Lab5_09_ - Author: Jack Reifert Page: 1 Happy Halloween...

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Author: Jack Reifert Page: 1 Week: 5 (Oct 26-30) Happy Halloween This Saturday! Laboratory #5 Quiz #2 next week in lab! Review labs 1-5. Lab #5 introduces another model organisms used for researching aspects of life. Echinoderms are a model organism primarily used to study fertilization and early development. First, however, we will start off by analyzing our restriction digest results from last lab. Remember we ran an agarose gel to visualize the DNA we cut up with restriction enzymes. A photo of the results was taken, and now we get to analyze the photo, Part I ) Review results from last weeks Restriction Digest: (Page 56-57 in Lab Book) - Main Point: Investigate DNA strand mobility through an agarose gel and how this is used as a tool. - Which strands will run the fastest (farthest) through the gel? Which will run the slowest (shortest) distance? - Understand cut probability of different restriction enzymes. - Hind III : recognizes 6 base pairs in DNA. 4 base pair options (A, T, G, C) - Gives 4 6 probability = 4096 So there is a 1:4096 chance a DNA strand will have that exact sequence for Hind III to cut. - Knowing lambda phage DNA is about 48,000 base pairs long, how many times would you predict Hind III to cut DNA? (48,000 / 4096) = 12 - Msp I : recognizes 4 base pairs in DNA. - Same calculation gives what probability? How many times would you expect Msp I to cut Lambda DNA? - Run the same calculations to determine the number of cuts on human genomic DNA @ about 3 billion base pairs. - What factors determine DNA mobility through the Agarose gel? - What does the agarose % do? - What does the voltage do? - What does length of the DNA electrophoresis run do? - Understand the resolution of different sized DNA strands on the gel? How could we separate DNA strands of smaller size? How about separating larger fragments of DNA?
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This note was uploaded on 10/16/2010 for the course MCDB MCDB 1A taught by Professor Senghuilow during the Spring '09 term at UCSB.

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Lab5_09_ - Author: Jack Reifert Page: 1 Happy Halloween...

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