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
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)
• 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.)
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
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
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