BMB 401 Lecture Notes - Lecture 4: Transcription Bubble, Dna Replication, Dna Supercoil
16 Dec 2016
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RNA Transcription 4.4
4.4a Transcriptional Machinery
• 3
o Transcribing DNA into RNA now
o 3 forms of RNA: rRNA and tRNA (both noncoding) and then mRNA
▪ Many other kinds of ncRNA also
o 3 RNA polymerases mediate it: RNAPI, RNAPII and RNAPIII
o Also need transcription factors along with RNAPs to initiate transcription
• 4
o 3 functions:
▪ RNA translation and protein synthesis
• mRNA has protein code and tRNA helps carry to ribosomes where
rRNA does building
▪ RNA transcription and DNA replication
• snRNA are spliceosome and snoRNA involved in modification of
nucleotides and telRNA helps as an RNA primer to extend
telomeres
▪ Gene regulation (mysterious RNAs)
• siRNA interferes with functions of normal RNAs such as binding to
mRNA and binds complementary and prevents translation
• 5
o RNAPI works with rRNA
o RNAPII works with mRNA
o RNAPIII works with tRNA
o They all need Mg2+ as a cofactor to neutralize – charge on incoming NTPs
• 6
o Get energy cause every nucleotide is like ATP so energy is embedded in the
substrate and get it through hydrolysis
o DNA polerases go 3’→5’ ad this is a ke feature ad epsilo ould proofread
o RNAP do ot hae the 3’→5’ ehais ut the a proofread in 2 ways
▪ 1 = They can backtrack
▪ 2 = they can sense whether to move on or to correct a mistake
• 7
o RNA trasriptio goes 5’→3’ ut ioles only copying one strand unlike DNA
replication
o NTPs added to 3’ groig ed ia NA
o Transcription requires transcription bubble formation just like DNA replication
bubble
• 8
o Bubble travels with machinery as it moves forward
find more resources at oneclass.com
find more resources at oneclass.com
RNA Transcription 4.4
o Antisense/noncoding is the strand acting as a template and other strand is the
sense/coding strand
• 9
o Dynamic process as bubble moves and opens it up and as it moves forward it
overwinds (+ supercoiling) ahead of it and it unwinds (- supercoiling) behind it
o Helicases unwind DNA double helix to generate transcription bubble
o Topoisomerase relieves stress again
o We need transcription bubble but how do we know where to start?
• 10
o Starts near a transcriptional start site (TSS) and this is called promoter
▪ Core component of cis-acting promoters
• Cis-acting = DNA stuff (cis is same thing like part of DNA)
• Trans-acting = protein stuff
o Promoters are docking sites for RNAP but also for trans-acting transcription
factors
o Genes also have cis-acting enhancers and silencers (can both be down or
upstream way far away controlling transcription)
▪ Enhance activate it so proteins that bind are called (co)activators
▪ Silencers downregulate transcription and proteins called repressors bind
to them
o 3 cis-acting things total
o On picture the loop could be 1000 base pairs so distance in sequence is long but
by folding over they come together and work in this way
• 11
o Majority of RNAPII promoters have several of following cis-acting promoter
sequences in order to recruit various trans-acting transcription factors:
▪ CAAT box – docking site for some TFs
▪ BRE – recognition site for TFIIB
▪ TATA – one of very few TFs that binds to DNA in minor groove whereas
most bind to major groove and binding site for TFIID and in particular the
TATA-binding protein part of it
▪ INR – docking site for TFIID which starts transcription and is very
important
▪ MTE – recruits TFIID in conjunction with INR
▪ DPE – substitute for TATA box
o Gene usually only has a couple of these core elements
• 12
o TFIIH unwinds DNA
find more resources at oneclass.com
find more resources at oneclass.com
