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MIT 7 012 - Quiz 2

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17.012 Practice Quiz 2 2004Actual Quiz 2 (closed book) will be given Monday 10/25 at 10:00 amNo Sections on MONDAY or TUESDAY 10/25-10/26 (No Kidding.)NOTE THE ROOM MAY BE DIFFERENT THAN THE ROOM YOUR WERE ASSIGNED FOR QUIZ 1Quiz Review Session Thursday, 10/21 7:00 - 9:00 pm Tutoring SessionFriday, 10/22 4:00 - 6:00 pmMIT Biology Department7.012: Introductory Biology - Fall 2004Instructors: Professor Eric Lander, Professor Robert A. Weinberg, Dr. Claudette Gardel2Question 1a) Indicate whether each of the following statements is true or false. If false, correct thestatement or provide a brief explanation for why it is false.i) DNA replication is initiated at promoter sequences in the DNA.ii) RNA polymerase requires primers to initiate RNA synthesis.iii) Okazaki fragments are the short fragments of DNA that are produced on the leading strand atthe DNA replication fork.iv) The 5' to 3' direction of DNA synthesis implies that deoxyribonucleotides are added to the 5' OHgroup on the growing strand.v) Transcription is terminated at stop codons in the mRNA.b) Shown below is the DNA sequence of a gene from a virus that encodes a short viral peptide. Alsoshown is the sequence of the mRNA synthesized from this gene.genomic DNA sequence:5'-AGCTCATGTGCGAGTCCTGACGCTGACTAGG-3'3'-TCGAGTACACGCTCAGGACTGCGACTGATCC-5'mature mRNA sequence (G* = G cap):5'-G*UCAUGUGCGAACGCUGACUAGGAAAAAAAA....-3'i) In the genomic DNA sequence shown above, draw a box around each of the two exons in thegene.ii) In the mRNA above, some nucleotides are present that are not coded for in the genomic DNAsequence. Name the two processes that have occurred to add these nucleotides to the mRNA.iii) How many amino acids are in the viral peptide encoded by this gene? _______iv) Is this virus more likely to replicate in prokaryotic or eukaryotic cells? Briefly explain yourreasoning.3 U C A GUUUU phe (F)UUC phe (F)UUA leu (L)UUG leu (L)UCU ser (S)UCC ser (S)UCA ser (S)UCG ser (S)UAU tyr (Y)UAC tyr (Y)UAA STOPUAG STOPUGU cys (C)UGC cys (C)UGA STOPUGG trp (W)UCAGCCUU leu (L)CUC leu (L)CUA leu (L)CUG leu (L)CCU pro (P)CCC pro (P)CCA pro (P)CCG pro (P)CAU his (H)CAC his (H)CAA gln (Q)CAG gln (Q)CGU arg (R)CGC arg (R)CGA arg (R)CGG arg (R)UCAGAAUU ile (I)AUC ile (I)AUA ile (I)AUG met (M)ACU thr (T)ACC thr (T)ACA thr (T)ACG thr (T)AAU asn (N)AAC asn (N)AAA lys (K)AAG lys (K)AGU ser (S)AGC ser (S)AGA arg (R)AGG arg (R)UCAGGGUU val (V)GUC val (V)GUA val (V)GUG val (V)GCU ala (A)GCC ala (A)GCA ala (A)GCG ala (A)GAU asp (D)GAC asp (D)GAA glu (E)GAG glu (E)GGU gly (G)GGC gly (G)GGA gly (G)GGG gly (G)UCAGQuestion 2The term "central dogma" refers to the flow of biological information from DNA to RNA to protein.DNA RNAProtein123a) i) In the spaces below, indicate the process that corresponds to each arrow.1. ___________ 2. ___________ 3. ___________ii) Name the initiation site for each processes, and on which molecule this site exists.1. ________________2. ____________________3. ________________iii) What cellular machinery carries out each process?1. ___________ 2. ___________ 3. ___________b) What is a gene? Please answer in one sentence. The first sentence written will be considered asyour answer.c) Many antibiotics are compounds that interfere with the transfer of genetic information from RNAto protein. Streptomycin is a compound that affects the small ribosomal subunit in prokaryotes.Streptomycin interferes with the binding of all Methionine-tRNAs to ribosomes. What two specificeffects will streptomycin have on protein synthesis in prokaryotes?4Question 3A.The primer shown below is used to sequence the following template DNA.primer: template DNA:5'-ACTGAC-3' 5'-ACCACTAACGTCAGT-3'Draw the resulting DNA fragments that would be produced from each of the 4 sequencing reactions atthe correct position (length in nucleotides) as they would appear on the diagram of the sequencing gelbelow.G A T C+DNA length (nts)15-14-13-12-11-10- 9- 8- 7- 6- 5- 4- 3- 2- 1-B.Polio has been practically eliminated from the American population, however, in countries where peoplehave little or no access to vaccinations, it is still prevalent. As a biologist with a global vision, youseek to create a transgenic banana that produces the protein used in the vaccine against polio. Byconsuming these bananas, individuals will develop immunity against the disease. The gene for thisprotein has already been cloned into a plasmid with a kanamycin-resistance gene (pKR-polio). You needto attach to the gene a banana-specific promoter and DNA sequences that will allow the gene to beincorporated into banana DNA. These sequences are contained in the pBAN plasmid, which carries agene for ampicillin resistance. Maps of these two plasmids are shown on the next page, includingimportant restriction sites and distances (in base pairs) between the sites.5Question 3 continuedoriamp geneRBanana specificpromoterbanana insertion sequenceswhich allow DNA to integrate into banana genomeBamHIEcoRIpBAN8900 bp120pKR-polio4500 bporikan geneRBglIIBglIIBamHIstart codonstop codongene for polio antigenEcoRI2801120BglII:!!!!!! BamHI:!! EcoRI:5'...A G A T C T...3'!!! 5'...G G A T C C...3' 5'...G A A T T C...3'3'...T C T A G A...5'!!! 3'...C C T A G G...5' 3'...C T T A A G...5'a) An end generated by digestion with BamHI can be ligated to an end generated by digestion withBglII. Why is this possible?b) You want to insert the gene encoding the polio antigen into pBAN. Devise a strategy to accomplishthis. Identify the enzyme(s) you would use to cut pBAN, the enzyme(s) you would use to cut pKR-polio, and the steps necessary to generate the intact plasmid.c) You next transform E. coli with the plasmids you have made. You grow the transformed cells onmedia containing (circle one):ampicillin kanamycinboth ampicillin and kanamycin neither ampicillin nor kanamycinWhy?6Question 3 continuedYou isolate plasmid DNA from three colonies that pass your antibiotic resistance test. You digest theDNA with the restriction enzyme EcoRI. You size separate the resulting fragments from each plasmidon an agarose gel. You find the following results. DNA fragment sizes are indicated to the left.10 kb9 kb.4 kb1.2 kb1 23d) i) Draw plasmids associated with the colonies 1, 2,


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MIT 7 012 - Quiz 2

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