7.012: Introductory Biology-Fall 2004 Instructors: Professor Eric Lander, Professor Robert A Weinberg, Dr. Claudette Gardel Friday 11/12/04 7.012 Quiz 3 Answers A>85 18% of test takers b 72-84 41% of test takers c 60-71 23% of test takers D 50-59 11.4% of test takers F<58 6.6% of test takers REGRADE Requests with attached notes describing the problem due by November 24mnoon Question Value Score 25 2 19 3 15 15 5 26 100
Friday 11/12/04 7.012 Quiz 3 Answers A > 85 18% of test takers B 72-84 41% of test takers C 60-71 23% of test takers D 50-59 11.4% of test takers F < 58 6.6% of test takers REGRADE Requests with attached notes describing the problem due by November 24th noon. Question Value Score 1 25 2 19 3 15 4 15 5 26 100 MIT Biology Department 7.012: Introductory Biology - Fall 2004 Instructors: Professor Eric Lander, Professor Robert A. Weinberg, Dr. Claudette Gardel��
Question 1 a)Circle whether the following antigens can be specifically and directly recognized by Antibodies and/or T cell receptors. 9 points-Graded horizontally. 1 Point each row, both have to be correct to get the point. The bottom row is 2 points an be Can b recognized by recognized by Antigen Antibodies cell receptors NO yES No\ Lipids ES NO yES NO Carbohydrates yES NO yES No Bacterial surface proteins yES NO yES No Viral capsids yES NO yES NO 3-Dimensional polypep otide folds in native proteins yES NO yES NO Linear oligopeptides yES NO yES Non -self MHc Class I/II molec yES NO ES NO MHC Class I/II molecules complexed with linear lse. 7 points t F i)B cells can generate higher affinity antibodies for antigens over time F ii)T cells can generate higher affinity T cell receptors for antigens over time T F ii)A single B cell might make antibodies that recognize many different epitopes I capsid pre F iv) Each of us is born with hundreds of genes each of which encodes an antibody to recognize a specific virus F v) Macrophages envelope and digest foreign antigens nonspecifically T F vi) T-cell receptors are membrane bound and thus can signal the T cell to ingest T F vi) Cytotoxic T cells can activate B cells to proliferate
Question 1 a) Circle whether the following antigens can be specifically and directly recognized by Antibodies and/or T cell receptors. 9 points-Graded horizontally. 1 Point each row,both have to be correct to get the point. The bottom row is 2 points. Can be Can be recognized by recognized by Antigens Antibodies T cell receptors YES NO YES NO Lipids YES NO YES NO Carbohydrates YES NO YES NO Bacterial surface proteins YES NO YES NO Viral capsids YES NO YES NO 3-Dimensional polypeptide folds in native proteins YES NO YES NO Linear oligopeptides YES NO YES NO Non-Self MHC Class I/II molecules YES NO YES NO MHC Class I/II molecules complexed with linear oligopeptides b) True or False. 7 points T F i) B cells can generate higher affinity antibodies for antigens over time. T F ii) T cells can generate higher affinity T cell receptors for antigens over time. T F iii) A single B cell might make antibodies that recognize many different epitopes on a viral capsid protein. T F iv) Each of us is born with hundreds of genes each of which encodes an antibody to recognize a specific virus. T F v) Macrophages envelope and digest foreign antigens nonspecifically. T F vi) T-cell receptors are membrane bound and thus can signal the T cell to ingest antigen. T F vii) Cytotoxic T cells can activate B cells to proliferate. 2
d)Which ONE of the following does Not provide innate immunity against pathogens? 2pts blinking macrophages ciliated cells in trachea mucous membranes low pH of stomach plasma cells lysozyme in tears skin e)Which of the following cells can you be sure CAN NoT have the same genetic content of a skin cell. For any circled, on the adjacent line, explain why in 5 words or less. 4 pts Helper T dna rearrangement of TCR_ or_VDJ rec Lung cell Macr Plasma Cell VDJ REC or somatic mutation or hypermutation or junctional diversity f) Continue the graph following the exposure to rabies virus in this laboratory mouse Concentration 10 of polio Virus antibodies Rabies virus In serum iniection of lab mouse
Name__________________________________ d) Which ONE of the following does NOT provide innate immunity against pathogens? 2pts blinking macrophages ciliated cells in trachea mucous membranes low pH of stomach plasma cells lysozyme in tears skin e) Which of the following cells can you be sure CAN NOT have the same genetic content of a skin cell. For any circled, on the adjacent line, explain why in 5 words or less. 4 pts Helper T cell ___dna rearrangement of TCR____ or ___VDJ rec.__ Lung Cell ______________________________________ Macrophage ______________________________________ Plasma Cell _____VDJ REC or somatic mutation or hypermutation or junctional diversity____ f) Continue the graph following the exposure to rabies virus in this laboratory mouse. 3 points Concentration 104 of Polio Virus antibodies in serum of lab mouse 102 Rabies virus injection Polio virus injection Time 3
Question 2 Winston, an avid cigarette smoker, detects tumors in 3 of his 6 dogs. Lucky Strike has an ear tumor, Virginia Slims has a paw tumor, and Kool has a tail tumor. Bob, a biologist friend, takes cells from each tumor as well as cheek cell samples from the dogs as controls and cultures them in Petri dishes. All of the cheek cell cultures grow as a monolayer but all of the tumor cell cultures exhibit foci a)Which ONE of the following properties do the tumor cells lack, resulting in this growth difference. 3 pts ATP hydrolysis tact inhibition G5 processing Retinoblastoma Signaling cascade b)Bob brushes up on the molecular nature of different cancer mutations. Match the following mutations to their respective phenotypes at the cellular level. 4 pts D dominar o_ Tumor Suppressor mutation m)G5 processing defective n)opportunistic o recessive p)none of these To determine the cause of each of the dogs tumors, he performs the following experiments. cheek cells isolate DNA→ (inject DNA) ear tumor cells transfection isolate DNA→ inject DNA→ wild type cell uncontrolled growth paw tumor cells isolateD→0×mtem tail transfection eDNA→ ject DNA)→> Figure by MIT OCW
Question 2 Winston, an avid cigarette smoker, detects tumors in 3 of his 6 dogs. Lucky Strike has an ear tumor, Virginia Slims has a paw tumor, and Kool has a tail tumor. Bob, a biologist friend, takes cells from each tumor as well as cheek cell samples from the dogs as controls and cultures them in Petri dishes. All of the cheek cell cultures grow as a monolayer but all of the tumor cell cultures exhibit foci. a) Which ONE of the following properties do the tumor cells lack, resulting in this growth difference.3 pts ATP hydrolysis Contact Inhibition G5 processing Retinoblastoma Signaling cascade b) Bob brushes up on the molecular nature of different cancer mutations. Match the following mutations to their respective phenotypes at the cellular level. 4 pts l) dominant ___o_ Tumor Suppressor mutation m) G5 processing defective n) opportunistic o) recessive ___l_ Oncogene mutation p) none of these To determine the cause of each of the dogs’ tumors, he performs the following experiments. cheek cells isolate DNA transfection (inject DNA) wild type cell controlled growth ear tumor cells transfection isolate DNA (inject DNA) wild type cell uncontrolled growth paw tumor cells transfection isolate DNA (inject DNA) wild type cell controlled growth tail tumor cells transfection isolate DNA (inject DNA) wild type cell uncontrolled growth Figure by MIT OCW. 4
Name c)Based on previous data, which tumor(s)has/have a mutation in a tumor suppressor gene? Circle aLL that apply 2 pts Cheek d) Based on the data above, which tumor(s)has/have a mutation resulting in an oncogene? Circle ALL that apply. 4 pts Paw Bob isolates the cells from each dish and fractionates them to isolate the membranes Bob measures the amount of phosphorylated amino acids present, using a specific antibody. See the results below Binding of Antibody Tail Specific for phosphorylated amino acids some Cheek Ear Paw Membrane fractions from Cells Bob reads that the three most likely causes for canine tumors are 1)Ras oncogene mutations 2)Mutations resulting in constitutively active tyrosine kinase receptors 3)Mutations inactivating the p53 tumor suppressor gene e)Based on the data above, match the different tumor types with the likely cancer causes listed above 6 points Ear tumor 3 Paw tumor 2 Tail tumor
Name__________________________________ c) Based on previous data, which tumor(s) has/have a mutation in a tumor suppressor gene? Circle ALL that apply. 2 pts Cheek Ear Paw Tail d) Based on the data above, which tumor(s) has/have a mutation resulting in an oncogene? Circle ALL that apply. 4 pts Cheek Ear Paw Tail Bob isolates the cells from each dish and fractionates them to isolate the membranes. Bob measures the amount of phosphorylated amino acids present, using a specific antibody. See the results below. lots Binding of Antibody –Specific for phosphorylated amino acids some Cheek Paw Tail Ear Membrane Fractions from Cells Bob reads that the three most likely causes for canine tumors are… 1) Ras oncogene mutations. 2) Mutations resulting in constitutively active tyrosine kinase receptors. 3) Mutations inactivating the p53 tumor suppressor gene. e) Based on the data above, match the different tumor types with the likely cancer causes listed above. 6 points __1___Ear tumor ___3__Paw tumor ___2__Tail tumor 5
Question 3 Bob grows dog cheek cells and adds Telohalt, a chemical that arrests cells at the end of mitosis. After removing Telohalt, he adds H-Thymidine to the cells and measures its incorporation over time Cheek cells after Amount of removal of telohalt incorporated 0510152025303540455 hours a)Bob knows M phase is 5 hours long in these cells. Label and fill in the durations of the remaining phases you must write legibly to receive credit. 5 hrs G 1-5 hrs. s-10 hrs G2-5 hrs 9p1 5 hrs G2 G1 5 h b)In a similar experiment Bob adds a drug with unknown effects, 27 hours after the removal of Telohalt and gets the results shown below Amount of Cheek cells Test Drug added incorporated at 27 hours 05101520253035404550 Circle the phase in the cell cycle where the drug acts.3 pts G1-G2 transition G1-s transit G2-G3 transition G2-S transition G3-s transition G2-M transition Cyclin G3-G4 transition processing Bob repeats the experiments above with p53 tumor suppressor deficient tumor cells, and gets the following results. assume the cell cycle phase times of the tumor cells are similar to those of cheek cells. p53- cells without drug Test Drug added 05101520253035404550 c)Circle the point in the cell cycle where the p53 tumor suppressor mutation acts. 3 pts G1-G2 transition G1-s transit G2-G3 transition G2-S transition G3-S transition G2-M transition G3-G4 transition
Question 3 Bob grows dog cheek cells and adds Telohalt, a chemical that arrests cells at the end of mitosis. After removing Telohalt, he adds 3 H-Thymidine to the cells and measures its incorporation over time. Cheek cells after removal of Telohalt Amount of 3 H-Thymidine incorporated hours a) Bob knows M phase is 5 hours long in these cells. Label and fill in the durations of the remaining phases. You must write legibly to receive credit. 5 hrs G1 -5 hrs, S –10 hrs, G2 -5 hrs 9pts M 5 hrs G2 G1 5 hrs S 10 hrs b) In a similar experiment Bob adds a drug with unknown effects, 27 hours after the removal of Telohalt, and gets the results shown below. Test Drug added at 27 hours Cheek cells Amount of 3 H-Thymidine incorporated Circle the phase in the cell cycle where the drug acts…3 pts G1-G2 transition G1-S transition G2 G2-G3 transition G2-S transition G3-S transition G2-M transition Cyclin G3-G4 transition G4 G5 processing Bob repeats the experiments above with p53 tumor suppressor deficient tumor cells, and gets the following results. (Assume the cell cycle phase times of the tumor cells are similar to those of cheek cells.) p53- cells without drug p53- cells Test Drug added at 27 hours c) Circle the point in the cell cycle where the p53 tumor suppressor mutation acts.3 pts G1-G2 transition G1-S transition G2 G2-G3 transition G2-S transition G3-S transition G2-M transition Cyclin G3-G4 transition G4 G5 processing 6
Name Question 4 Efficient infection by HIV requires the expression of the Hiv tat gene. All tat mutants are unable to spread from the cells of an initial infection to infect other cells a)What cell type would you use to study wildtype HIv infectivity? 3 pts canine kidney cells E coli uman neurons none of these you choose to study how tat works so you can design a drug to combat HIv infection you find that cells infected with WT HIV make a long viral rna that hybridizes to the iral DNa probes, A, B and C shown below. In contrast, cells infected with tat mutants produce shorter viral rNAs that can only hybridize to the A probe HIV DNA 3’[ B C b)Which of the following statements could be true based on the above observation? 3 pt i The tat gene product allows RNA polymerase to transcribe through a transcriptional terminator located in the dna between probes a and B ii) The tat gene product is necessary for initiation of transcription. ii) The tat gene product is necessary for initiation of translation of the+ sense mRNA iv)In the tat-mutant, a single nucleotide insertion causes a frameshift and changes the downstream DNA making it unable to hybridize to probes b and C In the early 1990's AIDS researchers began to see strains of hiv that were resistant to the treatment drug aZT, a thymidine analogue c)What enzyme is the target of AZT? 2 pts_Reverse Transcriptase d)Explain briefly why HIV is liable to develop drug resistance to AZT. 3 pts error-prone Replication> Mutation in Reverse Transcript e)A group of Eastern Europeans is resistant to infection by HIv. what is the best explanation for their immunity to infection? 4 pts i) Their RNa polymerase does not recognize DNA of viral origin ii) Their cells do not use the same genetic code as HIv ii) Their CD4 T-cells lack a T-cell receptor iv) Their CD4 T-cells have a mutated CD4 co-receptor v) Their neurons have an unusual shape vi) There is a mutated receptor on HIv
Name__________________________________ Question 4 - Efficient infection by HIV requires the expression of the HIV tat gene. All tat mutants are unable to spread from the cells of an initial infection to infect other cells. a) What cell type would you use to study wildtype HIV infectivity? 3 pts canine kidney cells E. coli human neurons yeast none of these You choose to study how tat works so you can design a drug to combat HIV infection. You find that cells infected with WT HIV make a long viral RNA that hybridizes to the - viral DNA probes, A, B and C shown below. In contrast, cells infected with tat mutants produce shorter viral RNAs that can only hybridize to the A probe. HIV DNA 5’ 3’ A B C b) Which of the following statements could be true based on the above observation? 3 pt i) The tat gene product allows RNA polymerase to transcribe through a transcriptional terminator located in the DNA between probes A and B. ii) The tat gene product is necessary for initiation of transcription. iii) The tat gene product is necessary for initiation of translation of the + sense mRNA. iv) In the tat- mutant, a single nucleotide insertion causes a frameshift and changes the downstream DNA making it unable to hybridize to probes B and C. In the early 1990’s AIDS researchers began to see strains of HIV that were resistant to the treatment drug AZT, a thymidine analogue. c) What enzyme is the target of AZT? 2 pts ____Reverse Transcriptase______________ d) Explain briefly why HIV is liable to develop drug resistance to AZT. 3 pts ______error-prone Replication Mutation in Reverse Transcriptase__________ e) A group of Eastern Europeans is resistant to infection by HIV. What is the best explanation for their immunity to infection? 4 pts i) Their RNA polymerase does not recognize DNA of viral origin. ii) Their cells do not use the same genetic code as HIV. iii) Their CD4 T-cells lack a T-cell receptor. iv) Their CD4 T-cells have a mutated CD4 co-receptor. v) Their neurons have an unusual shape. vi) There is a mutated receptor on HIV. 7
Question 5 Part a a)Which of the following is true about viruses?( Circle all that apply. )3 pts i) They encode genes for synthesizing their own ATP ii) They are single cell organisms ii They can have a genome made of dNA iv)They package ribosomes into their virion v) They can have a single stranded or double stranded RNa genome vi) They can have a membrane-like envelope to respond to an influenza infection. Circle all that apply. )pts scan b some viruses like inf luenza can cause disease in humans which of the following can iB cells i) Macrophages ii Killer T cells(Ctls iv) CD4+T cells v)Neurons c)Both bacterial viruses and plasmids can be used as cloning vectors. Which of the following is true and distinguishes a virus from a plasmid?( Circle all that apply. )2 pts i) Plasmids use the translation machinery of the cell ii Viruses have a protein capsid i)Viruses can replicate in the absence of a cellular host. iv)Plasmids carry genes v Plasmids have restriction sites. d)Which of the following is true about retroviruses?(Circle all that apply. )6pts i A viral genome is integrated into the host genome during infection ii)Viral genome can be made of lipids ii viral genome encodes gene for reverse transcriptase iv)Viral genome encodes gene for RNa polymerase v Virus packages reverse transcriptase protein in its virion vi) Virus packages RNa polymerase protein in its virion vii)Virus encodes genes for synthesizing lipid envelope
Question 5 Part A a) Which of the following is true about viruses? (Circle all that apply.) 3 pts i) They encode genes for synthesizing their own ATP. ii) They are single cell organisms. iii) They can have a genome made of DNA. iv) They package ribosomes into their virion. v) They can have a single stranded or double stranded RNA genome. vi) They can have a membrane-like envelope. b) Some viruses like influenza can cause disease in humans. Which of the following can clonally expand to respond to an influenza infection. (Circle all that apply.) 6 pts i) B cells ii) Macrophages iii) Killer T cells (CTLs) iv) CD4+ T cells v) Neurons c) Both bacterial viruses and plasmids can be used as cloning vectors. Which of the following is true AND distinguishes a virus from a plasmid? (Circle all that apply.) 2 pts i) Plasmids use the translation machinery of the cell. ii) Viruses have a protein capsid. iii) Viruses can replicate in the absence of a cellular host. iv) Plasmids carry genes. v) Plasmids have restriction sites. d) Which of the following is true about retroviruses? (Circle all that apply.) 6pts i) A viral genome is integrated into the host genome during infection. ii) Viral genome can be made of lipids. iii) Viral genome encodes gene for reverse transcriptase. iv) Viral genome encodes gene for RNA polymerase. v) Virus packages reverse transcriptase protein in its virion. vi) Virus packages RNA polymerase protein in its virion. vii) Virus encodes genes for synthesizing lipid envelope. 8
Part B you are studying a tumor virus that is capable of transforming healthy cells into cancer cells. 5 pts e) What is the single most likely explanation for this viral transforming property? i Virus genome encodes an oncogene ii)Virus genome encodes a tumor-suppressor gene ii) Virus genome encodes an inactivated tumor-suppressor gene iv)Virus genome encodes an inactivated proto-oncogene v)Virus packages growth factors in its virion. To further study this transforming property, you make a radioactive probe that is dentical to the viral genome f)would you expect this probe to hybridize with genomic dNa from healthy uninfected cells? 1 pt yes g)Would you expect this probe to hybridize with genomic DNa from infected cancerous cells? 1 pt h) How can you best explain your choices from f)and g)? 2 pts i Uninfected cells do not contain the virus, infected cells do ii) Virus does not affect host genome ii)Virus and host both encode a version of the capsid gene iv) Integrated viral genome cannot be recognized by viral probe v) Virus and host both encode a version of the cancer-causing gene vi) Viral and host rna polymerase genes are similar vii)Viral and host ribosomal genes are similar
Name__________________________________ Part B You are studying a tumor virus that is capable of transforming healthy cells into cancer cells. 5 pts e) What is the single most likely explanation for this viral transforming property? i) Virus genome encodes an oncogene. ii) Virus genome encodes a tumor-suppressor gene. iii) Virus genome encodes an inactivated tumor-suppressor gene. iv) Virus genome encodes an inactivated proto-oncogene. v) Virus packages growth factors in its virion. To further study this transforming property, you make a radioactive probe that is identical to the viral genome. f) Would you expect this probe to hybridize with genomic DNA from healthy uninfected cells? 1 pt Yes No g) Would you expect this probe to hybridize with genomic DNA from infected cancereous cells? 1 pt Yes No h) How can you best explain your choices from f) and g)? 2 pts i) Uninfected cells do not contain the virus, infected cells do. ii) Virus does not affect host genome. iii) Virus and host both encode a version of the capsid gene. iv) Integrated viral genome cannot be recognized by viral probe. v) Virus and host both encode a version of the cancer-causing gene. vi) Viral and host RNA polymerase genes are similar. vii) Viral and host ribosomal genes are similar. 9