Name five differences between prokaryotic transcription and eukaryotic transcription.
1. eukaryotes have three types of RNA polymerases
2. eukaryotes don't have a generic promoter; there are three different types for the three different RNA polymerases
3. many proteins take part in promoter recognition; different proteins for different pro
Name two proteins that have roles in chromatin modification so that transcription can be initiated.
1. acetyltransferases - add acetyl groups to histones so that the DNA is more accessible
2. chromatin-remodeling proteins - bind to chromatin and displace nucleosomes from promoters and other important regions for transcription
a class of accessory proteins that bind to eukaryotic promoters near the start site and are a part of the basal transcription apparatus that initiates transcription
general transcription factors (TFs)
complex of transcription factors, RNA polymerase, and other proteins (transcription activator proteins) that assemble on the promoter and are capable of igniting minimal levels of transcription
basal transcription apparatus
a class of accessory proteins in eukaryotic cells that bind to consensus sequences in regulatory promoters or enhancers and affect transcription initiation by stimulating the assembly of the basal transcription apparatus
transcriptional activator proteins (TAPs)
How is promoter recognition carried out in eukaryotes?
Promoter recognition is carried out by accessory proteins that bind to the promoter and then recruit a specific RNA polymerase (I, II, or III) to the promoter.
A promoter for a gene transcribed by RNA polymerase II typically consists of what two parts?
1. the core promoter
2. the regulatory promoter
located immediately upstream of the gene; DNA sequences to which the basal transcription apparatus binds
core promoter
consensus sequence (TATAAAA) commonly found in eukaryotic RNA polymerase II promoters; usually located 25 bp upstream of the transcription start site; determines the start point for transcription
TATA box
True/False: The core promoter typically includes one or more consensus sequences.
true
What do the consensus sequences in an RNA polymerase II promoter do?
They are recognized by transcription factors that bind to them and serve as a platform for the assembly of the basal transcription apparatus.
True/False: SOME general transcription factors are required, but no transcription activator proteins are.
true
DNA sequence located immediately upstream of the core promoter that affects transcription; contains consensus sequences to which transcription regulator proteins bind
regulatory promoter
_____ bind to the consensus sequences in the regulatory promoter and either directly or indirectly make contact with the basal transcription apparatus and affect the rate at which transcription is initiated.
transcriptional activator proteins
sequence that stimulates maximal transcription of distant genes; affects only genes on the same DNA molecule (is cis acting), contains short consensus sequences, is not fixed in relation to the transcription start site, can stimulate almost any promoter i
enhancer
True/False: An enhancer may be upstream OR downstream of a gene it stimulates.
true
The DNA between an enhancer and the promoter must _____ so TAPs bound to the enhancer can interact with the basal transcription machinery through protein-protein interactions.
loop out
promoter located within the sequences of DNA that are transcribed into RNA (the RNA-coding region); found in the transcription units that are transcribed by RNA polymerase III
internal promoter
polypeptide chain found in several different general transcription factors that binds to sequences (consensus) in eukaryotic promoters (core)
TATA-binding protein (TBP)
general transcription factor that transports TBP
TFIID
In eukaryotes, the transcriptional machinery on the promoter consists of at least how many polypeptides?
50
unnecessary component of the basal transcription apparatus that passes chemical signals on to the RNA polymerase from transcriptional activator proteins
mediator
At what position is the TATA box located?
-25
At what position is the TFIIB recognition element located?
-35
consensus sequence that attracts TFIIB
TFIIB recognition element
Name two absolutely necessary transcription factors.
TFIIB and TFIID
basal transcription apparatus + TAPS + winded DNA
closed complex (pre-initiation complex)
TFIID consists of at least _____ polypeptides.
9
The TATA-binding protein binds to the _____ groove. Then it _____ the DNA and ____ it a little.
minor; bends; unwinds
What is the main job of the transcription factors?
to position the RNA polymerase's active site of the transcription start site
After the RNA polymerase and transcription factors have assembled on the core promoter, what happens?
conformational changes take place in both the DNA and the polymerase; these changes cause from 11 to 15 bp of DNA surrounding the TSS to separate
basal transcription apparatus + TAPs + unwound DNA
open complex
True/False: Eukaryotic initiation may undergo several abortive attempts before elongation begins.
true
Watch the video I made on the structure of RNA polymerase II.
I did.
DNA-RNA hybrid
DNA-RNA duplex
After about _____ bp of RNA have been synthesized, RNA polymerase leaves the promoter.
30
True/False: (If true, explain why.) Many of the transcription factors are left behind by RNA polymerase II at the promoter.
true; they serve to quickly reinitiate transcription with another RNA polymerase enzyme
man who received the Nobel Prize in chemistry in 2006 for his work uncovering the structure of RNA polymerase II; his dad was also a biochemist who won a Nobel Prize
Roger Kornberg
How many nucleotides remain bound in the DNA-RNA duplex within RNA polymerase II?
8
How is large tRNA transcription by RNA polymerase I terminated?
termination factor-mediated (TTF1); the termination factor binds to downstream DNA (analogous to rho-dependent termination in eubacteria, except termination factor does not bind to new RNA molecule)
How is tRNA transcription by RNA polymerase III terminated?
termination sequence-mediated (UUUUU) (analogous to rho-independent termination, except no hairpin is required as it is eubacteria)
How is pre-mRNA transcription by RNA polymerase II terminated?
1. RNA polymerase II transcribes RNA way past the end of the gene.
2. Some consensus sequence on the new pre-mRNA signals cleavage.
3. It's cleaved into protein-coding and useless pre-mRNA.
4. Useless pre-mRNA remains bound to the DNA and RNA polymerase I
core promoter element present at the +30 position; it's sometimes present and can help initiate transcription by binding to transcription factors
downstream core promoter element
What do transcription factors that are not required do?
They turn the volume up or down on transcription.
consensus sequence
recognition site
The basal transcription apparatus does not include _____ and _____.
transcriptional activator proteins and optional general transcription factors
What are the seven steps of eukaryotic pre-mRNA transcription initiation?
1. TFIID/TBP causes DNA to bend and unwind at TATA box
2. essential and optional TFs bind
3. RNA polym. II is attracted and binds to docking station forming basal transcription apparatus
4. TAPs bind regulatory promoter and enhancers and repressors
5. DNA
What is the purpose of two exit holes in RNA polymerase II?
so the DNA and RNA separated and don't remain a hybrid
only large enough to accommodate one rNTP at a time
pore
holding cell for rNTP
funnel