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Chapter 17 - Transcriptional Regulation in Eukaryotes

Terms in this set (75)

Where does translation occur?
cytoplasm
T/F The separation of space of transcription and translation is a feature of cell regulation
true
How is the amount of mRNA affected for translation?
because eukaryotic transcripts are processed before transport into the cytoplasm
T/F Prokaryotic transcripts have a longer half-life than average eukaryotic transcripts in cell regulation.
F - Eukaryotic transcripts have a longer half-life
How does organization of DNA influence expression?
because chromatin must be remodeled before transcription of genes can occur
main difference between eukaryotic and bacteria DNA
Eukaryotic DNA is packaged into chromatin that has nucleosomes
chromosomes occupy discrete _____________ during interphase
territories
F.I.S.H
Fluorescent In Situ Hybridization
What is FISH?
method for visualizing specific locations on a chromosome to detect chromosomal abnormalities
1st step in FISH
fixation of the cell by a formaldehyde that causes cross links between proteins and nucleic acids
2nd step in FISH
a ds RNA or ds DNA probe that has special nucleotides with fluorescent proteins
3rd step in FISH
denaturation of probe and chromosomal target DNA by heating to 95 degrees Celsius
4th step in FISH
probe can hybridize (bind) to target DNA sequence
If no binding occurs between the probe and complementary DNA sequence in FISH, what does this mean?
a mutation has been detected
If a stained location of a chromosome occurs under a microscope in FISH, what does this mean?
probe and complimentary DNA sequence bind, so inflorescence occurs
Where are the transcription factories that contain most of the active RNA pol/transcription regulatory machine located?
in the nucleus
basic structure of chromatin
nucleosome
what results from chromatin being closed?
DNA is tightly associated with histone and other proteins inhibiting access to DNA
Who discovered open chromatin and when?
Weintraub and Groudine in 1976
Open chromatin
associated with histone proteins but that have been altered
What are the 3 ways to modify nucleosomes?
Nucleosome composition can be modified
Histones may be modified
chromatin can be remodeled
If a nucleosome has H2A.Z at a gene promoter region, how does this affect the nucleosome?
It affects its mobility/positioning on DNA making it more accessible for RNA pol
If a nucleosome doesn't have H2A.Z at at promoter region of a gene, how does this affect the nucleosome?
inappropriate transcription can occur
How does HATs modify histones?
They can add acetyl groups to histone tails decreasing their positive charge
What is the end result of acetylation of histones by HATs?
open conformations of open chromatin are formed allowing for binding of transcription regulatory proteins to DNA
How does repositioning/removing nucleosomes occur?
complexes use ATP hydrolysis
T/F H2A and H2A.Z are 70% identical at the amino acid level
F- 60%
What effect does SWI/SNF do to DNA and histones?
It loosens attachment between DNA and histones causing histones to "slide" down DNA
What effect does SWI/SNF do to DNA and nucleosomes?
It loosens DNA to nucleosomes or reorganization of internal nucleosome components causing histone variants to be swapped in and out
Where is methylation most likely to occur at?
position 5 of cytosine
cis-acting sequences
sequences located on same chromosome as gene that it regulates
T/F There is a "universal" promoter i.e. TATA box
F - there are none
2 subcategories of promoters
Proximal promoter element
Core promoter
2 major types of core promoter
Focused core promoter
Dispersed core promoter
Core promoters
The minimum part of a promoter needed for accurate initiation of transcription (TSS) by RNA pol II
Proximal promoter elements
located upstream of the TSS that contains binding sites for DNA-binding proteins that modulate efficiency of transcription
Focused core promoters
are associated with highly regulated genes that contain a single specific start site
Focused core promoters is used mainly in __________ ___________
lower eukaryotes
Dispersed core promoters
direct initiation from several weak TSS and are associated with constitutive genes
Dispersed core promoters are used mainly in ________ ____________
higher eukaryotes
3 components of focused core promoter
lnr element
TATA box
BRE
name 2 proximal promoter elements
CAAT and GC Box
Enhancers
increase the rate of transcription that are bound by protein activators or can activate a promoter
T/F Enhancers can be moved around relative to gene it influences and still "work"
T
How do insulators effect enhancers?
they can prevent enhancers from inappropriately affecting gene expression
What may allow/disallow enhancer-promoter interactions?
When proteins bind to insulators that then induce formation of DNA loops
Enhancers are responsible for ____________ and ___________________ ________________
time and tissue-specific expression
How do silencers block activators?
Because they will bind to repressors
Silencers often act in _________ or ___________ __________
tissue or time-specific ways
When can transcription factors bind to DNA?
when the DNA has been modified
When may transcription factors be expressed?
in tissue specific ways
certain times of development
a response to an environmental signal
MT2A gene
metallothionein 2A gene
When does the expression of MT2A gene occur?
in the presence of heavy metals and oxidative stress
What hormone is involved in the expression of MT2A gene?
glucocorticoid
GCR
glucocorticoid receptor and is an activator
Where is GCR located?
In the cytoplasm
Name the three binding domains of transcription factors
Helix-turn-helix, zinc-finger motifs, and basic leucine zipper
What are the 2 functional domains of Eukaryotic transcription factors?
DNA binding domain and protein binding domain
Helix-turn-helix
A protein domain composed of two α helices joined by a short strand of amino acids that enables it to fit into major groove of DNA
Zinc-finger motifs
chains of AAs bound around a zinc atom via linkages with 2 cysteine and 2 histidine residues that create loops that look like fingers
Basic leucine zipper (bZIP)
a leucine zipper that if formed by 2 α-helices work together to grip DNA
enhanceosome
a large protein complex that acts synergistically to activate transcription
Example of enhanceosome
it increases the assembly on PIC
PIC
pre-initiation complex
PIC is an example of what kind of promoter?
a focused promoter
Function of PIC
it is a platform for RNA pol ll to recognize the transcription start site and initiate transcription
1st step in the formation of a PIC
TFIID binds to TATA box and other core promoter elements
2nd step in the formation of a PIC
TFIIB binds to BREs
TFIID
a multi-subunit complex composed of a transcription binding protein and additional proteins
TFIIB is considered a ...
recognition element
3rd step in formation of a PIC
GTFs bind to promoter and interact with RNA pol II to help recruit it to the promoter
4th step in formation of a PIC
formation of PIC has occurred and it mediates unwinding of DNA and transcription can start
5th step in formation of a PIC
RNA pol II travels down DNA in an elongation complex and TFs stay at promoter to set up next PIC
What occurs if repressor proteins bind to silencer DNA elements?
transcription can be repressed
What 3 ways can a silencer and repressor repress transcription?
by inhibiting chromatin remodeling, inhibiting formation of a PIC or physically blocking activators
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