Term
| how multicellular eukaryotes differentiate cells, in general |
|
Definition
| they differentially use transcriptional regulation of DNA common to all cells to create different cell types |
|
|
Term
| 3 important characteristics unique to eukaryotes that influence gene expression |
|
Definition
1: more complex transcriptional regulation
2: RNA processing
3: nuclear membrane |
|
|
Term
| depiction of transcription and translation |
|
Definition
|
|
Term
| how many types of RNA polymerases are there in bacteria? |
|
Definition
|
|
Term
| how many types of RNA polymerases are there in eukaryotes? |
|
Definition
|
|
Term
| table of the different types of eukaryotic RNA polymerases |
|
Definition
|
|
Term
| location of RNA polymerase I |
|
Definition
|
|
Term
| location of RNA polymerase II |
|
Definition
|
|
Term
| location of RNA polymerase III |
|
Definition
|
|
Term
| what RNA polymerase I synthesizes |
|
Definition
-18S rRNA
-5.8S rRNA
-28S rRNA |
|
|
Term
| what RNA polymerase II synthesizes |
|
Definition
|
|
Term
| what RNA polymerase III synthesizes |
|
Definition
|
|
Term
| depiction of additional classes of RNA |
|
Definition
|
|
Term
| something unique about RNA polymerase II |
|
Definition
| contains carboxyl-terminal domain (CTD) |
|
|
Term
| how RNA polymerase II is regulated |
|
Definition
| by phosphorylation mainly on the serine residues of the carboxyl-terminal domain (CTD) |
|
|
Term
| what phosphorylation of the carboxyl-terminal domain (CTD) does to RNA polymerase II |
|
Definition
| enhances transcription and recruits other factors required to process the RNA polymerase II product |
|
|
Term
| some types of eukaryotic RNA polymerase promoters |
|
Definition
-RNA polymerase I promoters
-RNA polymerase II promoters
-RNA polymerase III promoters |
|
|
Term
| depiction of common eukaryotic promoter elements (RNA promoters) |
|
Definition
|
|
Term
| characteristics of promoters for RNA polymerase I |
|
Definition
| have one at the start site (ribosomal initiator element (rInr)) and one 125-150 bp upstream of the start site (upstream promoter element (UPE)) |
|
|
Term
| ribosomal initiator element (rInr) |
|
Definition
| a sequence at the transcription start site that helps recruit RNA polymerase I to start transcription |
|
|
Term
| upstream promoter element (UPE) |
|
Definition
| sequence 150-200 bp further upstream of ribosomal initiator element (rInr); helps recruit RNA polymerase I to initiate transcription |
|
|
Term
| how ribosomal initiator element (rInr) and upstream promoter element (UPE) aid transcription |
|
Definition
| by binding proteins that recruit RNA polymerase I |
|
|
Term
| how transcription gets started |
|
Definition
| ribosomal initiator element (rInr) and upstream promoter element (UPE) aid transcription by binding proteins that recruit RNA polymerase I |
|
|
Term
| characteristics of promoters for RNA polymerase II |
|
Definition
-have set of conserved-sequence elements that define the start site and include the polymerase
-can contain any combination of possible elements, such as enhancer elements, which are unique to eukaryotes |
|
|
Term
| characteristics of promoters for RNA polymerase III |
|
Definition
| they are within the transcribed sequence, downstream of the start site |
|
|
Term
|
Definition
| DNA sequences that regulate the expression of a gene located on the same molecule of DNA |
|
|
Term
| trans-acting elements aka transcription factors |
|
Definition
| proteins that recognize cis-acting elements and regulate RNA synthesis |
|
|
Term
| importance of the regulation of RNA polymerase II |
|
Definition
| accounts for cell differentiation and development in higher organisms |
|
|
Term
|
Definition
| the most common cis-acting element for our genes transcribed by RNA polymerase II |
|
|
Term
| depiction of the TATA box |
|
Definition
|
|
Term
| the TASTA box is often paired with... |
|
Definition
| an initiator element (Inr) |
|
|
Term
|
Definition
| sequence found at the transcriptional start site |
|
|
Term
| downstream core promoter element (DPE) |
|
Definition
| found downstream of the start site and is commonly found in conjunction with the Inr in transcripts that lack the TATA box |
|
|
Term
|
Definition
| genes that tend to be continuously expressed instead of regulated |
|
|
Term
| genes that tend to have GC boxes in their promoters |
|
Definition
|
|
Term
| strands GC and CAAT boxes can be effective on |
|
Definition
-template (antisense)
-coding (sense) |
|
|
Term
| depiction of the CAAT and GC boxes |
|
Definition
|
|
Term
| RNA polymerase II is guided to the start site by... |
|
Definition
a set of transcription factors known collectively as TFII
TF stands for transcription factor and II stands for RNA polymerase II |
|
|
Term
| how transcription initiation using TFII begins |
|
Definition
| TFIID binding to the TATA box |
|
|
Term
| depiction of transcription initiation |
|
Definition
|
|
Term
| the key initial event in TATA-box promoters |
|
Definition
| recognition of the TATA box by the TATA-box-binding protein (TBP); this widens the minor groove |
|
|
Term
| the part of TFIID that binds to the TATA-box |
|
Definition
| the TATA-box-binding protein (TBP) |
|
|
Term
| depiction of the complex formed by the TATA-box-binding protein and DNA |
|
Definition
|
|
Term
| essential catalytic activities of TFIIH |
|
Definition
-it is an ATP-deppendent helicase that unwinds the DNA as a prelude to transcription
-the protein is also a kinase that phosphorylates the CTD of the polymerase |
|
|
Term
| this marks the transition from initiation to elongation |
|
Definition
| phosphorylation of the CTD by TFIIH |
|
|
Term
|
Definition
a type of cis-acting element that greatly increases the activities of many promoters in higher eukaryotes
they have no promoter activity of their own, but can exert their stimulatory actions over the span of several thousand base pairs |
|
|
Term
|
Definition
| upstream, downstream, or even in the midst of a transcribed gene |
|
|
Term
| something enhancers have in common with promoter sequences |
|
Definition
| they are bound by transcription activators that participate in the regulation of transcription |
|
|
Term
| transcription factors in eukaryotes don't act on their own, but instead... |
|
Definition
| recruit other proteins to form a complex that interacts with the transcriptional machinery to activate or repress transcription |
|
|
Term
|
Definition
| huge complex of 25-30 subunits that joins the transcription machinery (transcription factor and RNA polymerase II) before transcription takes place |
|
|
Term
|
Definition
refer to p. 680
in this case, it's basically acting in combinatorial control |
|
|
Term
|
Definition
| means of controlling gene expression in eukaryotes in which each transcription factor, rather than acting on its own to effect transcription, recruits other proteins to build up large complexes that regulate the transcription machinery |
|
|
Term
| advantage of combinatorial control |
|
Definition
a given regulatory protein can have different effects, depending on the other proteins present in the cell
helps eukaryotes with different cell types |
|
|
Term
| one way steroid receptors are different from other receptors |
|
Definition
| they are soluble and found in the cytoplasm or nucleoplasm rather than being bound to the membranes |
|
|
Term
| the general mode of action for steroid hormone receptors |
|
Definition
| on binding with the signal molecule (geberic term ligand), the ligand-receptor complex modifies the expression of specific genes by binding to control elements in the DNA |
|
|
Term
| nuclear hormone receptors |
|
Definition
| large family of transcription factors that, on the binding of a signal molecule such as a steroid hormone, modify the expression of specific genes by binding to control elements in DNA |
|
|
Term
|
Definition
| specific DNA sites that nuclear hormone receptors bind to |
|
|
Term
| 2 highly conserved domains of the nuclear hormone-receptor family |
|
Definition
-DNA-binding domain
-ligand-binding domain |
|
|
Term
|
Definition
| DNA-binding domains in which eight of the cysteine residues bind zinc ions to form DNA-binding domains that are called zinc-binding domains |
|
|
Term
| depiction of the structure of 2 nuclear hormone-receptor domains |
|
Definition
|
|
Term
| how ligand binding leads to transcription |
|
Definition
| causes significant structural change in the receptor and allows the receptor to recruit other proteins that facilitate transcription |
|
|
Term
| depiction of ligand binding to nuclear hormone receptor |
|
Definition
|
|
Term
|
Definition
| proteins that bind to the receptor only after it has bound to the steroid |
|
|
Term
| when the site for the interaction between the nuclear hormone-receptor complex and the coactivators is fully formed |
|
Definition
| only when the ligand is bound |
|
|
Term
| depiction of coactivator recruitment |
|
Definition
|
|
Term
|
Definition
| binds to a site in the ligand-binding domain that overlaps the coactivator binding site |
|
|
Term
| the template for RNA synthesis in eukaryotes |
|
Definition
|
|
Term
|
Definition
| complex of DNA and histones |
|
|
Term
| one way DNA gets loosened around histones |
|
Definition
| enzymatic attachment of acetyl groups to histones |
|
|
Term
| depiction of acetylation of histones |
|
Definition
|
|
Term
| histone acetyltransferases |
|
Definition
| catalyzes the acetylation of histones |
|
|
Term
| depiction of the structure of histone acetyltransferase |
|
Definition
|
|
Term
| how histone acetylation loosens DNA |
|
Definition
| dramatically reduces the affinity of the histone for DNA by neutralizing the positive charge of the lysine residfue while adding a negative charge to it |
|
|
Term
|
Definition
an acetyl binding domain that is present in many proteins that regulate eukaryotic transcription
these proteins serve as docking sites to recruit proteins that play a variety of roles in transcription and chromatin remodeling |
|
|
Term
| how acetylation of histone tails provides a mechanism for recruiting other components of the transcriptional machinery |
|
Definition
| they serve as docking sites to recruit proteins that play a variety of roles in transcription and chromatin remodeling |
|
|
Term
| a large complex bromodomains are also present in |
|
Definition
| chromatin-remodeling engines |
|
|
Term
| chromatin-remodeling engines |
|
Definition
-large complexes that contain bromodomains and domains somilar to those of helicases
-utilize the free energy of ATP hydrolysis to shift the positions of nucleosomes along the DNA and induce other conformational changes in the DNA |
|
|
Term
| 3 mechanisms histone acetylation can activate transcription |
|
Definition
1: reducing the affinity of the histones for DNA
2: recruiting other components of the transcriptional machinery
3: initiating the remodeling of the chromatin structure |
|
|
Term
| some means by which histones can be modified |
|
Definition
-acetylation
-methylation
-phosphorylation |
|
|
Term
| depiction of chromatin remodeling |
|
Definition
|
|
Term
| table of selected histone modifications |
|
Definition
|
|
Term
| general effect of acetylation on histones |
|
Definition
|
|
Term
| general effect of methylation on histones |
|
Definition
|
|
Term
| general effect of phosphorylation on histones |
|
Definition
|
|
Term
| key reaction in repression |
|
Definition
| deacetylation of acetylated lysine |
|
|
Term
|
Definition
| catalyze deacetylation of lysine residues in histone tails |
|
|
