Lieb_Prob_Set_8-Key

Lieb_Prob_Set_8-Key - Biology 202-Lieb Problem Set 8-Key...

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Biology 202-Lieb Problem Set 8-Key 4/15/06 Page 1 of 5 his problem is due the week of April 16. It covers some material from past lectures, but most of the problems are derived from the April 9-13 lectures. Also, by the end of the April 18 lecture, you should be able to work through all of the problems at the end of Chapter 11. It is almost impossible to learn this stuff conceptually by just listening to the lecture or reading. You really have to get into the details and work through some problems. Therefore, for this material, it is critical that you work the problems in the back of the book, and this problem set. 1.Some restriction enzymes have degenerate recognition sequence. For example, Sty I cuts at the sequence 5'-CCWWGG-3', where W = A or T (W stands for weak, because A–T has only two H-bonds). a) Which of the following sequences will be cut by Sty I? 5’–CCAAGG–3’ 5’–CCTAGG–3’ 5’–CCGAGG–3’ 5’–GGTTCC–3’ 3’–GGTTCC–5’ 5’–GGATCC–3’ 3’–GGCTCC–5’ 3’–CCAAGG–5’ YES YES NO NO b) How often, on average, would you expect to find a site for Sty I? (4)(4)(2)(2)(4)(4) = 1024; about every 1024 bp c) Sty I cuts between the two C’s on each strand. The enzyme Nco I cuts at the sequence 5'-CCATGG-3', between the two C’s on each strand. What fraction of sites cut with Sty I will give ends that can be ligated to DNA cut with Nco I? Will the product contain a site for Sty I? For Nco I? The middle two bases for Sty I can be AA, AT, TA, or TT. Only the 5’-CCATGG-3’ will have the proper overhang to ligate to Nco I sites. This resulting ligated product will be recognized by Sty I and Nco I. Sty I can cut any Nco I site, but Nco I can cut only one in four Sty I sites. d) The enzyme Ocn I cuts the sequence 3'-CCATGG-5' (note that this is written 3’ to 5’) between the two C’s on each strand. Can DNA cut with Ocn I be ligated to DNA cut with Nco I? Explain.
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This note was uploaded on 04/02/2008 for the course BIOL 202 taught by Professor Kieber-hogan during the Spring '08 term at UNC.

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Lieb_Prob_Set_8-Key - Biology 202-Lieb Problem Set 8-Key...

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