Midterm 2 .pdf - Question 1(12pts One of the nucleotide...

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2 Question 1 (12pts): One of the nucleotide salvage enzymes is unique in that it can catalyze salvage reactions using two different bases. Name this enzyme. Write out the two reactions that this enzyme catalyzes. Abbreviations are acceptable and chemical structures are not necessary. Of the four standard ribonucleosides, which is NOT a direct product of any of the salvage reactions? Write its full name. One of the ribonucleosides produced by salvage cannot be phosphorylated into one of the standard nucleotide triphosphates, but is still useful for nucleotide synthesis. Which ribonucleoside is this, and how is it useful? Name two enzymes of the nucleotide biosynthetic pathway that can use rGDP as a substrate. In the space below, draw the chemical structure of the fully oxidized form of purine bases and name this molecule.
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3 Question 2 (12pts). This picture illustrates different parameters used to define the geometry of bases in nucleic acids double helices. Above each picture write the name of each parameter studied in class that each picture illustrates. Note that some of these have not been covered. For these, write an “X” – 6pts. Fill the missing words on the sentences below. Please limit your answers to relevant terms that have been discussed or presented in this class. (1pt each). Typically the answer should consist in just one word. The major groove is ______________________________________in A DNA than in B DNA. The helix diameter is ______________________________________in B DNA than in A DNA. The minor groove is _____________________________________in Z DNA than in B DNA. The rise per residue is______________________________________A DNA than in B DNA. The glycosidic bond conformation of guanosines is _________________________in Z DNA. The sugar pucker conformation of nucleotides of a DNA strand is _____________________ when this DNA is hybridized to a complementary RNA strand.
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4 Question 3 (12pts). The images on the right show two nucleotides joined in a base pair, viewed from different angles. The nucleotides are part of a double-stranded structure. A - On the top image, draw the hydrogen bonds between the two bases using dashed lines. Write in the hydrogen atoms as necessary and indicate whether each group is a hydrogen bond donor (D) or acceptor (A) – 3pts B- On the bottom image, label the 5’ and 3’ carbons on the backbone sugars. What is structurally different about these backbone sugars compared to those seen in nucleotide pairs in standard (B- form) DNA? – 3pts C- Explain how these two nucleotides are still able to form Watson-Crick base pairs in spite of the structural oddities with the paired nucleotides that you observed in (B) – 3pts D- Given the structure shown above, explain why the “pseudo-dyad” axis would not be an appropriate name for this axis in this particular structure.
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5 Question 4 (12pts) This picture shows the structure of amino acids in a protein binding to a nucleotide. The carbons are shown in green.
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  • Summer '15
  • paul tarr

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