Term
| Where must RNA polymerases be directed and by what? |
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Definition
| To the CAP site by trans-acting factors bound to cis-acting sequences in the promoter and regulatory regions |
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Term
| transcription initiation site |
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Definition
| +1 site or CAP site where the 7-MeG cap is added |
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Term
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Definition
| Transcribes only the large rRNA genes. Enriched in the nucleolus, the site of ribosomal RNA synthesis and initiation of ribosome biogenesis |
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Term
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Definition
| transcribes hnRNA(heterogeneous nuclear RNA, mostly mRNA) and most snRNA (small nuclear RNA). found throughout the nucleoplasm, but appears to exist in clusters at transcription "factories" |
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Term
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Definition
| transcribes RNA(tRNA) genes, the small 5s rRNA, the u6 spliceosomal RNA (in yeast), the 7SL RNA, and active Alu repeats. Located at the nucleolar periphery in yeast, but no yet localized in metazoan cells. |
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Term
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Definition
| A fungal toxin that inhibits RNA polymerases. The polymerases have differential sensitivity which allowed dissection of the types of RNA made by each polymerase. Pol II was very sensitive. PolIII is sensitive at only high levels. PolI is insensitive |
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Term
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Definition
| Carboxy Terminal Domain. Part of the largest subunit (RPB1) of RNA pol II. when unphosphorylated it is in the IIA form and called the initiating form. When phosphorylated its in the IIO form and is in the elongation form. |
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Term
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Definition
| Won nobel prize in 2006 for structure of yeast RNA pol II. He is the son of Arthur Kornberg. |
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Term
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Definition
| (H = helicase) After the RNA polymerase binds the DNA it must be unwound to allow reading of the template. Stimulated by TF II E. |
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Term
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Definition
| cis acting sequences near genes that bind to and direct RNA polymerase to the proper CAP site to initiate transcription. Each RNA polymerase recognizes distinct classes of promoters. |
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Term
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Definition
| site of transcription factor binding |
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Term
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Definition
| proteins that bind DNA (usually to a specific sequence) and regulate transcription of their target genes. |
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Term
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Definition
| an A-T rich sequence about 25 bases upstream of the CAP site in animals , very variable in yeast. binding site for the general transcription factor TBP( TATA binding protein). Involved in regulating both the efficiency of transcription, and in directing Pol II to the proper start site of transcription. |
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Term
| BRE- TF IIB recognition element. |
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Definition
| A non-sequence specific general transription factor. Provides additional interaction site for the general transcription factor TF II B |
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Term
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Definition
| initiator centered around the CAP site. Provide additional interaction sites for the general transcription factor TFIID. |
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Term
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Definition
| downstream promoter element- downstream from CAP site |
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Term
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Definition
| Linker Scanning Mutagenesis. The goal is to create a collection of plasmids containing mutation within a promoter sequence. if a promoter sequence that binds a critical transcription factor or RNA polymerase itself, is mutated, the resulting weakened DNA- protein interaction results in a decrease in transcription rate from the promoter |
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Term
| what 3 proteins are necessary for PolII to efficiently locate the promoter site on a gene and iniate transcription |
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Definition
| a critical general transcription factor, the TATA binding protein, and a transcription factor protein SP1 that can bind to GC boxes |
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Term
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Definition
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Term
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Definition
| (erythroid Kruppel-like factor) made only in erythroid cells, where it binds to the beta globin promoter to activate transcription. |
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Term
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Definition
| Have ICRs (internal control regions) where transcription factors bind to sequences within the transcribed region of the gene. |
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Term
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Definition
| Orientation independent and distance independent. These characteristics distinguish it from promoters |
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Term
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Definition
| histone acetyltransferase, |
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Term
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Definition
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Term
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Definition
| histone methyl transerase |
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Term
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Definition
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Term
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Definition
| Sequences near genes that lead to repression of transcription, sort of the opposite of an enhancer. Generally funtion at the level of chromatin by leading to the modification of histones that allows binding of other repressive proteins to chromatin. |
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Term
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Definition
| (PIC) the complex of RNA polymerase, GTFs, and promoter DNA |
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Term
| General transcription factors |
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Definition
| (GTFs)can interact with RNA polymerases themselves and with DNA sequences near the start site of transcription to direct basal level transcription. |
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Term
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Definition
| (transcription activators) further enhance the frequency of transcription initiation by binding upstream DNA sequences and helping to recruit GTFs and or RNA polymerases to the proper site of the gene for transcription to begin |
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Term
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Definition
| Electrophoretic Mobility Shift Assay, studies DNA protein interactions. |
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Term
| Order of assembly for PIC |
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Definition
1. TF II D a complex of protiens
2. TF II B: a single polypeptide
3. Pol II, a complex but requires the presence of TF II F to bind. |
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Term
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Definition
| Bind protein to end-radiolabeled DNA fragment. Add low concentration of DNase I(or DNA damaging material). Cleavage occurs all along the DNA except at location of protein binding. Resolve fragments at base pair resolution on polyacrylamide gel. |
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Term
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Definition
| bind to the TATA box. a large complex of proteins. |
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Term
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Definition
| (TATA binding protein) is the centerpiece attached to 8-10 TAFs. DNA binding is unusual in that it binds predominantly in the minor groove and sits on DNA like a saddle. Also induces a sharp bend in the DNA upon binding. Required by all 3 DNA polymerases. |
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Term
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Definition
| links TBP and polymerase, and with TF II A helps impart directionality to the PIC. Extends toward the downstream side of TBP to position polymerase toward the CAP site. |
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Term
| Pol I transcription factors |
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Definition
| Core region is bound by a complex of proteins called SL1. this complex is essientail to recruit Pol I to rRNA genes. SL1 contains TBP and three TAFs. |
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Term
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Definition
| first TF discovered, belongs to the Zinc finger class of TFs. Required only for the transcription of the 5s rRNA, a very specific and dedicated funtion. |
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Term
| Working model of Pol III Transcription |
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Definition
1. TF III C binds to the box A and box B
2. BOund TF III C recruits TF III B
3. TF III B recruits Pol III
4. TF III C now dispensable |
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Term
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Definition
| a portion of a polypeptide that folds into a specific structure and can carry out its function independent of the rest of the polypeptide chain. |
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Term
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Definition
| an amino acid sequence that is characteristic of a domain( or portion of one) that forms a characteristic type of struture (determined by the amino acid sequence), that is responsible for its funtion( DNA binding, enzyme activity, membrane proteins, etc. ) |
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Term
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Definition
| Common DNA binding motif. zinc clusters and zinc fingers. Corridnated zinc ions hold the DNA binding domain into the proper structure for recognizing bases within the double helix. |
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Term
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Definition
| a common DNA binding motif. a 60 amno acid motif found in many TFs, has structural similarities to prokaryotic helix-turn-helix DNA binding proteins. |
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Term
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Definition
| common DNA binding motifs. DNA binding motif linked to versatile dimerization domains. |
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Term
| Major classes of transcriptional activation domains |
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Definition
1. Acidic activation domians- rich in glutamate and aspartate residues (Gal4)
2. Glutamine rich domains- Sp1
3. Proline rich- EKLF (also has an acidic domain) |
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Term
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Definition
| wide enough (-20 A) to accommodate various protein substructures, such as an alpha helix. |
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Term
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Definition
| rich in information in the form of H- bonding and hydrophobic interaction potential. |
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Term
| Helix-turn-Helix DNA binding motif |
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Definition
| structure consists of 20 amino acids, containing two short alpha helices separated by a beta turn. Amnio acid side chains within the recognition helix form specific interactions with the base pairs within the major groove of the DNA binding sequence. |
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Term
| Glutamine can speficically H-bond to adenine. |
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Definition
| some binding affinity comes from interactions with the phosphate backbone. Sometimes, multiple amino acids come together within the protein structure to form an H-bonded network specific for a particular base. |
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Term
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Definition
| First identified in TF III A, which has 9 repeated domains of 30 amino acids that have striking similarities, especially a pattern of cysteines and histidines. The xinc finger domian folds into a particular Zn dependent strucutre that allows sequence spefici DNA binding. THE structure is an anti Parallel Beta sheet connected to an Alpha helix. |
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Term
| Many DNA binding proteins utilize arginine to recognize guanine |
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Definition
| 17 total hbonds form upon DNA binding |
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Term
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Definition
One of the first eukaryotic transcription factors characterized in detain. A multi domain protein: Amino acids 1-74 DNA binding and nuclear localization signal. Called a binuclear zinc cluster, or more genrally a bimetal thiolate cluster. AA 75-147 Dimerization domain. AA 148-196 transcriptional activation domain I, rich in acidic amino acids.
768-881 transcriptional activation domain II and Gal80p interaction domain, also rich in acidic amino acids. This type of domain organization (DNA binding, dimerization, transcriptional activation) is very common among transcription factors. Gal4p binds to a split palindrome, cggn11ccg. Dimerization of Gal4p position the recongition helices on opposite sides of the center to allow each to bind to its respective cgg subsite, regardless of the sequence of the intervening n11 bases. The dimerization domain is called a coiled-coil, as each monomer contains an alpha helix, each of which is coiled around each otehr. Gal4 is a member of the fungal zinc binuclear cluster superfamily of DNA bindind proteins. |
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Term
| 3 classes of zinc module TFs |
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Definition
1. C2H2/ C2HC-EKLF, TF IIIA
2. C4- hormone receptors, GATA
3. C6 fungal (Zn2) |
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Term
| Nuclear hormone receptors |
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Definition
| TFs that are sequestered in the cytoplasm until the hormone ligand is present. Hormone binding results in relocation of the receptor to the nucleus, where it can bind DNA and activate transcription. one of the simplest and best understood mechanisms of singal transduction. |
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Term
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Definition
| Valine contacts methyl groups on successive thymidine residues |
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Term
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Definition
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Term
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Definition
| basic leucine zipper. Dimerization domain is an alpha helical structure that generally contains hydrophobic reisdues every seven amino acids( a heptad repeat). This positioning allows the hydrophobic residues to successively interact by placing them on the same side of the helix, allowing formation of a coiled-coil. The adjacent basic domain makes both backbone and sequence spefici contacts in the major groove of the DNA. |
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Term
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Definition
| basic helix loop helix. Similar to bZIPs, but they form an additional globular-like domain that provides a second module for dimerization. the end result is the same, as tow basic helices are positioned into the major groove to make base-specific contacts. |
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Term
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Definition
| the heptad repeats of leucine (or other hydrophobic residues) allows hydrophobic interaction to occur at every twist of the alpha helix holding the polypeptide chains together. can form homodimers or heterodimers. |
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Term
| ectopic or homeologous recombination |
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Definition
| when recombination occurs between different regions of chromosomes, or even different chromosomes, with similar sequences. Can cause gross chromosomal rearrangement( deletions, inversions, or translocations). |
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Term
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Definition
| the region of connection between two double stranded DNA regions undergoing recombination |
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Term
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Definition
| For a true crossover recombination to occur, phosphodiester bonds must be broken and rejoined. |
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Term
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Definition
| the site of breaking and rejoining of two DNA molecules during homologous recombination. Breaking and rejoining requires endonucleases, DNA polymerases, and DNA ligases. |
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Term
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Definition
the region of complementary base pairing between the two different chromosomes or DNA molecules. Can originate from:
1. two copies of the same chromosome in a diploid cell.
2. newly replicated chromosomes.
3. a chromosome and DNA transformed, transduced, or conjugally transferred into cells. |
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Term
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Definition
(double strand invasion model) 1964. Step 1. two single strand breaks are made on each DNA molecule at the same location.
Step 2. Free ends cross over, base pair with their homologous sequences, and are ligated to their new strands. This is called strand invasion and heteroduplex formation, and then branch migration follows until resolution. Step 3. Ixomerization- alsters the spatial relationship of the strands. Step 4. Resolution, separation of the two joined recombining DNAs . AFter breakage and re-ligation, the holliday strucutre is said to be resolved. Resul is a splice/crossover recombination or a patch/non-crossover recombination |
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Term
| Problems with the holliday model |
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Definition
| requires that both strands are prealigned and cut at the same site to initate recombination. there is no evidence for proteins that specifically carry out this function. |
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Term
| Meselson and Radding single strand invasion model |
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Definition
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Term
| Double strand break repair model |
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Definition
| Rothstein and Stahl. 1983. Recombination is initiated by a double strand break in one DNA duplex. 5' to 3' exonucleolytic digestion of each end exposes a single strand with a free 3' hydroxy. |
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Term
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Definition
| initiates yeast meiotic recombination. a meiosis-specific endonuclease. its catalytic domain is homologous to topoisomerases, and contains a catalytic tyrosine that forms a covalent link to the phosphodiester backbone in creating the DSB. |
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Term
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Definition
| where the diploid cell undergoes meiosis to form four haploid spores containing mixed combinations of the genes of the original parents. |
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Term
| Yeast genes to determine mating type |
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Definition
| located on chromosome 3. and in wild type yeast will swithc mating types back and forth due to recombination induced by the HO endonuclease. For switching to occur, the HO endonuclease must first induce a double strand break within the MAT locus. |
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Term
| Direct PCR construction of knockout constructs for yeast |
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Definition
| only about 45-50 bp of homology are needed to promote homologous recombination in yeast. |
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Term
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Definition
| allows addition of protein coding sequence in frame to any yeast gene. You use antibodies that are specific for the epitope you entered. |
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Term
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Definition
| Help metabolize galactose when glucose is not present. |
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Term
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Definition
| codes for galactokinase, phosphorylates galactose at C1. |
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Term
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Definition
| Codes for galactose permease. Required for transport of galactose from the medium into the cell. |
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Term
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Definition
| the inducer, senses the presence of galactose in the cell. |
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Term
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Definition
| the main transcription factor that regulates the induction of transcription of the GAL metabolic genes. |
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Term
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Definition
| galactose-1-phosphate uridyl transferase, transfers UDP to galactose from UDP glucose, generating UDP-galactose and glucose-1-phosphate. |
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Term
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Definition
| UDP-galactose-4-epimerase, converst UDP-galactose to UDP-glucose. |
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Term
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Definition
| inhibits the transcriptional activation function of GAL4 in the absence of galactose |
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Term
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Definition
| part of the mediator transcriptional co-activator complex. |
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Term
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Definition
| proteins that do not directly activate transcription, but assist in the interaction between TFs and Pol II. |
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Term
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Definition
| a transcriptional regulatory protein, activates transcription of GAL1, GAL2, GAL3, GAL7, GAL10, and GAL80 only in the absence of glucose and the presence of galactose. |
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Term
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Definition
| responds to the presence of galactose to induce GAL4 activity. |
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Term
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Definition
| inhibits transcriptional activation by GAL4 in the absence of galactose; gal80 mutants consitutively transcribe GAL genes even in glucose. |
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Term
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Definition
| in the presence of glucose Mig1p binds to elements of these promoters to repress transcritipon ieven in the presence of galactose. Mig1p binds to regulatory regions of many other genes that are repressed in the presence of glucose. In the absense of glucose, Mig1p is kept in the cytoplasm as it is phosphorylated by the Snf1 kinase complex protein complex. |
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Term
| Gal4p is a modular protein |
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Definition
| the DNA binding domain can be separated from the rest of the protein and still bind to DNA. Also, the coding sequences of transcritpional activation domains from other activator proteins van be cloned in frame to the first 94 amino acids of GAL4 to form a gene that codes for a chimeric transcription factor. |
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Term
| GAL gene regulation; GAL1 promoter |
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Definition
| the GAL1 promoter is preceded by the UAS(upstream activation sequence-galactose). THis element contains four binding sites for the Gal4p. Between the UAS and the CAP site is a binding site for Mig1p, a transcriptional repressor protein. |
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Term
| the function of the DNA binding domain of TFs is .... |
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Definition
| simply to tether the activation domain to the proper location. |
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