midterm_3_key

midterm_3_key - / . Last Name: Flrst Name: i a. W 8”...

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Unformatted text preview: / . Last Name: Flrst Name: i a. W 8” \‘-_ 1/ (; 7A” Lab (day and time): TAs: Midterm Total: BISC 320 - Midterm 3 (100 pts) P : Nov 9, Fall 2005 “£9 Total (10 pts) 1. How do the proteins, known as conservative site-specific tyrosine recombinases, cause recombination in vivo between two double stranded DNA sequences? __\\ Answer: Recombinases first cause nic .. in one strand of eachiof the two duplex DNAs that are in register with each other. A Holliday structur i en forms between the two duplexes. Rotation of the Holliday structure, followed by strand cleavage and ligation, causes two independent, recombinant, duplexes to be formed. ._ 2. L“ P bill/"Lt ,1, ILLIL re, _ Fm Hg IVA. ............... _('®LAK_V'C\E"j/Cx {Z— i 49361 LLK RX Mama/mm" (Mb/VA were a (10 pts) 2. When a transposon “jumps” to a new site (target) and integrates there, why does the target sequence, as direct repeats, often appear at each end of the now integrated transposon‘? _ . .r 3*- Q m} Lt she: J] _ -.-———-— r__|——-"-'- __._—-. Answer: A transposase (or, an integrase) lands at a target site on duplex DNA and creates staggered nicks, one on each DNA strand at this site. The incoming, square- ended duplex DNA transposon inserts itself, leaving single stranded gaps at each end. The gaps are filled by DNA repair and ligation, creating direct repeats at each end of the transposen. Fansjfasaéé /}/i/;(j;/g;.g,( “Hedi—aw __‘__'_._______.-—-'-_-_" ("oi/Vi ' ‘”""‘”;:i:t, ______ __,;,; , g i C /‘ 1- - I ' . (at! “’I‘I U, . (.1 ."7 and £3 Page Total: (10 pts) 3. (a) When they “jump,” why do poly A—type transposons (and also retroviral transposons) always leave a copy of the transposon behind at the original (integrated) position? (b) Do some bacterial transposons utilize an RNA intermediate in “jumping” from an original position to a new target site? (Please explain your ‘yes’ or ‘no’ answer.) Answer: (a) The RNA intermediate in the jump is a transcript of the integrated double stranded DNA-version of the transposon (which stays where it is integrated and is not excised). (b) No. Bacterial cells do not contain reverse transcriptase and cannot convert RNA strands into double stranded DNA. {eve-r: twinge-w r ate-try? 521. 5 l” V flu or, '__.J 00% = . . “fl? l9- ? J , C. ill/VA Ila/f. :46er “3' (ft? «1/97? (b l N ‘ Rec-«gem. 5c f _ I]: I) (10 pts) 4. In creating new genes that code for immunoglobulin (antibody) light olypeptide chains, how are the proteins RAG] and RAGZ utilized in combining a particular V region with a particular I region in chromosomal DNA? Answer: Intervening V regions and J regions are deleted to allow an upstream V to be attached to a downstream J. RAGl and 2 cause the deletion by attaching to an upstream R1 sequence and a downstream R2 sequence and then delete the DNA in between, including the R1 and R2 sequences. Each V region has an R1 sequence (Vfl and each J region has an R2 sequence (R_2J). R1 '5’? 7 \a-F 2. l ,4 .. DB-lE‘fQ- fit a. [CW/3t zit/L when " i t Page Total: (10 pts) 5. Why is the carboxyl terminal domain (CTD tail) of the large subunit of eukaryotic RNA pol II able to load specifically the capping and splicing factors on to a nascent, growing pre-mRNA strand? Answer: After phosphorylation of specific serines in the CTD tail, the tail picks up the correct factors and then loads them onto the pre-mRNA strand. [For full credit, it is not necessary to have mentioned phosphorylation of the #2 serines (allows loading of splicing factOrs) or the #5 serines (allows loading of capping factors) in the repeating heptapeptide in the CTD tail.] grading standard: phOSphon/tation (5 points). serines in the CTD tail(5 points). If students mention #2 and #5 serines, but confused about the serines and factors, #2 for capping and #5 for splicing. then reduce 1 point. (10 pts) 6. How do most cukaryotic premeNA strands come to have a poly A tail at their 3‘ ends? Answer: Immediately after the sequence AAUAAA has been transcribed into a pre- mRNA strand, the protein CPSF binds to this sequence. Then, 10 to 30 bases further downstream at a G or GIU rich region, the protein CstF binds and the strand is cleaved close by. The terminal 3’ OH is then extended by poly A polymerase and poly A binding polymerase II. grading standard: CPSF (1 point), AAUAAA (1point). CstF(‘i point). G or GfU rich region (1point). PAP add less than 10As (2points), PABIip add 50-200 As (2 points). / (10 pts) 7. How do SR proteins initiate spliceosomal splicing within pre—mRNA strands? (It is not necessary to describe the entire assembly of new spliceosomes—just how they start to be made.) C, a? - / h} Answer: On a pre-mRNA strandiMllmfligfiE sequences Within exonsfand Page Total: _,_._— causerUifiRNPs‘jp become attached to nearby 5’ splice sites. \g u ‘i (10 pts) 8. Why is it necessary that cells carry many species of aminoacy] synthetase (tRNA “charging” enzymem-the enzymes that attach an amino acid to a tRNA)? Answer: Different species of tRNAs have different anticodnns. A specific kind of amino acid must be attached (via the enzyme) to the proper specie of {RNA with proper kind of anticodon. That is, a particular codon on an mRNA must be able to bind the anticodon on a tRNA that is carrying the correct amino acid. Page Total: ‘(10 pts) 9. What effect does deamination of the cytosine in a CAA codon in an mRNA strand have on synthesis of protein when the strand is translated by ribosomes? (Assume that prior to deamjnation, the CAA would have been translated in the correct translational reading frame.) a)“ %" Answer: Deamination converts CAA to UAA, which is a translation stop codon. Thus, . W . . synthesrs of,t.l_1©__translated protein chaln would be terminated at the UAA stop codon, res ultrng is ashortened chain.“ "7 (10 pts) 10. During initiation of translation of eukaryotic mRNAs, how does the protein factor eIF4F cause circularization of the mRNA strand? Answer: eIF4F binds to the 5’ CAP and the 3’ poly A tail of the mRNA strand, allowing the strand to be held in a circular form. owl 91 p4 F E ...
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This note was uploaded on 09/17/2009 for the course BISC 320L taught by Professor Baker,aparicio during the Fall '07 term at USC.

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midterm_3_key - / . Last Name: Flrst Name: i a. W 8”...

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