18081338
Description
Flashcards by Samantha Padoran, updated more than 1 year ago
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Created by Samantha Padoran
almost 5 years ago
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| Question | Answer |
| What is transcription? | It is a process in which a segment of DNA is copied into a complementary RNA sequence. |
| What enzyme mediates transcription in eukaryotes? | RNA polymerase |
| How many types of RNA polymerases are there in eukaryotes? | There are 5 types of RNA polymerases in eukaryotes: 3 in the nucleus (RNA pol 1, 2, and 3) 2 in the mitochondria and chloroplast |
| What are the differences between the three nuclear RNA polymerases in eukaryotes? | RNA pol 1 transcribes mostly ribosomal RNA RNA pol 2 transcribes mostly messenger RNA RNA pol 3 transcribes mostly transfer RNA |
| What is the role of alpha-amanitin in transcription? | alpha-amanitin is a toxin derived from a fungus used as a selective inhibitor for RNA synthesis. RNA pol 1 is not sensitive to alpha-amanitin RNA pol 2 and are increasingly sensitive to alpha-amanitin |
| How does alpha-aminitin inhibit transcription? | Alpha-aminitin binds to RNA polymerase resulting in degradation |
| How does actinomycin d inhibit transcription? | Actinomycin d binds to DNA, preventing the formation and binding of the pre-initiation complex of basal transcription factors and RNA polymerase to DNA required for transcription. |
| What are the four key phases of transcription in eukaryotes? | 1. RNA polymerase binding to RNA 2. Initiation of transcription 3. Elongation of RNA transcript 4. Termination of transcript |
| How does RNA pol 1 bind to DNA? | Ribosomal DNA has a promoter element upstream of the DNA-coding region. The promoter element contains: 1. Core motif - contains the TSS 2. Upstream Control Element (UCE) 3. T0. |
| How does RNA pol 2 bind to DNA? | Protein-coding DNA has a promoter element upstream of the protein-coding region. The promoter contains: 1. TATA-box 2. Initiator - contains the TSS |
| How does RNA pol 3 bind to DNA? | Transfer DNA is so short the promoter element can overlap the coding region. The promoter contains: 1. A box 2. B box 3. TSS |
| What is a TATA box? | It is a DNA sequence that.. 1. indicates where a genetic sequence can be read and decoded 2. defines the direction of the transcription 3. indicates the DNA strand to be read |
| What is the TATA box-binding protein (TBP) | The TATA box-binding protein (TBP) is one of the 44 accessory proteins associated with RNA pol 2 during transcription initiation. |
| What is the role of a TATA box and the TATA box-binding protein (TBP) in transcription? | The TATA-box binding protein (TBP) binds to the TATA box and recruits RNA polymerase for transcription. In humans, not all RNA pol 2 promoters have a TATA box but all the RNA polymerases have a TBP. |
| How does RNA pol 2 initiate transcription? | RNA pol 2 recruits 44 accessory factors, including TBP, to form the General Transcription Factor (GTF) complex. When the GTFs and RNA pol 2 bind to the promoter on the minor groove of DNA, all together this makes the Pre-Initiation Complex (PIC). As phosphorylation of the C-terminal domain (CTD) of RNA pol 2 increases, the affinity of RNA pol 2 towards the GTFs decrease, while the affinity to Elongation Initiation Factors (eIFs) increases. This in turn releases the the RNA pol 2 from the promoter |
| What is the C-terminal domain of RNA polymerase 2 and its role in transcription initiation? | The C-terminal domain (CTD) is part of the Rpb1 subunit of RNA pol 2 and is the largest subunit thereof. It is highly conserved among eukaryotes and consists of multiple heptapeptide repeats with the consensus sequence YSPTSPS. CTD kinases, TF2H and P-TEFbeta phosphorylate the CTD. There are five potential phosphoacceptor amino acids in the YSPTSPS consensus sequence - Serine (S) and Threonine (Y) for example. There are 2 types of RNA pol 2 based on the phosphorylation status of CTD: 1. Hypo-phosphorylated RNA pol 2A enters formation of the pre-initiation complex (PIC) at the promoter 2. Hyper-phophorylated RNA pol 2O is associated with Elongation Initiation Factors (eIFs) |
| How does RNA pol 1 initiation transcription? | Similar to RNA pol 2, RNA pol 1 also recruit accessory factors. RNA pol 1 accessory factors are completely different from factors recruited by RNA pol 2 except for the TATA-binding protein (TBP). |
| How does RNA pol 3 initiate transcription? | RNA pol 3 does not recruit any accessory factor to initiate transcription. The A box and B box of the promoter region of RNA pol 3 are bound by the TF3C complex of RNA pol 3 all throughout transcription. The TF3C complex binds to the TF3B complex, which contains the TATA-binding protein (TBP), to bind RNA pol 3 upstream of the TSS. |
| How does RNA pol 1 elongate RNA synthesis? | Elongation phase of RNA synthesis of RNA pol 1 is largely identical to the mechanism used of RNA pol 2. By recruiting the Elongation Initiation Factors (eIFs) and forming the Transcription Elongation Complex (TEC). RNA pol 1 is more efficient at transcribing rDNA than RNA pol 2 due to meet the demand of ribosomes required for normal cell function. rDNA is polycistronic while protein-coding DNA is monocystronic; this ensures that the large quantity of ribosomes needed for translation is met. |
| How does RNA pol 2 elongate RNA synthesis? | RNA pol 2 recruits the Elongation Initiation Factors (eIFs) and forms the Transcription Elongation Complex (TEX) during the elongation phase of RNA synthesis. |
| How does RNA pol 3 elongation RNA synthesis? | Transfer DNA is so short, formation of the Transcription Elongation Complex (TEX) is not needed for RNA pol 3 to elongate the tRNA transcript. |
| How is transcription terminated by RNA pol 1? | RNA pol 1 receives termination signals from the DNA - the T0 site in the promoter region, upstream of the coding region. The T0 site binds to TTF1 which brings RNA pol 1 back to the TSS for transcription initiation. Contrasting to RNA pol 2 which receives signals from the mRNA. |
| How is transcription terminated by RNA pol 2? | RNA pol 2 is signalled by the poly-A site of the transcript product to terminate transcription. Contrasting to RNA pol 1 which receives signals from the ribosomal DNA itself. At the end of transcription, RNA pol 2 is dephosphorylated, released from the DNA and then binds to TF2F to be recruited to GTFs bound to the promoter region for another round of transcription. |
| How is transcription terminated by RNA pol 3? | Subunits 11, 37, and 53 of RNA pol 3 recognises 6-9 T bases at the end of the coding strand DNA (Tn). Recognition of Tn bases pauses the RNA pol 3 enzyme and subunit 11 cleaves and releases the RNA. Nab2 protein directs RNA into the tRNA processing system. |
| How do we know where RNA transcripts are produced from the genome? | RNA-seq gives information as to where transcripts are produced from the genome. NET-seq gives information as to where transcription begins on the genome (mapping of the TSS and promoter regions). |
| What is RNA-seq? | RNA-seq is a process in which complimentary DNA that can be amplified and sequenced is generated from purified mRNA through reverse transferase enzymes. 1. Cells in a suspension are purified to get mRNA. 2. mRNAs are sonicated to produce RNA fragments. 3. Reverse transcriptase is added to the mRNA to produce complimentary DNA (cDNA is dsDNA). 4. cDNA library is amplified and sequenced through NGS. 5. Sequence reads are aligned back to the reference genome. 6. A graph is |
| What is NET-seq? (Nascent Elongation Transcript) | Nascent Elongation Transcript (NET)-seq is a newly developed technique derived from RNA-seq which allows for mapping the location of the TSS and promoter regions. cDNA is generated from "nascent" new transcripts attached to RNA pol tagged with an antibody. This cDNA library is then amplified, sequenced and mapped. |
| Characteristics of ribosomal DNA | Ribosomal DNA is a poly-cistronic operon that encodes multiple gene products in the same RNA molecule. Ribosomal DNA is transcribed as one long transcript (47 rRNA). 47 rRNA is processed in the nucleolus, separating it into 8S, 5.8S, and 23S. Ribosomal DNA genes are huge tandem repeats in eukaryotic genomes to generate sufficient quantity of ribosomes. |
| Which proteins regulate phosphorylation of the CTD of RNA pol 2? | CTD kinases add phosphate groups on residues of the CTD of RNA pol 2. TF2H and P-TEF-beta are examples of CTD kinases. |
| Characteristics of transfer RNA-encoding genes | Most of the promoter is within the coding region. The A box and B box are conserved elements of the promoter which become the D- and T-loops of tRNA. |
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