Term
| POL II is the only RNAP used to transcribe ___. |
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Definition
| POL II is the only RNAP used to transcribe mRNA. |
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Term
| POL II requires more transcription factors ("GTF's," "TF's") than I and III. The first TF binds to the core promoter, located at ___. |
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Definition
| POL II requires more transcription factors (TF's) than I and III. The first TF binds to the core promoter, located at THE TATAAT BOX. |
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Term
| The proximal promoters are the ___ and ___ boxes. The ___ is bound by SP1 factor, which affects the frequency of initiation. The proximal elements are required for initiation; the core promoter alone is not enough. |
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Definition
The proximal promoters are the GC and CAAT boxes. The GC is bound by SP1 factor, which affects the frequency of initiation. The proximal elements are required for initiation; the core promoter alone is not enough.
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Term
| In eukaryotes, deletion of the TATAAT box can result in ___. |
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Definition
| In eukaryotes, deletion of the TATAAT box can result in HETEROGENEITY OF TRANSCRIPTION START SITE. (It plays a different role than it does in prokaryotes.) |
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Term
| Define cis-acting sequence. |
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Definition
| Cis-acting sequence - sequences of DNA, which may be distant from the start site, upstream or downstream, acting in either direction, which can enhance or silence the rate of initiation. |
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Term
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Definition
| INR - a functionally analogous element to the TATAAT box, present in 65% of eukaryotic genes. It spans from -6 to +11 and is not well-defined. |
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Term
| Define trans-acting factor. |
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Definition
| Trans-acting factor - TF's which are not nucleotide sequence on the DNA. |
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Term
Define the role of the following domains found in TF's:
1. Activation domain.
2. Dimerization domain.
3. Ligand-binding domain. |
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Definition
TF domains
1. Activation domain - binds to machinery to affect transcription levels.
2. Dimerization domain - mediates protein-protein interactions.
3. Ligand-binding domain - binds to ligands, which may alter the TF's function. |
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Term
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Definition
| BRE - DNA sequence adjacent to core promoter (TATA or INR) which recognizes TFIID. |
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Term
Define the role of the following general ("basal") TF's:
1. TFIID
2. TFIIA
3. TFIIB
4. TFIIF
5. TFIIE
6. TFIIH |
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Definition
General TF's:
1. TFIID - consists of TBP (TATA-binding protein) & TAF (TBP-associated factors). TFIID is the first TF to bind and binds at the core promoter at the minor groove and kinks the DNA at each end. TAF binds to activators.
2. TFIIA - increases TBP binding affinity in vitro.
3. TFIIB - binds to TBP and BRE.
4. TFIIF - binds to RNAP II, assists in initiation and elongation.
5. TFIIE - assembles TFIIH into the pre-initiation complex (PIC).
6. TFIIH - contains helicases for each direction (required to form transcription bubble; -11 and -7 pockets not present) and a kinase to phosphorylate S5 on the CTD of RNAP. The phosphorylation is critical for promoter escape and termination.
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Term
The CTD of RNAP II contains heptapeptide repeats with S residues at locations ___.
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Stage of transcription
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S residues phosphorylated
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Promotes…
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Pre-initiation
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Promoter escape
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Elongation
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Definition
The CTD of RNAP II contains heptapeptide repeats with S residues at locations 2,5 and 7.
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Stage of transcription
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S residues phosphorylated
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Promotes…
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Pre-initiation
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none
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--
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Promoter escape
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5
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mRNA capping
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Elongation
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2
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Splicing
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Term
| The five GTF's ("general transcription factors") needed by RNAP II are ___. They do not, however, respond to ___. It was discovered a complex known as ___ is responsible for interacting with activators and transmitting that to RNAP. |
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Definition
The five GTF's ("general transcription factors") needed by RNAP II are TFIID, TFIIB, TFIIF, TFIIE, TFIIH (note TFIIA is only required by TFIID, not RNAP II directly). They do not, however, respond to ACTIVATORS. It was discovered a complex known as THE MEDIATOR is responsible for interacting with activators and transmitting that to RNAP. (Note it was also found the mediator is required for activator-independent transcription, plays a part in all stages of transcription and may also play a part in repression.)
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Term
| The rate of transcription of a gene is the sum of positive and negative influences exerted by proteins on cis-acting sequences. The level of transcription in eukaryotes is controlled by regulating the rate of ___. |
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Definition
| The rate of transcription of a gene is the sum of positive and negative influences exerted by proteins on cis-acting sequences. The level of transcription in eukaryotes is controlled by regulating the rate of INITIATION. |
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Term
| Describe the process of how a poly-A tail is added to nascent mRNA's. |
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Definition
| RNAP II continues elongation well past the end of a gene and through several AATAAA sequences (on coding strand), giving the mRNA AAUAAA sequences which are recognized by an endonuclease. The endonuclease cleaves 11-30 residues from the 3' end of the mRNA and a poly-A tail is added by poly-A polymerase (PAP). Simultaneously, the tail is bound by poly-A binding protein (PABP), which protects it from degradation. |
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Term
| Give two roles of poly-A tails. |
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Definition
Poly-A tails:
1. increase mRNA stability.
2. enhance translation. |
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Term
| Enzymes involved in RNA processing including capping, poly-A addition and splicing sit on the scaffold created by ___. |
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Definition
| Enzymes involved in RNA processing including capping, poly-A addition and splicing sit on the scaffold created by THE CTD OF RNAP II. |
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Term
| Termination is not well defined in eukaryotes. It is thought once the endonuclease cleaves the mRNA due to the AAUAAA signals, an attached ___ dissociates from RNAP II and chews up the stub of the mRNA still attached. |
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Definition
Termination is not well defined in eukaryotes. It is thought once the endonuclease cleaves the mRNA due to the AAUAAA signals, an attached RNAase dissociates from RNAP II and chews up the stub of the mRNA still attached.
[image]
Once the RNAase reaches the RNAP II, the RNAP undergoes a conformational change which, when coupled with pulling from the RNAase, pulls the transcript out. |
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Term
How do each of the following molecule inhibit transcription? Do they work in prokaryotes or eukaryotes?
1. Antinomycin D
2. Acridine
3. Rifampicin
4. Alpha-amanitin |
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Definition
Transcription inhibitors
1. Antinomycin D (prokaryotes & eukaryotes)- goes in between G and C nucleotides in dsDNA and prevents elongation.
2. Acridine (prokaryotes & eukaryotes) - same as antinomycin D.
3. Rifampicin (prokaryotes) - prevents promoter clearence by binding to the beta subunit of bacteria RNAP.
4. Alpha-amanitin (eukaryotes) - from fungus, interacts with the bridge helix and prevents translocation. It affects RNAP II more than III and does not affect I. |
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Term
| Would antinomycin D, acridine, rifampicin or alpha-amanitin work best as an antibiotic? |
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Definition
| Rifampicin would work best as an antibiotic, because it only works on prokaryotes, whereas alpha-amanitin only works on eukaryotes and antinomycin D and acridine on both. |
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