Transcription 2 Flashcards

Terms Definitions
-single stranded-Ribose sugar-pyrimidine uracil in place of thymine
loop formed from snurps
-PolII sometimes continues to transcribe past the end of a gene-Cleavage of pre-mRNA at a specific site occurs-Rat1, 5-> 3' exonuclease degrades the extra RNA-once Rat1 reaches PolII transcription terminates
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deoxyribose sugars no free hydroxyl group , so more stable 2 polynucleotide strands joined by hydrogen bonding btwn complementary bases not many secondary structures so has fewer roles in cell double helix
mRNA is the product of
Structural genes
-Step 1-initiated at RNA polymerase II
promoters when the TFIID transcription factor binds to the TATA box, followed
by the binding of a preassembled holoenzyme containing general transcription factors, RNA polymerase II,
and the mediator.
It occurs at transcription or translation when RNA polymerase or the ribosome, respectively, ignores a termination signal because of a mutation of the template or the behavior of an accessory factor.
Sequences proceeding farther in the direction of expression.
Which prokaryotic RNA subunit binds the DNA template?
RNA Polyerase II
Responsible for transcribing mRNA
Initiation (Bacterial transcription)
transcription apparatus assembles on the promoter and begins the synthesis of RNAs then the selectivity of transcription is enforced, binding of RNA polymerase to the promoter determines which prts of the DNA template are
 to be transcribed & how oftenpromoter binding is responsible for determining the frequency of transcription for a genpromoter recognition, formation of the transcription bubble, creation of the first bonds btwn rNTPs and escape of the transcription apparatus form the promoter
at the end of initiation RNA polymerase undergoes a change in shape and so is no longer able to bind to the consensus sequence in the promoter this change allows the polymerase to escape from the promoter and begin transcribing downstreamas it moves downstream along the template RNA polymerase unwinds the DNA at the leading (dwn stream) edge of the transcription bubble, joins nucleotides to RNA molecule according to sequence on template and rewinds DNA at the trailing edge (upstream) of bubble
3 Phases of Transcription
1. Initiation2. Elongation3. Termination
Acetylations on K9/14 on H3 recruit which protein for transcription?
The sequence between sites of initiation and termination by RNA polymerase; it may include more than one gene.
transcription unit
An acronym for rho utilization site, the sequence of RNA that is recognized by the rho termination factor.
The complex in initiation of transcription that consists of RNA polymerase and DNA and a dinucleotide that represents the first two bases in the RNA product.
ternary complex
Where does Sigma factor bind?
Only at promoters
copy of DNA that leaves the nucleus
Central Dogma
information in the DNA (genotype) is first transferred to RNA and then to protein (phenotype) DNA ---> RNA ----> Protein
Terminator (transcription unit)
sequence of nucleotides that signals where the transcription should end apart of the coding sequencetranscription stops only after the terminator has been copied into RNA
EUK Transcription
Very similar to the process in prokaryotes, with the following exceptions
Role of RNA
RNAs serve diffeclrent important roles as well including structural
roles, role in processing pre-mRNA and roles in silencing of other mRNAs
A mutation in a promoter that increases the rate of transcription.
up mutation
A region of DNA where RNA polymerase binds to initiate transcription.
Portions in premature RNA that need to be excised out. 5` end always GU, 3` end always AG.
Introns & Exons
exons= coding regions , introns = noncoding regions (intervening sequences)all introns and exons are initially transcribed in RNA but after transcription the introns are removed by splicing and exons are joined to yield the mature RNA common in eukaryote genes but rare in bacterial genes
Rho dependent terminators
two features 1. DNA sequences produce a pause in transcription 2. DNA sequence encodes a stretch of RNA upstream of the terminator that is devoid of secondary structures unstructured RNA serves a s binding site for the rho protein which binds the RNA and moves toward the 3' end when RNA polymerase encounters the terminator it pauses allowing rho to catch up rho protiein has helicase activity which it uses to unwind the RNA-DNA hybrid in the transcription bubble , ending transcription
Transcription Initiation
1. TBP binds the TATA box and partially unwinds DNA2. TFIIs bind3.PolII is position over start site4. Transcription bubble formed5. Poll II transcripting
Genes in phage lambda that are equivalent to the early class of other phages. They are transcribed immediately upon infection by the host RNA polymerase.
immediate early genes
It describes a process in which RNA polymerase starts transcription but terminates before it has left the promoter. It then reinitiates. Several cycles may occur before the elongation stage begins.
abortive initiation
Sequences in which many examples of a particular nucleic acid or protein are compared and the same individual bases or amino acids are always found at particular locations
conserved sequences
writing DNA sequences
sequence of the non template strand is the same as the sequence of the RNA transcribed from the template (with exception of the U replacing the T in the RNA strand) nontemplate strand: 5' end is on the left and 3' end is on the right first nuclotde transcribe (the transcription start site) is numbered +1 nucleotides downstream of start site are positive nucleotides upstream of start site are negative
PROK: How fast is elongation?
30 to 50 bases per second
When does enzyme induction occur?
high substrate concentration - signals to transcribe the gene that makes needed enzyme
small nuclear ribonucleoprotiens (snRNPs)
found in euk cells small nuclear RNAs combined with small protein subunitsconvert pre-mRNA into mRNAin euk nucleus
Which histones are known to be modified in transcription? How are they modified?
H2B Ub and H3 methylation
The DNA strand that has the same sequence as the mRNA and is related by the genetic code to the protein sequence that it represents.
coding strand (sense strand)
Difference in Prokaryote Eukaryote Transcription
1) Co-regulating multiple gene via expression on one mRNA 2)Coupling Transcription and Translation
Sigma factors (subunit of core enzyme)
control the binding of of RNA polymerase to the promoter without sigma RNA polymerase would initiate transcription at a random point along the DNA sigma + core enzyme = holoenzyme (binds to -35 and -10 )when holoenzyme is formed RNA polymerase binds stably only to the promoter region and initiates transcription holoenzyme unwinds double stranded DNAsigma only needed for promoter binding and initiation when a few RNA nucleotides have been joined together the sigma detaches from the core enzyme
What does Slu7 and U2AF do?
Select the 3' splice site (splice acceptor site)
Which TF inititiates complex formation and how does it do so?
TFIID begins initiation by binding the TATA Box
There are 2 models for chromatin regulation during transcription initiation. 1. What is the first step?
2. What is the next steps of both models?
1. HAT and chromatin remodelers to remodel chromatin
2. Model 1: histone eviction, initiation complex binds

Model 2: Partial initiation complex, histone eviction, and Pol II and TFIIH join to complete the complex
PROK: 2 steps of holoenzyme binding
1st: it binds to the dsDNA at the –35 box, 2nd: it binds to the –10 box, opening 17 basepairs of the helix as it binds.
What is U2 responsible for in splicing? How does it do it?
U2 defines the branchpoint A by base complementarity
In eukaryotic transcription what is the function of the transcription factors (TFs)?
Form a complex with RNA Pol II which effectively creates a holoenzyme
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