Name: ________________________________ 1 The Genetic Code 2nd base in codon U C A G U UUU phe UUC phe UUA leu UUG leu UCU ser UCC ser UCA ser UCG ser UAU tyr UAC tyr UAA STOP UAG STOP UGU cys UGC cys UGA STOP UGG trp UC A G C CUU leu CUC leu CUA leu CUG leu CCU pro CCC pro CCA pro CCG pro CAU his CAC his CAA gln CAG gln CGU arg CGC arg CGA arg CGG arg UC A G A AUU ile AUC ile AUA ile AUG met ACU thr ACC thr ACA thr ACG thr AAU asn AAC asn AAA lys AAG lys AGU ser AGC ser AGA arg AGG arg U C A G G GUU val GUC val GUA val GUG val GCU ala GCC ala GCA ala GCG ala GAU asp GAC asp GAA glu GAG glu GGU gly GGC gly GGA gly GGG gly U C A G 1st base in codon 3rd base in codonName: ________________________________ 2 7.012 Exam Two -- 2006 Exam starts at 10:05 am and ends at 10:55 am. There are 9 pages including this cover page & the genetic code. Please write your name on each page. Only writing on the FRONT of every page will be graded. (You may use the backs, but only as scratch paper.) Question 1 24 pts________ Question 2 11 pts________ Question 3 24 pts________ Question 4 25 pts________ Question 5 16 pts________ TOTAL out of 100_______Name: ________________________________ 3 1. (24 pts) You are working with a piece of DNA of the sequence: 5’-TATTGAGCTCCCGGAT-3’ 3’-ATAACTCGAGGGCCTA-5’ (a, 5 pts) You cut the above piece of DNA with a restriction enzyme that recognizes the sequence 5’-GAGCTC-3’ and cuts on the 3’ side of the A within this sequence. Draw all products that result from this digestion. Make sure to draw the nucleotide sequence of both strands, and label all 5’ and 3’ ends. (b, 5 pts) Now you ligate the DNA you produced in part (a) to the sequence below, which you have also cut with the same restriction enzyme. Draw the shortest DNA product that could form from ligating a piece of DNA from part (a) to a piece of DNA from part (b). Make sure to draw the nucleotide sequence of both strands, and label all 5’ and 3’ ends. 5’-TAGAGCTCCGCAATG-3’ 3’-ATCTCGAGGCGTTAC-5’Name: ________________________________ 4 (c, 6 pts) Restriction enzymes have DNA binding domains. Name three other different types of proteins (that are not restriction enzymes) that have DNA binding domains. Which reaction is catalyzed by each of the enzymes listed below? Answer by stating which specific type of bond is affected (e.g. “covalent” is not specific enough), and whether each enzyme catalyzes the formation or the breaking of that type of bond. (d, 4 pts) the T. aquaticus “Taq” polymerase used in PCR (e, 4 pts) a restriction enzyme 2. (11 pts) Below is shown a picture of a replication bubble. (a, 3 pts) The primer 5’-CUU-3’ is being used to replicate this piece of DNA. Would that primer anneal to the upper strand of DNA in the picture or the lower strand? A T A T T G T C C T A T A A C A G G C A T T C A T T G A G T A T G A A C 3’ 5’ … … … …Name: ________________________________ 5 (b, 5 pts) Write what the product of DNA replication would be if the first five nucleotides had been added onto this primer by DNA polymerase. Label the 5’ and 3’ ends. Make sure to include the primer. (c, 3 pts) Would that strand that you have drawn in part (b) be a leading strand or a lagging strand? 3. (24 pts) You are studying a very short protein-encoding gene whose sequence is shown below. The region of sequence shown is from the transcriptional start site to the transcriptional stop site. The gene’s one small intron is shown for you in bold. 5’-CTACGTACTAGCTATTCCGATCTATACTCGATCTAGTCGCATTCCGATTCGATCGTAC-3’ 3’-GATGCATGATCGATAAGGCTAGATATGAGCTAGATCAGCGTAAGGCTAAGCTAGCATG-5’ (a, 4 pts) Which strand is used as a template in transcription, the upper strand or the lower strand? (b, 4 pts) How many nucleotides long would the final processed mRNA made from this gene be (not including the 5’ cap and the 3’ polyA tail)? (c, 4 pts) How many amino acids long would the protein product of this gene be? (d, 4 pts) What is the sequence of the anticodon of the tRNA that would bind to the third codon of this mRNA as it was being translated? Make sure to label the 5’ and 3’ ends of the anticodon sequence.Name: ________________________________ 6 (e, 4 pts) What is the amino acid that would be on the C-terminus end of the protein produced from this gene? (f, 4 pts) Say that the C:G basepair that is underlined in the sequence above were changed to an A:T basepair to make a mutant form of this gene. Which kind of mutation would this be? Your choices are: a frameshift mutation, a nonsense mutation, a silent mutation, or a missense mutation. 4. (25 pts) You are interested in how a specific protein-encoding mouse gene named Hrt1 is regulated. Full activity of the Hrt1 gene product is present in heart cells, but no activity of this gene product is present in liver cells. You hypothesize that the Hrt1 gene product is regulated in one of the following ways (which are listed in no particular order): -- 1) whether the mRNA is translated or not -- 2) whether the protein product is stable or immediately completely degraded -- 3) whether the gene is transcribed or not -- 4) whether the protein product is phosphorylated or not -- 5) whether the pre-mRNA is spliced to include all 5 exons or only 4 of those exons You prepare four samples from cells: all of the mature mRNAs in heart cells, all of the mature mRNAs in liver cells, all of the proteins in heart cells, all of the proteins in liver cells. You load each sample into a separate lane in a gel, and separate the components by size via gel electrophoresis. You then detect presence/absence of any band corresponding to Hrt1 RNA or protein. (a, 5 pts) Towards which pole of the gel will the Hrt1 RNA run? Your choices are: positive, negative, neither, both, or inconclusive. Explain your answer.Name: ________________________________ 7 (b, 5 pts) Towards which pole of the gel will the Hrt1 protein run? Your choices are: positive, negative, neither, both, or inconclusive. Explain your answer. You perform the type of experiment described above, and detect any Hrt1 mRNA
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