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RNA Polymerase II: Regulation
Key Terms
31
Biology
Undergraduate 2
06/11/2010

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Term
activation domain
Definition
independently folding domain of transcription activator protein that recruits components of the transcription machinery to the gene and then interacts with various components of the machinery to stimulate transcription
Term
basic region/leucine zipper (bzip) protein
Definition
binds to DNA as dimers that are held together through coiled coil interactions
Term
bzip DNA binding domain
Definition
basic amino acid sequence combined with the leuzine zipper
Term
CCAAT box
Definition
sequence motif 50-200 bp upstream from initiation site inside regulatory/proximal promoter
Term
chromatin remodeling
Definition
event that alters nuclease sensitivity of a region of chromatin, or a wide variety of changes in chromatin structure that occur during regulatory processes
Term
dimerization domain
Definition
loop formed by residues between first two cysteine residues in zinc finger in DNA-binding domain that interacts with another dimerization loop in other DNA-binding domain to stabilize homodimer
Term
DNA affinity chromatography
Definition
can be used to purify transcription activator proteins; beads have tandem repeats of sequence motif that binds transcription activator protein; put mixture through calf thymus DNA with a few transcription activator proteins bound, then through affinity column with beads
Term
DNA binding domain
Definition
domain of transcription activator proteins that makes sequence-specific contacts with control elements in a gene's regulatory promoter or enhancer, classified by structure
Term
enhancer
Definition
can stimulate transcription even when they are far away from the transcription initiation site and when inserted in either orientation
Term
euchromatin
Definition
open chromatin
Term
GAL4
Definition
yeast transcription activator protein belonging to Cys_6 zinc cluster family that regulates the transcription of genes involved in galactose metabolism, has DNA binding and activation domains
Term
gene silencing
Definition
genes within blocked chromatin regions are silenced
Term
helix-loop-helix motif
Definition
dimers, binds to DNA sites as homodimers or heterodimers in manner reminiscent of bzip protein
Term
heterochromatin
Definition
closed chromatin
Term
histone acetylase (HAT)
Definition
modifies histones on N-terminal tail to activate transcription
Term
histone deacetylase (HDAC)
Definition
removes acetyl groups from histone N-terminal tails, which lowers transcriptional activity
Term
homeobox
Definition
conserved sequence that specifies the 60-amino acid residue helix-turn-helix DNA binding domain, its proteins bind to regulatory promoters and enhancers and enhancers (sequence-specific), may act as activator proteins or repressor proteins
Term
homeodomain
Definition
DNA-binding domain formed by C-terminus of homeobox protein, contains a helix-turn-helix motif
Term
homeotic gene
Definition
assigns positional identities along axes to cells during embryonic development, first clue to existence of helix-turn-helix activator protein structure
Term
hormone response element
Definition
imperfect palindrome to which homodimer binds (zinc finger binding)
Term
leucine zipper
Definition
coiled coil dimerization domain
Term
ligand-binding domain
Definition
domain and ligand undergo conformation changes when bound together
Term
linker-scanning mutagenesis
Definition
reveals regulatory promoter's presence just upstream from core promoter by systematically replacing short upstream DNA sequences with DNA linker with random sequence of same size and inserting plasmid to see if transcription machinery works
Term
nuclear receptor
Definition
superfamily that has Cys_4 zinc finger motifs, allows cells in higher organisms to respond to variety of external and internal chemical signals by increasing or decreasing the transcription of specific genes
Term
POU domain
Definition
tandem pair of helix-turn-helix motifs which can bind DNA (one homeobox, one POU), joined by linker, has activation domain on each side
Term
POU protein
Definition
transcription activator proteins that belong to Pit, Oct, Unc superfamily, contain POU and homeobox domain
Term
remodeling complex
Definition
Term
transcription activator protein
Definition
needed to stimulate RNA synthesis, has DNA-binding domain and activation domain
Term
two-hybrid assay
Definition
detects polypeptides that interact through non-covalent interactions; first protein fused with DNA binding domain, second fused with activation domain. If they bind, then transcription occurs.
Term
upstream activating sequence (UAS)
Definition
spans 118-bp and contains four Gal4 binding sites, only one of four 17-bp sites must be present to stimulate transcription, binds in absence of galactose and glucose
Term
zinc finger
Definition
Cys2His2 biound to zinc ion in each repeating sequence causing each unit to fold independently
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