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 3 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 I Problem sets will not be accepted late Solutions will be posted on the web October 2, 2003. Question 1 You have two pure-breeding colony of mice. Colony I mice have black fur and long tails, Colony II mice have golden fur and short tails You cross mice from each of these colonies Fo black fur and golden fur and short tails F1 Brown fur and long tails a) Predict genotypes for the mice shown in the cross above. Define your notation. i) black fur and long tails ii) golden fur and short tails i) Brown fur and long tails: b) You mate a male and a female from the Fi generation. Given your prediction in(a), what genotypes and phenotypes do you see in the F2 generation, and in what ratios? 7012Fall2003
Name:___________________________________ Section:_____ 7.012 Fall 2003 7.012 Problem Set 3 Question 1 You have two pure-breeding colony of mice. Colony I mice have black fur and long tails, Colony II mice have golden fur and short tails. You cross mice from each of these colonies. F0 black fur and long tails X golden fur and short tails ⇓ F1 Brown fur and long tails a) Predict genotypes for the mice shown in the cross above. Define your notation. i) black fur and long tails: ii) golden fur and short tails: iii) Brown fur and long tails: b) You mate a male and a female from the F1 generation. Given your prediction in (a), what genotypes and phenotypes do you see in the F2 generation, and in what ratios? 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 1. Problem sets will not be accepted late. Solutions will be posted on the web October 2, 2003. MIT Biology Department 7.012: Introductory Biology - Fall 2004 Instructors: Professor Eric Lander, Professor Robert A. Weinberg, Dr. Claudette Gardel
Name Section FIGURE 1: plate plate 2 plate 3 plate plate 5 minimal medium+phe a) Plate l is the original rich medium plate that the mutagenized cells were grown on. It is standard practice for the last plate in a series of replica plates to have the same growth medium as the original plate. What purpose might this serve? b)You obtain some phe" colonies in this manner. Identify the colonies from FIGURE 1 that are c) You notice that some colonies do not grow on plates containing minimal medium phenylalanine(plate 2). Identify these colonies and give one possible explanation for the growth behavior of these colonies d)This strategy for isolating phe" mutants works well so you repeat the mutagenesis and replica plating experiment to isolate more phe" mutants. You then perform a complementation test on these phe- mutants i)What is a complementation test? ii)What is the purpose of a complementation test? 7012Fall2003
Name:___________________________________ Section:_____ 7.012 Fall 2003 FIGURE 1: A B C D E F G H X Y A F A B F A C E F G H Y A B C D E F G H X Y plate 1 plate 2 plate 3 plate 4 plate 5 rich medium minimal medium + phe minimal medium minimal medium + PEP rich medium a) Plate 1 is the original rich medium plate that the mutagenized cells were grown on. It is standard practice for the last plate in a series of replica plates to have the same growth medium as the original plate. What purpose might this serve? b) You obtain some phe- colonies in this manner. Identify the colonies from FIGURE 1 that are phec) You notice that some colonies do not grow on plates containing minimal medium + phenylalanine (plate 2). Identify these colonies and give one possible explanation for the growth behavior of these colonies. d) This strategy for isolating phe- mutants works well so you repeat the mutagenesis and replica plating experiment to isolate more phe- mutants. You then perform a complementation test on these phe- mutants. i) What is a complementation test? ii) What is the purpose of a complementation test?
Name Section Question 2 tinued In the table below, a()indicates that the diploid created grows on minimal media, a(-) indicates that the diploid fails to grow on minimal media Im1 m2m3 m4 7m8m9m10 3 m4+ m++++++++ + n10|+ ii)Assign the mutants 1-10 into complementation groups e) You also characterize your mutants based upon which of the intermediates accumulates lates x m 3: accumulates z m4 accumulates pep m5: accumulates y m6: accumulates w Based on the above data, you predict that m1 has a mutation ir ge m2 has a mutation in gene iii) m3 has a mutation in ge iv) m4 has a mutation in gene v) m5 has a mutation in gene 7012Fall2003
Name:___________________________________ Section:_____ 7.012 Fall 2003 Question 2, continued In the table below, a (+) indicates that the diploid created grows on minimal media, a (-) indicates that the diploid fails to grow on minimal media. m1 m2 m3 m4 m5 m6 m7 m8 m9 m10 m1 - - + + + + - + + + m2 - - + + + + - + + + m3 + + - + + + + + + + m4 + + + - + + + + + - m5 + + + + - + + + - + m6 + + + + + - + - + + m7 - - + + + + - + + + m8 + + + + + - + - + + m9 + + + + - + + + - + m10 + + + - + + + + + - ii) Assign the mutants 1-10 into complementation groups. e) You also characterize your mutants based upon which of the intermediates accumulates m2: accumulates X m3: accumulates Z m4: accumulates PEP m5: accumulates Y m6: accumulates W Based on the above data, you predict that i) m1 has a mutation in gene______ ii) m2 has a mutation in gene______ iii) m3 has a mutation in gene______ iv) m4 has a mutation in gene______ v) m5 has a mutation in gene______
Name ection: Question 3 Replica plating has been used to address profoundly important questions in bacterial genetics For example, in the 1940,'s there was much debate regarding the issue of whether or not mutants pre-exist in a population of bacteria. Researchers observed that when they inoculated wild type(pens) bacteria onto growth medium containing penicillin, and thus selected for bacteria that had mutated to become penicillin resistant a small fraction(-10-6)of cells would always grow. Inus, pen colonies had arisen from a pen population. There were two models for this Model A: "Directed Mutations"One grou line of reasoning was that the bacteria can sense the up of researchers argued that these mutants originated as a result of the selective pressure. thei need to grow on penicillin and that a small fraction of them successfully mutate in a directed manner so that they become pen Model B: " Pre-existing Mutations"A second group of researchers argued that pen mutants pre-existed within the wild type population before ever coming into contact with penicillin thus,(they argued) penicillin doesn't direct mutations, it simply reveals mutants Replica plating provided a rapid means for testing these two hypotheses. The following is a simplified version of the experiment. Plate 1 contains a lawn"of cells(a solid layer of cells packed together), all of which are the offspring of a single, wild type cell. About 5 X 106 cells were spread on a plate, and after a day of growth, they formed a lawn containing about 10 cells. Plate 1 was used as the master plate that was replicated onto plates 2, 3, 4, and 5 = lawn colony plate 1 plate 2 plate 3 plate 4 plate 5 The distribution of colonies on plates 3, 4, and 5 is identical a)Which of the two hypotheses( directed mutations or pre-existing mutations) does this result more strongly support. Explain your reasoning 7012Fall2003
Name:___________________________________ Section:_____ 7.012 Fall 2003 Question 3 Replica plating has been used to address profoundly important questions in bacterial genetics. For example, in the 1940's there was much debate regarding the issue of whether or not mutants pre-exist in a population of bacteria. Researchers observed that when they inoculated wild type (penS) bacteria onto growth medium containing penicillin, and thus selected for bacteria that had mutated to become penicillin resistant, a small fraction (~10-6) of cells would always grow. Thus, penR colonies had arisen from a penS population. There were two models for this: Model A: "Directed Mutations" One group of researchers argued that these mutants originated as a result of the selective pressure. Their line of reasoning was that the bacteria can sense the need to grow on penicillin and that a small fraction of them successfully mutate in a directed manner so that they become penR. Model B: "Pre-existing Mutations" A second group of researchers argued that penR mutants pre-existed within the wild type population before ever coming into contact with penicillin; thus, (they argued) penicillin doesn't direct mutations, it simply reveals mutants. Replica plating provided a rapid means for testing these two hypotheses. The following is a simplified version of the experiment. Plate 1 contains a "lawn" of cells (a solid layer of cells packed together), all of which are the offspring of a single, wild type cell. About 5 X 106 cells were spread on a plate, and after a day of growth, they formed a lawn containing about 109 cells. Plate 1 was used as the master plate that was replicated onto plates 2, 3, 4, and 5. The distribution of colonies on plates 3, 4, and 5 is identical. a) Which of the two hypotheses (directed mutations or pre-existing mutations) does this result more strongly support. Explain your reasoning
Name ection: Question 4 Shown below is a diagram of a replication fork in a double-stranded (ds) DNA molecule found in a prokaryotic cell. Each DNA strand(a and B)serves as a template for polymerization by DNA polymerase, resulting in the formation of a newly synthesized"daughter"DNA strand strand a Replication fork in this 5′ i)On which template strand (A or B)would there be continuous replication by dNA polymerase? What is this newly synthesized daughter strand called during DNA replication? olymerase? What is this newly synthesized daughter strand called during DNA NA ii)On which template strand (a or B)would there be discontinous replication b replication? i)Chemicals that inhibit the enzyme dNa ligase will primarily affect synthesis on one of the two template strands(a or B). Explain on which template strand (a or B) polymerization will be primarily affected and why this occurs b) There are inaccuracies in the dna molecule shown below 5AGTCCGAUGC3 i) Name three things that are wrong in the above DNA sequence ii)What type of chemical interaction is indicated by a" I"in the above diagram? What happens to these interactions during DNA replication? 7012Fall2003
Name:___________________________________ Section:_____ 7.012 Fall 2003 Question 4 Shown below is a diagram of a replication fork in a double-stranded (ds) DNA molecule found in a prokaryotic cell. Each DNA strand (A and B) serves as a template for polymerization by DNA polymerase, resulting in the formation of a newly synthesized "daughter" DNA strand. Replication fork moves in this direction 5’ 3’ 3’ 5’ strand A strand B a) i) On which template strand (A or B) would there be continuous replication by DNA polymerase? What is this newly synthesized daughter strand called during DNA replication? ii) On which template strand (A or B) would there be discontinous replication by DNA polymerase? What is this newly synthesized daughter strand called during DNA replication? iii) Chemicals that inhibit the enzyme DNA ligase will primarily affect synthesis on one of the two template strands (A or B). Explain on which template strand (A or B) polymerization will be primarily affected and why this occurs. b) There are inaccuracies in the DNA molecule shown below. 1 5 10 5' A G T C C G A U G C 3' | | | | | | | | | | 5' T C A G G C T A T G 3' i) Name three things that are wrong in the above DNA sequence. ii) What type of chemical interaction is indicated by a "|" in the above diagram? What happens to these interactions during DNA replication?
Name ection: c) Shown below is the structure of a monomer used in nucleic acid sy N o2。-PBo-↓o-c, iWould this monomer be used to form part of an rna strand or a dna strand? Briefly explain your answer ii)In nucleic acid synthesis, one of the phosphate groups of this monomer is covalently linked to a new strand that is being elongated. In the figure above, draw a circle around the phosphate group that would be linked iii)When this monomer is already part of the newly synthesized strand one of the hydroxyl groups of this monomer will be linked to the phosphate group of the next monomer added. In the figure above, draw a box around the hydroxyl group that will be linked 7012Fall2003
Name:___________________________________ Section:_____ 7.012 Fall 2003 c) Shown below is the structure of a monomer used in nucleic acid synthesis. γ β α OH H H O P O P O P O CH2 HO N N N N NH2 O O O H H O– O– O– O– i) Would this monomer be used to form part of an RNA strand or a DNA strand? Briefly explain your answer. ii) In nucleic acid synthesis, one of the phosphate groups of this monomer is covalently linked to a new strand that is being elongated. In the figure above, draw a circle around the phosphate group that would be linked. iii) When this monomer is already part of the newly synthesized strand, one of the hydroxyl groups of this monomer will be linked to the phosphate group of the next monomer added. In the figure above, draw a box around the hydroxyl group that will be linked