Control of Gene Expression 1: Transcriptional Controls Flashcards
Different cells contain the same genes but express different what?
sets of protein; gene expression is different in different cells
What is an example of a “housekeeping protein”?
glucose metabolism
Hemoglobin is an example of what type of protein?
specifically limited protein
True or false?
Typical human cells express 30-60% of its 25,000 genes but level of gene expression varies
true
Alternative splicing (dystrophin gene) and post translational modification are other factors that occur when?
after transcription
What two things does gene regulation require?
- short stretches of DNA of defined sequence -recognition sites for DNA binding proteins
- gene regulatory proteins - transcription factors
True or False?
Recognition sequences can only be proximal to first exon
false; can be proximal or distal to first exon
In regards to DNA motif recognition, regulatory proteins associate with what?
major groove in DNA - presents a specific face for each of the specific base pairs
True or false?
The surface of the protein is extensively complementary to the surface of the DNA region to which it binds
true
A series of contacts between the regulatory protein and DNA is made which involves how many possible configurations?
4 configurations of base pairs
A typical gene regulatory protein-DNA interaction ivolves how many interactions?
10-20
The parts of a DNA transcription factor can be modular. What are some of these modules?
DNA binding module, dimerization module, activation module, regulatory module
What is the simplest, most common DNA binding motif?
helix-turn-helix
Describe the structure of the helix-turn-helix domain
two alpha helices are connected by short chain of amino acids that make the “turn” at a fixed angle
The longer helix in the helix-turn-helix domain is what type of module?
recognition module - DNA binding module that fits into major groove
This DNA binding motif binds to the major groove of DNA and includes a Zn atom and when the amino acid sequence is drawn out, the structure looks like a finger.
Zinc finger domain
Are Zn Finger domains found in tandem clusters? If so, why?
yes; stabilizes interaction with DNA and provides multiple contact points
This motif has a dimerization domain, activation domain and DNA binding domain and has a two alpha helical structure with leucine side arms.
Leucine zipper motif
Where do interactions occur in the leucine zipper motif?
between hydrophobic amino acid (leucine) side chains
In the leucine zipper motif there is a leucine residue every __ amino acids down one side of the alpha helix in the dimerization domain
7
note: this forms zipper structure
In the leucine zipper motif, which domain does the activation domain overlap?
dimer domain
Describe the structure of the helix-loop-helix domain
consists of a short alpha chain connected by a loop to a second longer alpha chain
True or false?
the helix-loop-helix domain can only occur as a homodimer.
false; can occur as homodimer or heterodimer
How many modules are there in the helix-loop-helix domain? What are they?
3; DNA binding domain, dimerization domain, activation domain
What is hereditary spherocytosis (HS)?
a hemolytic anemia characterized by spherical and fragile RBCs that lyse and release hemoglobin
What is the clinical presentation of hereditary spherocytosis?
hemolysis, anemia, splenomegaly
note: presentation ranges from mild to severe anemia and can be fatal
What is HS caused by?
mutations in genes for the erythrocyte membrane skeleton of RBCs
Is HS dominantly or recessively inherited?
dominantly
The erythrocyte membrane skeleton (EMS) confers what to RBCs?
durability and stability
How many EMS passages are in the circulation?
1/2 million
What is the incidence rate of HS?
1/2000
note: HS is the most common hereditary anemia in people of Northern European Descent
True or false?
HS can be caused by a mutation in zinc finger protein gene Klf1
true
note: the Klf1 zinc finger protein binds to promoters of all genes in EMS - turns them on
Where is the HS mutation found in the Klf1 gene?
GAA to GAT or Glutamic acid (Glu) to Aspartic acid (Asp) in exon 3 (zinc finger domain 2)
note: the mutation causes there to be less RNA made from target promoter
What is the chain of amino acids in the mutated form of Klf1 DNA binding motif?
Arg-Asp-Arg
In normal Klf1, the R (Arg) interacts with E (Glu Acid) in RER to stabilize interaction with C in the major groove of what?
CACCC recognition sequence
What is the result of the HS Klf1 mutation?
DNA cannot be unwound - no transcription
In regards to detection of sequence-specific DNA proteins, how does affinity chromatography work?
DNA binding protein is isolated, then the purification of sequence specific binding proteins
What does CHIP: chromatin immune precipitation allow one to identify?
allows identification of the sites in the genome that a regulatory protein binds; the pcr product at the end can be used to screen a microarray gene chip
What is the gene control region of a typical eukaryotic gene?
DNA region involved in regulating and initiating transcription of a gene
Does the gene control region of a typical eukaryotic gene include the promoter?
yes; where transcription factors and RNA polymerase II assembles
Of the 25,000 human genes, __% encode gene regulatory proteins
8
In regards to the gene control region of a typical eukaryotic gene, RNA polymerase and general transcription factors assemble at the promoter. Other gene regulatory proteins bind to regulatory sequences located where?
can be adjacent, far upstream, or in introns downstream of the promoter
What is the model for Transcriptional activation?
DNA looping and a mediator complex allowing regulatory proteins to interact with the proteins that assemble at the promoter
In regards to transcriptional activation, the mediator serves as an intermediary between what?
gene regulatory proteins and RNA polymerase II
Gene activator proteins modify local chromatin structure. Histone acetylation does what?
makes it easier to remove histones - favors transcription
What is the sequence of events starting from gene activation to transcription initiation?
gene activator protein binds to chromatin; chromatin remodeling; covalent histone modification; additional activator proteins bound to gene regulatory region; assembly of pre-initiation complex at the promoter; transcription initiation
Gene repressors inhibit transcription in different ways. The first being that gene activators and repressers compete for the same what?
binding site
Another way gene repressors inhibit transcription when both activator and repressor bind to DNA but the repressor also binds to what?
the activation domain of the activator protein - masks the activation surface
Another way gene repressors inhibit transcription is by binding DNA and directly interacting (blocking) with what?
general transcription factors
Another way gene repressors inhibit transcription is by recruiting a ___ ___ __ which returns the promoter to the pre-transcriptional nucleosome state
chromatin remodeling complex
Another way gene repressors inhibit transcription is by recruiting a ___ ___ to the promoter which makes it harder to remove deacetylated histones
histone deacetylase
Another way gene repressors inhibit transcription is by recruiting a ___ ___ ___ which methylates histones. These methylated histones are bound to proteins which act to maintain chromatin in a transcriptionally silent form..
histone methyl transferase
True or false?
depending on their composition, the complexes can be either activating or repressing. The same protein can be part of an activating or repressing complex
true
What are the seven ways gene regulatory proteins are controlled?
- synthesis
- ligand binding
- covalent modificaiton-phosphorylation
- addition of subunit
- unmasking
- nuclear entry
- proteolysis
In regards to the globin genes, what are alpha like chains? and beta like chains?
alpha like: zeta and alpha
beta like: epsilon, gamma, delta, and beta
In regards to beta globin gene regulation, what do regulatory proteins bind to?
LCR
