Term
| Name two genes that have an internal promoter. |
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Definition
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Term
| What size of genes does RNA polymerase III transcribe |
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Definition
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Term
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Definition
| They bind to the promoter elements of genes and they recruit RNA polymerase III and position it correctly at the start of a gene. |
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Term
| What nucleotide sequence does transcription terminate at? |
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Definition
| TTTT (think T for termination), usually on the 2nd T, but sometimes the 3rd or 4th. |
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Term
| In genes, what are Box A, Box B, and Box C? |
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Definition
| They are internal promoters. |
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Term
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Definition
| TATA box binding protein. |
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Term
| What three accessory factors are involved at internal promoters of genes transcribed by pol III? |
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Definition
| TFIIIA, TFIIIB, and TFIIIC |
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Term
| WHat is the role of TFIIIB in the initiation of RNA transcription when there's an internal promoter? |
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Definition
| It positions the RNA polymerase III correctly. |
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Term
| What is the role of TFIIIA and TFIIIC in the initiation of RNA transcription when there is an internal promoter? |
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Definition
| They are assembly factors that recognize the internal promoter boxes. TFIIIA recognizes box c and recruits TFIIIC, or TFIIIC recognizes box b directly. Then TFIIIC recruits TFIIIB. |
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Term
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Definition
| PSE stands for proximal sequence element. It is found upstream of the gene to be transcribed by polII, and increases the efficiency of transcription. |
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Term
| With an upstream promoter, which 3 elements are required for efficient pol III transcription? |
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Definition
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Term
| What 3 kinds of proteins can bind to DNA? |
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Definition
-Metabolic proteins that bind to DNA and act on it such as restriction enzymes.
-Regulatory proteins that bind to DNA and control gene expression etc...
-Structural proteins like histones that bind nonspecifically and weakly. |
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Term
| What is the most common secondary structure in DNA binding elements? |
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Definition
| An alpha helix that fits into the major grooves. |
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Term
| What is the typical number of hydrogen bonds in a specific protein/DNA interaction? |
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Definition
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Term
| Why do purines have more possible hydrogen bonding site than pyramidines? |
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Definition
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Term
| How long are the 2 alpha helices in a helix turn helix recognition motif? |
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Definition
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Term
| What residues are commonly found in the turn of a helix turn helix motif? |
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Definition
| Glycine, 'cause they're bendy. |
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Term
| Give an example of a protein that uses helix turn helix motif? |
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Definition
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Term
| What can affect whether a particular TF acts to activate or repress transcription? |
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Definition
| Binding partners and covalent modification. |
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Term
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Definition
| They regulate the developmet of body patterns. It encode 60 amino acids that serve as the DNA binding domains of some transcription factors. They have a HTH motif, and can form a stable structure by themselves unlike HTH domains. |
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Term
| Which part of a zinc finger binds zinc? |
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Definition
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Term
| What does the zinc do in a zinc finger? |
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Definition
| Stabilizes the domain and keeps it in the right conformation. |
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Term
| What is the most common secondary structure of a zinc finger? |
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Definition
| An antiparallel B sheet and a helix. |
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Term
| How do zinc fingers interact with DNA? |
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Definition
| The fingers fit into the DNA's major groove. |
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Term
| How often does leucine occur in a leucine zipper? |
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Definition
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Term
| What is the secondary structure of a leucine zipper? |
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Definition
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Term
| What 2 types of regions does a helix loop helix protein have? |
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Definition
| It has a basic region of amino acids for DNA binding and 2 amphipathic helices connected by a loop that allow formation of dimers. |
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Term
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Definition
| It stands for electrophoretic mobility shift. Same as a gel shift assay, where you see DNA migrate higher on a gel when a protein is attached to it, and even higher when a protein and an antibody are attached to it. |
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Term
| What is promoter bashing? |
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Definition
| It's where you make reporter genes with less and less of the promoter until it doesn't work. It lets you figure out which bits are important. |
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Term
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Definition
| CHIP stands for Chromatin IP. You add formaldehyde to the cells to make DNA and protein bind more tightly, then do an IP with an antibody to the protein you think is binding the DNA, then release the DNA and PCR it using specific primers and detect the products by running them out on a gel. |
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Term
| What is a nice size of segment to amplify by PCR for a CHIP assay? |
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Definition
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Term
| How long is a typical siRNA? |
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Definition
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Term
| What is reverse genetics? |
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Definition
| It's where you manipulate the genotype and make mutants to see what the phenotype will be. |
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Term
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Definition
| Post translational gene silencing. Introduction of dsRNA by any method so that mRNA is rapidly degraded. |
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Term
| What is RNA interference? |
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Definition
| PTGS introduced by direct addition of dsRNA to an organism or cell culture. |
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Term
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Definition
| RNA induced silencing complex. It's a combination of enzymes and siRNA that is directed to degrade complimentary RNAs. |
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Term
| When was PTGS stumbled upon and how? |
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Definition
| 1990 while trying to make purpler petunias |
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Term
| What are 4 ways to make siRNAs? |
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Definition
-chemical synthesis
-in vitro transcription
-Digestion of dsRNA by RNAse III or dicer
-Transfection via plasmid or viral vector (most common and most stable) |
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Term
| 3 siRNA design considerations: |
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Definition
-50-100 nucleotides downstream from start codon
-GC content ~50%
-Blast it and make sure it only targets one gene. |
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Term
| what is an example of an siRNA expression vector? |
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Definition
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Term
| What is microRNA? What does it do? |
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Definition
| It's a little RNA that can bind to the 3' sequence near the polyA tail and inhibit translation. They are transcribed in the nucleus and exported to the cytoplasm, and target specific mRNAs through RISC |
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Term
| what happens to mRNAs that are not properly processed? |
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Definition
| They don't leave the nucleus. |
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Term
| What serves as an assembly platform for proteins involved in splicing and capping? |
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Definition
| The phosphorylated tail of RNA pol II |
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Term
| Why does the 5' phosphate cap protect the mRNA from degradation? |
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Definition
| It makes it basically not have a 5' end. |
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Term
| What type of enzyme does the splicing of most mRNAs? |
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Definition
| snRNPs (small nuclear ribonucleoproteins) |
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Term
| What do introns start with? What do they end with? |
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Definition
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Term
| What nucleotide always serves as a branch point during intron snipping? |
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Definition
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Term
| What types of reactions are splicing reactions? |
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Definition
| phosphoester bond transfers. |
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Term
| How many proteins and sRNAs does a splicosome have. |
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Definition
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Term
| Name 3 kinds of splice variants: |
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Definition
exon skipping: an entire exon is missed
cryptic: part of an exon is skipped |
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Term
| What are group I and II introns? |
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Definition
| They are found in some genes encoding mRNA, rRNA, and tRNA. They require no ATP or external enzymes for their removal. |
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Term
| What is the signal for RNA pol II termination? |
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Definition
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Term
| What happens if you cleave the untranslated regions of a piece of mRNA? |
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Definition
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Term
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Definition
| They are RNA molecules capable of catalyzing biochemical reactions. |
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Term
| What are the principal reactions catalyzed by ribozymes? |
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Definition
| RNA transesterfication and RNA cleavage |
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Term
| What do most ribozymes need to function? |
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Definition
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Term
| What are hammerhead ribozymes? |
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Definition
| They are parts of some viruses. THey have a catalytic pocket and they look a bit like a hammerhead. |
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Term
| What does pol I transcribe? |
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Definition
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Term
| What does Pol II transcribe? |
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Definition
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Term
| What does pol III transcribe? |
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Definition
| tRNAs, 5s, and additional small RNAs. |
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Term
| What does pol III transcribe? |
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Definition
| tRNAs, 5s, and additional small RNAs. |
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Term
| What are trans acting factors? |
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Definition
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Term
| What are cis acting factors? |
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Definition
| sequence elements on the dna the transcription factors bind to |
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Term
| How do pol I and pol III differ from pol II when it comes to initiation complexes? |
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Definition
| pol I and III rely on a small number of ubiquitous transcription factors, while Pol II uses a variety of specific ones as well. |
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Term
| How do eukaryotes and prokaryotes compare when it comes to control over RNA processing and degradation? |
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Definition
| eukaryptes have more of it. |
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Term
| What direction do RNA polymerases read the template in? |
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Definition
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Term
| What does actinomycin do? |
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Definition
| Inhibits transcription in eukaryotes and prokaryotes by intercalating between bases. |
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Term
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Definition
| It's a toxin from the death cap mushroom that inhibits pol II, and pol III to a lesser degree. |
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Term
| What percent of a cell's RNA is ribosomal? |
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Definition
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Term
| Where are CAAT boxes and GC boxes on a typical pol II promoter? |
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Definition
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Term
| Where are TATA boxes in the typical pol II promoter? |
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Definition
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Term
| Where might one find enhancer sequences that regulate a gene? |
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Definition
| anywhere in the general vicinity |
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Term
| What are general transcription factors? |
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Definition
| Those that can be used on all promoters for a particular polymerase. |
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Term
| What are the steps to building a pol II initiation complex at a typical TATA box promoter? |
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Definition
-TFIID binds with TBP and associated factors
-TFIIA and TFIIB join TFIID
-TFIIF delivers pol II to the +1 position.
-Several other TFIIs assemble before the beginning of transcription.
-TFIIH opens up the DNA duplex (helixase activity) and phosphorylates pol II to release it from the other transcription factors. |
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Term
| What are the three big differences between Eukaryotic mRNA and prokaryotic mRNA? |
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Definition
-prokaryotes have a mature transcript that requires no processing.
-prokaryotes couple transcription and translation
-prokaryotes have polycistronic messages. |
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