Week_6_2009_Berk_Sharp_ANSWERS

Week_6_2009_Berk_Sharp_ANSWERS - Group size 4~5 people,...

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• Group size 4~5 people, please • The key to quiz #1 is posted on the course website. I will hand the quiz back to you during class. • Deadline for regrading: Please submit a written note explaining the question(s) you have for regrading, and hand them to Kristina after the class on May 13 th , Wednesday
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Week 6 Make-Up Assignment Write a 1-2 page summary of the Berk and Sharp paper. In your summary, explain the “paradoxical observations” that prompted Berk and Sharp to do the work described in the paper as well as the strategy used. Finally, write a concise but complete explanation of the data and state the conclusions made from the data.
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Highlights : 1. Must read the paper prior to the discussion section. 2. Must attend the section you are enrolled in ( will take points off if not informed ahead of time to attend a different section). 3. You only have ONE opportunity to complete a make-up paper, from Week 1 to Week 9 (Week 10 is for quiz#2). 4. Meeting outside of discussion and office hours by appointment only to ensure no time conflict (li@lifesci.ucsb.edu)
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Spliced early mRNAs of simian virus 40 Arnold Berk and Phillip Sharp PNAS 75: 1274-78 (1978) MCDB 134: Week 6 Discussion li@lifesci.ucsb.edu
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Background: SV40 Family: Papovaviridae Virion: small (~45 nm), icosahedral, naked Genome: –closed circular dsDNA, ~5.2 kb ½ is expressed early in infection as two proteins: •large T antigen (T) •small T antigen (t)
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SV40 Genome Depicted in 2 different orientations 1) 12:00 noon = 0/100, an EcoRI site. All other sites are assigned a fraction number (0-1.0 or 0-100). This orientation is what we’ll use today. 2) 12:00 noon = 0/5243, the origin of replication. All other sites are assigned a base pair number (0- 5243). This orientation is what was seen on SV40 map on the class handout from this week. Early Late Early genes: •Expressed before DNA replication •Large and small T antigen Late genes: •Expressed after DNA replication •Structural proteins
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EcoRI (100/0) Rationale for this Paper Some paradoxical observations: – Nearly the entire early region of the SV40 genome (2500-2600 bp) would be needed to encode for a protein the size of large T antigen. – However, deletions in the area mapping to 0.59-0.54 do not alter the production of large T. (These deletions do alter the production of small T.) – Moreover, a transcript encoded by the early region would contain two termination codons in all three reading frames near position 54. 54 59 = stop codons
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1 1’ 2 5’a 5’b 5’a UAG T Ag Pre-mRNA 1 1’ 2 UAG Small T Ag mRNA 1 2 Large T Ag mRNA Large T Ag protein Small T Ag protein 5’b 3’ Large and Small T Antigen Arise From Alternative Splicing
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Answer: Question #1 Nearly all of the early region is needed to encode large T, but deletions in the region 0.54-0.59 (or 54- 59) of the SV40 genome do not affect expression of large T because this region is spliced out of the mRNA for Large T. These deletions do affect small T
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This note was uploaded on 06/08/2010 for the course MCDB 134 taught by Professor Samuels during the Spring '10 term at UCSB.

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Week_6_2009_Berk_Sharp_ANSWERS - Group size 4~5 people,...

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