8.1 - 8.3 Flashcards
what does RNA pol I transcribe
rRNA
what does RNA pol II transcribe
mRNA, miRNA, snRNA
what does RNA pol III transcribe
tRNA
what are the similarities between prokaryotic and eukaryotic polymerase
what are the differences between prokaryotic and eukaryotic polymerase
what is the function of the clamp structure in RNA pol II
clamp domain swings over the cleft between the jaws of the polymerase during formation of the transcribing complex, trapping the template DNA strand and transcript
list eukaryotic promoter elements
- TATA box
- initiator
- CpG islands
- BRE and DPE (in combination with TATA or Inr)
what is CpG island
stretch of 20-50 CG nucleotides located approx. 100 bp upstream from transcription start site
what is the first element to bind to promoter DNA
TFIID: TATA-binding protein (TBP) and TATA-associated factors (TAFs)
what happens after TFIID binds
TFIIA and TFIIB come along and bend the DNA (this is essential)
what happens after DNA is bent
RNA pol II comes along with CTD and TFIIF forming core PIC
before ATP, is the PIC closed or open
closed
after ATP, is the PIC closed or open
open
CTD must be ____________ for elongation to begin
FULLY PHOSPHORYLATED
what is the first step in the formation of the pre-initation complex (PIC)
TATA-binding protein binds to the minor groove of DNA
what is happening in a mutated region where transcription is completely abolished
there is a mutation in the TATA box region
what does DNase I footprinting tell us
reveals the region of a DNA sequence where a transcription factor binds
defines the regions where proteins are being bound
what does gel electrophoresis tell us
if the DNA is free or if there is a protein bound (the slower moving one will be the one with the protein bound)
all transcription factors that function as activators have what
a DNA binding domain and an activator domain
what are the 3 common structures of DNA binding domains
helix-turn-helix
zinc fingers
leucine zipper
coiled-coil
where do the majority of DNA binding domains bind
in the MAJOR GROOVE
what is cooperative binding
the cooperative binding of two transcription factors to neighboring sites (strengthens binding)
what is the DNA recognition code
the edge of each base pair contains a distinctive pattern of hydrogen bond donors, hydrogen bond acceptors and methyl groups
why do majority of transcription factors bind to major groove
from the major groove, each base pair has a distinct pattern that is recognizable but this is not the case from the minor groove
what is a homeodomain
binds DNA through 3 helix structures (recognition helix) and the major groove
