Exam 3 Chapter 12 Flashcards
memorize and comprehend
regulatory transcription factors (RTFs)
proteins that affect whether RNAP can go forth with transcription of a certain gene/how fast it occurs
general transcription factors (GTFs)
required for RNAP to bind to core promoter and for elongation to occur
ex. TBP, TFIID
what do RTFs recognize
cis regulatory elements near the core promoter
other words for regulatory elements
control elements, regulatory sequences
activator
RTF that increases the rate of transcription
enhancer
sequences that activators bind to
repressor
RTF that decreases the rate of transcription
silencer
sequence that a repressor binds to
DNA methylation does what
can inhibit transcription
- prevent activator binding
- recruit proteins that compact the chromatin
possible functions of domains of transcription factors
- DNA binding
- binding site for effector molecules
up-regulation
increasing rate of transcription by binding to an enhancer
can be 10-fold to 1000-fold increase
down-regulation
decreasing rate of transcription by binding to a silencer
orientation independent/bidirectional
response elements that can function in forward or reverse orientation
where are response elements located
within a few hundred nucleotides upstream of the promoter (usually)
can be up to 100,000 nucleotides away
can be downstream of the promoter
can be within introns
TFIID can be used ______ or ______
directly or through cofactors
transcription enhanced via TFIID
activator binds to the enhancer
coactivator binds to activator and recruits TFIID to the core promotor
and/or activates its functions
transcription enhanced
transcription silenced via TFIID
repressor protein binds to the silencer, stops TFIID from binding to the core promoter
transcription activated via mediator
activator protein interacts with mediator ->
carboxy-terminal domain of RNAP is phosphorylated
GTFs are released
RNAP proceeds to elongation
transcription repressed via mediator
repressor protein interacts with mediator to prevent the phosphorylation of RNAP -> no elongation -> no transcription
small effector molecule i.e. hormone
binds to the transcription factor before it binds to the response element
protein-protein interactions
two transcription factors (proteins) bind and form a homodimer that attaches to the response element
covalent modification
groups are covalently bonded to he transcription factors, ex. phosphate groups (phosphorylation)
what carries out ATP-dependent chromatin remodeling
different kinds of multiprotein machines
closed conformation of chromatin
chromatin is tightly packed
transcription may be difficult/impossible
open conformation of chromatin
chromatin is accessible to transcription factors
transcription can take place
nucleosome positioning in B-globin
changes in the promotor region as part of gene activation
role of some transcriptional activators
induce changes in chromatin structure
what causes ATP-dependent chromatin remodeling
energy of ATP hydrolysis drives changes in nucleosome location/composition, making it easier or harder to transcribe
DNA translocase
catalytic ATPase subunit found in all remodeling complexes
eukaryotic families of chromatin remodelers
SWI/SNF
ISWI
INO80
Mi-2
3 ways chromatin remodeling complexes change chromatin structure
change in nucleosome position
evicting histone octamers
change in nucleosome composition
change in nucleosome position
making some relatively closer together
or changing the spacing of all of them over a long distance
change in nucleosome composition
replacement of histones with histone variants
5 histone genes
H1, H2A, H2B, H3, H4
human genome contains _____ histone genes
over 70
most histone genes encode
standard histones
histone variants
caused by histone genes with mutations that alter the amino acid sequence
specialized chromatin
created when histone variants are incorporated into some nucleosomes
common types of histone modification
acetylation, methylation, phosphorylation
effects of histone modification
affect the level of transcription
may affect interactions between nucleosomes
_____ enzymes in mammals that can modify histone amino terminal tails
over 50
histone code
pattern of modifications that provide binding sites for proteins that specify which changes will be made to chromatin structure
effect of acetylation
DNA is less tightly bound to histones
histone acetyltransferase -> histone deacetylase
nucleosome-free region (NFR)
found at the beginning and end of genes
nucleosome positioning in a gene
precise near the beginning and end
less regularly distributed in the middle
formation of the pre-initiation complex
GTFs and RNA poly II bind to the core promotor to form a pre-initiation complex
elongation
histones ahead of the open complex - covalently modified by acetylation and evicted
histones behind the open complex - deacetylated and
become tightly bound to the DNA
DNA methylation is carried out by
DNA methyltransferase
species with very little DNA methylation
yeast, drosophila
species with abundant DNA methylation
vertebrates and plants
mammals have _____ methylated DNA
2-7%
DNA methylation usually _______ transcription in eukaryotes
inhibits
CpG islands
1,000 to 2,000 nucleotides long
high amount of CpG sites
common in vertebrates and plants
CpG islands in housekeeping genes
unmethylated
genes are expressed in most cell types
CpG islands in tissue-specific genes
expression of genes may be silenced by methylation of the islands
methylation may influence the binding of transcription factors
methyl-CpG-binding proteins may recruit factors that lead to the chromatin being compacted
enzyme adaptability
more substrate -> more enzymes
mediator
large co-activator/co-repressor molecule
3 ways to regulate eukaryotic gene expression
- use of transcription factors (GTFs or RTFs)
- chromatin remodeling complexes or histone modifying enzymes to change structure/composition of nucleosomes
- DNA methylation
RNA editing
can delete codons to alter base sequence of mRNA
combinatorial control
most eukaryotic genes are regulated by many factors
common combos of factors
1 or more activator proteins may stimulate transcription
1 or more repressor proteins may inhibit transcription
number of bps in a nucleosome
~146-147
histones in a core/octamer
2 H2A
2 H2B
2 H3
2 H4
width of a DNA double helix
2 nm
width of “beads on a string” DNA wrapped around histones
11 nm
width of chromatin fiber of packed nucleosomes
30 nm
width of a section of the extended form of a chromosome
300 nm
width of a condensed section of a metaphase chromasome
700 nm
width of an entire metaphase chromosome
1400 nm
purpose of H1
linker - holds DNA in place on the histone
what AA gets acetylated
lysine (K)
process of acetylation
add acetyl group -> done by HAT histone acetyl transferase -> histones become less positive -> less attraction with DNA -> more open conformation -> transcription ON
process of deacetylation
remove acetyl group -> done by HDAC histone deacetylase -> histones become more positive -> closed conformation favored -> transcription OFF
phosphorylation most common on which AAs
tyrosine (Y)
threonine (T)
Serine (S)
process of phosphorylation
add phosphate group -> done by kinases -> histones are less positive -> DNA unwinds -> open conformation -> transcription ON
process of de-phosphorylation
remove phosphate group -> done by phosphotases -> histones are more positive -> DNA wraps tightly -> closed conformation -> transcription OFF
AAs that are methylated
lysine (k)
histidine (H)
arginine (R)
process of methylation
add methyl group -> carried out by histone methyl transferase
can lead to EITHER turning transcription ON or OFF - not clear-cut - depends on # of times the AA is methylated
histone demethylase
removes methyl group from histones
lysine can be methylated ____
1x, 2x, or 3x
histidine can be methylated ____
only 1x
arginine can be methylated ______
1x or 2x
extent of ATP-dependent chromatin remodeling
can affect a few nucleosomes or a lot on a large scale
