7.012 Central Dogma Section

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1 MIT Biology Department 7.012: Introductory Biology - Fall 2004 Instructors: Professor Eric Lander, Professor Robert. Weinberg, Dr. laudette ardel Part entral Dogma Section Shown below is a 240 base pair segment of a modified version of an E. coli gene. It includes the moter and the first codons of the gene. The sequences of both strands of the DN 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'-TTTTTTTTTTTTTTTTTTT '-TTTTTTTTTTTT TTTTTTTTTTTTTTTT a d---e+--f-----c TTTTTTTTTTTTTTTTTTT TTTTTTTT g TTTTTTTTTTTTTTTTTTT TTTTTTTTTTTTT-3' x TTTTTTTTTTTT-5' a) RN polymerase binds to the sequence (underlined above) and shown below. 5'-...TTTTTT...14bp space...tttt...-3' 3'-...TT...14bp space...t...-5' Once bound, RN polymerase starts making mrn at the 6th nucleotide after the end of the sequence (at position a, also underlined above). Synthesis of the mrn ceeds 5' to 3' left to right on the sequence above. Write the sequence of the first 10 nucleotides of the resulting mrn. b) What are the first five amino acids of the resulting tein? c) Does translation terminate at the underlined T at position 108 (c, bold)? Why or why not?

2 d) How would your answer to b) change if the / base pair at position 95 (d, bold) was deleted? e) How would your answer to b) change if an /T base pair were added between 98 & 99 (e, bold)? f) How would your answer to b) change if the /T base pair at position 103 (f, bold) were changed to /? g) ive 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 T codon 147 (g, underlined). h) ive a nonsense mutation (codon --> stop codon). i) ive a missense mutation (codon --> codon for another amino acid). j) ive a snt mutation (codon ---> codon for the same amino acid). The enetic ode ser tyr ser tyr ser STOP ser STOP trp phe phe met his his gln gln asn asn lys lys asp asp glu glu cys cys STOP ser ser

3 Part 2 iven 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'-TTTTTTTTTTTTTTTT '-TTTTTTTTTTTTTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTTTTTTTTT TTTTTTTTTTT TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT TTTTTTTTTTT TTTTTTTTTTTTTTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTTTTTTTTTTTTTTT TTTTTTTTTTTTTTT TTTTTTTTTTTTTT TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT TTTTTTTTT TTTTTTTTTTTTTTTTTTT TTTTTTT TTTTTTTTTTTTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTTTTTTTT TTTTTTTTTTTTTTTTTTTTTTTTTTTT TTTTT-3' TTTTTTTTT-5' Figure 1: enomic DN 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 "+".

4 ENOMI DN: 251 TTTTTTT 300 mrn: 49 ENOMI DN: 301 TTTTTTTTT 350 mrn: ENOMI DN: 351 TTTTT 400 mrn: ENOMI DN: 401 TTTTTTTTTTTTTTT 450 mrn: ENOMI DN: 451 TTTTTTTTTTTTTTTTTT 500 mrn:... ENOMI DN: 501 TTTTTTT 550 mrn: ENOMI DN: 551 TTTTTTTTTT 600 mrn: ENOMI DN: 601 TTT 650 mrn: ENOMI DN: 651 TTT 700 mrn: ENOMI DN: 701 TTTTTTTT 750 mrn: ENOMI DN: 751 TTTTTTTTTTT 800 mrn: ENOMI DN: 801 TTTTTTTTTTTT 850 mrn: ENOMI DN: 851 TTTTTTTTTTTTTT 900 mrn: Figure 2: Sequence alignment of con-6 genomic DN and mrn sequences. The top line of each pair of sequences is the sequence of con-6 genomic DN. The genomic DN nucleotides are numbered as in figure 1. The bottom line is the sequence of a con-6 mrn isolated from Neurospora crassa. The nucleotide numbers of the mrn begin at the 5' end with #1, and end with #539 at the 3'end. Vertical dashes indicate nucleotides identical in both sequences. Dots indicate nucleotides in the genomic sequence that are not found in the mrn sequence. (@ represents 5' -cap)

5 Part 2 continued iven the previous figures draw a schematic of the con-6 gene below. Include the transcription start and stop sites, start and stop codons, untranslated regions, introns and exons phe phe met The enetic ode ser tyr ser tyr ser STOP ser STOP his his gln gln asn asn lys lys asp asp glu glu cys cys STOP trp ser ser

7.013 Problem Set 3 FRIDAY October 8th, 2004

7.013 Problem Set 3 FRIDAY October 8th, 2004 MIT Biology Department 7.012: Introductory Biology - Fall 2004 Instructors: Professor Eric Lander, Professor Robert. Weinberg, Dr. laudette ardel Name: T: 7.013 Problem Set 3 FRIDY October 8th, 2004 Problem