CHEM 1050 Final: chem 1050 final 2007

This question uses a program "Coot" which can be downloaded here http://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/

23. Fetch the coordinates for PDB code 2BAM. This is the structure of BamHI, a restriction endonuclease. Switch the display manager to CAs + ligands.

a. What is the quaternary structure of this enzyme? Only consider the protein components, and use terminology that describes not only the number of subunits, but also if they are the same or not.

b. Does this enzyme mainly interact with the DNA in its major groove or minor groove? Does this enzyme bind a specific DNA sequence? Explain.

24. Switch the view back to “Bonds” in Display Manager. Zoom in on nucleotide 7 of chain D. It might help to turn on environmental distances (under the Measures menu).

a. Which nucleotide is this?

b. Which amino acid residues interact with this nucleotide base? Identify the atoms.

c. Considering the structures of the other three nucleotide bases, identify any structural basis for the DNA sequence specificity for nucleotide 7 of chain D of BamHI (i.e. why does BamHI recognize the nitrogenous base you identified above and not a different one?). Be specific.

(v) Plot the three spectra on the same axes (constructing a spreadsheet may aid you here and in the following questions). What colour is the suspect car paint that you are attempting to match? (4 marks) (Graduate Capabilities - Chemistry knowledge & skills; Quantitative literacy) Now follow the Tristimulus colour matching procedure. (vi) By using the 1964 CIE standard weighting factors table (which can be downloaded at www.cie.co.at or located in Bell Ed 2 Chapter 14 Table 1 pp 457) to deconstruct each spectra into its RGB components. Then convert these RGB components to chromaticity coordinates. On a copy of a chromaticity diagram, locate these three car paint colours. What sample colour is the closest match to the suspect car colour? (12 marks) (Graduate Capability - Quantitative literacy) (vii) Comment on your perception of these two specific paint colours in relation to the chromaticity diagram. Is it easier or more difficult to distinguish between variations of this colour due to the asymmetric distortions of the diagram? Would you say they are both pure spectral colours? (4 marks) (Graduate Capabilities - Chemistry knowledge & skills; Critical Thinking) You have now performed a quantitative colour test, you wish to follow up by performing a chemical test on the paint sample itself. (viii) With your knowledge of colorants introduced in the lecture slides, locate in the literature a paint pigment of similar colour you could target for chemical analysis. Draw its structure and circle the chromophore. What class is the colorant? What would be a suitable particle size for the pigment to maximise scattering? (8 marks) (Graduate Capabilities - Chemistry knowledge & skills; Inquiry /Research; Critical Thinking)