Flashcards in Transcription And Translation I Deck (93):
True or false: DNA controls protein synthesis directly.
False. DNA uses RNA as an intermediary.
What is transcripton?
When an appropriate piece of DNA (a gene) is copied into RNA
When RNA is used as a template to direct the synthesis of a protein.
What are two similarities between RNA and DNA?
Both are linear polymers
Both are made of nucleotides connected by phosphodiester bonds.
What are the major differences (4) between DNA and RNA?
RNA is single stranded
RNA has ribonucleotides instead of deoxyribonucleotides
RNA has uracil instead of thymine
RNA can fold into complex 3-dimensional structures allowing some RNAs to have precise structural and catalytic functions.
What is messenger RNA (mRNA)?
RNA that codes for proteins.
What is ribosomal RNA?
RNA that forms the basic structure of the ribosome and catalyzes protein synthesis.
What is transfer RNA?
RNA that is central to protein synthesis as adaptors between mRNA and amino acids. They select and hold amino acids during protein synthesis.
What is small nuclear RNA?
RNA that directs the splicing of pre-mRNA to form mRNA.
What is small interfering mRNA?
RNA that regulates eukaryotic gene expression by degrading select mRNA.
They turn off gene expression by directing the degradation of selective mRNAs and the establishment of compact chromatin structure.
What is micro RNA?
RNA that regulates gene expression by blocking translation of selective mRNA.
What element is required at the active site of RNA polymerase?
What is the function of RNA polymerase?
It catalyzes the formation of phosphodiester bonds that link nucleotides.
It also has proof-reading nuclease activity.
Why can a low fidelity of RNA synthesis be tolerated by organisms?
Because mistakes are not transmitted to progeny.
What is the first step in transcription?
Binding of polymerase to a promoter on DNA.
It is then followed by unwinding a portion of DNA double helix.
During transcripton, DNA is unwound and one strand is bound to DNA polymerase at a promoter site. What is the function of the other strand?
It acts as a template for the synthesis of RNA.
How are nucleotides bound together?
By phosphodiester bonds.
In what direction does RNA polymerase transcribe RNA?
In a 5 -> 3 direction.
Is the RNA that is transcribed single or double stranded?
After transcription, the RNA sequence is extactly ____ to the template strand and _____ to the coding strand.
After transcription, the RNA sequence is exactly COMPLEMENTARY to the template strand and IDENTICAL to the coding strand.
What is the most important step in prokaryotic transcription?
What occurs during initiation?
RNA polymerase assembles and slides down the DNA until it locates a promoter.
It unwinds a short segment of DS DNA to form a transcription bubble.
Which subunit binds to the promoter to form an open promoter complex?
What provides energy for the transcripton (formation of phosphodiester bonds) and drives the reaction forward?
The hydrolysis of nucleoside triphosphates (ATP, CTP, UTP, GTP)
What are promoters?
Special sequences of nucleotides that direct the RNA polymerase to the proper initiation site for transcription.
What are two common motifs for prokaryotic transcription?
-35 sequence (TTGACA)
-10 sequence (TATAAT)
When does elongation begin?
After the formation of nascent RNA with ~10 nucleotides.
What is an initial step in elongation?
RNA breaks its interaction with the promoter, and it binds more strongly to the DNA template.
What is the function of RNA polymerase in elongation?
It moves stepwise alon gthe DNA, unwinding the helix just ahead of its active site and exposing anew region for complementary base pairing.
Elongation generates superhelical tension. What enzyme eases the tension?
Transcripton continues until RNA polymerase meets what?
True or false: transcription is very efficient during elongation.
When does transcription end?
When RNA polymerase encounters a termination signal on the DNA template.
What is a termination signal?
A GC rich region followed by an AT rich region.
It is a stable hair pin structure with a stem and loop, and is known as a poly (U) tail.
What happens as RNA polymerase encounters the poly(U) tail?
Formation of phosphodiester bonds stops
RNA-DNA hybrid destabilized to rU-dA bonds and dissociates.
Hairpin structure destabilizes the interaction of RNA with RNA polymerase, and RNA dissociates
Unwound region of DNA rewinds with its partner to form a DNA duplex
Transcription bubble closes.
How many polymerases are used in prokaryoties?
1 RNA polymerase
In eukaryotes, how many RNA polymerases are used?
Eukaroyotic RNA polymerase II requires additional proteins during transcription. What is the term for them?
General transcription factors.
Why does eukaryotic transcription require additional proteins?
Because eukaryotic transcription needs to deal with a higher order packing of DNA (nucleosomes, chromatin etc).
What is a unique feature of RNA polymerase II?
It contains a carboxyl-terminal domain called CTD.
What regulates the activity of RNA polymerase II?
Phosphorylation on Ser residues of the CTD
Where are the generatl transcription factors (TFIIA-D) found prior to transcripton?
At the promoter
What are the functions (3) of TFIIs?
Help to position the RNA polymerase correctly at the promoter.
Aid in pulling apart the two strands of DNA to allow transcription to begin.
Release RNA polymerase from the promoter into the elongation mode once transcription has begun.
What is the initial step of eukaryotic transcription?
The binding of TFIID to the TATA box.
What is the TATA boxi binding protein?
A subunit of TFIID that recognizes TATA.
After TFIID has bound to the TATA box, what other factors are recruited?
TFIIB, TFIIF, TFIIE, TFIIH, RNA polymerase II.
What factors joint to form the transcription initiation complex?
TFIIB, TFIIF, TFIIE, TFIIH, RNA polymease II.
Which transcription initiation factor unwinds the DNA double helix and exposes the DNA template strand?
What must be done in order for eukaryotic initiation to end and elongation to begin?
Phosphorylation of CTD by TFIIH.
This causes RNA polyemrase to leave the promote and begin elongation.
What are the three possible promoters for RNA polymerase II?
What prevents the dissociation of RNA polymerase II during elongation until it reaches the termination signals?
RNA polymerase II creates superhelical tension as it moves along DNA during eukaryotic elongation. What enzyme removes the tension?
What is eukaryotic DNA packaged into?
Nucleosomes, which are arranged in higher order chromatin structures.
Why does eukaryotic transcription require additional proteins?
Because there are physical barries that prevent access to DNA.
What proteins help to attract RNA polymerase II to the transcription initiation start site?
Transcriptional activator proteins.
What is the function of the mediator protein complex?
It allows the activator proteins to communicate with RNA polymerase II and the general transcription factors.
In order to get greater access to DNA, what enzyms are recruited?
Chromatin modifying enzymes. These include:
Chromatin remodeling complexes
Histone modifying complexes
What is transcription elongation in eukaryotes tightly coupled to?
What is the immediate product of RNA polymerase II?
Pre-mRNA or primary transcript.
What allows a eukaryotic cell to assess whether both ends of an mRNA molecule are present before it exported from the nucleus to the cytosol for translation?
What is RNA capping?
Modification of the 5' end of mRNA
What is RNA splicing?
Removal of non-coding sequences
What is polyadenylation?
Modification of the 3' end of mRNA
What are the three types of processing that occur in eukarotic RNA?
The 5' end of the nascent RNA molecule is modified by the addition of a cap. What is the role of the cap?
It distinguishes mRNA from other RNAs.
It defines the translational start site.
It stabilizes mRNA by protecting their 5' ends from phosphatases and nucleases.
It binds a protein complex that helps in RNA processing and export.
Why are eukaryotic genes discontinuous?
Because they are composed of exons and introns.
What must be done to introns and exons in order make the final mRNA?
The introns must be excised and exons linked to form the final mRNA. This is carried out by spliceosomes.
The 3' end of an mRNA is specified by a signal in DNA. This signal is transcribed into mRNA.
These unique sequences are AUAAA, GU or U rich seqeunces and CA.
They are recognized by RNA binding proteins and RNA processing enzymes.
What is the function of cleavage and polyadenylation specificity factor (CPSF) and cleavage stimulation factor (CstF)?
Both proteins travel on RNA polymerase tail and are transferred to RNA as it emerges from the polymerase.
What is the AAUAAA and the 3' end of RNA bound by?
Cleavage and polyadenylation factor (CPSF)
What is the GU rich element of RNA bound by?
Cleavage stimulation factor (CstF)
What is CA on RNA bound by?
A third factor (no CPSF or CSTf).
What cleaves the CA sequence of RNA?
What is the function of Poly A polymerase?
It adds 200 A nucleotides to the 3' end produced by the cleavage.
The souce of A is ATP
What is invoved in 3' polyadenylation.
CPSF and CstF are bound to their respective ends (AAUAAA and GU).
RNA is cleaved at the CA sequence.
PAP adds 200 A nucleotides to the 3' end produced by the cleavage.
Poly A binding proteins assemble.
Bacterial mRNAs are ___, whereas eukaryotic mRNAs are mostly ___.
True or false: the 5' and 3' ends of a bacterial mRNA are unmodified.
The 5' and 3' ends of bacterial mRNA are unmodified. What is found at the corresponding ends of a eukaryotic mRNA?
A 5' cap and a 3' poly A tail.
True or false: bacterial mRNA has introns.
False. They do not have introns. Their eukaryotic counterparts have introns which are removed by splicing.
What is a quick summary of transcription?
Is catalyzed by RNA polymerase
Usese one of the DNA strands as the template
Usese ribonucleoside triphosphates
In the 5' -> 3' direction
What is prokaryotic RNA polymerase?
A multisubunit enzyme with a sigma factor.
What does the process of transcription include?
What is initiation?
Binding of RNA polymerase to the promoter sites via a sigma subunit, unwinding of the DNA and formation of the first phosphodiester bond.
What occurs during prokaryotic elongation?
The sigma subunit dissociates from the holoenzyme.
What occurs during prokaryotic termination?
The RNA chain stops growing as the polymerase encounters stop signals in the DNA.
Where does transcription take place in eukaryotes?
In the nucleus
What does RNA polymerase I make?
What does RNA polymerase II make?
What does RNA polymerase III make?
What is a necessary component of transcription in eukaryotes?
What is the function of TATA-box binding protein of TFIID?
It unwinds and bends DNA at TATA-box sequences to start transcription initiation.
What is involved in the processing of eukaryotic mRNA?
Capping and methylation of the 5' end of pre mRNA
Addition of poly (A) tail at the 3' end of pre mRNA
Splicing of pre-mRNA by spliceosomes to remove introns.