MIT Department of Biology 7.013: Introductory Biology - Spring 2005 Instructors: Professor Hazel Sive, Professor Tyler Jacks, Dr. Claudette Gardel 7.013 Central Dogma Section-Replication/Transcription/Translation Part 1 Shown below is a 240 base pair segment of a modified version of an E. coli gene. It includes the promoter and the first codons of the gene. The sequences of both strands of the DNA duplex are shown in Figure 1. The top strand reads 5' to 3' left to right (1 to 240); the bottom, complimentary, strand reads 5' to 3' right to left (240 to 1). 5'-ATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTA 1 ---------+---------+---------+---------+---------+---------+ 60 3'-TACACTCAATCGAGTGAGTAATCCGTGGGGTCCGAAATGTGAAATACGAAGGCCGAGCAT TGTTGTGTGGAATTGTGAGCGGATAACAATGTCACACAGGAAACAGCTAAGACCATGTTT 61 ---------+a--------+---------+----d---e+--f-----c+---------+ 120 ACAACACACCTTAACACTCGCCTATTGTTACAGTGTGTCCTTTGTCGATTCTGGTACAAA ACGCCAAGCTCGGAATTAACCCTCACTAAAGGGAACAAAAGCTGGAGCTCCACCGCGGTG 121 ---------+---------+-------g-+---------+---------+---------+ 180 TGCGGTTCGAGCCTTAATTGGGAGTGATTTCCCTTGTTTTCGACCTCGAGGTGGCGCCAC GCGGCCGCTCTAGAACTAGTGGATCCCCCGGGCTGCAGGCATTCGATATCAAGCTTATCG-3' 181 ---------+---------+---------+---------+---------+-x-------+ 240 CGCCGGCGAGATCTTGATCACCTAGGGGGCCCGACGTCCGTAAGCTATAGTTCGAATAGC-5' a) RNA polymerase binds to the sequence (underlined above) and shown below. 5'-...CTTTACACTTT...14bp space....TATGTTG...-3'||||||||||| |||||||3'-...GAAATGTGAAA...14bp space....ATACAAC...-5' Once bound, RNA polymerase starts making mRNA at the 6th nucleotide after the end of the sequence (at position a, also underlined above). Synthesis of the mRNA proceeds 5' to 3' left to right on the sequence above. Write the sequence of the first 10 nucleotides of the resulting mRNA. b) What are the first five amino acids of the resulting protein? c) Does translation terminate at the underlined TAA at position 108 (c, bold)? Why or why not?d) How would your answer to b) change if the C/G base pair at position 95 (d, bold) was deleted? e) How would your answer to b) change if an A/T base pair were added between 98 & 99 (e, bold)? f) How would your answer to b) change if the A/T base pair at position 103 (f, bold) were changed to G/C? g) Give a single base change (substitution, deletion, or addition of a single base and it's partner on the other strand) that would cause termination of the polypeptide chain at TAA codon 147 (g, underlined). h) Give a nonsense mutation (codon --> stop codon). i) Give a missense mutation (codon --> codon for another amino acid). j) Give a silent mutation (codon ---> codon for the same amino acid). The Genetic Code U C A G U UUU UUC UUA UUG phepheleu leu UCU UCC UCA UCG ser ser ser ser UAU UAC UAA UAG tyr tyrSTOP STOP UGU UGC UGA UGG cys cysSTOP trp U C A G C CUU CUC CUA CUG leu leu leu leu CCU CCC CCA CCG pro pro pro pro CAU CAC CAA CAG his his glngln CGU CGC CGA CGG arg arg arg arg U C A G A AUU AUC AUA AUG ile ile ile met ACU ACC ACA ACG thr thr thr thr AAU AAC AAA AAG asn asn lyslys AGU AGC AGA AGG ser ser arg arg U C A G G GUU GUC GUA GUG val val val val GCU GCC GCA GCG ala ala ala ala GAU GAC GAA GAG asp aspgluglu GGU GGC GGA GGG glyglyglygly U C A GPart 2 Given the sequences on these next two pages, your goal is to draw a schematic of the con-6 gene. Determine the transcription start and stop sites, start and stop codons, untranslated regions, introns and exons. 5'-CGGTGAATAAATACGTCATGACGGTGCTGTCAGCATCATCGATAGGTAGGAGCGAACAAACAACCTAACATCGGATTGCA 1 +---------+---------+---------+---------+---------+---------+---------+---------3'-GCCACTTATTTATGCAGTACTGCCACGACAGTCGTAGTAGCTATCCATCCTCGCTTGTTTGTTGGATTGTAGCCTAACGT GGACCGCGGGGCAGGATTGCTCCGGGCTGTTTCATGACTTGTCAGGTGGGATGACTTGGATGGAAAAGTAGAAGGTCATG 81 +---------+---------+---------+---------+---------+---------+---------+---------CCTGGCGCCCCGTCCTAACGAGGCCCGACAAAGTACTGAACAGTCCACCCTACTGAACCTACCTTTTCATCTTCCAGTAC GGGTGGCCAACTTGGGCGAGAAAAGGTATATAAAGGTCTCTTGCTCCCATCAACTGCCTCAAAAGTAGGTATTCCAGCAG 161 +---------+---------+---------+---------+---------+---------+---------+---------CCCACCGGTTGAACCCGCTCTTTTCCATATATTTCCAGAGAACGAGGGTAGTTGACGGAGTTTTCATCCATAAGGTCGTC ATCAGACAACCAAACAAACACACTTCATTCCCAAGACATCACTCACAAACAACCAACCTCTTCCAATCCAACCACAAACA 241 +---------+---------+---------+---------+---------+---------+---------+---------TAGTCTGTTGGTTTGTTTGTGTGAAGTAAGGGTTCTGTAGTGAGTGTTTGTTGGTTGGAGAAGGTTAGGTTGGTGTTTGT AAAATCAGCCAATATGTCCGACTTCGAGAACAAGAACCCCAACAACGTCCTTGGCGGACACAAGGCCACCCTTCACAACC 321 +---------+---------+---------+---------+---------+---------+---------+---------TTTTAGTCGGTTATACAGGCTGAAGCTCTTGTTCTTGGGGTTGTTGCAGGAACCGCCTGTGTTCCGGTGGGAAGTGTTGG CTAGTATGTATCCTCCTCAGAGCCTCCAGCTTCCGTCCCTCGTCGACATTTCCTTTTTTTTCATATTACATCCATCCAAG 401 +---------+---------+---------+---------+---------+---------+---------+---------GATCATACATAGGAGGAGTCTCGGAGGTCGAAGGCAGGGAGCAGCTGTAAAGGAAAAAAAAGTATAATGTAGGTAGGTTC TCCCACAATCCATGACTAACCAGAAATATCACAGATGTTTCCGAGGAAGCCAAGGAGCACTCCAAGAAGGTGCTTGAAAA 481 +---------+---------+---------+---------+---------+---------+---------+---------AGGGTGTTAGGTACTGATTGGTCTTTATAGTGTCTACAAAGGCTCCTTCGGTTCCTCGTGAGGTTCTTCCACGAACTTTT CGCCGGCGAGGCCTACGATGAGTCTTCTTCGGGCAAGACCACCACCGACGACGGCGACAAGAACCCCGGAAACGTTGCGG 561 +---------+---------+---------+---------+---------+---------+---------+---------GCGGCCGCTCCGGATGCTACTCAGAAGAAGCCCGTTCTGGTGGTGGCTGCTGCCGCTGTTCTTGGGGCCTTTGCAACGCC GAGGATACAAGGCCACCCTCAACAACCCCAAAGTGTCCGACGAGGCCAAGGAGCACGCCAAGAAGAAGCTTGACGGCCTC 641 +---------+---------+---------+---------+---------+---------+---------+---------CTCCTATGTTCCGGTGGGAGTTGTTGGGGTTTCACAGGCTGCTCCGGTTCCTCGTGCGGTTCTTCTTCGAACTGCCGGAG GAGTAAGCTCAGAGTTCACGAAAGAACCATTCGACGAGGGGAAGCACGGGGTTATCTCGTTCGAAACATGGGCCTGGTTA 721 +---------+---------+---------+---------+---------+---------+---------+---------CTCATTCGAGTCTCAAGTGCTTTCTTGGTAAGCTGCTCCCCTTCGTGCCCCAATAGAGCAAGCTTTGTACCCGGACCAAT ATGCAAATGCATAATGGGGAGGATAATGAATCATGAGGTGTACGATATGGACGATATTGACGGATCTTAATTTGATGACA 801 +---------+---------+---------+---------+---------+---------+---------+---------TACGTTTACGTATTACCCCTCCTATTACTTAGTACTCCACATGCTATACCTGCTATAACTGCCTAGAATTAAACTACTGT GTAATGAAATCACACCATAGT-3' 881 +---------+---------+ 901 CATTACTTTAGTGTGGTATCA-5' Figure 1: Genomic DNA sequence of con-6 gene from Neurospora crassa. The sequence of both strands (5' to 3' on top, 3' to 5' on bottom) is shown above with nucleotides numbered 1 to 901. The dashed lines are interrupted every tenth nucleotide with a
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