Name_____________________________________
MBMB 451A Section 1
Fall 2002 9-19-02
Total of 70 points
1. List and definefour different parameters that are used to characterize A, B, and Z DNA thathelp describe the helical properties of these nucleic acid structures. (8 points)
2. List the contents of a nucleosome, the 10 nm fiber, and 30nm fiber? (6 points)
3. Diagram what are the typical promoterelements found in a eukaryotic (1) rRNA, (2) mRNA, and (3) tRNA genes and theirrelative position in DNA with regard to the transcription start site.
(8points)
4. What are the three classes of ATP-dependent chromatinremodeling complexes and how are they different or the same? (8 points)

5. A closed-circular DNA molecule in its relaxed form has an Lkof 500. Approximately how manybase pairs are in this DNA? (2points)
6. Which transcription factors contain TBP? Why are they called positioningfactors? Propose a model for howall three RNA polymerases can interact with TBP. (7 points)

7. What are the three basic DNA components (based on frequencyof occurence) found within the eukaryotic genome and what are theirproperties? What genes are found associatedwith these different DNA components? (8 points)
8. What factors are required for basaltranscription by RNA polymerase II and what factors might be required foractivated transcription? (8 points)

9. TFIIIA is a transcription factorrequired for the expression of 5S rRNA genes. This protein contains nine zinc finger domains, and binds toan internal region of 5S rRNA genes and to 5S rRNA itself.
(a) Describe how you would map the DNAbinding sites of the TFIIIA protein
(b) What specific mutations would demonstrate that the zincfingers are required for
DNA binding?
(c) You find that a deletion of 19 aminoacids from the C-terminus of TFIIIA binds DNA as well as wild type, but failsto activate 5S rRNA transcription. Propose an explanation
(d) Xenopus oocytes synthesize and store largeamounts of 5S rRNA. As 5S rRNAaccumulates, TFIIIA binds to it. What effect will this have on transcription of 5S genes?
What kind of regulatory mechanism isworking here?
(10 points)
10. In the figure below is shown ChIP (chromatinimmunoprecipitation) results for the mating type locus in Saccharomycescerevisiae. Antibodies thatrecognize histone H3 N-terminal tails with methylated lysine 4 or lysine 9 wereused to probe the state of methylation of chromatin within this region. Theinverted repeats, depicted as IR-L and IR-R for inverted repeat left and rightrespectively, are chromatin boundary elements. The Mat2 and Mat3 genes are silenced and inactive, whereasthe Mat1 gene is active.
What is the correlation ofthese two different kinds of methylation sites with transcriptionally activeand inactive regions - please specify?
Where would you expectheterochromatin and euchromatin to be located within this locus?
Please explain what you mightexpect to happen to the methylation patterns shown here if the boundary domainswere deleted.
(5points)