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Shine-Dalgarno Motif

Shine-Dalgarno Motif. Ribosome binding site located about 13 bases upstream of AUG start codon SD sequence is: 5’-AGGAGGU-3’ Middle GGAG is more highly conserved Degree of match is positively correlated with translation rate. Assignment (due 9/9/04).

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Shine-Dalgarno Motif

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  1. Shine-Dalgarno Motif • Ribosome binding site located about 13 bases upstream of AUG start codon • SD sequence is: 5’-AGGAGGU-3’ • Middle GGAG is more highly conserved • Degree of match is positively correlated with translation rate

  2. Assignment (due 9/9/04) • Write perl code to detect Shine-Dalgarno motifs in E. coli DNA sequences. • I will give you about 15 files, each has a single gene and one SD motif. (Ecoli.1, Ecoli.2, etc. in “examples”. • You do not know which ORF to use (except that it is in the forward direction, so only 3 choices). • S-D will be 6 bp (±5) upstream of ATG. • Perfect matches are the exception, not the rule. • Which ATG is a start codon? (Hint: gene will be at least 250 bp long, so if you encounter a stop codon early, it is not a gene. If you do not encounter a stop codon ever, it is not a gene.)

  3. Eukaryotes (eucaryotes) Cells with a nucleus (us)

  4. Gene expression: eukaryotes vs. prokayotes

  5. RNA polymerase II promoters • BRE - TFIIB recognition element • TATA box • INR - Intiator region Py.Py.A*.N.T/A.Py.Py • (Py = pyramidine C/T) • DPE - downstream promoter element • Other elements 100-300 bp upstream CAT box and GC box

  6. Initiation of transcription • TFIIA, B, C … general transcription factors • TBP - TATA binding protein • Over 100 proteins involved • TFIIH pulls DNA apart • Then transcription factors are released so that transcription can occur • Similar to sigma factor in prokaryotic transcription

  7. In vivo is even more complex; note long distance regulatory proteins

  8. Recognition sequences for most common splice (Y =C/U(T), R=A/G)

  9. “Lariat” mechanism for removing intron

  10. GT(U) - AG rule • Most common splice mechanism • U1, U2, U4, U5, U6 are snRNPs (small nuclear ribonucleoproteins) • snRNPs are made up of snRNAs and proteins • Assembly of snRNPs and other proteins is called a spliceosome

  11. Alternative splicing!

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