PS_5_key_05 - Bio 115 Problem set #5 February 11, 2005 1....

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February 11, 2005 Problem set #5 1. In group I introns, why is a guanosine cofactor required for the first chemical step of splicing but not the second? Answer: In the first step, the 3'-hydroxyl group of the guanosine provides the nucleophile that attacks the phosphodiester bond. In the second step, a 3'-hydroxyl group at the end of the 5' exon (created in the first step) serves as the nucleophile. 2. Considering group I, group II and pre-mRNA introns, describe where energetic inputs are required to drive the splicing process. Answer: The actual chemical steps of splicing for these three types of introns do not require energetic inputs. However, in pre-mRNA splicing, there are multiple ATP dependent steps. The first of these occurs when the U2-snRNP binds the pre-mRNA. Other ATP requiring steps occur when RNA helicases are used. 3. What feature of RNA makes it ideal for performing chemical reactions? Answer: The 2'-hydroxyl group of RNA (missing in DNA-deoxy- ribonucleic acid) can serve as a nucleophile in chemical reactions. 4. Rank DNA, RNA and proteins in terms of: a. the amount of genetic information that they carry DNA > RNA > protein b. their ability to form complex structures protein > RNA > DNA 5. Briefly, what is the "RNA world" hypothesis? Answer This refers to the idea that life began with RNA molecules that could self replicate and that proteins and DNA were later elaborations on life. 6. In group one introns, what function does the "internal guide sequence" perform? How is this function carried out in pre-mRNA splicing? Answer: The internal guide serves to hold the 5' and 3' exons in the correct orientation to the ribozyme and to each other. In pre-mRNA splicing, the U5 snRNA holds the exons next to one another and the active site of the spliceosome. 7. In terms of the fundamental mechanisms by which splicing occurs, how does tRNA splicing differ from splicing of group I, group II and pre-mRNA splicing? Answer: tRNA splicing is entirely dependent on protein-only enzymes. 8. What enzymatic activity does RNAseH possess? Answer: The ability to degrade RNA that is base-paired to DNA (hence the 'H' for hybrid). 9. Some group I introns require proteins. called maturases, in order to splice. What is the function of a maturase? Answer: These proteins help the group I introns fold into the correct structure to catalyze their splicing.
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PS_5_key_05 - Bio 115 Problem set #5 February 11, 2005 1....

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