Lecture 5 - Overview of transcription and mRNA formation Flashcards
During transcription, incoming ________________ base-pair with bases in the ________________. They are joined together by ______ from ___ to ______ on the RNA**
ribonucleoside triphosphates (rNTPs). template DNA strand. RNA polymerase. 5’ to 3’
Why is polymerization energetically favoured during elongation.
High energy bond between alpha and beta phosphates on rNTPs is replaced by low energy phosphodiester bond between the rNTPs
Transcription starts at the ____ position. The coding sequence is ________ from this position and the promoter is _________. The ______ strand is read from ___ to ____.
+1. downstream. upstream. template DNA. 3’ to 5’
________ is the critical mechanism for gene expression regulation
initiation
During initiation, 3 things that RNAP does
Binds to promoter sequence. Denatures DNA. Catalyzes first phosphodiester linkage
During elongation, RNAP advances from ___ to ____ down the _______ strand and ________ DNA. It polymerizes _______.
3’ to 5’. template. denatures. polymerizes RNA
During termination, 3 things RNAP does
polymerase recognizes stop site, releases completed RNA, dissociates from DNA.
_______ (which type) RNAP requires associated proteins called _________ which help it _________ and ________
eukaryotic. GTFs. find promoter. initiate transcription
When RNAP binds to promoter sequence on DNA ____, we call that ________ complex. when DNA melted and ___________ (__bp longs) is created, the ________ complex is formed
duplex, closed, transcription bubble - 14bp, open
During elongation, there is a ____________ behind the nascent RNA. Multiple _________ can transcribe the ________ DNA strand at the ________ time. This is shown on the _________.
hybrid region (DNA:RNA). polymerases. same template. same. EM image
Speed of elongation is around ___________. small genes are transcribed in __________ whereas big genes (with big ____) can take ________.
1000 nt/min. a few minutes. introns. hours.
Completed RNA molecule is called the __________
primary transcript
What signals the bound RNAP to terminate transcription
specific sequence in the TEMPLATE DNA strand
the terminating sequence has to be on the ________ strand
template
E.Coli RNAP has ___________ which are ___, ___, ___, ___, ___
five subunits. alpha, beta, alpha prime, beta prima, omega.
RNAPs have structures that are ________ because _________
similar. all deal with DNA.
What happens to DNA when it enters RNAP (an enzyme) (3)
1) Bends sharply 2) Template strand is open 3) Template strand can go in active site of enzyme
Gene organization in prokaryotes. How it is called and amount of non coding genes
Genes with common function arranged linearly in operons and transcribed together on a SINGLE mRNA. Called coordinate expression. Few non coding gaps of DNA prokaryotic genomes.
Gene organization in eukaryotes. In eukaryotes, gene _______________ is not achieved by simple _______________.
Analogous genes (related proteins) are scattered on several chromosomes. co-regulation. physical linkage.
mRNA in prokaryotes vs mRNA in eukaryotes
in prokaryotes mRNAs directly transcribed from DNA. in eukaryotes, transcripts go through several PROCESSING steps before becoming mRNAs.
The cap of the primary transcript will be __________ by other _________ when _________ does its function
recognizes. molecules. RNA
Steps of RNA processing. RNA retains ____________ at its ____ and _____ ends.
Capping, cleavage at poly(A) site and polyadenylation. Intron excision. Exon ligation. RNA retains untranslated regions (UTRs) at its 3’ and 5’ ends.
What process can increase protein diversity and how
Alternative splicing. Cell types produce different forms of the protein encoded by a gene.
Exemple of alternative splicing
Fibronectin gene. in fibroblasts, the fibronecting mRNA transcript contains EIIIB and EIIIA regions of the gene but in liver cells, hepatocyte fibronectin mRNA doesn’T contain EIIIB and EIIIA regions of the gene
Different forces and mechanisms that unwind DNA (2)
1) TFIIH helicase activity necessary for ATP hydrolysis which provides energy for a TFIIH subunit to unwind DNA at start site (it also pushes DNA into the polymerase)
2) As DNA is held in place in the PIC (preinitiation complex) by binding of TBP of TFIID to tatabox, this force and force of TFIIH unwinding subunit both ASSIST N-terminal region of TFIIB and pol II to melt the DNA at transcr. site
