Transcription in Eukaryotic - Week 4 Flashcards
(42 cards)
how is transcription different in eukaryotes and bacteria
The transcription in eukaryotes is more complex than in bacteria, some of the key main differences are:
- eukaryote cells contain 3 different RNA polymerases, (the 3 different RNA polymerases are able to transcribe distinct categories of the genes), whereas bacterial cells only contain 1 RNA polymerase
- eukaryotic polymerases need to interact with additional proteins to initiate transcription rather than binding directly to the promoter sequence as in bacteria.
what are the additional proteins and regulatory elements does eukaryotic RNA polymerase need to integrate with to initiate transcription
These additional proteins are called general transcriptional factors and there are 5 different types.
RNA polymerases also interact with additional regulatory elements which are called enhancers, silencers, chromatin modifiers and etc.
what are the 3 different types of eukaryotic RNA polymerase and what are they responsible for
The 3 different RNA polymerases are:
- RNA polymerase I
Which is responsible for the synthesis of all ribosomal RNAs, except for the 5S ribosomal RNA.
- RNA polymerase II
Which is responsible for the synthesis of all mRNA (messenger RNA).
- RNA polymerase III
Which is responsible for the synthesis of all tRNA (transfer RNA) and 5S ribosomal RNA.
RNA polymerase II and III are also involved in the synthesis of ssRNA (small nuclear RNA) which is important for the regulation of gene expression.
what is the function of mitochondrial RNA polymerase
RNA polymerases in the mitochondria are responsible for the transcription of mitochondrial genes.
what is the function of RNA polymerase in the chloroplast
RNA polymerases in the chloroplast are responsible for the transcription of chloroplast genes.
what is the similarity between prokaryotic/bacteria polymerase and eukaryotic polymerase
Both eukaryotic and bacterial RNA polymerases have core catalytic subunits that are responsible for synthesizing RNA from a DNA template. In bacteria, the core enzyme consists of five subunits: two α subunits, one β subunit, one β’ subunit, and one ω subunit. In eukaryotes, the core enzyme consists of 12 subunits, including homologs of the bacterial α, β, and β’ subunits.
what is the difference between prokaryotic/bacteria polymerase and eukaryotic polymerase
Eukaryotic RNA polymerases recognize complex promoter sequences, often with the help of additional transcription factors, while bacterial RNA polymerases recognize relatively simple promoter sequences called “sigma factors.” This difference in promoter recognition requires eukaryotic RNA polymerases to have additional subunits and mechanisms for promoter recognition, which are not present in bacterial RNA polymerases.
which subunit is found in all 3 RNA polymerases
the subunit that is found in RNA polymerase I, II and III is RPB6
how many subunits does RNA polymerase II consist of and which is the largest
Polermase II consists of 12 subunits and cannot initiate transcription by itself as it needs transcription factors to initiate transcription.
The largest subunit of Pol II has a carboxy-terminal domain (CTD), which consists of multiple repeats of 7 amino acids. CTD is subjected to phosphorylation and is important for initiation, elongation and all aspects of mRNA processing.
what are the transcription factors polymerase ll needs and why are they important
Pol II needs a set of transcription factors which are:
- General transcription factors (GTF) – important for initiation by Pol II. They are identified as TFNX.
- Regulatory transcription factors – important for regulating gene expression.
what is a promoter
The promoter is a short DNA sequence that is required for transcription to take place.
what 2 sequences are found in the core promoter
In eukaryotes, the core promoter contains 2 important sequences, which are:
- TATA box
- initiator box
where is the TATA box located and why is it important
The TATA box is a sequence that is located about -25 base pairs upstream from the transcription start site.
This TATA box is important for the binding of RNA polymerases.
what is the initiation site and why is it important
The initiation site is where the transcription starts. If the initiation site is missing from the core promotor, the transcription can start at the wrong location. Therefore it is an important site for the initiation of the transcription at the right place.
where are regulatory elements found and what is their function
Regulatory elements are found several thousand bp upstream of the start site. They affect the ability of RNA polymerase to recognize the core promoter and begin transcription.
what are the 2 types of regulatory elements and what is their function
There are two types of regulatory elements:
- activating sequences which are called Enhancers
- inhibiting sequences which are called Sliencer elements
These 2 distinct elements have different functions
The enhancer elements promote transcription whereas the silencer elements inhibit the transcription, thus both these elements affect the rate of transcription.
why are trans-acting factors called trans-acting factors
the regulatory transcription factor is also called the trans-acting factor because while the enhancer elements and the silencer elements are located within the chromosome of the genes that they regulate, the genes that transcribe the trans-acting factors are located on different chromosomes.
what are the 6 general transcription that RNA polymerase II requires for the initiation of transcription
Six general transcription factors are required for the initiation of transcription by RNA Pol II.
RNA polymerase II requires 6 general transcription factors, which are:
- TFIID
- TFIIA
- TFIIB
- TFIIF
- TFIIE
- TFIIH
( TF stand for transcription factor, II stands for RNA polymerase II)
what are the different general transcription factors and how many subunits does each general transcription factor have
GTFs Number of subunits
TBP 1
TFIIA 2
TFIIB 1
TFIIE 2
TFIIF 3
TFIIH 10
TAFs 11
why are the 6 transcription factors required
The 6 general transcription factor is required for the initiation of transcription by RNA polymerase II, there are a series of interactions between the 6 general transcription factors and RNA polymerase II which results in the formation of the open complex or in the result in the formation of a pre-initiation complex.
which transcription factor bind to the TATA box and in which order
The first transcription factor that binds to the TATA box is TFIID (TFIID is composed of several subunits which also include the TATA-binding protein which is TBP).
After TFlID binds to the TATA box, TFIIB joins the complex, (the function of TFIIB is to promote the binding of the RNA polymerase II to the promoter).
RNA polymerase II is already associated with TFIIF, so together they join to make the complex.
The last 2 general transcription factors that join the complex are TFIIE and TFIIH.
When all the general transcription factor is associated with the RNA polymerase II and they assemble at the promoter, they form the closed complex.
what happens after the general transcription factor binds to RNA polymerase II
When all the general transcription factor is associated with the RNA polymerase II and they assemble at the promoter, they form the closed complex.
Then the TFIIH (which is a multisubunit factor) unwinds the DNA locally to form the transcription bubble. Essentially TFIIH acts as a helicase that unwinds the DNA at the initiation site.
Why is TFIIH important other than the fact it’s able to unwind DNA
TFIIH is also able to phosphorylate the RNA polymerase II into the carboxyl-terminal domain (CTD), this phosphorylation event is important because it marks the transition from the initiation step to the elongation step of the transcription.
why is the phosphorylation of RNA polymerase II by TFIIH important
TFIIH is a multi-subunit protein complex that plays a crucial role in transcription initiation by serving as a DNA helicase and a kinase.
phosphorylation of RNA polymerase II by TFIIH is a critical step in the regulation of transcription initiation in eukaryotic cells, facilitating the recruitment of additional factors and influencing the transition from initiation to elongation during transcription.
