MIT Biology Department 7.012: Introductory Biology - Fall 2004 Instructors: Professor Eric Lander, Professor Robert A. Weinberg, Dr. Claudette Gardel Name:___________________________________ Section:_____ 7.012 Problem Set 4 Please print out this problem set and record your answers on the printed copy. Answers to this problem set are to be turned in at the box outside by 4:10 Wednesday, October 8. Problem sets will not be accepted late. Solutions will be posted on the web October 9, 2003. Question 1 Below is an electron micrograph of a single gene being transcribed. The DNA strand runshorizontally with RNA transcripts extending vertically outward. Image removed due to copyright reasons. a) Draw an arrow indicating the direction that the RNA polymerases are transcribing. Whydid you choose this direction? b) Below is a partial sequence of the above gene. Its orientation is the same as pictured above.Which strand is the template strand, the top or the bottom strand? Explain your choice. 5’ACTCGATGCTAG3’ 3’TGAGCTACGATC5’ c) What would be the mRNA sequence transcribed from the above sequence? Be sure to labelthe 5’ and 3’ ends. 7.012 Fall 2003 1_____________________ _____________________ _____________________ Name:___________________________________ Section:_____ Question 2 A tRNA molecule (shown below) is composed of an RNA chain that folds into a 3-D shape likethat shown below. At one end it has an anti-codon that base pairs with the appropriate codonon the mRNA and at the other end it has an amino acid arm that binds to a specific amino acid.Below are three anti-codon sequences for three tRNAs, fill in the corresponding amino acid onthe blanks. Amino acid arm Anticodon Amino acid armAnticodonAmino acid armAnticodonAmino acid armAnticodonFigure by MIT OCW. anticodon found on tRNA amino acid attached to tRNA 5’ AGU 3’ 5’ AUG 3’ 5’ CUG 3’ b) You are studying a certain enzyme. You have two mutant versions, one that works just aswell as the wild-type and another that doesn’t work at all. When you sequence the genes thatcode for these two mutant enzymes you find the enzyme that works has a 9 base pair deletion,whereas the enzyme that does not work has only a single base pair deletion. Explain why thesequence with the 9 base pair deletion results in an active enzyme when the sequence with asingle base pair deletion produces an inactive enzyme. c)The first 17 nucleotides from an mRNA molecule are 5’ GAAUGGCCACUUAGCAA…3’ Write out the first 5 amino acids encoded by this sequence. 7.012 Fall 2003 2Name:___________________________________ Section:_____ Question 3 a) How does the structure of the lac operon ensure that the lac genes are coordinatelycontrolled? Why would this be beneficial? b) Describe the regulation of the lac operon (inducible, uniducible, or constitutive) in the caseof each of the following mutants. In all cases the concentration glucose is low. Explain yourchoice. i) A mutation in the lac repressor such that it can’t bind DNA ii) A mutation that makes lac permease nonfunctional iii) A mutant promoter that has a high affinity for polymerase iv) A mutant lac repressor that doesn’t bind lactose c) You have a cell where the expression of the lac operon is constitutive due to a mutation inthe operator. If you add to that cell a completely wild-type version of the lac operon would normal regulation be restored? Explain. 7.012 Fall 2003 3Name:___________________________________ Section:_____ Question 4 Lambda phage is a virus that infects E. coli bacteria. After infecting the bacteria it can take oneof two paths, lysis or lysogeny. In the lysis path, the phage makes many copies of itself, breaks out of the cell and infects new cells. In lysogeny, the phage incorporates its DNA into thebacterial DNA and lays dormant in the cell. The presence of a protein called lambda repressorinfluences which path is taken by inhibiting lysis. When lambda repressor is present it turnsoff or represses the genes that allow the virus to reproduce, thus no phage progeny areproduced and no cell lysis occurs. a) In studying this protein you find that lambda repressor binds DNA at a site that overlapsthe promoter for the lysis genes. Propose a mechanism for repression based on thisinformation. b) Activators typically work by binding near a promoter site and recruiting RNA polymeraseto the promoter by forming non-covalent bonds with it. This helps the polymerase attach tothe promoter and increases transcription from that promoter. Although Lambda repressor turns off the transcription of the lysis genes, it stimulates the expression of its own lambda repressor gene (acts as an activator). In studying lambdarepressor you find that there are two amino acids, Asp and Glu, which are essential to theactivator function. Based on this information what type of bonds do you expect Lambdarepressor to make with RNA polymerase and what type of amino acids do you expect to findon polymerase participating in these bonds? 7.012 Fall 2003
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