MCB121 MT1 Winter 2010

MCB121 MT1 Winter 2010 - Name_ ID #_KEY_ FIRST MIDTERM...

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Name_______________________________ MCB121 Spring 2010 Page of 9 ID #______KEY__________________________ FIRST MIDTERM January 26, 2010 Question Points Score 1 12 2 16 3 20 4 25 5 15 6 12 7 12 8 20 9 12 10 6 Total 150 This examination is closed book. There are 9 pages to the exam. Please count them before you start to make sure all are present . Please write your name on each page of the exam . Answer each question in the space provided. If additional space is required use the back of the page and indicate clearly that you continued your answer on the back. Do not attach additional pages. GOOD LUCK AND HAVE FUN! 1
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Name_______________________________ MCB121 Spring 2010 Page of 9 1. (12 points) Origins of replication can be analyzed using 2-D gel electrophoresis where the first dimension separates fragments by shape and size and the second dimension separates fragments by size only. The output of this analysis is shown below. Panels b and c show migration patterns for Y-arc and bubble-arc forms, respectively. Panel d shows the migration pattern of these fragments when the origin of replication is asymmetrically positioned with respect to the restriction sites used that flank the origin of replication. For each panel, label the region of the gel that corresponds to each fragment shown above it. 2. (16 points ) Draw all the nucleic acids of a bidirectional replication fork. A. Identify and label all newly synthesized strands by name. (4) B. Show DNA segments using straight lines and the location of RNA using zig-zag lines. (2) C. Indicate all relevant 5’ and 3’ ends (6) D. Indicate direction of fork movement using arrows. (2) E. Mark the region where the origin of replication would be (2) 2
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Name_______________________________ MCB121 Spring 2010 Page of 9 3. ( 20 points ) Gillyweed is a magical plant that when eaten gives a person gills to breathe underwater and webbed hands and feet for swimming. Harry Potter used it for the underwater event at the tri-wizard tournament. Professor Sprout has assigned her herbology class to determine the genome sequence of this plant. a. (8) Briefly outline a general strategy (in 4 or 5 steps) that you would use to create a draft sequence (about 4X coverage) of the Gillyweed genome without using any magic. There are several ways you could approach this problem. Method 1-mapping -Isolate DNA from cells and cut with restriction enzymes to create large fragments (100 kb) - Assign sequences in BACS to chromosome location using RFLPs -sequence subcloned regions of BACs -align overlapping sequences to form contigs -Build contigs to form a scaffold de novo or by using Arabidopsis genome sequence Method 2-shot gun -isolate gillyweed DNA from cells -shear into small fragments (few hundred basepairs) -add primers for illumina or other NGS -align overlapping regions into contigs -use scaffold from another plant such as Arabidopsis to build sequence for 4x coverage every base will be sequenced 4 times. Miminally you need to 1: isolate DNA from Gillyweed, 2. shear or use restriction enzymes
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MCB121 MT1 Winter 2010 - Name_ ID #_KEY_ FIRST MIDTERM...

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