7.014 Quiz II Handout• Quiz II: Friday, March 1812:05 - 12:55Walker**This will be a closed book exam**• Quiz Review Session: Wednesday, March 167:00 - 9:00 pmroom 54-100• Open Tutoring Session: Thursday, March 174:00 - 6:00 pmroom 66-1562Question 1Shown below is a representation of an origin of replication.5'3'5'3'ACBDGGAAC CAAGGGGAAC CAAGG fork 1 fork 2a) For the following, use sites A and B with respect to fork 1 and sites C and D with respect tofork 2.i) On which strand(s) will replication be continuous?template 1 template 2 template 3 template 4ii) To which site or sites (A, B, C, or D) can the primer 5'-GUUCC-3' bind to initiatereplication?iii) When DNA ligase is inhibited, it differentially affects the synthesis from the leadingand the lagging strands. Explain which strand (leading or lagging) is more affected bythe lack of DNA ligase and why. template 4 template 3 template 1 template 2ORI3Question 1, continuedb) The next nucleotide to be added to a growing DNA strand is dCTP (shown).• Circle the part of the growing DNA chain to which the next base is attached.• Circle the part of the dCTP that is incorporated into the growing DNA chain. CCHOHCH2O OP--OOP-OP-NN NH 2 O O O C O C O O Oc) DNA Replication involves many different enzymatic activities. Match each enzyme activitylisted below with the function(s) that it has in the replication process. The first one is done foryou.Enzyme ActivityFunction(s)Choose From:Topoiosmeraseka)3’ 5’ growth of new DNA strandPrimase (synthesizes primer)b)5’ 3’ growth of new DNA strandDNA polymerase to elongate newDNA strandc)3’ 5’ exonucleaseHelicase to unwind DNAd)5’ 3’ exonucleaseDNA polymerase to replace RNAwith DNAe)Makes RNA primer complementaryto the lagging strandProcessivity factor f)Makes RNA primer complementaryto the leading strandg)Makes peptide bondsh)Separates the two DNA strandsi)Maintains DNA polymerase ontemplatej)Provides 3’ hydroxyl for initiationof DNA polymerizationk)Untangles super-coiled DNAOCCCCHOHCH2ONNOCH3Growing DNA chaindCTP4Question 2Below is the partial sequence of the sevenohwunforin (7014in) gene, hypothesized to be mutantin students who take 7.013 Introductory Biology and in those students at the other school upthe river. The promoter is underlined and transcription begins at and includes the bold G/Cbase pair.5’ TGCCA TCCGA TTGGT GTTCC TTCCA TGAAG GATGC ACAAC GCAAA 3’3’ ACGGT AGGCT AACCA CAAGG AAGGT ACTTC CTACG TGTTG CGTTT 5’5’ TACAC GCTTA GCTGA CTATA AGGAC GAATC GCTAC AACGA TGCGA 3’3’ ATGTG CGAAT CGACT GATAT TCCTG CTTAG CGATG TTGCT ACGCT 5’5’ TGCCA TCCGA TTGGT GTTCC TTCCA TGAAG GATGC ACAAC GCAAA 3’3’ ACGGT AGGCT AACCA CAAGG AAGGT ACTTC CTACG TGTTG CGTTT 5’a) What are the first 12 nucleotides of the transcript encoded by the 7014in gene? Label the 5’and 3’ ends.__’--__’b) On the DNA sequence above, circle the DNA bases that encode the first amino acid of theprotein.c) What are the first four amino acids encoded by the 7014in transcript? Label the N- and C-terminus____- - ___d) You want to create a system to translate a specific mRNA in a test tube. To an appropriatewater and salt solution you add many copies of this mRNA and ATP (energy). What other keycomponents must you add?You succeed in translating the mRNA in your test tube. You repeat the experiment with twoidentical test tubes. You add limiting amounts of the antibiotic puromycin to test tube 2 only.Puromycin is a molecule that has structural similarities to the 3’ end of a charged tRNA. It canenter the ribosome and be incorporated into the growing protein. When puromycin isincorporated into the polypeptide, it stalls the ribosome and the polypeptide is released. Youdo not know if puromycin recognizes a specific codon or not.e) What effect would puromycin have on transcription?f) What effect would puromycin have on translation?5Question 2, continuedg) You examine the length of the polypeptide produced in both test tubes.i) In test tube 1 (no puromycin) you get a polypeptide that is 100 amino acids long. Atleast how many bases was the mRNA that you added?ii) Which of the following would you find in test tube 2 (has limiting amounts ofpuromycin) if puromycin does NOT recognize a specific codon.Only a single type of polypeptideOnly 2 types of polypeptides that are each different lengthsOnly 3 types of polypeptides that are each different lengthsOnly 4 types of polypeptides that are each different lengthsPolypeptides of all sizes, i.e., dipeptides, tripeptides, … a polypeptide that is 100amino acids longiii) Which of the following would you find in test tube 2 (has limiting amounts ofpuromycin) if puromycin recognizes a specific codon that occurs three times in themRNA.Only a single type of polypeptideOnly 2 types of polypeptides that are each different lengthsOnly 3 types of polypeptides that are each different lengthsOnly 4 types of polypeptides that are each different lengthsPolypeptides of all sizes, i.e., dipeptides, tripeptides, … a polypeptide that is 100amino acids long6Question 2, continuedThe 7014in gene encodes a protein (7014IN) that binds the neurotransmitter serotonin, asshown below. The five amino acids 7014IN involved in binding serotonin are shown.To understand the difference between introductory biology students, you have determined theDNA sequence for the 7014in gene in a group of 7.013 and 7.014 students. Below is the 7014INprotein and the DNA sequence that encodes it. The amino acids depicted in the picture aboveare underlined.From a 7.014 student:DNA 5’ ACC AAT GGA CCA GCA GGA AGC GGG GTA GCT GAG TAC 3’3’ TGG TTA CCT GGT CGT CCT TCG CCC CAT CGA CTC ATG 5’Protein N- Thr Asn Gly Pro Ala Gly Ser Gly Val Ala Glu Tyr –Ch) You find that 7.013 student 1 has the following DNA sequence for the 7014IN:5’ ACC AAT GGA CCA GCA GGA TAG CGG GGT AGC TGA GTAC 3’3’ TGG TTA CCT GGT CGT CCT ATC GCC CCA TCG ACT CATG 5’i) Indicate (circle/underline) the site of the mutation on the sequence directly above.ii) Does student 1 have an insertion, deletion, or substitution mutation?iii) Would you expect this DNA sequence to encode a protein that binds serotonin?Why or why not? A chart of the amino acids is found on page 10.i) You find that 7.013 student 2 has the following DNA sequence for the 7014IN:5’ ACC AAT GGA CCA GCA GGA AGC GGG GTA GCT GAT TAC 3’3’ TGG TTA CCT GGT CGT CCT TCG CCC CAT CGA CTA ATG 5’i)
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