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| Eukaryotes have ___ types of RNA polymerase that differ in which types of RNAs which types of RNAs they transcribe and in the promoters they recognize |
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| RNA polymerase II contains how many subunits? Are they all unique to this enzyme |
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Definition
| 12, some of them are, but some are also in the other polymerases |
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| One or more discrete elements |
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| RNA polymerase II requires what for specific transcription from a promoter |
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Definition
| General transcription factors |
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| To identify the transcription start site what tools would you need? |
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Definition
| S1 mapping, primer extension, and run-off transcription. |
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| What tools can be used to measure gene activity? |
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Definition
| S1 mapping and primer extension |
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| __ ____ provide another means for measuring the level of gene expression. |
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| RNA polymerase II requires what general transcription factors for transcription |
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Definition
| TFIIA, B, D, E, F, and H must bind to the promoter |
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Term
| How does preinitiation begin |
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Definition
| The TFIID or TBP binds to the promoter, and the complex formation begins. The TBP contacts the TAT box, and the TAFs contact other promoter elements. |
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Term
| After the preinitiation complex has begun, in what is added in the correct order |
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Definition
| TFIIA, TFIIB, TFIIF-RNA poly II complex, TFIIE, and finally TFIIH |
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Term
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Definition
| is a cyclic peptide of eight amino acids. It is an inhibitor of RNA poly II (which is why it is a deadly toxin). Can also be used to to determine which types of RNA poly are present. RNA I is insensitive to it, II is highly sensitive, and III is slightly sensitive. |
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Definition
| Are typically defined as the minimal complement of proteins necessary to reconstitute accurate transcription from a minimal promoter (such as a TATA element or initiator sequence) They are distinct from regulatory transcription factors, which bind to sequences farther way from the initiation site and serve to modulate levels of transcription. |
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Definition
| is the minimal portion of the promoter required to properly initiate gene transcription. It contains a binding site for RNA poly I, II or III. |
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Definition
| Carboxyl terminal domain- (C Terminus) is the end of the amino acid chain terminated by a free carboxyl group. |
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Definition
| (EMSA) is a common affinity electrophoresis technique used to study protein-DNA or protein RNA interactions. Performed in vitro concurrently with DNase footprinting, and primer extension. |
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Term
| general transcription factor |
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Definition
| are protein transcription factors that have been shown to be important in the transcription of class II genes to mRNA templates. They form the preinitiation complex, which with RNA Poly II bind to and read the single stranded DNA gene template. |
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Definition
| is a technique whereby the 5' ends of DNA or RNA can be mapped. It requires a a radiolabelled primer, which is complementary to a region near the 5' end. It is allowed to anneal to the RNA and reverse transcriptase is used to synth. cDN until it reaches the 5' end of the RNA. It is then run on a polyacrylamide gel allowing for determination of the transcriptional start site. |
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Definition
| is a gene that researchers attach to a regulatory sequence of another gene of interest in cell culture, animals or plants. A plasmid is a reporter gene, luciferase, green fluorescent protein, the lacZ gene, |
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Definition
| the only enzyme that transcribes ribosomal RNA. |
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Definition
| This catalyzes the transcription of DNA to synthesize precursors of mRNA and most snRNA and microRNA. |
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Definition
| transcribes DNA to synthesize tRNA and small RNAs. The genes that it transcribes fall into the category of housekeeping genes-is tied to the regulation of cell growth |
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Definition
tells us two things- where transcription initiates and how much of this accurate transcription occurred.
1-Start with DNA, cut it up with restriction enzyme
2-transcribe the fragments
3-measure the length of the run off transcript |
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Definition
| A probe is prepared and allowed to attach to the mRNA. S1 then digests anything that is not anealled, |
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| TATA binding protein (TBP) |
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Definition
| is a transcription factor that binds specificially to a DNA sequence called the TATA box. The DNA sequence is about 35 base pairs upstream of the transcription site |
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Definition
| is a DNA sequence (cis-regulatory element) found in the promoter region of genes in archaea and eukaryotes. It is considered to be the core promoter sequence, it is the binding site of either general transcription factors or histones, and is involved in transcription. |
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Term
| TBP associated factors (TAFS) |
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Definition
| These are the subunits that make up TFIID (there are 16). These add promoter selectivity, especially if there is no TATA box sequence for TBP to bind to. |
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Term
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Definition
| interacts with the TBP subunit of TFIID and aids in the binding of TBP to TATA box containing promoter DNA. Although it does not recognize DNA itself, its interactions with TBP allow it to stabilize and facilitate formation of the preinitiation complex. Results in the exclusion of negative (repressive) factors. |
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Term
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Definition
| This localizes to the nucleus where it forms a complex with the transcription factors IID and IIA. Serves as a bridge between IID and RNA poly II |
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Term
| TFIIB-recognition element (BRE) |
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Definition
| This is a core promoter element that is recognized by TFIIB. The selected sequences contain a strong representation of G and T bases and a striking preference against A. Contact takes place via the minor groove. |
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Term
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Definition
| this is a form of eukaryotic RNA poly II that is recruited to the promoters of protein coding genes in living cells. Consists of RNA poly II, a subset of general transcription factors and regulatory proteins (SRB proteins). It binds to the TATA box |
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Definition
| Is thought to be involved in DNA melting at the promoter, contains a zinc ribbon motif that can bind single stranded DNA |
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Definition
| DNA is thought to be wrapped one complete turn around the preinitiation complex, and TFIIF helps keep this tight wrapping. May also aid in forming the transcription bubble. Most similar to bacterial sigma factor. |
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Definition
| Has helicase and ATPase activities and help create the transcription bubble-also involved in nucleotide excision repair |
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Term
| RNA poly I creates ____, RNA poly II creates _____, RNA poly III creates _____? |
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Definition
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Term
| What is not a common characteristic of nucleotide sequence elements within eukaryotic core promoters? |
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Definition
| They are not uniform in structure and position within all actively transcribed genes |
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Term
| The protein complex(es) required for recognition of the core promoter and binding of the core promoter by RNA polymerase II is (are) called? |
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Definition
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Term
| The initial placement and interaction of TBP within the minor groove of DNA and the interaction of TBP with other transcription factors is facilitated by a set of proteins called what? |
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Definition
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Term
| The CTD tail of RNA polymerase II does what? |
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Definition
| requires phosphorylation for promoter clearance and progression through transcription. |
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Term
| Promoters are cis acting. The promoter is considered a cis-acting site because: |
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Definition
| it exclusively influences the expression of a gene that it is proximal to. |
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Term
| Transcriptional activators do what? |
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Definition
| They regulate the specificity and efficiency with which a promoter is recognized by RNA polymerase. |
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Term
| Eukaryotic RNA polymerases can be distinguished by their sensitivities to ____- |
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Definition
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| Pre-initiation beings with either ______ or TATA binding protein to the core promoter |
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| The C terminal domain of the largest RNA polymerase subunit must be _____ for chain elongation to occur. |
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| What is the process called when foreign DNA is introduced into a eukaryotic cell |
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