. A more realistic representation of the tRNA is the spacefilling model ; here, the size of each molecule is represented by its bonding properties and van der Waals radius. A cartoon representation is a good way to see the overall folding of the tRNA molecule.

The Tutorial

Yeast phenylalanine tRNA is the adaptor molecule which brings phenylalanine (phe) to the ribosome when a phenylalanine codon is read on the messenger RNA. This phenylalanine is then incorporated into the growing protein chain. The tRNA folds into the defined L-shaped structure shown on the right. This structure is stabilised by many different types of interactions; these include Watson-Crick base-pairs, which are shown in the "clover leaf" representation shown below:

Fig. 22-3 (pg. 682) The World of the Cell by Becker et al, published by Pearson Education

The structure on the right is colour coded the same as the diagram above. This structure contains three "leaves", the anticodon loop (green), the D loop (blue) and the T loop (orange) and a fourth variably sized loop (coloured pink). Regions between loops are referred to as stems. The anticodon and D stems fold into a helix as do the T and Acceptor stems . Interactions between the variable loop and the D stem (red) and between the D and T (cyan) loops are important for maintaining the L-shape fold of the tRNA. This is shown in molecular detail . The codons for phenylalanine are 5'-UUU-3' and 5'-UUC-3'. For this tRNA the anticodon is 3'-AAG-5' (dark grey) and is located in the anticodon loop (coloured green). To perform its function tRNA^phe must first be attached to (charged with) phenylalanine. The enzyme aminoacyl-tRNA synthetase attaches phe at the end of the amino acid acceptor stem (coloured light purple). The charged tRNA then interacts with the messenger RNA at the surface of the ribosome.

The tRNA contains several modified nucleotides .

The loops and the regions of helical conformation are important for the specific interactions the tRNA must make with the aminoacyl-tRNA synthetase and the messenger RNA and ribosome.

Further information about the structure of yeast phenylalanine tRNA can be found in Rich,A. & Kim,S.H. (1978) The three-dimensional structure of transfer RNA Scientific American 238:52-62. This includes a discussion about how the structure is stabilised by non Watson-Crick base-pairing which has not been discussed in this tutorial.

More Tutorials

• To view a DNA tutorial here.
• To view a GC base pair click here.
• To view a TA base pair click here.
• To view three base pairs click here.
• More Tutorials & Animations

Using directory /Users/minchisd/Documents/Documents/Teaching/Teaching Material/BIO124/Web Material & Movies/DNA tutorial/jmol/Tutorials/tRNA/tRNA
  adding JmolPopIn.js
  ...jmolApplet0
      ...adding Reset.png
      ...copying
/Users/minchisd/Documents/Documents/Teaching/Teaching Material/BIO124/Web Material & Movies/DNA tutorial/jmol/Tutorials/tRNA/tRNA.pdb
         to
/Users/minchisd/Documents/Documents/Teaching/Teaching Material/BIO124/Web Material & Movies/DNA tutorial/jmol/Tutorials/tRNA/tRNA/tRNA.pdb
      ...adding Reset.spt
  ...jmolApplet1
      ...adding Spacefill.png
      ...adding Spacefill.spt
  ...jmolApplet2
      ...adding Cartoon.png
      ...adding Cartoon.spt
  ...jmolApplet3
      ...adding Anticodon.png
      ...adding Anticodon.spt
  ...jmolApplet4
      ...adding Anticodon_and_D_Stems.png
      ...adding Anticodon_and_D_Stems.spt
  ...jmolApplet5
      ...adding Acceptor_and_T_Stems.png
      ...adding Acceptor_and_T_Stems.spt
  ...jmolApplet6
      ...adding Interactions.png
      ...adding Interactions.spt
  ...jmolApplet7
      ...adding Interactions__Detailed_.png
      ...adding Interactions__Detailed_.spt
  ...jmolApplet8
      ...adding Modified_Bases.png
      ...adding Modified_Bases.spt