Download Study Guide MBMB 451A Fall 2002

Study Guide MBMB 451A Fall 2007
Nucleic Acid Structures and Manipulation
1. Know nucleotide and nucleoside structure and nomenclature.
2. What are the forces that help stabilize DNA double helical structure?
3. What is Tm?
4. What are the differences between A, B, and Z DNA? What conditions and
sequence favor the formation of Z DNA?
5. How is DNAse I footprinting done and what are its applications?
6. Be able to "read" a DNA sequencing gel and understand the process of
dideoxy sequencing.
7. What is the shorthand notation used to display DNA or RNA structure?
8. What are type I, II, and III restriction endonucleases?
9. What are sticky and blunt ends?
10. What is Southern blotting and its applications?
11. Explain the process of PCR. What is RFLP?
12. What is restriction mapping?
13. What is cDNA?
14. What is pulsed gel electrophoresis and why is it used for genomic DNA?
15. What is a DNA microarray and for what is it used?
Chromatin
1. What is the composition of a nucleosome, chromatosome, 10 nm and 30 nm
fibers?
2. What are core histones and linker histone? What are the "tails" of histone
proteins?
3. What is the structure of the nucleosome core particle?
4. What is translational and rotational positioning?
5. Describe how to do "indirect" labeling and what is it useful for?
6. What is the nuclear matrix and nuclear scafold?
7. Give specifice xamples of known covalent modification of the histone
octamer.
Explain how these modifications might affect the structure of the nucleosome
core particle.
8. What is euchromatin and heterochromatin?
9. How do you determine the L, T, and W values for a closed circular DNA?
10. Define DNA supercoiling and topoisomerases.
11. How does writhe changes when DNA is wrapped around protein in either a
left-handed or right-handed direction?
12. What are DNase hypersensitive sites and what is their relationship with
chromatin?
13. What is chromatin remodeling and what proteins are involved in this
process?
14. Explain how histones are acetylated and deacetylated and how that relates
to gene regulation.
Transcription
1. What is the subunit organization of E. coli RNA polymerase? What are the
three different eukaryotic nuclear RNA polymerases and the genes they
transcribe?
2. What are the two classes of eukaryotic transcription factors and how are they
different from each other?
3. What is a promoter element? What is the structure/organization of a typical
E. coli gene, eukaryotic mRNA gene, tRNA gene, rRNA gene, or 5S rRNA
gene?
4. Define basal versus activated transcription.
5. Describe the different ways in which the activity of transcription factors can
be regulated in the cell.
6. Describe the properties of the transcription factors TFIID, IIA, IIB, IIE, IIF,
and IIH. What are TAFs and are they important for basal transcription.
7. What is an enhancer? What is a response element?
8. Describe two models for how an enhancer could effect the level of
transcription.
9. What are the transcription factors called that are used by Pol I and Pol III?
10. Discuss how transcription activity can be regulated by protein
phosphorylation of RNA polymerase or the transcription factors.
11. Discuss methods that can be used to identify promoter elements in a
transcriptional unit.
12. What are the three different kinds of subunits associated with eukaryotic
RNA polymerases?
13. Give details about three different kinds of DNA binding motifs found in
promoter-specific transcription factors. What are some other separable domains
that can be identified in these transcription factors?
14. What are the differences between Pol IIO, IIA, and IIB?