Worksheet+4+MCB110 2

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University of California, Berkeley *

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110

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Biology

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Apr 24, 2024

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pdf

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4

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MCB110 Discussion Week 5 Worksheet GEL ELECTROPHORESIS 1. You ran a DNA gel; however, you forgot whether or not the gel was denaturing or not. The samples you ran are described below. Lane 1: Ladder Lane 2: Plasmid DNA isolated from E. coli Lane 3: Linear ssDNA annealed to a shorter linear ssDNA strand Lane 4: Linear dsDNA, both strands of equal length Lane 5: A 100 bp linear ssDNA Lane 6: A 100 bp linear ssDNA bound by SSBs a. Which of the samples will allow you to differentiate between the gel being native or denaturing? b. Based on the gel to the right, did you run a native or denaturing gel? How did you tell? 2. You run the following gel and stain the gel with ethidium bromide after running. Your samples contain plasmid DNA, a buffer with various cofactors, and an unknown enzyme. You incubated your samples for differing amounts of time and ran them on an agarose gel (Gel 1). a. Based on the banding pattern, what is most likely to be this unknown enzyme? b. You go to repeat the experiment, but you realize that you have run out of the buffer you used before! In a pinch, you instead use another unlabeled buffer given to you by a lab member. Why does this gel (Gel 2) look different?
MCB110 Discussion Week 5 Worksheet 3. You are studying the mismatch repair pathway in vitro (in a test tube). In all of your samples, you have a linear, hemi-methylated piece of dsDNA which has a mismatch at a known site (mismatch noted with an arrow and dashed line; methylated strand in gray). Only the unmethylated strand (in black) is internally-labeled with radioactivity. Samples: Lane 1: Ladder Lane 2: DNA only Lane 3: DNA + MutS Lane 4: DNA + MutS + MutH Lane 5: DNA + MutS + MutH + MutL Lane 6: MutS + MutH + MutL a. Draw the pattern you would expect to see below if these samples were run on an alkaline agarose gel. Note, you give enough time for each enzyme to act on all substrates. b. Describe how the gel would appear if you instead internally labeled the methylated strand. c. How would the gel appear if you instead end-labeled the unmethylated strand? d. Why is it beneficial to use a denaturing gel, rather than a native gel in this case?
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