MIT Biology Department 7.012: Introductory Biology -Fall 2004 Instructors: Professor Eric Lander, Professor Robert A Weinberg, Dr. Claudette Garde Final Exam Practice Final Exam is on monday dECEMBER 13 9: 00 AM-12 NOON BRING PICTURE工D. Exam Review on Thursday, Dec 9(new material only 7-9PM Exam Tutorial Friday, Dec 10th 1-3 PM Spring 2004 Final Exam Practice
1 Final Exam Practice Final Exam is on Monday, DECEMBER 13 9:00 AM - 12 NOON BRING PICTURE I.D. Exam Review on Thursday, Dec. 9 (new material only) 7-9 PM Exam Tutorial Friday, Dec 10th 1-3 PM Spring 2004 Final Exam Practice MIT Biology Department 7.012: Introductory Biology - Fall 2004 Instructors: Professor Eric Lander, Professor Robert A. Weinberg, Dr. Claudette Gardel
Question 1 In the space provided next to each definition or description, clearly write the letter of the appropriate term from the list of terms given on the last page A short, single-stranded DNA that serves as the necessary starting material for the synthesis of the new DNA strand in PCR The synthesis of DNA using DNA as a template The building blocks of dna and rNa The synthesis of protein using information encoded in mRNA The location in a eukaryotic cell where the electron transport chain occurs The major component of cell membranes The genetic composition of an organism a gene that lies on one of the sex chromosomes An organism without membrane-bound organelles a cell with ln chromosomes The building blocks of proteins a cell with 2n chromosomes A major source of energy that has the general formula( CH2O)n An enzyme needed for completion of lagging strand synthesis, but not leading strand synthesis The synthesis of RNA using one strand of DNA as a template An observed characteristic of an organism Spring 2004 Final exam practice
Spring 2004 Final Exam Practice 2 Question 1 In the space provided next to each definition or description, clearly write the letter of the appropriate term from the list of terms given on the last page. ____ A short, single-stranded DNA that serves as the necessary starting material for the synthesis of the new DNA strand in PCR ____ The synthesis of DNA using DNA as a template ____ The building blocks of DNA and RNA ____ The synthesis of protein using information encoded in mRNA ____ The location in a eukaryotic cell where the electron transport chain occurs ____ The major component of cell membranes ____ The genetic composition of an organism ____ A gene that lies on one of the sex chromosomes ____ An organism without membrane-bound organelles ____ A cell with 1n chromosomes ____ The building blocks of proteins ____ A cell with 2n chromosomes ____ A major source of energy that has the general formula (CH2O)n ____ An enzyme needed for completion of lagging strand synthesis, but not leading strand synthesis ____ The synthesis of RNA using one strand of DNA as a template ____ An observed characteristic of an organism
on 1. continued A DNA molecule that is distinct from the chromosome this molecule can be sed to move foreign dna in or out of a cell The dna from a eukaryote formed by the enzyme reverse transcriptase thi DNA lacks introns An organism with 2 identical alleles for the same gene a membrane protein involved in signal transduction; activation involves binding a gTP molecule An organism with genetic material inside a nucleus An organism with 2 different alleles for the same gene A measure of the affinity of an enzyme for its substrate a gene that lies on any chromosome except the sex chromosomes The membrane that surrounds the cell One of the alternate forms of a gene found at a given locus on a chromosome A technique for the rapid production of millions of copies of a particular region of dNA Proteins with a signal sequence are directed to this cellular organelle Spring 2004 Final exam practice
Spring 2004 Final Exam Practice 3 Question 1, continued ____ A DNA molecule that is distinct from the chromosome; this molecule can be used to move foreign DNA in or out of a cell ____ The DNA from a eukaryote formed by the enzyme reverse transcriptase; this DNA lacks introns ____ An organism with 2 identical alleles for the same gene ____ A membrane protein involved in signal transduction; activation involves binding a GTP molecule ____ An organism with genetic material inside a nucleus ____ An organism with 2 different alleles for the same gene ____ A measure of the affinity of an enzyme for its substrate ____ A gene that lies on any chromosome except the sex chromosomes ____ The membrane that surrounds the cell ____ One of the alternate forms of a gene found at a given locus on a chromosome ____ A technique for the rapid production of millions of copies of a particular region of DNA ____ Proteins with a signal sequence are directed to this cellular organelle
uestion The following double-stranded dNA contains sequence of a eukaryotic gene b123 5-ATGGCCTTCACACAGGAAACAGCTATGGCCATGAGCACGC 3'-TACCGGAAGTGTGTCCTTTGTCGATACCGGTACTCGTGCG CAGTCTCGGCAT TATCCTATTAAAGGGAACTGAGGTGA-3 GTCAGAGCCGTAATAGGATAATTTCCCTTGACTCCACT-5 a)Transcription begins at the underlined A/T at base pair 17(b)and proceeds to the right What are the first 12 nucleotides of the resulting mRNA? Indicate the 5 and 3 ends of the mrNA b)The first 7 amino acids of the protein encoded by this gene are NH3+-met-ala-met-ser-thr-pro-his-tyr.COO- i)underline the nucleotides which correspond to the 5 untranslated region of the primary RNA transcript made from this gene ii)draw a box around the intron region in this gene c) Consider each of the following three mutations independently i)How would the resulting protein change if the underlined G/C base pair at position 22 (1) was deleted from the DNA sequence? Briefly explain was changed to a C/g base pair? Briefly expla underlined G/C base pair at position 27(2) ii)How would the resulting protein change if the iii)How would esulting protein change if the underlined A/T base pair at position 31 (3)was deleted d from the DNA sequence? Briefly explain Spring 2004 Final exam practice
Spring 2004 Final Exam Practice 4 Question 2 The following double-stranded DNA contains sequence of a eukaryotic gene: b 1 2 3 5'-ATGGCCTTCACACAGGAAACAGCTATGGCCATGAGCACGC 1 ---------+---------+---------+---------+ 40 3'-TACCGGAAGTGTGTCCTTTGTCGATACCGGTACTCGTGCG ii CAGTCTCGGCATTATCCTATTAAAGGGAACTGAGGTGA-3' 41 ---------+---------+---------+---------+ 80 GTCAGAGCCGTAATAGGATAATTTCCCTTGACTCCACT-5' i a) Transcription begins at the underlined A/T at base pair 17 (b) and proceeds to the right. What are the first 12 nucleotides of the resulting mRNA? Indicate the 5' and 3' ends of the mRNA. b) The first 7 amino acids of the protein encoded by this gene are: NH3+ -met-ala-met-ser-thr-pro-his-tyr....COOi) underline the nucleotides which correspond to the 5' untranslated region of the primary RNA transcript made from this gene. ii) draw a box around the intron region in this gene. c) Consider each of the following three mutations independently. i) How would the resulting protein change if the underlined G/C base pair at position 22 (1) was deleted from the DNA sequence? Briefly explain. ii) How would the resulting protein change if the underlined G/C base pair at position 27 (2) was changed to a C/G base pair? Briefly explain. iii) How would the resulting protein change if the underlined A/T base pair at position 31 (3) was deleted from the DNA sequence? Briefly explain
Question 2, continued d) Puromycin is an antibiotic that has an effect on both prokaryotes and eukaryotes Puromycin, which is structurally similar to the aminoacyl terminus of an aminoacyl-tRNA (see diagram), inhibits protein synthesis by releasing nascent polypeptide chains before their synthesis is completed CH HOCHO Rrepresents the side group of the amino acid r'is the remainder of the tRNA H一NO Aminoacyl-tRNA Explain how puromycin can affect this result on growing polypeptide chains and why the peptide chain is released Question 3 a) Many patients are coming into the emergency room with a disease caused by an unknown pathogen! A doctor studies this pathogen in order to create a vaccine against it. She discovers that the infectious agent is an intracellular bacterium and its cell surface is coated with human- like proteins. Considering the mechanism of the pathogen, the doctor decides to generate a live-attenuated vaccine instead of a heat-killed vaccine i)What are the two advantages of using a live-attenuated vaccine vs a heat killed vaccine in this case? ii)What is a disadvantage of using a live-attenuated vaccine? b)When a rabbit protein is injected into rabbits, no antibodies against this protein are generated. If, however, the same rabbit protein is injected into guinea pigs, the guinea pigs generate antibodies against the rabbit protein. Briefly (in one or two sentences)explain this observation c) The genomes contained in almost all of the somatic cells in an adult human are identical Name one(diploid) cell type that is an exception to this and specify the process by which the genetic variation occurred d)will siblings have the exact same antibody repertoire? What about identical twins? Briefly olai in <plain your reasoning Spring 2004 Final exam practice
Spring 2004 Final Exam Practice 5 Question 2, continued d) Puromycin is an antibiotic that has an effect on both prokaryotes and eukaryotes. Puromycin, which is structurally similar to the aminoacyl terminus of an aminoacyl-tRNA (see diagram), inhibits protein synthesis by releasing nascent polypeptide chains before their synthesis is completed. R represents the side group of the amino acid R' is the remainder of the tRNA Explain how puromycin can affect this result on growing polypeptide chains and why the peptide chain is released. Question 3 a) Many patients are coming into the emergency room with a disease caused by an unknown pathogen! A doctor studies this pathogen in order to create a vaccine against it. She discovers that the infectious agent is an intracellular bacterium and its cell surface is coated with humanlike proteins. Considering the mechanism of the pathogen, the doctor decides to generate a live-attenuated vaccine instead of a heat-killed vaccine. i) What are the two advantages of using a live-attenuated vaccine vs. a heat killed vaccine in this case? ii) What is a disadvantage of using a live-attenuated vaccine? b) When a rabbit protein is injected into rabbits, no antibodies against this protein are generated. If, however, the same rabbit protein is injected into guinea pigs, the guinea pigs generate antibodies against the rabbit protein. Briefly (in one or two sentences) explain this observation. c) The genomes contained in almost all of the somatic cells in an adult human are identical. Name one (diploid) cell type that is an exception to this and specify the process by which the genetic variation occurred. d) Will siblings have the exact same antibody repertoire? What about identical twins? Briefly explain your reasoning
Question 4 a) Below is the pedigree for a family with an autosomal recessive disease, disease X A ○= unaffected female affected female unaffected male affected male i)What is the genotype of individual a at the disease X locus? Use"+"to indicate the wildtype allele and "to indicate the mutant allele ii)What is the probability that individual B is a carrier of disease X? ii)Individuals C and d decide to have a child. What is the probability that the child will have disease x? iv) What is the probability that the child of individuals C and d will be a carrier of disease X? b) The most common mutant allele of the disease x gene is a deletion of three nucleotides which eliminates a phenylalanine at amino acid residue 508. Although the mutant X protein is made, it is not localized to the plasma membrane i)Assuming the altered X protein is stable, where might it be found? ii)Describe another mutation in this gene that could prevent the disease X protein from localizing to the plasma membrane Spring 2004 Final exam practice
Spring 2004 Final Exam Practice 6 Question 4 a) Below is the pedigree for a family with an autosomal recessive disease, disease X. ? = unaffected female = affected female = unaffected male = affected male A B C D i) What is the genotype of individual A at the disease X locus? Use “+” to indicate the wildtype allele and “-“ to indicate the mutant allele. ii) What is the probability that individual B is a carrier of disease X? iii) Individuals C and D decide to have a child. What is the probability that the child will have disease X? iv) What is the probability that the child of individuals C and D will be a carrier of disease X? b) The most common mutant allele of the disease X gene is a deletion of three nucleotides which eliminates a phenylalanine at amino acid residue 508. Although the mutant X protein is made, it is not localized to the plasma membrane. i) Assuming the altered X protein is stable, where might it be found? ii) Describe another mutation in this gene that could prevent the disease X protein from localizing to the plasma membrane
Question 4, continued c)Researchers are currently working on gene therapy for disease X patients. The most adenovirus is a double-stranded DNA virus that target wivip thelial cells, it can be used to promising therapy has involved incorporating the disease x gene into an adenovirus. Becau deliver the disease X gene to the lung cells of the affected individual display of MHC I molecules on the surface of cells. Why is this a desirable property of the virus used to deliver the disease x gene? ii)Using the plasmids and restriction enzymes provided, design a procedure to create a double-stranded dna to incorporate into the adenovirus particle. The final product should be linear, contain the majority of the virus genome and have the disease x gene under control of the El promoter(Pel). Nhel and Spel create the same sticky ends. All the other restriction enzymes create unique cuts P BamHI HindIll start Spel disease X cdnA BR-Ad2-7 Adenovirus pCMV-diseaseX HindII BamhI EcoRI Spring 2004 Final exam practice
Spring 2004 Final Exam Practice 7 Question 4, continued c) Researchers are currently working on gene therapy for disease X patients. The most promising therapy has involved incorporating the disease X gene into an adenovirus. Because adenovirus is a double-stranded DNA virus that targets lung epithelial cells, it can be used to deliver the disease X gene to the lung cells of the affected individual. i) The adenovirus used in these studies is able to produce gp19, a protein that inhibits the display of MHC I molecules on the surface of cells. Why is this a desirable property of the virus used to deliver the disease X gene? ii) Using the plasmids and restriction enzymes provided, design a procedure to create a, double-stranded DNA to incorporate into the adenovirus particle. The final product should be linear, contain the majority of the virus genome and have the disease X gene under control of the E1 promoter (PE1). NheI and SpeI create the same sticky ends. All the other restriction enzymes create unique cuts. pBR-Ad2-7 PE1 BamHI NheI HindIII SpeI BamHI Adenovirus genome pCMV-diseaseX EcoRI HindIII SpeI disease X cDNA start stop
Question 5 The figure below shows GDP in the binding pocket of a G protein. o|P|O HO OHOH y r HNN→C=NH O Arg Glu a) Circle the strongest interaction that exists between i)the side chain of Lys and the phosphate group of GDP van der waals covalent hydrogen bond lonIc ) the side chain of Glu and the ribose group of GDp van der waals covalent hydrogen bond Ionic ii)the side chain of Tyr and the guanine base of gDp van der waals covalent hydrogen bond ionIc b) You make mutations in the gDp-binding pocket of the g protein and examine their effects on the binding of GDP. Consider the size and the nature(e. g charge, polarity, hydrophilicity, hydrophobicity) of the amino acid side chains andand give the most likely reason why each mutation has the stated effect. Consider each mutation independently i)Arg is mutated to a Lys, resulting in a G protein that still binds GDP ii)Asp is mutated to a Tyr, resulting in a G protein that cannot bind GDP. Spring 2004 Final exam practice
Spring 2004 Final Exam Practice 8 Question 5 The figure below shows GDP in the binding pocket of a G protein. NH NH H N C NH C O C O HO Lys Arg Asp Glu Tyr 3 + 2 2 + P P O O O O O OH OH N N NH NH N O CH 2 O- OO- 2 O- O - a) Circle the strongest interaction that exists between: i) the side chain of Lys and the phosphate group of GDP van der Waals covalent hydrogen bond ionic ii) the side chain of Glu and the ribose group of GDP van der Waals covalent hydrogen bond ionic iii) the side chain of Tyr and the guanine base of GDP van der Waals covalent hydrogen bond ionic b) You make mutations in the GDP-binding pocket of the G protein and examine their effects on the binding of GDP. Consider the size and the nature (e.g. charge, polarity, hydrophilicity, hydrophobicity) of the amino acid side chains and and give the most likely reason why each mutation has the stated effect. Consider each mutation independently. i) Arg is mutated to a Lys, resulting in a G protein that still binds GDP. ii) Asp is mutated to a Tyr, resulting in a G protein that cannot bind GDP
Question 6 The bos/seven receptor is required for differentiation of a particular cell, called R7. It is a receptor tyrosine kinase with the structure below. As a monomer, the protein is inactive Binding of ligand causes the receptor to dimerize, causing phosphorylation of the intracellular domain, activating the protein. During processing of the protein, the extracellular domain is cleaved and a disulfide bridge forms between two cysteines, tethering the ligand-binding domain to the rest of the protein ligand-binding domain extracellular S-s S-s membraneITITIIIITTTIIiIli intracellular NACTIVE ACTIVE i) How would receptor activity be affected by changing one of the two cysteines shown above to an alanine? explain ii) What effect would this mutation have on the differentiation of r7? b) Name three amino acids that would be likely to be found in the transmembrane domain. What property do those amino acids have in common, and why do they cause the transmembrane domain to stay in the membrane? d) Draw a schematic of the receptor tyrosine kinase(discussed above) prior to any cleavage or modification using the template below. Include the domains of this protein that are required for targeting to and insertion in the plasma membrane. Also label the intracellular and extracellular domains C e)Activation of the above receptor causes Ras to exchange GDP for GTP, thereby activating it This activated Ras can activate a signal transduction cascade, which ultimately results in the Spring 2004 Final exam practice
Spring 2004 Final Exam Practice 9 Question 6 The bos/seven receptor is required for differentiation of a particular cell, called R7. It is a receptor tyrosine kinase with the structure below. As a monomer, the protein is inactive. Binding of ligand causes the receptor to dimerize, causing phosphorylation of the intracellular domain, activating the protein. During processing of the protein, the extracellular domain is cleaved and a disulfide bridge forms between two cysteines, tethering the ligand-binding domain to the rest of the protein. -S-Sligand-binding domain intracellular extracellular membrane -S-S- -S-Sligand INACTIVE ACTIVE P P a) i) How would receptor activity be affected by changing one of the two cysteines shown above to an alanine? Explain. ii) What effect would this mutation have on the differentiation of R7? b) Name three amino acids that would be likely to be found in the transmembrane domain. What property do those amino acids have in common, and why do they cause the transmembrane domain to stay in the membrane? d) Draw a schematic of the receptor tyrosine kinase (discussed above) prior to any cleavage or modification using the template below. Include the domains of this protein that are required for targeting to and insertion in the plasma membrane. Also label the intracellular and extracellular domains. N C e) Activation of the above receptor causes Ras to exchange GDP for GTP, thereby activating it. This activated Ras can activate a signal transduction cascade, which ultimately results in the
transcription of genes required for r7 differentiation. In different cells in the same animal, ras can be activated by an activated growth factor receptor. This leads to transcription of genes required for cell division egl A GDP GDP GTP transcription of genes for R7 development transcription of genes for cell division How is it possible for the activation of Ras to lead to transcription of different sets of genes? ii)Given that these cells exist in the same animal, name one component in the pathway that could be mutated to give each of the following results(consider each situation independently). Describe how the mutant component differs from the wild-type component, and whether it is a loss-of-function or gain-of-function mutation You never see differentiation of rz cells You see uncontrolled cell proliferation Question 7 You are studying a common genetic condition. The mutant allele differs from the wild-tyrexg allele by a single base-pair(bp)substitution. This substitution eliminates a Nhel restriction si that is present in the wild-type allele. The mutant allele is not cut by Nhel. )a pedigree of a family exhibiting this condition is shown below: normal female affected male affected female Spring 2004 Final exam practice
Spring 2004 Final Exam Practice 10 transcription of genes required for R7 differentiation. In different cells in the same animal, Ras can be activated by an activated growth factor receptor. This leads to transcription of genes required for cell division. i) How is it possible for the activation of Ras to lead to transcription of different sets of genes? ii) Given that these cells exist in the same animal, name one component in the pathway that could be mutated to give each of the following results (consider each situation independently). Describe how the mutant component differs from the wild-type component, and whether it is a loss-of-function or gain-of-function mutation. • You never see differentiation of R7 cells. • You see uncontrolled cell proliferation. Question 7 You are studying a common genetic condition. The mutant allele differs from the wild-type allele by a single base-pair (bp) substitution. This substitution eliminates a NheI restriction site that is present in the wild-type allele. (The mutant allele is not cut by NheI.) A pedigree of a family exhibiting this condition is shown below: normal male affected male normal female affected female 1 2 3 4 5 6 7 8 boss/sev Ras GDP GTP transcription of genes for R7 development Ras GDP GTP EGF receptor EGF transcription of genes for cell division
