Term
| Transcriptions role in gene expression |
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Definition
| repression and activation of genes to produce specific gene products |
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Term
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Definition
| proteins are produced at low rates |
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Term
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Definition
| DNA sequences to which RNA polymerase and sigma factors bind to begin transcription |
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Term
| How is the strength of a promoter regulated? |
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Definition
| Consensus sequence has the most commonly occurring base at each of the positions in the -35 and -10 regions |
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Term
| What is meant by the term “strength” of a promoter |
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Definition
| Optimal binding site for RNA polymerase and sigma factor |
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Term
| role of the sigma factor (sigma) in the initiation of transcription in E. coli |
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Definition
| Sigma factor binds to RNA polymerase and to promoter DNA sequences, bringing the RNA polymerase enzyme to a promoter |
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Term
| Where does sigma factor bind? |
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Definition
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Term
| What enzyme does sigma factor associate with? |
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Definition
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Term
| What is the most common sigma factor |
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Definition
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Term
| What types of transcription is sigma factor involved with |
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Definition
| Operon transcription, bacterial transcription |
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Term
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Definition
| Clustered genes which encode enzymes involved in a particular metabolic pathway or proteins that interact to form one multi-subunit protein |
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Term
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Definition
Lac mRNA is repressed when E.coli is in an environment where there is no lactose. When there is glucose and lactose, E.coli prefers to metabolize glucose. When lactose is the only sugar available to metabolize E.coli represses transcription of the lac operon until lactose is present and this allows synthesis of only low levels of lac mRNA until the cytosolic concentration of glucose galls to low levels
Lac operon encodes three proteins required for the metabolism of lactose |
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Term
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Definition
| specific DNA sequence in the lac transcription-control region, controlled by lac repressor. When no lactose is present, the lac repressor binds to the lac operator, and the operon cannot be transcribed. When lactose is present, it binds to the lac repressor which causes it to dissociate from the lac operator which allows for operon transcription |
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Term
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Definition
| tetrameric protein which controls the lac operator, it is bound to operator when lactose is not present. When lactose is present, it binds to the repressor, which causes it to dissociate from the operator. |
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Term
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Definition
| sugar present in milk, a low levels repressor it bound to operator, a high levels it binds to repressor allowing for dissociation and gene transcription. |
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Term
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Definition
| a sugar favorably used for metabolism by E.coli. When it is in high concentrations, the repressor binds the lac operon. When the concentration falls E.coli synthesizes cAMP which binds to CAP protein and interacts with the polymerase bound to the promoter which stimulates the rate of transcription initiation |
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Term
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Definition
| catabolite activator protein, controls lac operon transcription under low glucose levels, dimeric protein, bound by cAMP when glucose levels are low |
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Term
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Definition
| synthesized by E.coli when glucose levels are low in order to bind to CAP and interact with polymerase bound to the promoter and increase lac operon transcription initiation |
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Term
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Definition
| activators whose binding sites are 80-160 base pairs upstream from the start site, regulates transcription of genes by RNA polymerase containing sigma 54 |
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Term
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Definition
| Sigma 54 associates with enhancers as activators which can be far away from the start site |
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Term
| Two-component regulatory system |
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Definition
| o Depending on two proteins for control, they control many responses of bacteria to changes in their environment |
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Term
| example of a two-component regulatory system |
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Definition
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Term
| Factors, which regulate transcription elongation in E. coli |
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Definition
cytoplasm concentration of tryptophan
amino-acylated tRNA concentration |
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Term
| transcriptional control in Prokaryotes |
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Definition
| gene control serves mainly to allow a single cell to adjust to changes in its environment so that its growth and division can be optimized |
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Term
| transcriptional control in eukaryotes |
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Definition
| Primary purpose of gene control in eukaryotes is the execution of precise developmental decisions so that proper genes are expressed in the proper cells during embryonic development and cellular differentiation |
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Term
| transcriptional control in both eukaryotes and prokaryotes |
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Definition
| Transcriptional control is the primary means of regulating gene expression |
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Term
| three different types of RNA polymerases found in eukaryotes |
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Definition
RNA polymerase I- transcribes pre rRNA
RNA polymerase II- transcribes mRNA, snRNAs, siRNAs, and miRNAs
RNA polymerase III- transcribes tRNAs, 5s rRNA, snRNA U6, and 7S RNA |
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Term
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Definition
| CTD of RNA polymerase II is the carboxyl-terminal domain, heptapeptide repeat with a consensus sequence. It is critical for viability in yeast |
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Term
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Definition
| It becomes phosphorylated during transcription initiation and remains phosphorylated as the enzyme transcribes the template |
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Term
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Definition
| conserved sequence in highly transcribed genes, found ~ 26-31 base pairs upstream of the transcription start site, acts similarly to an E.coli promoter to position RNA pol II for transcription initiation |
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Term
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Definition
| alternative promoter element (to TATA box), contain a cytosine at the -1 position and an adenine reside at the transcription start site (+1), nucleotide sequence directly surrounding the start site determines the strength of the initiator |
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Term
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Definition
| transcription factor recognition element |
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Term
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Definition
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Term
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Definition
| downstream core promoter element |
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Term
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Definition
| promoter regions for genes that encode proteins which are not required in large numbers, occur relatively rarely in genomes of mammals, CG sequences |
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Term
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Definition
| first protein to bind to a TATA box promoter, domain folds into a saddle shape, interacts with the minor groove of the DNA, and bends the helix |
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Term
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Definition
| monomeric protein, smaller than TFB, C-terminal domain makes contact with TBP and DNA on either side of the TATA box, N-terminal domain is inserted into the RNA exit channel of RNA pol II, N- terminal assists Pol II in melting the DNA strands at the transcription site and interacts with the template strand near the Pol II active site |
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Term
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Definition
| performed complex, binds with Pol II in positioning the polymerase over the start site |
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Term
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Definition
| creates a docking site for TFIIH |
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Term
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Definition
| completes assembly of the transcription pre-initiation complex |
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Term
| Helicase Activity of TFIIH |
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Definition
| uses energy from ATP to help unwind the DNA at the start site allowing Pol II to form an open complex in which DNA around the start site is melted and the template strand id bound at the polymerase active site |
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Term
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Definition
| Completes assembly of transcription pre-initiation complex and has Helicase activity |
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Term
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Definition
| When a transcribing RNA pol becomes stalled, TFIIH recognizes the stalled pol and the associates with other proteins to repair the damaged DNA region. In mutations, repair of genes is inactive, and affected individuals have extreme skin sensitivity to sunlight and have incidence of cancer |
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Term
| how enhancer sequences can regulate transcription of specific genes at a distance |
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Definition
| Stimulate transcription from a promoter far away |
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Term
| Relationship between activators and their domains and enhacers and their domains |
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Definition
Activators use activation domains
Enhancers use repressors |
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Term
| How does DNAase footprinting reveal where a transcription factor bind |
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Definition
| Takes advantage of the fact that when a protein is bound to a region of DNA, it protects that DNA sequence from digestion by nucleases. The appearance of a footprint (region protected by the bound protein that appears as a gap) indicates the presence of a transcription factor that binds that control element in the protein sample being assayed |
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Term
| Constitutive gene expression |
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Definition
| Constitutive regulated gene expression is unregulated, abnormally high expression due to mutation. Results from inactivation of a repressor that normally inhibits the transcription of those genes |
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Term
| Mutation of repressors and activators |
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Definition
Mutation of repressor binding site = increased expression of a reporter gene
Mutation of an activator binding site = decreased expression of the linked reporter gene |
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Term
| typical characteristics of the DNA binding domains of activators |
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Definition
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Term
| typical characteristics of the DNA binding domains of repressors |
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Definition
| can inhibit transcription from a gene they do not morally regulate when their cognate binding sites are placed close or far from the gene’s start site. Two functional domains: DNA binding domain and repressor domain |
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Term
| typical characteristics of DNA binding domains of repressors and activators |
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Definition
| Both domains continue to function when fused to another type of DNA-binding domain. Both domains function by interacting with other proteins |
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Term
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Definition
| conserved 60-residue DNA-binding motif, present in eukaryotic transcription factors that function during development, similar to helix-turn-helix, found in genes that have master-control functions in human development |
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Term
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Definition
| development genes of drosophila |
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Term
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Definition
| regions that fold around a central zinc ion, producing a compact domain from a relatively short length of the polypeptide chain, common in DNA binding and transcription factors |
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Term
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Definition
| DNA binding domains, mutagenesis of leucine was required for dimerization |
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Term
| Example of leucine zipper domains |
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Definition
| DNA-binding domain of yeast GCN4 transcription factor |
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Term
| Basic Helix-Loop-Helix (bHLH) proteins |
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Definition
| DNA-binding domains of another class of dimeric transcription factors, form heterodimers |
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Term
| modular nature of transcription factors in terms of DNA binding and RNA polymerase activation domains |
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Definition
| Structural motifs bind specific DNA sequences, results in a noncovalent interaction between atoms in an alpha helix in the DNA-binding domain and atoms on the edge of the bases within the major groove in the DNA |
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Term
| how chromatin remodeling influences transcription regulation |
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Definition
| Activators or repressors exert their effects by binding to multi-subunit co-activators or co-repressors that influence assembly of Pol II transcription pre-initiation complexes by modulating chromatin |
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Term
| What proteins play a role in the process of remodeling |
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Definition
| Histones tail (H3 and H4) |
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Term
| How does post-translational modification of chromatin proteins lead to regulation of transcription |
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Definition
| Post-translational modification can aceylate Histones to mediate chromatin repression |
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Term
| mechanism by which steroid hormone receptors regulate transcription |
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Definition
Induced conformational changes that modify their interactions with other proteins
Steroid hormones are homodimeric nuclear receptors, when bound to their ligands they can translocate to the nucleus and activate transcription of target genes |
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Term
| five members of the nuclear receptor superfamily |
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Definition
Estrogen receptor
Progesterone receptor
Glucocoticoid receptor
Thyroxine receptor
Retinoic acid receptor |
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Term
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Definition
| inherited changes in the phenotype of a cell that do not result from changes in DNA sequence |
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Term
| mechanisms observed in epigenetic regulation of transcription |
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Definition
| Repression or activation that is maintained after cells replicate as the result of DNA methylation and/or post-translation modification of Histones, especially histone methylation |
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Term
| Operator consitiuative mutants of the lac operon would ... |
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Definition
| express beta-galactosidase constitutively |
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Term
| E.coli two-component regulatory system |
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Definition
| PhoB is a cytosolic protein |
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Term
| How does the binding of the lac repressor to the lac operator block transcription initation |
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Definition
| Lac repressor blocks RNA polymerase from interacting with DNA at the start site |
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Term
| Which proteins "footprint" the lac operon control region? |
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Definition
| Lac repressor, RNA polymerase, cAMP-CAP but NOT beta-galactosidase |
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Term
| Fundamental difference between gene regulation in bacteria compared to eukaryotes |
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Definition
| in eukaryotes trancription is influenced by how effectively the DNA sequence of promoter interacts with histone octomers |
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Term
| CTD of RNA Pol II ... (3) |
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Definition
can be phosphorylated, is crutial for viability, and contains more than 50 repeats of heptapeptide
NOT present in RNA pol I II and III |
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Term
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Definition
| acts to position RNA polymerase II for transcription initiation |
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Term
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Definition
TATA box
initiator element
CpG islands
NOT an enhancer |
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Term
| Correct order of binding transcription factor to RNA pol II promoters |
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Definition
| TFIID, TFIIB, Pol II, and TFIIH |
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Term
| What is the function of TFIIH? |
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Definition
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Term
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Definition
| promoter for 60-70% of eukaryotic genes and a control region for genes that are transcribed at low rates |
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Term
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Definition
| DNA element that stimulates transcription of eukaryotic promoters |
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Term
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Definition
radiolabled DNA fragment
polyacrimide gel
DNA binding protein
NOT DNase I |
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Term
| Leucine Zipper motif contains |
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Definition
| a leucine residue at every 7th position |
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Term
| Strictual motifs of DNA binding domain |
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Definition
| Homeodomain, zinc-finger, helix-loop-helix, NOT random coil acidic domain |
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Term
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Definition
stains more darkly with DNA dyes
contains more highly condensed DNA
associated with inactive genes
NOT susceptible to DNase I |
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Term
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Definition
| has histone acetylase activity |
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Term
| transcriptionally inactive genes |
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Definition
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Term
| lipid soluble hormones activate transciption by |
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Definition
| binding to nuclear receptor |
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Term
| Which protein domains are found in nuclear receptor family members |
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Definition
| variable regions, DNA binding domain, and ligand-binding domain |
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Term
| regulation of transcription by steroid hormones |
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Definition
| involves cytoplasmic hormone receptors that can move to the nucleus |
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Term
| X chromosome inactivation is mediated by |
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Definition
| short RNA directed methylation of histones and DNA |
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Term
| transcription initation and pol II activity (3) |
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Definition
| does not require ATP, Pol II is responsible for synthesizing tRNAs and 5S-rRNA, and the promoter element of tRNA genes lie entirely within the transcribed sequence |
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