Transcription Flashcards
(36 cards)
How does the chemical structure of RNA differ from DNA?
1) Ribose sugar instead of deoxyribose
2) Uracil instead of thymine
In what direction does transcription proceed?
It goes from left to right in a 5’ –> 3’ direction.
Why is polymerization of the rNTP to the growing RNA strand favoured in transcription?
The high energy bond between the alpha and beta phosphates of the incoming rNTP (ribonucleotide triphosphate) is replaced by a lower-energy phosphodiester bond.
RNA polymerase begins transcription at gene nucleotide designated ____.
The polymerase travels “downstream” where the bases are ______.
“Upstream” bases are _______.
+1
positive
negative
Where do important features like promoter sequences with transcription factors that recruit RNA polymerase lie on the transcription site?
Upstream!
What are the three stages of transcription? Briefly describe them.
1) Initiation: polymerase binds to the promoter sequence, locally denatures the DNA, and catalyzes the first phosphodiester linkage
2) Elongation: Polymerase advances 3’->5’ down template strand (RNA is being made 5’ -> 3’), melting duplex DNA and polymerizing the RNA by adding rNTPs.
3) Termination: Polymerase recognizes a STOP site, releases the completed RNA and dissociates from DNA.
Match the following steps of initiation:
- Step 1
- Step 2
- Step 3
A. Polymerase catalyzes phosphodiester linkages of two initial rNTPs.
B. Polymerase binds to PROMOTER SEQUENCE in duplex DNA. “Closed Complex.”
C. Polymerase melts duplex DNA near transcription start site, forming a transcription bubble. “Open Complex.”
Step 1: Polymerase binds to PROMOTER SEQUENCE in duplex DNA. “Closed Complex.”
Step 2: Polymerase melts duplex DNA near transcription start site, forming a transcription bubble. “Open Complex.”
Step 3: Polymerase catalyzes phosphodiester linkages of two initial rNTPs.
What do eukaryotic RNA polymerase require to find promoter regions and initiate transcription?
General transcription factors (associated proteins)
(T/F) Elongation complex is quite clumsy, the polymerase tends to fall quite often.
False! Elongation complex is very stable; polymerase doesn’t fall until a stop site is reached.
*small genes transcribed in few mins, big genes can take hours
Fill in the blank:
The completed RNA molecule (after the three stages of transcription) is called the ______ ______.
Primary transcript
What are sigma factors found in bacterial RNA polymerase?
Sigma factors are INITIATION FACTORS of transcription that recognize promoter regions and recruit RNA polymerase to the site. Once transcription is initiated, sigma factor is released.
Match the following sigma factors to their definition:
1) Sigma factor 70
2) Sigma factor 54
A) recognizes promoters of genes involved in nitrogen metabolism
B) is the best known, recognizes TTGACA…TATAAT & is for growth related genes
Sigma factor 70: is the best known, recognizes TTGACA…TATAAT & is for growth related genes
Sigma factor 54: recognizes promoters of genes involved in nitrogen metabolism
How is organization of genes different in prokaryotes compared to eukaryotes?
In prokaryotes, genes with a common function are often arranged linearly in OPERONS and transcribed together on a SINGLE mRNA. Very few non-coding gaps of DNA (introns) in prokaryotic genomes.
In eukaryotes, genes analogs are scattered on several chromosomes. Co-regulation can not be achieved by physical linkage. They can’t be transcribed together on a single mRNA. Lots of introns!
(T/F) In both prokaryotes and eukaryotes, transcripts must go through several processing steps to become mRNA.
False!
In prokaryotes, mRNAs are directly transcribed from DNA.
(T/F) For eukaryotes, regulatory sites can be tens of kilobases upstream or downstream of the promoter.
True!
*Transcription factors bind to regulatory sites and affect the expression of a gene!
The three eukaryotic RNA polymerases are ______ complex than the bacterial RNA polymerase.
MORE
Eukaryotic RNA polymerases contain ____ large subunits and _______ smaller subunits, some which are common to all and others specific.
two
10-14
What is the bacterial RNA polymerase composed of?
Has two large subunits (β’ and β) and three small subunits (two α and one ω).
Which eukaryotic RNA polymerase contains C-terminal domain (CTD)? In which subunit?
RNA polymerase II
In its largest subunit (RPB1)
Fill in the blanks:
RNA polymerases that initiate transcription have __________ CTD, while RNA polymerases that are actively transcribing have __________ CTD.
Unphosphorylated; phosphorylated
Briefly describe and compare the structures of eukaryotic RNA polymerases.
There are three; RNA pol I, II and III.
All of them contain two large subunits, b and b’ like of bacterial large subunits.
RPB1 and RPB2 in polymerase II!
And multiple same or differing small subunits.
RNA pol II is the only one with a C-terminal domain in its RPB1.
RNA pol I and pol III contain the same α-like subunits, while pol II has different α-like subunits.
They have all share the same ω-like subunit and four other common subunits.
Which RNA polymerase mostly transcribes mRNA?
RNA polymerase II
What happens to the clamp domain of RPB1 during before and during elongation?
Clamp domain is open when downstream DNA is inserted into RPB1.
Clamp domain SHUTS by swinging over the cleft between the jaws of the polymerase when enzyme is in elongation mode, anchoring polymerase onto the downstream dsDNA.
*talking about eukaryotic RNA pol II
How is transcribing RNA pol II different than free RNA pol II?
Position of a clamp domain; clamp is shut of the transcribing RNA pol II to trap the template DNA strand and transcript.
