Lecture 01 - Eukaryotic Transcription Flashcards
What is transcription
the DNA dependent synthesis of RNA
What makes transcription different than replication
- only specific genes are transcribed at a time
- only one strand is typically transcribed
- regulatory sequences in DNA designate beginning and end of DNA segments that are templates for transcription
What is the coding strand used for
it matches the sequence of the RNA an is used as as a reference
What is the antisense strand used for
used by RNA polymerase to synthesize the RNA
What does gene mean
specific DNA sequences associated with products
What is mRNA used for
to direct protein synthesis
What is tRNA used for
delivery of amino acids to ribosomes during translation
What is small interfering and micro RNA used for
sequence-specific inactivation of mRNA
What is large intergenic noncoding RNA used for
transcriptional control
What is small nuclear RNA used for
RNA splicing
What is small nucleolar RNA used for
sequence-specific methylation of rRNA
How do cells differentiate
expression of genes vary from cell to cell
What is an example of long term control
cell differentiation
What is an example of short term control
metabolic control
What does RNAP I do
transcription of rRNA precursors
What does RNAP II do
transcription of mRNA precursors
What does RNAP III do
transcription of 5S, rRNA, tRNA and other small RNA precursors
What subunit is shared between RNAP I, II, III
omega homolog
What subunit is shared between RNAP I and II
alpha homolog
How many subunits does yeast RNA polymerase II have
12
What is the largest subunit of yeast RNA polymerase II
Rpb1
What are the phases of transcription
assembly, initiation, elongation, termination
What does the clamp portion of Rpb2 do
locks over bound dNA to increase processivity
Where are contacts between RNAP and hybrid duplex
the backbone
What are enhancers
variable in terms of location, specific sequences of DNA where proteins can bind
What do accessory proteins do
identify promoters and recruit RNAP to transcription start site
How many general transcription factors are there
6
What is the TATA binding protein
the first protein to bind to a promoter in initiation which distorts the DNA partially unwinding the duplex
How does the TATA binding protein associate
via hydrogen bonding, van der waals interactions and aromatic sidechain interactions
What is the pre-initiate complex
when TF2D binds to the TATA box of the promotor, then TF2B and TF2A bind which becomes a stable complex. TF2F binds to RNAP2 and escorts it to the complex where it binds. TF2E and TFH are recruited which completes the complex
What does TF2B interact with
RNAP2 and TBP
What does TF2A do
stabilizes TBP and TAF binding
What does TF2B do
stabilizes TBP binding, recruits RNAP2, influences start site selection
What does TF2D do
recognizes TAT box, recruits TF2A and TF2B, regulatory function
What does TF2E do
its an alpha 2 beta 2 heterotetrametric, recruits TF2H and stimulates its helicase activity, enhances promoter melting
What does TF2F do
facilitates promoter targeting, stimulates elongation
What does TF2H do
contains an ATP-dependent helicase that functions in promoter melting and clearance
What initiates transcription
after the PIC is assembled Pol II CTD is phosphorylated
How does TF2H repair errors in the DNA
at the site of a DNA lesion Pol II halts and TF2H interacts with the lesion and recruits entire nucleotide-excision repair complex
Where is repair of damaged DNA most effective
on actively transcribed genes and the template strand
What is a cis acting enhancer
its on the same chromosome thats being transcribed
What is a trans acting enhancer
it is on a different chromosome that comes close and the mediator proteins bind
What is a mediator used for
regulating expression of most RNA polymerase II transcripts
How is a mediator usually targeted
sequence-specific DNA-binding transcription factors that work to control gene expression programs in response to developmental or environmental cues
What is endonucleolytic cleavage
post-transcription processing which creates more consistent 3’ ends
What does ripfampicin do
inhibits bacterial beta subunit of RNA polymerase, prevents promotor clearance, antibiotic
What does Actinomycin D do
inhibits bacterial and eukaryotic RNA polymerase, intercalates into dsDNA preventing movement of RNA and RNAP along the template, anti-cancer agent
What does alpha-amanitin do
inhibits eukaryotic RNA polymerase, blocks RNAP2 and at higher concentrations RNAP3, does not block bacterial polymerase or RNAP1
