Molecular Bio (Exam 3): Eukaryotic Transcription

Competition, repression by blocking activation domain, translocation of repressor to the nucleus, are examples of what mechanism?

suppression by repressors.

DNA-binding and transcription-activities are carried by __________ domains of an activator.

independent.

What are the two independent domains of an activator?

DBD + activation domain.

Some activating proteins do not have __________ and instead bind DNA through protein-protein interactions.

DBD.

Coactivators don’t have a DBD and bind DNA through what interactions.

protein-protein.

A DNA-binding domain determines __________ for the target promoter or enhancer.

specficity.

An activator that does not have an activation domain (or has weak activation domain) may work by binding a __________ that has an activation domain.

coactivator.

Several factors in the __________ apparatus are targets with which activators or coactivators interact.

basal.

Activators increase binding for what?

RNA polymerase.

Activators may alter efficiency of transcription complex by inducing what?

conformational change.

Leucine zipper, helix-turn-helix, helix-loop-helix, zinc finger, are all examples of what?

DNA-binding domain structures.

Some histone methylations are associated with ________ methylation.

DNA.

The target residues for histone methylation are:

Lysine and Arginine.

Histone methylation is mediated by ________.

HMTs (histone methyltransferase).

Zinc finger is composed of what 2 structures?

alpha helix and beta sheet.

Zinc ion is coordinated by ________ or ________/histidine.

cystein.

Multiple zinc fingers may be present in one ________.

protein.

The lac repressor and homeodomain contain this DBD structure.

helix-turn-helix.

Helix3 inserts into the ________ groove (helix-3 is recognition helix).

major.

N-terminal arm of the helix-turn-helix lies in the ________ groove.

minor.

The region of the alpha-helix that binds DNA contains ________ amino acid residues.

basic.

In helix-loop-helix, a ________ is formed from two helical regions.

dimer.

A leucine zipper has a stretch of amino acids with a leucine residue in every ________ position.

seventh.

The stretch of amino acids in a leucine zipper is ________.

hydrophobic.

The upper part of leucine zipper is a short stretch of ________ ________ structure, wherein the two helices held together by hydrophobic interactions with appropriately spaced leucine.

coiled coil.

The lower part of alpha helix inserting into the ________ groove, basic region binds to DNA (bZIP).

major.

Chromatin remodeling is an ________ process (uses ATP).

active.

If nucleosomes form at a ________, transcription factors (and DNA polymerase) cannot bind.

promoter.

________ ________ is the energy-dependent displacement of reorganization of nucleosomes during transcription.

chromatin remodeling.

There are numerous chromatin remodeling complexes that use energy provided by what?

hydrolysis of ATP.

A major role is to change the organization of nucleosome at the ________, resulting in activation or repression.

promoter.

Which nucleosome dimers can only be replaced?

H2A-H2B.

The ATPase subunits of all remodeling complexes are related members of a large ________ of proteins.

superfamily.

Remodeling complexes are classified based on the subfamily of ________ subunit.

ATPase.

Different ATPase subfamilies have different modes of ________.

remodeling.

The sequence-specific factor may be released once the ________ complex has bound.

remodeling.

A remodeling complex itself does not have ________ for any particular target site on DNA.

specificity.

Remodeling complexes are recruited by ________ or ________ that binds specific DNA sequence.

activators/repressors.

Some activators or repressors can bind DNA in ________.

nucleosome.

Swi5 binds to HO ________ at the end of mitosis and recruits SWI/SNF complex. It is subsequently released.

promoter.

Transcription activation often involves nucleosome displacement at the ________.

promoter.

RNA pol II-bound promoters contain nucleosome-free regions flanked by ________ containing the H2A variant H2AZ (Htz1 in yeast).

nucleosomes.

Nucleosome is not always inhibitory for transcription, it is sometimes required for ________ of transcription.

activaton.

Mouse mammary tumor ________  binds to hormone receptor and NF1.

promoter.

Mouse mammary tumor virus (MMTV) activators can not bind naked ________ simultaneously.

DNA.

Nucleosome structure provides ________ allowing concomitant binding of MMTV promoter activators.

structure.

Histone acetylation is usually associated with ________ of gene expression.

activation.

Histone acetylation can be ________ (small area within a chromatin) or ________ (entire chromatin).

local; global.

Acetylation is mediated by ________.

HATs (KATs).

Acetyl groups are removed by histone ________.

deacetylases (HDACs).

Absence of histone acetylation is a feature of ________.

heterochromatin.

Transcription activators are associated with ________ activities in large complexes.

HAT.

Multiple HATs are recruited at a promoter region to target different ________.

histones.

Acetylated lysine binds to ________-containing proteins.

bromodomain.

Acetylated ________ binds to bromodomain-containing proteins.

lysine.

Corepressors recruit ________ ________, which are enzymes that remove acetyl groups from histones.

histone deacetylases (HDACs).

What recruits histone deacetylases (HDACs) to remove acetyl groups from histones?

corepressors.

A ________ complex contains three components: DNA binding subunit, a corepressor, and a histone deacetylase.

repressor.

What domain is found in a variety of proteins that interact with chromatin, and is used to recognize acetylated lysins on histones?

bromodomain.

The ________ is a ~60 amino acid long domain that binds methylated lysines in histones.

chromodomain.

The chromodomain is ~60 amino acid-long domain that binds methylated ________ in histones.

lysines.

Methylated cytosine on DNA recruits HDACs and ________ transcription.

represses.

Methylated ________ on DNA recruits HDACs and represses transcription.

cytosine.

Methylation of DNA is associated with transcriptional ________.

repression.

Methylated histones are associated with transcriptional activation and repression depending on ________ of methylation.

sites.

H3K4 di- or tri-methylation is associated with ________, but methylated H3K0 or K27 is associated with ________.

activation; repression.

Lysines and arginines on H3 and H4 are major targets for ________ by histone methyltransferases (HMTs).

methylation.

Lysines and arginines on ___ and ___ are major targets for methylation by HMTs.

H3; H4.

Methylation is removed by KDM1 or Jumonji family ________.

demethylases.

KMD1 and Jumonji family demethylases enzymes do what?

remove methylation.

Chromodomains and other conserved domains can bind to specific methylation sites on ________.

histones.

PHD, Tudor, and WD40 are ________ ________ that can bind to specific methylation sites on histones.

conserved domains.

H3K9 methylation is associated with transcriptional ________.

repression.

H3K9 ________ is associated with transcriptional repression.

methylation.

H3K9 is linked to ________ methylation.

DNA.

H3K9 is ________ by SET domain-containing KMT, Suv39h1.

methylated.

H3K9me recruits HP1 (________ protein).

chromodomain.

HP1 recruits DNA ________ (DNMTs).

methyltransferase.

DNMTs methylate ________ in CpG islands.

cytosine.

CpG ________ also reinforces histone methylation and deacetylation.

methylation.

Some HMTs and HDACs have binding ________ for methylated CpG.

domains.

Gene activation involves multiple changes to ________.

chromatin.

During initiation, sequence-specific factor (activator or repressor) binds to DNA (chromatin or free DNA), and recruits ________ ________ complexes and/or HAT/HDAC/HMT.

chromatin remodeling.

Alternative histones are incorporated to nucleosomes in ________ regions.

transcribed.

Htz1 alternative histone (H2AZ) is present in poised ________ and evicted before transcription.

poised.

During elongation, ________ ________ (FACT and Spt6) help disassembly and reassembly of nucleosome.

histone chaperone.

During ________, histone chaperons (FACT, Spt6) help disassembly and reassembly of nucleosome.

elongation.

FACT and Spt6 are ________ ________ that help disassembly and reassembly of nucleosomes during elongation.

histone chaperones.

Immediate ________ of nucleosome at the back of RNA pol is crucial to prevent “cryptic transcription”.

reassembly.

GAL genes for galactose metabolism is under numerous________ regulation.

transcriptional.

GAL: CUT (antisense RNA cryptic unstable transcript), assists in maintaining repressed ________.

chromatin.

GAL: CUT recruits ________ to GAL 1/10.

HMTs.

What sequence is the equivalent in yeast of the enhancer in higher eukaryotes and is bound by transcriptional activator proteins?

UAS (upstream activating sequence).

GAL1/10 genes are ________ regulated by the activator Gal4.

positively.

There are __ Gal4-binding sites in UAS.

4.

________-dependent repressors inactivates gene transcription (catabolite repression).

transcription.

Gal80 binds ________ masks its activation domain.

Gal4.

Gal3 (galactose inducible) sequesters Gal80 in the ________.

cytoplasm.

Gal3 is activator for ________.

Gal4.