ps_4_05_key - Bio 115, February 4, 2005 Problem Set #4 1....

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Bio 115, February 4, 2005 Problem Set #4 1. If you want to differentiate between euchromatin and heterochromatin under an electron microscope, what stain would you use? In which of these regions does Pol II transcription occur? Answer- Feulgen. In the euchromatin. 2. What is a karyotype? How is karyotypic analysis performed and how is it useful? Answer- Karyotype refers to the normal complement of chromosomes of an individual, with respect to number, size, structure etc. Karyoypic analysis is carried out by making a preparation of chromosomes from an individual, staining them with Giemsa dye, and determining if they are normal or abnormal (by looking carefully at the alternating patters of dark and light chromosome bands) . 3. In chromatin, what determines the width of the 10 nm fiber? Answer- The width of the nucleosome core particle 4. How do micrococcal nuclease and DNAse I differ in their ability to digest DNA that is assembled into chromatin? How are these different activities used to study nucleosome structure and positioning? Answer- Micrococcal nuclease can cut DNA between nucleosomes and DNAse I can cut DNA that is wrapped around or that is between nucleosomes. Micrococcal nuclease is used to map nucleosome positioning whereas DNAse I is used to map the fine structure of DNA’s interactions with histones, i.e. the exact positioning of a histone octamer on DNA (to single bp resolution, this is known as mapping the rotational positioning of a nucleosome) and slight variations in the path of DNA around a nucleosome. At low concentrations, DNAse I can be added to isolated nuclei andused to identify DNAse I hypersensitive sites, which often correspond to transcriptional controls sites-promoters and enhancers. 5. What is a chromatin remodeling machine (CRM)? How can a CRM effect transcription? Do CRM’s consume energy when performing their function? Answer: A multisubunit protein complex that uses ATP-derived energy to directly alter DNA-histone contacts and chromatin structure. By altering histone-DNA contacts or assembling or removing nucleosomes, CRM’s can modulate accessibility of DNA binding proteins to their binding sites in DNA. The catalytic subunit of all known CRM’s shows homology to the Snf2/Swi2 protein of the Snf/Swi complex (the first CRM to be discovered). 6. Name two strategies used by cells to manipulate chromatin structure to alter transcription. Answer: 1 -they use chromatin remodeling machines (which hydrolyze ATP) to directly alter chromatin structure. 2 - they post-translationally modify histones e.g. -phosphorylate, acetylate, methylate, ADP-ribosylate etc 3. –they substitute core histones with histone variants that can assemble into nucleosome core particles but that have altered properties in transcriptional regulation. 7.
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ps_4_05_key - Bio 115, February 4, 2005 Problem Set #4 1....

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