Q1. Recreating your own version of textbook Fig. 30.11 (threonyl-tRNA synthetase bound to tRNA and AMP). The response to this question should contain two components:

a. One high-quality JPEG (2pt) exported from the Jmol program (not a screenshot!). If you can't choose one angle that best captures what you want to show, then you should export two very different views (most likely one that clearly shows the anticodon and the other that very clearly shows the AMP near the 3' end of the tRNA), and label them 'Figure A' and 'Figure B' in your caption.

b. A clear and very detailed caption (4pt) that is customized to your own personal image(s) that you created - it should definitely contain differences compared with what your classmates are submitting! There are various orders in which you could present the following information, but at some point, with complete sentences, you should include all of the following:

-The name of the enzyme and what it is bound to (the tRNA, small molecule, and the cofactor), along with the specific colors used for each.
-The filename that you downloaded.
-The name of the program that you used to create the image(s).
-The specific names of the colors that you used for everything (e.g. 'the majority of the tRNA is colored T, while the individual bases in the anticodon were highlighted as follows:...)
-The styles that you chose for everything (e.g. the AMP molecule is displayed in the spacefill style...)
-The organism, the resolution in Angstroms, and the method by which the structure was obtained (X-ray diffraction? NMR? Other?) Remember, you can easily get this information from the appropriate page at http://www.rcsb.org/pdb
-Something that you want to draw the viewer's attention to. (Notice how close together two particular things are.. ? Notice how large or how small something is ? Notice how much or how little secondary structure something has. ? Notice how the color-coding reveals a that would otherwise have been hard of to see...?)

Q2. The ribosome (Jmol Exercise 19). The response to this question should contain two components (2pt each):

a. This should include the molecule window, captured at the indicated spot (final step) in the instructions the Script card. close together in the peptidyl transferase center (which of course Console The purpose is to, as best you can, show that where the two is the are opposite end from where the mRNA is!) there is predominantly rRNA, not ribosomal protein.

b. One paragraph reflecting on this Ribosome exercise. There were lacked three separate files to upload because the final intact' ribosome file of the ribosomal proteins and did not allow as good of an investigation many of the RNA vs. protein localization as the first two files did. Was this three-file exercise effective in its intended purpose of having you more deeply understand the embedded content in textbook Figs. 30.14 (showing that the ribosome contains both RNA and protein) and 30.16 (showing tRNA binding to the mRNA and the ribosome, and showing that the peptidyl transferase center is lined with rRNA, causing the ribosome to be described as a 'ribozyme' rather than as an 'enzyme')? If not, then do you have suggestions for how these messages could be better conveyed?

(Alternatively, if you thought that Exercise 19 went fine, you can instead give a detailed response to the Central Dogma animations. Were they valuable? Did they serve their intended purpose of helping you to visualize the complexity and speed of transcription and translation better? Or do you have suggestions for what types of animations would be more useful based on your impression of what Central Dogma-related processes remain the most difficult to visualize?)

Q1. Recreating your own version of textbook Fig. 30.11 (threonyl-tR...