MIT Biology Department 7.012: Introductory Biology -Fall 2004 Instructors: Professor Eric Lander, Professor Robert A Weinberg, Dr. Claudette Gardel 7.012 Practice quiz 2 2004 Actual Quiz 2 (closed book) will be given Monday 10/25 at 10: 00 am No Sections on MONDAy or TUESDAy 10/25-10/26(No Kidding. NOTE THE ROOM MAy BE DIFFERENT THAN THE ROOM yOUR WERE ASSIGNED FOR QUIZ 1 Quiz Review Session Thursday, 10/21 7:00-9:00pm Tutoring Session Friday, 10/22 4:00-6:00pm
1 7.012 Practice Quiz 2 2004 Actual Quiz 2 (closed book) will be given Monday 10/25 at 10:00 am No Sections on MONDAY or TUESDAY 10/25-10/26 (No Kidding.) NOTE THE ROOM MAY BE DIFFERENT THAN THE ROOM YOUR WERE ASSIGNED FOR QUIZ 1 Quiz Review Session Thursday, 10/21 7:00 - 9:00 pm Tutoring Session Friday, 10/22 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
uestion 1 a) Indicate whether each of the following statements is true or false. If false, correct the statement or provide a brief explanation for why it is false ODNA replication is initiated at promoter sequences in the dNA ii)RNA polymerase requires primers to initiate RNA synthesis ii) Okazaki fragments are the short fragments of dna that are produced on the leading strand at the dna replication fork iv)The 5 to 3 direction of DNA synthesis implies that deoxyribonucleotides are added to the 5 OH group on the growing strand v)Transcription is terminated at stop codons in the mRnA b)shown below is the DNA sequence of a gene from a virus that encodes a short viral peptide. Also hown is the sequence of the mRNa synthesized from this gene genomic DNA sequence 5 -AGCTCATGTGCGAGTCCTGACGCTGACTAGG-3 3 -TCGAGTACACGCTCAGGACTGCGACTGATCC-5 mature mRNA sequence(G = G cap) 5-G UCAUGUGCGAACGCUGACUAGGAAAAAAAA..-3 iIn the genomic DNA sequence shown above, draw a box around each of the two exons in the ii)In the mRNA above, some nucleotides are present that are not coded for in the genomic dNA sequence. Name the two processes that have occurred to add these nucleotides to the mrNA ii How many amino acids are in the viral peptide encoded by this gene? iv)Is this virus more likely to replicate in prokaryotic or eukaryotic cells? Briefly explain your
2 Question 1 a) Indicate whether each of the following statements is true or false. If false, correct the statement or provide a brief explanation for why it is false. i) DNA replication is initiated at promoter sequences in the DNA. ii) RNA polymerase requires primers to initiate RNA synthesis. iii) Okazaki fragments are the short fragments of DNA that are produced on the leading strand at the DNA replication fork. iv) The 5' to 3' direction of DNA synthesis implies that deoxyribonucleotides are added to the 5' OH group on the growing strand. v) Transcription is terminated at stop codons in the mRNA. b) Shown below is the DNA sequence of a gene from a virus that encodes a short viral peptide. Also shown is the sequence of the mRNA synthesized from this gene. genomic DNA sequence: 5'-AGCTCATGTGCGAGTCCTGACGCTGACTAGG-3' 3'-TCGAGTACACGCTCAGGACTGCGACTGATCC-5' mature mRNA sequence (G* = G cap): 5'-G*UCAUGUGCGAACGCUGACUAGGAAAAAAAA....-3' i) In the genomic DNA sequence shown above, draw a box around each of the two exons in the gene. ii) In the mRNA above, some nucleotides are present that are not coded for in the genomic DNA sequence. Name the two processes that have occurred to add these nucleotides to the mRNA. iii) How many amino acids are in the viral peptide encoded by this gene? _______ iv) Is this virus more likely to replicate in prokaryotic or eukaryotic cells? Briefly explain your reasoning
U UUU phe(F UCU ser(S UAU UGU cys(c) UUc phe(F) UCc ser(s) UAc tyr (n) UGc cys( C) UUa leu(L) UAA STOP UGA STOP UUG leu L) UCG ser(s) UAG STOP UGG trp(w) cCU leu( L) pro(P) CGU arg (r) CUc leu l) Ccc pro(P) CAc his(H) cGc arg(R) CUA leu l) CCa pro(P) CAA CGa arg(R) CUG leu lL) (P) caG gIn( Q CGG (R) A| AUU ile(工) ACU thr(t) AAU asn(N) AUC ile (I) acc thr D) N AGUAGUcAG AUa ile(工 ACa thr D AAa lys(k) AGa arg(r) AUG AAG (K) Gau ala(a) GAU asp(D) GGu gly(G) GAc asp(D) gly GUA val (v Gca ala(a) gaa glu(e) GGa glyG) A gcg ala(a gag glu(e) Question 2 The term"central dogma"refers to the flow of biological information from dNa to RNA to protein RNA Prote a) i)In the spaces below, indicate the process that corresponds to each arrow ii Name the initiation site for each processes, and on which molecule this site exists itWhat cellular machinery carries out each process? 1 b)What is a gene? Please answer in one sentence. The first sentence written will be considered as your answer c)Many antibiotics are compounds that interfere with the transfer of genetic information from RNA to protein. Streptomycin is a compound that affects the small ribosomal subunit in prokaryotes Streptomycin interferes with the binding of all Methionine -tRNAs to ribosomes. what two specific effects will streptomycin have on protein synthesis in prokaryotes?
3 U C A G U UUU phe (F) UUC phe (F) UUA leu (L) UUG leu (L) UCU ser (S) UCC ser (S) UCA ser (S) UCG ser (S) UAU tyr (Y) UAC tyr (Y) UAA STOP UAG STOP UGU cys (C) UGC cys (C) UGA STOP UGG trp (W) UC A G C CUU leu (L) CUC leu (L) CUA leu (L) CUG leu (L) CCU pro (P) CCC pro (P) CCA pro (P) CCG pro (P) CAU his (H) CAC his (H) CAA gln (Q) CAG gln (Q) CGU arg (R) CGC arg (R) CGA arg (R) CGG arg (R) UC A G A AUU ile (I) AUC ile (I) AUA ile (I) AUG met (M) ACU thr (T) ACC thr (T) ACA thr (T) ACG thr (T) AAU asn (N) AAC asn (N) AAA lys (K) AAG lys (K) AGU ser (S) AGC ser (S) AGA arg (R) AGG arg (R) U C A G G GUU val (V) GUC val (V) GUA val (V) GUG val (V) GCU ala (A) GCC ala (A) GCA ala (A) GCG ala (A) GAU asp (D) GAC asp (D) GAA glu (E) GAG glu (E) GGU gly (G) GGC gly (G) GGA gly (G) GGG gly (G) U C A G Question 2 The term "central dogma" refers to the flow of biological information from DNA to RNA to protein. DNA RNA Protein 1 2 3 a) i) In the spaces below, indicate the process that corresponds to each arrow. 1. ___________ 2. ___________ 3. ___________ ii) Name the initiation site for each processes, and on which molecule this site exists. 1. ________________2. ____________________3. ________________ iii) What cellular machinery carries out each process? 1. ___________ 2. ___________ 3. ___________ b) What is a gene? Please answer in one sentence. The first sentence written will be considered as your answer. c) Many antibiotics are compounds that interfere with the transfer of genetic information from RNA to protein. Streptomycin is a compound that affects the small ribosomal subunit in prokaryotes. Streptomycin interferes with the binding of all Methionine-tRNAs to ribosomes. What two specific effects will streptomycin have on protein synthesis in prokaryotes?
Question 3 The primer shown below is used to sequence the following template dNA template dna 5 -ACTGAC-3' 5 -ACCACTAACGTCAGT-3' Draw the resulting DNA fragments that would be produced from each of the 4 sequencing reactions at the correct position (length in nucleotides) as they would appear on the diagram of the sequencing gel DNA length G T C (nts) 111111 54321098765432 B Polio has been practically eliminated from the American population, however, in countries have little or no access to vaccinations, it is still prevalent. As a biologist with a global seek to create a transgenic banana that produces the protein used in the vaccine against consuming these bananas, individuals will develop immunity against the disease. The gene for this protein has already been cloned into a plasmid with a kanamycin-resistance gene(pkR-polio). you need to attach to the gene a banana-specific promoter and dna sequences that will allow the gene to be incorporated into banana DNA. These sequences are contained in the pBan plasmid, which carries a gene for ampicillin resistance. Maps of these two plasmids are shown on the next page, including mportant restriction sites and distances (in base pairs) between the sites
4 Question 3 A. The primer shown below is used to sequence the following template DNA. primer: template DNA: 5'-ACTGAC-3' 5'-ACCACTAACGTCAGT-3' Draw the resulting DNA fragments that would be produced from each of the 4 sequencing reactions at the correct position (length in nucleotides) as they would appear on the diagram of the sequencing gel below. G A T C + DNA length (nts) 15- 14- 13- 12- 11- 10- 9- 8- 7- 6- 5- 4- 3- 2- 1- B. Polio has been practically eliminated from the American population, however, in countries where people have little or no access to vaccinations, it is still prevalent. As a biologist with a global vision, you seek to create a transgenic banana that produces the protein used in the vaccine against polio. By consuming these bananas, individuals will develop immunity against the disease. The gene for this protein has already been cloned into a plasmid with a kanamycin-resistance gene (pKR-polio). You need to attach to the gene a banana-specific promoter and DNA sequences that will allow the gene to be incorporated into banana DNA. These sequences are contained in the pBAN plasmid, which carries a gene for ampicillin resistance. Maps of these two plasmids are shown on the next page, including important restriction sites and distances (in base pairs) between the sites
Question 3 continued Banana specific BamHI promoter 120 EcoRI Bglll gene for polio antigen pBAN KR-polio 280 8900bp 4500bp kan gene banana insertion sequences which allow dna to integrate into na genome Bg1I工 BamH工: ECORI 5AVG A T GG A A ATT C. C a)An end generated by digestion with BamHI can be ligated to an end generated by digestion with BgIII. Why is this possible? b)you want to insert the gene encoding the polio antigen into pBAN. Devise a strategy to accomplish this. Identify the enzyme(s)you would use to cut pBAN, the enzyme (s) you would use to cut pkR olio, and the steps necessary to generate the intact plasmid c)you next transform E. coli with the plasmids you have made. you grow the transformed cells on media containing(circle one) both ampicillin and kanamycin neither ampicillin nor kanamycin Why?
5 Question 3 continued ori amp gene R Banana specific promoter banana insertion sequences which allow DNA to integrate into banana genome BamHI EcoRI pBAN 8900 bp 120 pKR-polio 4500 bp ori kan gene R BglII BglII BamHI start codon stop codon gene for polio antigen EcoRI 280 1120 BglII: BamHI: EcoRI: 5'...A G A T C T...3' 5'...G G A T C C...3' 5'...G A A T T C...3' 3'...T C T A G A...5' 3'...C C T A G G...5' 3'...C T T A A G...5' a) An end generated by digestion with BamHI can be ligated to an end generated by digestion with BglII. Why is this possible? b) You want to insert the gene encoding the polio antigen into pBAN. Devise a strategy to accomplish this. Identify the enzyme(s) you would use to cut pBAN, the enzyme(s) you would use to cut pKRpolio, and the steps necessary to generate the intact plasmid. c) You next transform E. coli with the plasmids you have made. You grow the transformed cells on media containing (circle one): ampicillin kanamycin both ampicillin and kanamycin neither ampicillin nor kanamycin Why?