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Unformatted text preview: Department of Chemical Engineering ChE 170 University of California, Santa Barbara Fall 2010 Problem Set No. 3 Due: Thursday, 11/04/10 at the start of class Objective : To understand and develop models of protein binding and enzyme kinetics. To understand DNA and RNA structure, replication, transcription, and translation. Review problems You should pay special attention to these questions after reading. Note that the answers are given in the back of the book. Formulate your answers fully first and then check them. This can be a significant aid in your understanding of the material, and similar questions may be asked on the final. You do not need to provide written answers in the solutions you hand in. ECB 5-6 ECB 5-8 ECB 5-9 ECB 5-18 ECB 6-8 ECB 6-9 ECB 6-15 ECB 6-19 ECB 7-7 ECB 7-17 Problem 1 Leucine zippers are a family of proteins that play important roles as transcriptional factors in eukaryotic cells: by recognizing and binding to specific nucleotide sequences in DNA they can regulate the expression of various genes (i.e., the transcription of particular proteins). The structure of the activator GCN4 of the family of bZip leucine zippers in a complex with DNA has been solved and can be found on the Protein Databank with PDB code 1YSA. Download this file and view it with Pymol. You should view it in cartoon representation for more clarity. You want to split the protein and DNA into two separate objects. Follow these steps: 1. Display > Sequence 2. Display > Sequence Mode > Chains 3. Select the A and B chains corresponding to the two DNA strands by using the letters at the top of the display window. 4. A button next to (sele) > Create object. You should get a new row in the selection pane (obj1) and a new row of chain codes at the top of the display window. 5. Select the C and D chains corresponding to GCN4 by using the letters at the top of the display window. 6. A button next to (sele) > Create object. You should get a new row in the selection pane (obj2) and a new row of chain codes at the top of the display window. 7. A button next to 1YSA > Delete object. You should now be left with two objects, obj1 and obj2, corresponding to the DNA strands and GCN4, respectively. 8. S button next to all > Display As > Cartoon. a) What is the dominant secondary structure of GCN4? Is it a monomer, dimer, trimer, or other multimeric protein? What kind of structure is it (hint: consult figure 4-13 in the book)? b) What kinds of amino acid residues in the protein are interacting with the DNA nucleotides, and why do these interactions make sense? To answer this, you will display amino acid residues of different types according to the following color scheme: hydrophobic=gray, positively charged=blue, negatively charged=red: 1. S button next to obj2 > Sticks. This will show the stick models of the residues in addition to the cartoon representation....
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