1Name_________________________________________ Section_________7.014 Problem Set 7Answers to this problem set are to be turned in at the box outside 68-120 by 4:00 pmWednesday, May 8. Problem sets will not be accepted late. Solutions will be posted on theweb. (http://web.mit.edu/7.01x/www/intro.htm).Question 1The plasmid vector pet83 contains an ampicillin resistance gene (Amp) and a kanamycinresistance gene (Kan). The plasmid is cut at the BamHI site shown below, and successfullyligated with a compatible human BamHI fragment. The recombinant plasmid is thentransformed into E. Coli. The transformation mixture is then spread on petri plates andallowed to grow.a) What type of E. Coli cells would you choose as the host strain for your transformation?b) What antibiotic would you include in the medium to ensure that only bacteria containingthe pet83 plasmid will grow?c) What two antibiotic resistance phenotypes will be found among the transformed bacteria?d) Of the antibiotic resistance phenotypes listed above, which will contain the human BamHIfragment?Spring 2002 7.0142Question 1, continuede) The human BamHI fragment that you cloned into pet83 encodes the enzyme helicase. Youdecide to clone the mouse version of the helicase gene.i) Briefly explain how you would make a mouse genomic library in E. Coli.ii) Once you have the mouse genomic library in E. Coli, how would you find the cellsthat contain the mouse helicase gene?f) The restriction endonuclease sites for several enzymes are given below.BamHI: BglII: EcoRI t5'...G G A T C C...3'3'...C C T A G G...5' s t5'...A G A T C T...3'3'...T C T A G A...5' s t5'...G A A T T C...3'3'...C T T A A G...5' sPvuII PvuI EcoRV t5'...C A G C T G...3'3'...G T C G A C...5' s t5'...C G A T C G...3'3'...G C T A G C...5' s t5'...G A T A T C...3'3'...C T A T A G...5' si) DNA that has been cut with PvuII can be ligated to DNA that has been cut withEcoRV. Indicate what would be the DNA sequence of the ligated DNA by filling in theblanks below.5'...C A G _ _ _...3'3'...G T C _ _ _...5'Spring 2002 7.0143Question 1, continuedii) DNA fragments can be ligated together because the ends have compatible overhangs.• Which two enzymes on the previous page create compatible ends?• If a DNA fragment cut with one of these enzymes was ligated to DNA cut with theother, what would be the DNA sequence of the ligated DNA? Label 5' and 3' ends.• Can this new DNA be cut with either of the enzymes originally used?g) You successfully clone a DNA fragment (2.1 kb in length) carrying the mouse helicase geneinto a unique EcoRI restriction site of the plasmid pQE1 (4.1 kb in length). You digest this newplasmid with the restriction enzymes EcoRI, BamHI, and PstI alone and in pairs. After runningout the digests on an agarose gel you get the following results. Lengths are in kb.Draw a restriction map of the plasmid; include the fragment lengths and the restriction sites.Label the vector and the insert.EcoRI BamHI PstIEcoRI & BamHIEcoRI & PstIBamHI& PstI5.54.11.01.0 1.00.7 0.73.72.5 2.52.40.60.60.50.23.91.1 1.11.52.6Spring 2002 7.0144Question 2a) Complete the following life table for the gray squirrel. Gray Squirrel Life TablexnxlxdxmxLxTxex0-1 5301-2 1342-3 563-4 394-5 235-6 126-7 57-8 28-9 0b) Complete the Fecundity table for the gray squirrel.xbxlxlxbx0-1 0.01-2 2.562-3 4.563-4 6.484-5 6.485-6 4.966-7 4.567-8 4.568-9 0c) Is the population of squirrels increasing, decreasing, or remaining constant?Spring 2002 7.0145Question 2, continuedSurvivorship curves reveal information about survival strategies of species. They are plots ofthe survival over time of individuals in a cohort (group of individuals in same population,born in same time period).d) Draw three different types of survivorship curves (label your axes) and briefly explain thesurvival strategy associated with each.e) For each of the following cohorts, decide which type of survivorship curve best applies.Explain briefly.i) Cohort of 20 sugar maple seedlings growing in the shadow of the parent, a tall sugarmaple in mature forest.ii) Cohort of 100 babies born at Mass General Hospital.iii) Cohort of 1000 zooplankton in a lake containing a stable fish population which preys on zooplankton.iv) Cohort of 100 corn plants planted and cultivated on a farm.Spring 2002 7.0146Question 3A breeding pair of rabbits is introduced to a secluded island off the coast of Australia. At first,the population growth is far below K so the population may grow exponentially. The birthrate of the rabbits is 4 rabbits/(rabbit•month) and the death rate is 0.5 rabbits/(rabbit•month).a) What is the intrinsic growth rate of the rabbits?b) If the population grew exponentially, how many rabbits would there be after 15 months?c) What is the doubling time (td) of this exponentially growing population?d) You observe the rabbit population over 15 months. You find that the specific rate ofincrease is 1.2 rabbits/(rabbit•month). You tag the rabbits and find there are approximately678 rabbits on the island. Using the density-dependent model of logistic growth…i) calculate the carrying capacity of the island.ii) calculate the doubling time of this logistically growing population.e) What other factors besides density may play a role in controlling the actual growth rate ofthe rabbit population on the island?Spring 2002 7.0147Question 4Part1You are studying farm snakes in Western Massachusetts. Farm snakes may be one of twodifferent colors, blue (BB or Bb) or red (bb).genotype # snakesBB 15Bb 60bb 25a) What is the frequency of the B allele (p)?b) What is the frequency of the b allele (q)?c) Is this population at Hardy-Weinberg equilibrium? Why or why not?d) Given the p and q calculated above, how many snakes of each genotype are expected if thepopulation is in Hardy-Weinberg equilibrium?genotype # snakesBBBbbbe) Why are real populations in nature not usually found at Hardy-Weinberg equilibrium?f) Can a population be in Hardy-Weinberg equilibrium for one trait and not for another?Spring 2002 7.0148Question 4, continuedPart 2Researchers isolated the XYZ protein from 12 different organisms (some extinct and somepresent now) and determined the amino acid sequences of a particular region from each. Thesequences are listed below:Organism Sequence of
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