Q1. Exploring PDB files and secondary structure (Imol Exercise 1). The response to this question should contain two components (2pt each):

a) One photo captured at the indicated spot in the instructions manual from Exercise 1 (step xxxiv). This should include the molecule window, the Script Console window.

b. One paragraph reflecting on whether the exercise was successful in having you more vividly appreciate the distinctive order that allows secondary structure to form, compared with lecture coverage of the figures in Section 2.3 (Secondary Structure) of our textbook. Try to pick one portion of the exercise that was particularly helpful in improving your understanding of how secondary structure is arranged or stabilized (or where the R groups are with respect to the backbone), and use specific wording to say what you were doing in the exercise that was helpful. If you found the exercise unhelpful, then provide specific feedback regarding what you think an ideal exercise would contain, if its goal was to provide 3D enhancement to lecture coverage of secondary structure. (If you found part of the exercise confusing, too brief to be useful, etc., then please use this opportunity to convey that feedback.)

Q2. Exploring tertiary structure and disulfide bonds (Jmol Exercise 2). The response to this question should contain two components (2pt each):

a. One photo captured at the indicated spot in the instructions manual from Exercise 2 (final step). This should include the molecule window, the Script Console window

b. One paragraph describing what can be observed using the 'Slab' command with lysozyme (final steps of Exercise 2). Write a paragraph that describes what you saw when using this new command. This part of the exercise had a specific purpose - think about how the residues (amino acids) were color-coded and what you could observe when viewing the protein's exterior compared with when using the "Slab' observed for lysozyme on the surface vs. in the 'Slab' view. Also mention or represented, and the overall spatial distribution pattern that be command be sure to specifically describe the color-coding, what could it whether you could view empty (unoccupied) space in the 'Slab' view whether the interior was tightly packed with atoms.

Q3. Using the ProtParam tool (2pt). The response to this question should consist
of one paragraph that addresses the following in complete sentences:

Lysozyme's molecular weight (kD), most-represented residue (or indication that they are all equally represented), and pl.

Histone H3's pl, composition in terms of acidic and highly basic residues (and the direct relevance of this to its pl!), and a restatement of the definition of pl (textbook section 3.1).

An overall comment (your own judgment) regarding whether these two examples suggest that protein composition is largely evenly distributed (most amino acids represented at approximately similar frequency regardless of which protein you were to study) or not.

Q1. Exploring PDB files and secondary structure (Imol Exercise 1)....