Difference between revisions of "Blitvak Week 2"

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Individual Journal Assignment Week 2

Given Strand of DNA

5’-cgtatgctaataccatgttccgcgtataacccagccgccagttccgctggcggcatttta-3’

• Given strand is written from 5’ to 3’; each strand has a complementary antiparallel strand
• The given strand is the mRNA-like strand

Given Strand and the Complementary Strand

5’-cgtatgctaataccatgttccgcgtataacccagccgccagttccgctggcggcatttta-3’ - Given, mRNA-like strand
3’-gcatacgattatggtacaaggcgcatattgggtcggcggtcaaggcgaccgccgtaaaat-5’ - Found, template strand

• Since the given strand runs from 5’ to 3’, the complementary strand will run from 3’ to 5’
• Complementary strand was found by applying the base pairing of C-G, and A-T
• Under each base letter of the given strand, the corresponding base letter (that forms a base-pair) is written to find the complementary strand
• Since the given strand is 5’ to 3’, it is the strand that is the mRNA-like strand. This is due to the fact that DNA/mRNA must be synthesized from the 5’ to 3’ direction (via the template strand)

Reading Frames of the mRNA-like strand

+1 Reading Frame

Transcribed mRNA codons

5’-cgu aug cua aua cca ugu ucc gcg uau aac cca gcc gcc agu ucc gcu ggc ggc auu uua-3’

Translated Amino Acid Sequence

Nter-RMLIPCSAYNPAASSAGGIL-Cter

+2 Reading Frame

Transcribed mRNA codons

5’-c gua ugc uaa uac cau guu ccg cgu aua acc cag ccg cca guu ccg cug gcg gca uuu ua-3’

Translated Amino Acid Sequence

Nter-VC(STOP)YHVPRITQPPVPLAAF-Cter

+3 Reading Frame

Transcribed mRNA codons

5’-cg uau gcu aau acc aug uuc cgc gua uaa ccc agc cgc cag uuc cgc ugg cgg cau uuu a-3’

Translated Amino Acid Sequence

Nter-YANTMFRV(STOP)PSRQFRWRHF-Cter

• Convert the DNA strands to mRNA by applying A-U pairing rather than A-T pairing
• A reading frame is one of the ways of dividing a strand into triplets (or codons)
• Stop codons are designated by (STOP)
• There are three possible reading frames with the mRNA-like strand, the +1, +2, and +3
• +1 reading frame is from the first base to the last base in a given mRNA-like strand (the entire strand)
• +2 reading frame excludes the very first base from the reading frame
• +3 reading frame excludes the first two bases from the reading frame
• It is helpful to group the sequences into triplets and exclude incomplete triplets
• Use an RNA Codon Table to find the amino acids that correspond to the codons (triplets) in mRNA
• Different reading frames lead to different sequences of amino acids
• All reading frames are from 5’ to 3’

Reading Frames of the template strand

-1 Reading Frame

Transcribed mRNA codons

5’-uaa aau gcc gcc agc gga acu ggc ggc ugg guu aua cgc gga aca ugg uau uag cau acg-3’

Translated Amino Acid Sequence

Nter-(STOP)NAASGTGGWVIRGTWY(STOP)HT-Cter

-2 Reading Frame

Transcribed mRNA codons

5’-u aaa aug ccg cca gcg gaa cug gcg gcu ggg uua uac gcg gaa cau ggu auu agc aua cg-3’

Translated Amino Acid Sequence

Nter-KMPPAELAAGLYAEHGISI-Cter

-3 Reading Frame

Transcribed mRNA codons

5’-ua aaa ugc cgc cag cgg aac ugg cgg cug ggu uau acg cgg aac aug gua uua gca uac g-3’

Translated Amino Acid Sequence

Nter-KCRQRNWRLGYTRNMVLAY-Cter

• Finding reading frames is the same for the template strand as it is for the mRNA-like strand, but each is designated as -1, -2, and -3 respectively
• Since there are also 3 possible reading frames for the template strand, there are 6 total reading frames in double-stranded DNA
• Since the complementary template strand is 3’ to 5’, it must be reversed so that it is 5’ to 3’ (prior to finding its reading frames)

Open Reading Frames

• The +1, -2, and -3 reading frames are all open reading frames since they all contain no stop codons in their mRNA sequences

Brandon Litvak
BIOL 367, Fall 2015