Term
| What is human RNA Polymerase I responsible for transcribing? Where is it made? |
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Definition
| rRNAs (5.8S, 18S, 28S... everything but 5S), nucleolus |
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Term
| What is human RNA Polymerase II responsible for transcribing? Where is it made? |
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Definition
| mRNA (proteins), miRNA, lnc RNA, snRNA, snoRNA; nucleoplasm |
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Term
| What is human RNA Polymerase III responsible for transcribing? Where is it made? |
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Definition
| tRNA, 5SrRNA, snRNA; nucleoplasm & nucleolus |
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Term
| What are the four processing steps that Polymerase II transcripts undergo? |
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Definition
| Capping, tailing, splicing, and editing. |
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Term
| Differentiate between the location of transcription and translation in the eukaryotes and prokaryotes. |
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Definition
| In bacteria (prokaryotes), all the steps from DNA to protein are covered in the same compartment at the same time. In eukaryotic cells, DNA replication is restricted to a fraction of the cell cycle, and transcription and translation also occur during the cell cycle but in different compartments. |
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Term
| What happens to the final product of transcription in eukaryotes? |
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Definition
| The RNA is transported to the cytoplasm to carry out its job. |
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Term
| In both prokaryotes and eukaryotes, what is necessary for transcription? |
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Definition
| In both: DNA template, all 4 rNTPs, divalent cations (Mg2+ or Mn2+), initiates at promoter sequence, no primer, copies only one DNA strane, synthesis in 5' to 3' direction, no 3'-5' endonuclease activity (therefore low fidelity copying). |
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Term
| Where is ribosomal RNA combined with proteins necessary for its function as a ribosome? |
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Definition
| In the nucleolus, then shipped out to the cell. |
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Term
| What types of genes are clustered in the nucleolus during interphase in human cells? |
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Definition
| Genes for rRNAs and tRNAs are clustered here. |
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Term
| What is a pseudouridine modification and why is it important? |
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Definition
| This is a modification of uracil where it is attached in a different position to the sugar, which allows rRNA to fold and bind proteins as part of the final ribosomal structure. |
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Term
| Why is the 2' sugar of some rRNA residues methylated? |
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Definition
| It allows the rRNA to be tagged as part of a ribosome. |
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Term
| What is the relationship between the products of RNA Polymerase I and RNA Polymerase II? |
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Definition
| Pol I makes precursors, which are modified with Pol II. |
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Term
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Definition
| It is an A-T rich sequence about 25 bp up from the starter site, found commonly in eukaryotic promoter regions in most inducible genes (analogous to Pribnow boxes in bacteria). This is one of several consensus sequences found in human promoters. |
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Term
| What is the general transcription factor associated with a TATA box? |
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Definition
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Term
| How does the core transcription machinery know where to start in humans? |
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Definition
| The TATA box will bind TBP, and then a sequence of binding and a variety of proteins follows. This includes the polymerase, completing the machinery to begin RNA synthesis in that spot. |
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Term
| What signal breaks apart the machinery used to initiate RNA transcription in humans so that the process can continue? |
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Definition
| Phosphorylation of the C-terminal domain of the polymerase by a transcription factor will signal elongation. |
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Term
| What is the function of regulatory transcription factors, or activator proteins? |
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Definition
| These factors are needed for some specific promoters under some physiological conditions (special conditions like development, disease, etc.). Regulatory transcription factors are used to bind enhancer sequences on certain genes in these situations. |
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Term
| When and where do capping proteins bind RNA? |
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Definition
| They bind a new transcript to protect the ends of the RNA, binding the 5' end as it is being transcribed. |
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Term
| Why do splicing proteins bind an emerging RNA transcript? |
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Definition
| They scan it for splice sites and carry out splicing while the RNA is being made. |
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Term
| What is the significance of the 5'-5' triphosphate bridge formed in the capping procedure between guanosine and the 5' end of a transcript? |
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Definition
| Since the linkage is 5'-5', the conformation is changed from that of a naked RNA molecule. The cap for this reason will block and protect the end from 5' ribonucleases. |
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Term
| What is a second function of the 5' cap on RNA? |
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Definition
| If a piece is capped, then it is mRNA; this provides a unique initiation complex for translation, and a method of discriminating between RNA types. |
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Term
| How do you get different isoforms of a protein in different tissues, starting from the same gene? |
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Definition
| This is possible with varied intron splicing. |
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Term
| Describe the mechanism of the pre-mRNA splicing reaction. |
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Definition
1. In a given intron, a particular adenine moiety spaced from the junction with an exon will attack the 5' end of an intron with its 2' OH, cleaving the site and forming a "lariat" structure.
2. The free hydroxyl then attacks the other splice site, cleaves it, and frees the intron entirely.
3. The mRNA is rejoined by ligase, and the lariat is either broken down or used with miRNAs. |
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Term
| What is unique about the lariat branch point in pre-mRNA splicing? |
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Definition
| A 2'-5' phosphodiester bond forms at this branch point. |
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Term
| Give the basic structure of a finished mRNA ready to translate, from 5' to 3'. |
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Definition
| 5' cap... 5' untranslated region... AUG (start codon)... exons... UAA stop codon... 3' untranslated region... PolyA 3' tail |
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Term
| Name the 3 splicing sites commonly found in human introns. (These are conserved or "consensus" sequences.) |
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Definition
| At the 5' end, GU; at the 3' end AG; and an A in the middle (since we need an A at the branch point of the lariat). |
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Term
| What molecules help to carry out the splicing process? |
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Definition
| small nuclear rubonucleoprotein particles (snRNPs) |
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Term
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Definition
| These are proteins containing small pieces of snRNA used to carry out splicing. |
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Term
| What is alternative splicing? |
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Definition
| A method by which the same or a similar transcript can be spliced in different ways in different patterns in different tissue types to get the protein in that tissue that's used for that cell. |
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Term
| What two molecules are responsible for stopping the transcription process in humans? |
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Definition
| CPSF (Cleavage and polyadenylation specificity factor) and CstF (cleavage stimulation factor). They bind the stop codon in the RNA sequence. |
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Term
| What enzyme is responsible for adding the PolyA tail to an RNA molecule? |
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Definition
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Term
| How is the polyA tail related to the lifespan of an RNA molecule? |
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Definition
| The longer the tail, the longer the half-life within a cell. |
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Term
| What is the advantage of Poly(A)-binding protein attaching to the tail of an RNA molecule? |
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Definition
| It interacts with the 5' cap to make a stable, circular mRNA and allows the molecule to associate with initiation factors out in the cytoplasm so that ribosomes can begin translation. |
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Term
| What is apolipoprotein an example of? |
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Definition
| RNA editing; the RNA transcript has one codon changed so that part of the molecule won't be expressed in intestinal tissue though it is necessary in liver tissue. |
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Term
| RNA Polymerase III codes what two important molecules? |
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Definition
| The 5S RNA subunit and snRNAs. |
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Term
| What transcription factors are associated with Polymerase III? |
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Definition
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