2006 MT3 blank

2006 MT3 blank - Midterm 3 statistics 11:00 class Class...

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Unformatted text preview: Midterm 3 statistics: 11:00 class Class Average (out of 100 pts) Standard Deviation High Score Los Score 75.8 15.8 97 26 12:00 class 74.4 15.4 95 6 Midterm 3 pick-up and re-grade procedures: #1 Pick up your BISC 320 midterm 3 exam: Tuesday, Nov. 21 from noon -4 pm in ZHS 360A (BioSpace) Wednesday, Nov. 22 after your BISC 320 lecture in THH 101 Monday, Nov. 27 from 1-3 pm in ZHS 360A (BioSpace) You may not pick up anyone else's exam. Please bring your ID card with you when picking up your exam. #2 Deadline for submitting re-grade: Re-grade is not your opportunity to haggle for points! If you feel a factual or arithmetic error was made in the grading of an examination, not on judgments about how many points an answer was awarded. you submit a written re-grade request along with your exam to your TAs. Regardless of when you pick up your exam, the deadline to submit your re-grade request is 5:00 pm, Thursday, Nov. 30. This deadline is firm. Grading TAs need to complete all re-grade before the final exam week. #3 Pick up your re-grade: Monday, Dec 4 from 10 am to 2 pm in ZHS 357 Online gradebook will be updated before Monday Dec 4. #4 Still have issues after re-grade: Please see Dr. Baker during his office hours on Monday Dec. 4 from 2 to 3:45 pm. Re-grade for midterm 3 ends at 5:00 pm on Monday, Dec 4. Last Name: _____________________________First Name: ______________________ Lab (day and time): _____________________________ TAs: ___________________________ Please write your last and first name on every page (total of 5 pages). Points will be deducted if you fail to write your last and first name on every page. Answers written in pencil will NOT be eligible for re-grade. BISC 320 Midterm 3 (100 pts) Nov. 15, 2006 1. (10 pts) How are LTRs involved in transposition of an integrated retrotransposon? Answer: Transcription of a retrotransposon starts within the left hand LTR and stops within the right hand LTR. Then, after conversion of the viral RNA strand into double stranded DNA, the LTR ends of this DNA allow integration, via an LTR-specific transposase (integrase), into a new chromosomal site. 2. (10 pts) (a) What kind of mammalian cells make immunoglobulins? (b) Briefly, how do V and J regions contribute to combinatorial diversity of antibodies in a mammal? (c) Where does transcription start in synthesizing immunoglobulin light chain pre-mRNA? Answer: (a) B lymphocytes. (b) Different lengths and/or positions of a deletion within a V and J chromosomal DNA region results in the attachment of a specific V to a specific J. (c) Transcription, starting at the specific V (PLIV, where P is the transcription promoter sequence), now attached to the specific J, codes for a specific kind of light chain (including the downstream C region). 1 Last Name: _____________________________First Name: ______________________ 3. (10 pts) How do aminoacyl synthetase enzymes ("charging" enzymes) contribute to the accurate synthesis of polypeptide chains, each having the correct sequence of amino? Answer: These enzymes attach the correct kind of amino acid to the proper kind of tRNA. 4. (10 pts) (a) If a frameshift mutation occurs at a certain point within a gene, would you expect the transcribed mRNA to be translated in a reading frame that now includes a nonsense codon prior to the position of the original (non-frameshifted) stop codon? (b) If the nonsense codon acts as a translation stop codon, actually stopping translation, would you expect the translated protein to be the same length as the protein coded for by the non-mutated version of the gene? (c) Downstream from the mutation point, would the amino acid sequence in the translated protein be the same as the amino acid sequence translated from the non-mutated version of the gene? (To receive credit for your yes or no answers to these three questions, you must disclose your reasoning.) Answer: (a) Yes, a ribosome reading in a frame that is not the normal long open reading frame will likely soon encounter a nonsense codon. In the shifted frame, while the codons encountered are certainly not random, the translated codons would be biased toward the inclusion of nonsense codons not found in the long open reading frame. That is, on a completely random basis, statistically there would be approximately three nonsense codons in every 64 codons encountered. (b) No, since three out of every 64 codons are stop codons, the shifted reading frame would be shorter because a stop codon would, statistically, be encountered sooner by a traveling ribosome compared with a ribosome translating in the normal long open reading frame). A correct reading frame has a specific length. All out of frame transcripts when translated would produce proteins with different lengths. (c) No, downstream from the frameshift mutation, the translated codons would be different even though the RNA sequence would be the same. A frame shift mutation will alter the reading frame and the amino acid sequence downstream from the mutation would be different from the WT 2 Last Name: _____________________________First Name: ______________________ 5. (10 pts) How does glucose, via the CAP protein, control transcription of the lactose and arabinose operons in E. coli? Answer: Transcription from the operon's promoter DNA sequence requires that CAP be bound to the CAP binding DNA sequence. In order to bind, CAP itself must be bound to cAMP. Glucose reduces the concentration of cAMP and, thus, prevents mRNA transcription. Glu inc. cAMP production (2) . cAMP binds CAP and the complex binds to CAP binding site (2) Increase transcription (Opposite order -5) or not mentioning CAP protein (-5) 6. (10 pts) (a) How (and under what circumstance) does attenuation occur during transcription of the tryptophan operon in E. coli? (b) How (by what mechanism) do codons for tryptophan, in the first attenuation region of the tryptophan operon, influence the length of the operon's transcribed RNA? Answer: (a) When the concentration of tryptophan is high, a 3-4 "tennis racket" forms, causing transcription termination prior to transcription of the block of operon's genes. (The attenuated RNA transcript is 139 bases in length, rather than being longer than 6000 bases.) a) incr. [TRP] attenuations occur by... (Both incr. and decr. [TRP] attenuations occur -3) (b) Unless there is sufficient tryptophan available, there will not be sufficient tryptophancharged tRNAs to prevent stalling of ribosomes within the first region of the attenuation region. This cover-up in first attenuation region allows the formation of a 2-3 racket-- preventing formation of a 3-4 racket. b) Mechanism: inc TRP Inc. charged tRNA+ TRP availability ( -2 for not mentioning tRNA) under this condition ribosome rapidly cover region 1 and 2 thus, formation of 34 region stem loop STOP... if dec. [TRP] ribosome cover 1 and 2-3 stem loop. (Opposite -5) 3 Last Name: _____________________________First Name: ______________________ 7. (10 points) How is a specific repressor protein implicated in maintaining lysogeny of lambda prophage (integrated viral DNA)? Answer: CI repressor protein binds to OR2 and OR1, repressing the Pr and Pl promoters, allowing Prm to be active. CI protein continues to be synthesized. This prevents transcription of the viral genes that allow excision of the prophage, production of lambda phage, and lysis of the bacterial cell. 8. (10 points) During RNA splicing, how does the branch point in a pre-mRNA intron participate in forming a lariat structure? (What are the proteins, RNPs, splice site(s), etc. involved in forming a lariat?) Answer: An SR protein binds to an ESE (or ISE) sequence, U1snRNp binds to the 5' splice site, BPB protein and U2snRNP bind to the branch point, then the 5' end of the intron connects via a 5'-2' connection to the A in the branch point. 4 Last Name: _____________________________First Name: ______________________ 9. How is transcription of eukaryotic pre-mRNA terminated? Answer: CPSF binds to the AAUAAA sequence on the pre-mRNA strand. 10 to 15 bases downstream from the AAUAAA, in a G or G/U rich region, CstF binds and cleaves the premRNA strand loose by cutting in this region. 10. (a) How does a eukaryotic 43S ribosome complex form and (b) how does this complex participate in initiating protein synthesis? (It is not necessary to name the actual protein translation factors in describing these two processes.) Answer: (a) After a 40S subunit attaches at a CAP site, the 40S subunit picks up a number of translation initiating factors, becomes a 43S complex. (b) The 43S complex scans the mRNA as it travels to find the correct AUG codon. (There, the 60S ribosome subunit attaches, producing the 80S eukaryotic ribosome.) 5 ...
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