copilot cards exm 3
Call Kai
Learn
Practice Test
Spaced Repetition
Match
Flashcards
Knowt Play1/86
There's no tags or description
Looks like no tags are added yet.
87 Terms
How does eukaryotic gene regulation differ from prokaryotic regulation?
Eukaryotic regulation is more complex because DNA is packaged into chromatin, genes are in a nucleus, and RNA processing occurs before translation.
What is the default state of most eukaryotic genes?
OFF because chromatin often makes promoters inaccessible.
What are the major levels of eukaryotic gene regulation?
Chromatin accessibility, transcription, RNA processing, mRNA stability, translation, and protein modification/degradation.
What is pre-transcriptional regulation?
Control of gene expression before transcription begins, often through chromatin structure and transcription factor binding.
What is post-transcriptional regulation?
Control after transcription, including splicing, mRNA degradation, translation, and protein modification.
What is chromatin?
DNA associated with histones and other proteins.
What is a nucleosome?
The basic unit of chromatin; ~147 bp of DNA wrapped around a histone octamer.
What proteins make up the histone octamer?
Two copies each of H2A, H2B, H3, and H4.
What is the role of histone H1?
It binds linker DNA and helps stabilize chromatin packing.
What is a chromosome territory?
A distinct nuclear region occupied by a chromosome during interphase.
What are transcription factories?
Nuclear sites enriched in RNA polymerase II and transcription proteins.
Why does chromatin inhibit transcription?
It restricts access of transcription factors and RNA polymerase to DNA.
What is euchromatin?
Relatively open chromatin associated with active transcription.
What is heterochromatin?
Condensed chromatin associated with low transcriptional activity.
Does open chromatin mean naked DNA?
No. DNA remains associated with histones but is more accessible.
What is nucleosome remodeling?
Movement or removal of nucleosomes to expose DNA.
How does histone acetylation affect transcription?
It generally increases accessibility and promotes transcription.
How does histone methylation affect transcription?
It can activate or repress transcription depending on the residue modified.
How does DNA methylation affect transcription?
It often represses transcription, especially at promoter CpG islands.
What enzyme adds acetyl groups to histones?
Histone acetyltransferase (HAT).
How does histone acetylation promote transcription?
It reduces positive charge on histones and weakens DNA-histone interactions.
What is a histone variant?
A replacement histone protein that alters nucleosome properties.
Give an example of a histone variant.
H2A.Z.
What is ATP-dependent chromatin remodeling?
The use of ATP to reposition, remove, or restructure nucleosomes.
What is SWI/SNF?
A major ATP-dependent chromatin remodeling complex.
What can SWI/SNF do to nucleosomes?
Slide them, restructure them, remove them, or exchange histones.
How do specific transcription factors influence chromatin?
They recruit chromatin remodelers and histone-modifying enzymes.
What is the difference between cis-acting and trans-acting elements?
Cis elements are DNA sequences; trans factors are diffusible proteins that bind those sequences.
What is a core promoter?
The promoter region surrounding the transcription start site required for basal initiation.
What is a proximal promoter?
A nearby regulatory region upstream of the core promoter that binds specific transcription factors.
What is the transcription start site (TSS)?
The first nucleotide transcribed into RNA (+1 position).
What is the TATA box?
A core promoter element ~25–30 bp upstream of the TSS that binds TBP.
What is the initiator (Inr)?
A core promoter element overlapping the transcription start site.
What is a BRE element?
A TFIIB recognition element near the TATA box.
What is a DPE?
A downstream promoter element that helps recruit transcription machinery.
What is an MTE?
A motif ten element that supports transcription initiation.
What are general transcription factors (GTFs)?
Proteins required for RNA Polymerase II initiation at core promoters.
Name the six major general transcription factors.
TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIIH.
What is TFIID composed of?
TBP and TAFs.
What does TBP bind?
The TATA box.
What is the role of TFIIA?
Stabilizes TBP binding.
What is the role of TFIIB?
Helps position RNA Polymerase II.
What is the role of TFIIF?
Stabilizes RNA Polymerase II within the initiation complex.
What is the role of TFIIE?
Recruits and regulates TFIIH.
What is the role of TFIIH?
Opens promoter DNA and phosphorylates the Pol II CTD.
What is the pre-initiation complex (PIC)?
The assembled transcription machinery at a promoter before RNA synthesis begins.
What is basal transcription?
The low, inefficient level of transcription produced by general transcription factors and the core promoter alone.
What is a focused promoter?
A promoter with one major transcription start site.
What is a dispersed promoter?
A promoter with multiple transcription start sites spread across a region.
What are specific transcription factors?
Regulatory proteins that bind particular DNA sequences and control transcription.
What are the two functional domains of a specific transcription factor?
A DNA-binding domain and an activation/repression domain.
What is the function of a DNA-binding domain?
It recognizes specific cis-acting DNA sequences.
What is the function of an activation domain?
It interacts with cofactors and the transcription machinery.
What is an activator?
A transcription factor that increases transcription.
What is a repressor?
A transcription factor that decreases transcription.
What are proximal promoter elements?
Specific DNA sequences near the promoter such as GC boxes and CCAAT boxes.
What is an enhancer?
A cis-regulatory element that increases transcription and can function at a distance.
Where can enhancers be located?
Upstream, downstream, or within a gene.
What is a silencer?
A cis-regulatory element that decreases transcription.
What is an insulator?
A DNA element that blocks inappropriate enhancer-promoter interactions.
How do enhancers activate transcription at a distance?
Through DNA looping that brings enhancers near promoters.
What is Mediator?
A coactivator complex that links activators to RNA Polymerase II.
How can activators increase transcription?
By recruiting chromatin remodelers, recruiting HATs, recruiting Mediator, and stabilizing PIC assembly.
How do repressors reduce transcription?
By recruiting corepressors, compacting chromatin, or blocking activator function.
What is combinatorial control?
Regulation of transcription through the combined effects of multiple transcription factors.
What is a zinc finger?
A DNA-binding motif stabilized by zinc ions.
What is a helix-turn-helix motif?
A DNA-binding motif that contacts the DNA major groove.
What is a basic leucine zipper (bZIP)?
A DNA-binding protein motif that uses leucines for dimerization.
What is a helix-loop-helix motif?
A DNA-binding motif that also supports dimerization.
What conditions activate GAL genes in yeast?
Galactose present and glucose low.
Are GAL genes under positive or negative control?
Positive control because an activator is required.
What is GAL4?
A transcriptional activator required for GAL gene expression.
What is GAL80?
A repressor that binds GAL4 and blocks its activation domain.
What is GAL3?
A galactose sensor that relieves GAL80 inhibition.
What happens when galactose enters the cell?
Galactose binds GAL3, which binds GAL80 and releases GAL4.
What happens after GAL4 is released from GAL80?
GAL4 activates transcription of GAL structural genes.
What is a UAS?
Upstream Activating Sequence; a cis-regulatory site bound by GAL4.
What is the eukaryotic equivalent of a bacterial operator in the GAL system?
The UAS (Upstream Activating Sequence).
What two major domains are present in GAL4?
A DNA-binding domain and an activation domain.
How does GAL4 activate transcription?
It recruits Mediator, TFIID, chromatin remodelers, and transcription machinery.
Why are GAL4 mutants unable to express GAL genes?
Because the activator required for transcription is absent.
Why are GAL80 mutants constitutively active?
Because GAL4 is no longer repressed.
Why are GAL3 mutants uninducible?
Because GAL80 repression cannot be relieved.
How does glucose repress GAL genes?
High glucose activates Mig1-mediated repression.
What is Mig1?
A glucose-responsive repressor that suppresses GAL gene transcription.
How does Mig1 repress GAL genes?
It recruits Cyc8-Tup1 and histone deacetylase activity, preventing GAL4 activation.
What is DNase hypersensitivity?
A characteristic of open chromatin that is readily cut by DNase due to reduced nucleosome occupancy.