MIT Biology Department 7.012: Introductory Biology-Fall 2004 Instructors: Professor Eric Lander, Professor Robert A Weinberg, Dr. Claudette Gardel 7.012 Practice Quiz 1 Actual Quiz 1(closed book) will be given Monday10/4 at 10: 00 am No Sections on Monday or tuesday 10/4-10/5(No Kidding Quiz Review Session Thursday, 9/30 7:00-9:00pm Tutoring Session Friday, 10/1 4:00-6:00pm
7.012 Practice Quiz 1 Actual Quiz 1 (closed book) will be given Monday10/4 at 10:00 am No Sections on Monday or Tuesday 10/4-10/5 (No Kidding.) Quiz Review Session Thursday, 9/30 7:00 - 9:00 pm Tutoring Session Friday, 10/1 4:00 - 6:00 pm MIT Biology Department 7.012: Introductory Biology - Fall 2004 Instructors: Professor Eric Lander, Professor Robert A. Weinberg, Dr. Claudette Gardel
Question 1 Shown below are the structures of three amino acids NH NH, OH H-C-CH CH H-C-CH OH Phenylalanine Threonine (Phe) ( yr) Using the blanks below, rank these three in order of the hydrophobicity of their side chaIns b)工 ntermediate Leas↑ Hydrophobic d)Explain why(a) is more hydrophobic than(b) e)Explain why(b) is more hydrophobic than(c) Question 2 Shown below is a close up of a substrate(UDP-Glucose) bound to the active site of an enzyme (UTase). The shaded area is the enzyme; the structure of the substrate is shown. CHOH Ser161 NH2 HH CH2 OH H OH OH (Arg 31 Two amino acids of the enzyme are highlighted: Arg 31 and Ser 161
2 Question 1 Shown below are the structures of three amino acids. NH3 C C H O O CH OH CH3 NH3 C CH2 C H O O OH Threonine (Thr) Phenylalanine (Phe) Tyrosine (Tyr) NH3 C CH2 C H O O Using the blanks below, rank these three in order of the hydrophobicity of their side chains. a) Most Hydrophobic b) Intermediate c) Least Hydrophobic d) Explain why (a) is more hydrophobic than (b). e) Explain why (b) is more hydrophobic than (c). Question 2 Shown below is a close up of a substrate (UDP-Glucose) bound to the active site of an enzyme (UTase). The shaded area is the enzyme; the structure of the substrate is shown. N N H OH OH H H O H CH2 O O O P O O O P H CH2OH OH H OH H O H OH H O H NH2 O H Ser161 Arg 31 Two amino acids of the enzyme are highlighted: Arg 31 and Ser 161
Question 2, continued a)Part(I)of the figure below shows the relative positions of Arg 31 and the portion of the substrate with which it interacts; part(Ir)shows the structure of arginine (D) NH H 88 H-C-CH2--CH2-CH2-N The side chain of Arg 31 interacts with the portion of the substrate shown previously What type of interaction()is/are possible between the side chain of Arg 31 and this portion of the substrate?(circle all that apply hydrop orogen IonIc van der Interaction Interaction b)Part(r)of the figure below shows the relative positions of Ser 161 and the portion of the substrate with which it interacts: part(Ir) shows the structure of serine (I Ser161 O+1-O Serine i) The side chain of Ser 161 interacts with the portion of the substrate shown above What type of interaction(s) is/are possible between the side chain of Ser 161 and this portion of the substrate?(circle all that apply hydrophobic Hydrogen IonIc van der waa interaction bond bond interaction i) The side chain of Ser 161 interacts with the region of the substrate shown above Draw the structure of Ser 161 and the relevant portion of the substrate as they would interact with each other. Be sure to indicate (1) the interaction use a dotted line) (2)the places where Ser 161 connects with the backbone of the protein 3
3 Question 2, continued a) Part (I) of the figure below shows the relative positions of Arg 31 and the portion of the substrate with which it interacts; part (II) shows the structure of arginine. (I) (II) Arginine O O O P O O O P O Arg 31 C CH2 CH2 CH2 C H O N H C NH2 NH2 NH The side chain of Arg 31 interacts with the portion of the substrate shown previously. What type of interaction(s) is/are possible between the side chain of Arg 31 and this portion of the substrate? (circle all that apply) hydrophobic Hydrogen ionic van der Waals interaction bond bond interaction b) Part (I) of the figure below shows the relative positions of Ser 161 and the portion of the substrate with which it interacts; part (II) shows the structure of serine. Serine O O O P O O O P O Ser161 (I) C CH2 C H O OH NH i) The side chain of Ser 161 interacts with the portion of the substrate shown above. What type of interaction(s) is/are possible between the side chain of Ser 161 and this portion of the substrate? (circle all that apply) hydrophobic Hydrogen ionic van der Waals interaction bond bond interaction ii) The side chain of Ser 161 interacts with the region of the substrate shown above. Draw the structure of Ser 161 and the relevant portion of the substrate as they would interact with each other. Be sure to indicate: (1) the interaction (use a dotted line) (2) the places where Ser 161 connects with the backbone of the protein
Question 2, continued c)Suppose that you are studying the interactions between the substrate and the enzyme. It is possible to make variant enzymes that differ from the one above by a single amino acid substitution (For example, Asp 78 could be replaced with tryptophan). you could use this technique to investigate the roles of each amino acid shown above i)If you change Arg 31 to a lysine, would you predict that the substrate still binds, or that the substrate now fails to bind to the altered enzyme? Explain. Choose an amino acid substitution for ser 161 ii) Explain the possible outcome of this change Note: There are many possible full-credit answers for (i) and (ii). a table of amino acid structures can be found at the end of this exam Question 3 a)Brief ly define the following Dominant Recessive Phenotype enotype alleles Homozygous Heterozygous Mendel's first Law: Mendel,s second Law Diploid b)A yeast cell has the genotype AaBb, where the a and the b loci are on different chromosomes. Sketch the chromosome arrangement of this cell in meiosis I, when 2n 4 4
4 Question 2, continued c) Suppose that you are studying the interactions between the substrate and the enzyme. It is possible to make variant enzymes that differ from the one above by a single amino acid substitution. (For example, Asp 78 could be replaced with tryptophan). You could use this technique to investigate the roles of each amino acid shown above. i) If you change Arg 31 to a lysine, would you predict that the substrate still binds, or that the substrate now fails to bind to the altered enzyme? Explain. ii) Choose an amino acid substitution for Ser 161. iii) Explain the possible outcome of this change. Note: There are many possible full-credit answers for (ii) and (iii). A table of amino acid structures can be found at the end of this exam. Question 3 a) Briefly define the following: Dominant: Recessive: Phenotype: Genotype: Alleles: Homozygous: Heterozygous: Mendel's First Law: Mendel's Second Law: Haploid: Diploid: b) A yeast cell has the genotype AaBb, where the A and the B loci are on different chromosomes. Sketch the chromosome arrangement of this cell in meiosis I, when 2n = 4
Question 4 you have started a UROP in the behavioral genetics department at the University of Monterrey in Mexico. For your first assignment, your advisor asks you to figure out the genetics of a particular species of honeybee that has just been discovered- a red killer To begin your studies, you cross this true breeding red killer bee with the local true breeding blue gentle bee. The Fl progeny show the following phenotype misTy you have characterized the disposition as such gentle: will ignore he d simply gather poller killer:will attack and sting without provocation feisty: will approach humans threateningly, but will not sting n)Write the genotypes of the Fo parental types and the F1 progeny (Be sure to indicate which particular phenotype corresponds to each parental genotype. Use H"and"h"as your symbols for the alleles of the gene conveying color or hue and"D and d"as your symbols for alleles of the gene for disposition Fo F1 b)you want to determine if the gene for hue is linked to the gene involved in disposition you decide to set up a test cross for the F1. Indicate the genotypes of the strains you choose for the cross c)Using your chosen strains indicate the ratio of genotypes and phenotypes of the progeny if the traits are not linked 5
5 Question 4 You have started a UROP in the behavioral genetics department at the University of Monterrey in Mexico. For your first assignment, your advisor asks you to figure out the genetics of a particular species of honeybee that has just been discovered- a red killer bee! To begin your studies, you cross this true breeding red killer bee with the local true breeding blue gentle bee. The F1 progeny show the following phenotype: 54 red "feisty" bees You have characterized the disposition as such: gentle: will ignore humans and simply gather pollen killer: will attack and sting without provocation feisty: will approach humans threateningly, but will not sting a) Write the genotypes of the F0 parental types and the F1 progeny. (Be sure to indicate which particular phenotype corresponds to each parental genotype.) Use "H" and "h" as your symbols for the alleles of the gene conveying color or hue and "D and d" as your symbols for alleles of the gene for disposition. F0 F1 b) You want to determine if the gene for hue is linked to the gene involved in disposition. You decide to set up a test cross for the F1. Indicate the genotypes of the strains you choose for the cross: c) Using your chosen strains indicate the ratio of genotypes and phenotypes of the progeny if the traits are NOT linked