MMBIO 240 Ch 16 – Flashcards

question
activation domain does what
answer
recruits the transcription machinery
question
basic region/leucine zipper (bzip) protein
answer
is usually found as part of a DNA binding domain in various transcription factors, and are therefore involved in regulating gene expression. Functions as a dimerizaiton domain. Its presence generates adhesion forces in parallel alpha helices.
question
bzip DNA binding domain
answer
One part of the domain contains a region that mediates sequence specific DNA properties and the leucine zipper that is required for the dimerization of two DNA binding regions.
question
CCAAT box
answer
is a distinct pattern of nucleotides with GGCCAATCT consensus sequence that occure upstream by 75-80 bases to the initial transcription site. It signals the binding site for the RNA transcription factor -located upstream from the TATA box (in eukaryotes)
question
chromatin remodeling
answer
is the enzyme assisted movement of nucleosomes on DNA. At the core of a chromatin remodeling complexes is an ATPase capable of DNA translocation. By moving nucleosomes, transcription factors can get access to DNA that was unavailable.
question
Dimerization domain
answer
question
DNA affinity chromatography
answer
a method of separating biochemical mixtures and based on a highly specific biological interaction such as that between antigen and antibody, enzyme and substrate, or receptor and ligand.
question
DNA binding domain
answer
question
enhancer
answer
s a short region of DNA that can be bound with proteins (trans-acting factors much like transcription factors) to enhance transcription levels of genes. Enhancers are usually cis acting but it does not need to be particularly close to the genes it acts on., and sometimes not even on the same chromosome. It is typically close to the promoter and the gene.
question
euchromatin
answer
is a lightly packed form of chromatin that is rich in gene concentration and is often, but not always, under active transcription. Is the most active portion of the genome within the cell nucleus.
question
GAL4
answer
is a biochemical method used to study gene expression and function in organisms such as the fruit fly. Has two parts, the GAL4 gene, which encodes the yeast transcription activator protein Gal4 and the UAS (upstream activation sequence) a short section of the promoter region to which Gal4 specifically binds to activate gene transcription.
question
gene splicing
answer
Is the process of combining two or more sequences that would not normally occur together
question
helix-loop-helix motif
answer
is characterized by two a-helicies connected by a loop. The larger helix typically contains the DNA binding regions.
question
heterochromatin
answer
is a tightly packed form of DNA which comes in different varieties. These varieties lie on a constitutive and facultative.
question
histone acetylase (HAT)
answer
are enzymes that acetylate conserved lysine amino acids on histone proteins by transferring an acetyl group from acetyl CoA to fomr E-N-acetyl lysine. In general it is linked to transcriptional activation and associated with euchromatin.
question
histone deacetylase (HDAC)
answer
are a class of enzymes that remove acetyl groups from an E-N-acetyl lysine amino acid on a histone. It is opposite that of HAT
question
homeobox
answer
is a DNA sequence found within genes that are involved in the regulation of patterns of anatomical development in animals, fungi, and plants. It is about 180 base pairs long and encodes a protein domain (homeodomain) which when expressed can bind DNA.
question
homeodomain
answer
is a protein structural domain that binds DNA or RNA and is thus commonly found in transcription factors. Has three alpha helicies and it is the third helix that interacts directly with DNA.
question
homeotic gene
answer
are genes that determine which parts of the body form what what body parts.
question
hormone response element
answer
is a short sequence of DNA within the promoter of a a gene that is able to bind a specific hormone receptor complex and therefore regulate transcription. The sequence is most commonly a pair of inverted repeats separated by three nucleotides which also indicates that the receptor binds as a dimer.
question
leucine zipper
answer
is a motif that is involved as part of a DNA binding domain in various transcription factors, and are therefore involved in regulating gene expression. It involves parallel alpha helices, with a hydrophobic region running along one side.
question
ligand binding domain
answer
Ligand binding to a receptor alters the chemical conformation (3-D shape). This affects the functional state of the a receptor.
question
linker-scanning mutagenesis
answer
question
nuclear receptor
answer
are a class of proteins found within cells that are responsible for sensing steroid and thyroid hormones and certain other molecules. These work with other proteins to regulate the expression of specific genes, thereby controlling development, homeostasis, and metabolism of the organism.
question
POU domain
answer
(POU comes from the three transcription factors that are used) are eukaryotic transcription factors containing a bipartite DNA binding domain
question
POU protein
answer
question
remodeling complex
answer
is a complex with the capacity to remodel the structure of chromatin. It exhibits a DNA dependent ATPase activity stimulated by both free and nucleosomeal DNA and a capacity to perturb nucleosome structures.
question
transcription activator protein do what?
answer
they help recruit the transcription machinery
question
two hybrid assay
answer
this utilizes a genetically engineered strain of yeast in which the biosynthesis of certain nutrients (usually amino acids or nucleic acids) is lacking. When grown on a media that lacks these nutrients, the yeast dies. This mutant yeast strain can be made to incorporate foreign DNA in the form of plasmids
question
upstream activating sequence (UAS)
answer
is a cis-acting regulatory sequence. It is distinct from the promoter and increases the expression of a neighboring gene. Its binds GAL4
question
zinc finger
answer
is a protein structural motif that can coordinate one or more zinc ions to help stabilize their folds. They function as interaction modules that bind DNA, RNA, proteins, or small molecules.
question
What are the types of DNA binding domains?
answer
Zinc fingers, helix-turn-helix structures, basic region/ leucine zipper proteins and helix-loop-helix motifs.
question
What has been a key technique in identifying promoter elements
answer
Linker scanning mutagenesis
question
What binds just upstream of the core promoter elements to bind specific transcription activator protein?
answer
Promoter proximal elements
question
Enhancers do what?
answer
They modulate transcription and can act at a great distance from the promoter.
question
The DNA binding domain of transcription activators make sequence specific contacts with ____ or ______?
answer
Enhancers or promoter proximal elements
question
The _____ ______ recruits the transcription machinery
answer
activation domain
question
Nuclear localization and nuclear export signals do what?
answer
They permit activator proteins to move into or out of the nucleus.
question
What can be used to purify activator proteins?
answer
DNA affinity chromatography.
question
Homeotic genes do what
answer
they encode important transcriptional activators called homeobox proteins that help define the body axes during development.
question
The homeodomain of a homeobox protein contains what?
answer
a helix-turn-helix motif for DNA binding.
question
POU proteins have what
answer
Both a homeobox and a POU domain for DNA binding.
question
What is the classical zinc finger model
answer
Cys2His2- zinc residues are bound by two Cys and two His residues
question
Nuclear receptors have ____ ____ motifs. The nuclear receptors have a common structural design and are _____ or _____ with a recognition helix that bind to a hormone response element.
answer
Zinc Finger, homodimers or heterodimers.
question
_____ proteins bind to DNA as dimers that are held together through coiled coil interactions.
answer
Bzip
question
Where do activator proteins with a helix-loop-helix motif bind as dimers?
answer
To the major groove of DNA
question
In an activator, what must be bound to a DNA binding domain to stimulate transcription?
answer
The activation domain
question
How do activators work
answer
They can work through recruitment of the transcriptional machinery or by inducing a conformational change in the transcriptional machinery.
question
What is one of the best studied transcriptional activators? What has it shown?
answer
Gal4- It has been shown that the activation domain cannot stimulate transcription without a DNA binding domain.
question
Chromatin remodeling factors do what
answer
They alter histone-DNA or histone-histone interactions to make DNA accessible to the transcription machinery. These complexes work without producing covalent modification in chromatin.
question
Modifying complexes does what?
answer
it modifies the histone tails to activate or repress transcription.
question
What tends to activate transcription? What tends to repress transcription?
answer
Acetylation by HATs, Histone deacetylation by HDACs.
question
Chromatin remodeling and chromatin modifying complexes interact how?
answer
They interact with each other and with the transcription machinery to condense or decondense DNA to silence genes or make genes transcriptionally active
question
Enhancers differ from other regulatory sequences in what way?
answer
They act at a distance
question
Each transcription activator protein has at least two independently folding domains: an activation domain and what
answer
DNA binding domain
question
Genes that assign positional identities to cells along the anterior posterior axis of an embryo are called ____ genes
answer
homeotic
question
The helix turn helix motif or homeodomain is required for ____
answer
DNA binding
question
In a classical zinc finger, zinc ions...
answer
interact with histidine and methionine residues
question
Members of the nuclear receptor superfamily are induced to activate transcription by___?
answer
ligand binding
question
One reason that the number of nuclear receptors is greater than the total number of genes encoding nuclear receptors is that____?
answer
The proteins form heterodimers
question
Leucine zippers are characterized by ___
answer
coiled coil interactions
question
Leucine zippers have ____ DNA binding domains?
answer
fibrous
question
What does the b stand for in bZip of bHLH?
answer
basic
question
Myc, Max, and Mad are transcription factors of the ___ family.
answer
HLHbzip
question
Transcription will be stimulated as long as the DNA-binding domain and activation domain____.
answer
are both present, either covalently or noncovalently linked
question
What are two possible ways an activator protein can affect transcription?
answer
1. recruits transcriptional machinery
2. induces a conformational change in the transcriptional apparatus that stimulates transcription initiation.
question
Euchromatin, which contains many _____, is usually ____ accessible to transcription machinery
answer
protein coding genes; more
question
Histone deacetlyation lowers transcriptional activity by _____
answer
stabilizing compact chromatin structure
question
What are known post-translational histone modifications
answer
1. Serine phosphorylation
2. lysine methylation
3. lysine ubiquitination
question
A DNA that serves as a binding site for proteins that create a repressive chromatin environment is called a
answer
silencer
1 of

Unlock all answers in this set

Unlock answers
question
activation domain does what
answer
recruits the transcription machinery
question
basic region/leucine zipper (bzip) protein
answer
is usually found as part of a DNA binding domain in various transcription factors, and are therefore involved in regulating gene expression. Functions as a dimerizaiton domain. Its presence generates adhesion forces in parallel alpha helices.
question
bzip DNA binding domain
answer
One part of the domain contains a region that mediates sequence specific DNA properties and the leucine zipper that is required for the dimerization of two DNA binding regions.
question
CCAAT box
answer
is a distinct pattern of nucleotides with GGCCAATCT consensus sequence that occure upstream by 75-80 bases to the initial transcription site. It signals the binding site for the RNA transcription factor -located upstream from the TATA box (in eukaryotes)
question
chromatin remodeling
answer
is the enzyme assisted movement of nucleosomes on DNA. At the core of a chromatin remodeling complexes is an ATPase capable of DNA translocation. By moving nucleosomes, transcription factors can get access to DNA that was unavailable.
question
Dimerization domain
answer
question
DNA affinity chromatography
answer
a method of separating biochemical mixtures and based on a highly specific biological interaction such as that between antigen and antibody, enzyme and substrate, or receptor and ligand.
question
DNA binding domain
answer
question
enhancer
answer
s a short region of DNA that can be bound with proteins (trans-acting factors much like transcription factors) to enhance transcription levels of genes. Enhancers are usually cis acting but it does not need to be particularly close to the genes it acts on., and sometimes not even on the same chromosome. It is typically close to the promoter and the gene.
question
euchromatin
answer
is a lightly packed form of chromatin that is rich in gene concentration and is often, but not always, under active transcription. Is the most active portion of the genome within the cell nucleus.
question
GAL4
answer
is a biochemical method used to study gene expression and function in organisms such as the fruit fly. Has two parts, the GAL4 gene, which encodes the yeast transcription activator protein Gal4 and the UAS (upstream activation sequence) a short section of the promoter region to which Gal4 specifically binds to activate gene transcription.
question
gene splicing
answer
Is the process of combining two or more sequences that would not normally occur together
question
helix-loop-helix motif
answer
is characterized by two a-helicies connected by a loop. The larger helix typically contains the DNA binding regions.
question
heterochromatin
answer
is a tightly packed form of DNA which comes in different varieties. These varieties lie on a constitutive and facultative.
question
histone acetylase (HAT)
answer
are enzymes that acetylate conserved lysine amino acids on histone proteins by transferring an acetyl group from acetyl CoA to fomr E-N-acetyl lysine. In general it is linked to transcriptional activation and associated with euchromatin.
question
histone deacetylase (HDAC)
answer
are a class of enzymes that remove acetyl groups from an E-N-acetyl lysine amino acid on a histone. It is opposite that of HAT
question
homeobox
answer
is a DNA sequence found within genes that are involved in the regulation of patterns of anatomical development in animals, fungi, and plants. It is about 180 base pairs long and encodes a protein domain (homeodomain) which when expressed can bind DNA.
question
homeodomain
answer
is a protein structural domain that binds DNA or RNA and is thus commonly found in transcription factors. Has three alpha helicies and it is the third helix that interacts directly with DNA.
question
homeotic gene
answer
are genes that determine which parts of the body form what what body parts.
question
hormone response element
answer
is a short sequence of DNA within the promoter of a a gene that is able to bind a specific hormone receptor complex and therefore regulate transcription. The sequence is most commonly a pair of inverted repeats separated by three nucleotides which also indicates that the receptor binds as a dimer.
question
leucine zipper
answer
is a motif that is involved as part of a DNA binding domain in various transcription factors, and are therefore involved in regulating gene expression. It involves parallel alpha helices, with a hydrophobic region running along one side.
question
ligand binding domain
answer
Ligand binding to a receptor alters the chemical conformation (3-D shape). This affects the functional state of the a receptor.
question
linker-scanning mutagenesis
answer
question
nuclear receptor
answer
are a class of proteins found within cells that are responsible for sensing steroid and thyroid hormones and certain other molecules. These work with other proteins to regulate the expression of specific genes, thereby controlling development, homeostasis, and metabolism of the organism.
question
POU domain
answer
(POU comes from the three transcription factors that are used) are eukaryotic transcription factors containing a bipartite DNA binding domain
question
POU protein
answer
question
remodeling complex
answer
is a complex with the capacity to remodel the structure of chromatin. It exhibits a DNA dependent ATPase activity stimulated by both free and nucleosomeal DNA and a capacity to perturb nucleosome structures.
question
transcription activator protein do what?
answer
they help recruit the transcription machinery
question
two hybrid assay
answer
this utilizes a genetically engineered strain of yeast in which the biosynthesis of certain nutrients (usually amino acids or nucleic acids) is lacking. When grown on a media that lacks these nutrients, the yeast dies. This mutant yeast strain can be made to incorporate foreign DNA in the form of plasmids
question
upstream activating sequence (UAS)
answer
is a cis-acting regulatory sequence. It is distinct from the promoter and increases the expression of a neighboring gene. Its binds GAL4
question
zinc finger
answer
is a protein structural motif that can coordinate one or more zinc ions to help stabilize their folds. They function as interaction modules that bind DNA, RNA, proteins, or small molecules.
question
What are the types of DNA binding domains?
answer
Zinc fingers, helix-turn-helix structures, basic region/ leucine zipper proteins and helix-loop-helix motifs.
question
What has been a key technique in identifying promoter elements
answer
Linker scanning mutagenesis
question
What binds just upstream of the core promoter elements to bind specific transcription activator protein?
answer
Promoter proximal elements
question
Enhancers do what?
answer
They modulate transcription and can act at a great distance from the promoter.
question
The DNA binding domain of transcription activators make sequence specific contacts with ____ or ______?
answer
Enhancers or promoter proximal elements
question
The _____ ______ recruits the transcription machinery
answer
activation domain
question
Nuclear localization and nuclear export signals do what?
answer
They permit activator proteins to move into or out of the nucleus.
question
What can be used to purify activator proteins?
answer
DNA affinity chromatography.
question
Homeotic genes do what
answer
they encode important transcriptional activators called homeobox proteins that help define the body axes during development.
question
The homeodomain of a homeobox protein contains what?
answer
a helix-turn-helix motif for DNA binding.
question
POU proteins have what
answer
Both a homeobox and a POU domain for DNA binding.
question
What is the classical zinc finger model
answer
Cys2His2- zinc residues are bound by two Cys and two His residues
question
Nuclear receptors have ____ ____ motifs. The nuclear receptors have a common structural design and are _____ or _____ with a recognition helix that bind to a hormone response element.
answer
Zinc Finger, homodimers or heterodimers.
question
_____ proteins bind to DNA as dimers that are held together through coiled coil interactions.
answer
Bzip
question
Where do activator proteins with a helix-loop-helix motif bind as dimers?
answer
To the major groove of DNA
question
In an activator, what must be bound to a DNA binding domain to stimulate transcription?
answer
The activation domain
question
How do activators work
answer
They can work through recruitment of the transcriptional machinery or by inducing a conformational change in the transcriptional machinery.
question
What is one of the best studied transcriptional activators? What has it shown?
answer
Gal4- It has been shown that the activation domain cannot stimulate transcription without a DNA binding domain.
question
Chromatin remodeling factors do what
answer
They alter histone-DNA or histone-histone interactions to make DNA accessible to the transcription machinery. These complexes work without producing covalent modification in chromatin.
question
Modifying complexes does what?
answer
it modifies the histone tails to activate or repress transcription.
question
What tends to activate transcription? What tends to repress transcription?
answer
Acetylation by HATs, Histone deacetylation by HDACs.
question
Chromatin remodeling and chromatin modifying complexes interact how?
answer
They interact with each other and with the transcription machinery to condense or decondense DNA to silence genes or make genes transcriptionally active
question
Enhancers differ from other regulatory sequences in what way?
answer
They act at a distance
question
Each transcription activator protein has at least two independently folding domains: an activation domain and what
answer
DNA binding domain
question
Genes that assign positional identities to cells along the anterior posterior axis of an embryo are called ____ genes
answer
homeotic
question
The helix turn helix motif or homeodomain is required for ____
answer
DNA binding
question
In a classical zinc finger, zinc ions...
answer
interact with histidine and methionine residues
question
Members of the nuclear receptor superfamily are induced to activate transcription by___?
answer
ligand binding
question
One reason that the number of nuclear receptors is greater than the total number of genes encoding nuclear receptors is that____?
answer
The proteins form heterodimers
question
Leucine zippers are characterized by ___
answer
coiled coil interactions
question
Leucine zippers have ____ DNA binding domains?
answer
fibrous
question
What does the b stand for in bZip of bHLH?
answer
basic
question
Myc, Max, and Mad are transcription factors of the ___ family.
answer
HLHbzip
question
Transcription will be stimulated as long as the DNA-binding domain and activation domain____.
answer
are both present, either covalently or noncovalently linked
question
What are two possible ways an activator protein can affect transcription?
answer
1. recruits transcriptional machinery
2. induces a conformational change in the transcriptional apparatus that stimulates transcription initiation.
question
Euchromatin, which contains many _____, is usually ____ accessible to transcription machinery
answer
protein coding genes; more
question
Histone deacetlyation lowers transcriptional activity by _____
answer
stabilizing compact chromatin structure
question
What are known post-translational histone modifications
answer
1. Serine phosphorylation
2. lysine methylation
3. lysine ubiquitination
question
A DNA that serves as a binding site for proteins that create a repressive chromatin environment is called a
answer
silencer