Ch 17 Control of Gene Expression in Eukaryotes Flashcards
explain the differences between gene expression regulation in prokaryotes and eukaryotes
bacterial and archaeal genes organized into operons, and genes are transcribed together into a single mRNA molecule
eukaryotic genes have their own promoters and transcribed separately ; chromatin structure affects gene expression; transcription takes place in nucleus, whereas translation takes place in the cytoplasm
why is modification of chromatin structure important for gene expression?
DNA is tightly coiled to create chromatin, which is wrapped tightly around histones. transcription factors and regulatory proteins cannot access the DNA unless modifications to the chromatin are made to make the DNA more accessible
regions around the genes that become highly sensitive to DNase I, and develop upstream of transcription start site
DNase I hypersensitive sites
explain the significance of DNase I hypersensitive sites?
when genes become transcriptionally active, these sites become sensitive to DNase I, which digests the DNA. the chromatin structure relaxes, allowing regulatory proteins to access the binding sites. they support the fact that chromatin must have a more open configuration for transcription
what are three processes that affect gene regulation by altering chromatin structure?
- chromatin remodeling
- modification of histone proteins
- DNA methylation
protein complexes that bind directly to particular DNA sites and reposition nucleosomes to allow TFs and RNA polymerase to bind and initiate transcription
alters chromatin structure without altering the chemical structure of histones directly
chromatin-remodeling complexes
describe the two mechanisms by which chromatin-remodeling complexes reposition nucleosomes
CR complexes cause nucleosome to slide along DNA
CR complexes cause conformational change to DNA or nucleosomes or both
-both allow segment of DNA to be exposed and more accessible to TFs and RNA polymerase for transcription
what are the two domains of a histone and what do they associate with?
globular domain - associates with other histones and the DNA
positively charged tail - interacts with negatively charged phosphate groups on DNA
modifications of histone proteins that encode information affecting how genes are expressed
histone code
describe how histone proteins are modified
addition/removal of phosphate groups, methyl groups, or acetyl groups to phosphate tails
ubiquitination - ubiquitin added/removed from histones
describe how methylation of histones affect gene expression
addition of methyl groups to tails of histones may activate or repress transcription, depending on which histone and amino acid is methylated.
enzymes that add methyl groups to specific amino acids of histones
histone methyltransferases
what amino acids are usually methylated in histones?
lysine or arginine
enzymes that remove methyl groups from histones
histone demethylases
describe how acetylation of histones affect gene expression
addition of acetyl groups to histones usually stimulates transcription. acetyl groups destabilize the chromatin structure, allowing transcription to take place
enzymes that add acetyl groups to histone proteins, allowing transcription
acetyltransferases
enzymes that remove acetyl groups from histones, thus repressing transcription
deacetylases
describe DNA methylation and how it affects gene expression
methylation of cytosine bases to yield 5-methylcytosine, which represses transcription
where is DNA methylation most common
it is most common on cytosine bases adjacent to guanine nucleotides (CpG)
DNA regions with many CpG sequences
CpG Islands
describe the effect of CpG Islands being commonly around transcription start sites
when CpG sites are methylated, genes are not transcribed and transcription is repressed
when CpG sites are unmethylated, transcription is initiated
explain the association between DNA methylation and histone acetylation
DNA methylation attracts deacetylases, that remove acetyl groups from histones; both play role in repressing transcription
Demethylation allows acetyltransferases to add acetyl groups, thus stimulating transcription
describe the function of transcription factors
TFs bind to DNA and regulate transcription
can recruit cofactors that either stimulate or repress transcription
other proteins stimulate or repress transcription when recruited by transcription factors
cofactors
transcription factors that are part of the basal transcription apparatus and bind to the core promoter
general transcription factors
what is required for initiation of transcription
general transcription factors that are part of the basal transcription apparatus
transcription factors that bind to regulatory promoter and enhancers
transcription activator proteins (TAPs)
transcription factors that stimulate transcription
activators
transcription factors that inhibit transcription
repressors
proteins that help stimulate or stabilize the basal transcription apparatus at the core promoter
coactivator proteins
complex of proteins that interact with TFs in regulatory promoter (or enhancer) and RNA polymerase, affecting the rate at which transcription is initiated
mediator
regulatory elements that affect the transcription of distant genes (usually stimulate transcription)
enhancers
how can enhancers affect initiation of transcription at a promoter that is far away?
binding of transcription factors to enhancer causes the DNA to loop out, bringing the enhancer closer to the promoter
what are super-enhancers and what is the purpose of them?
enhancers clustered together, which are then occupied by a higher number of transcription factors, and stimulate higher levels of transcription
sequences that have an inhibitory effect on transcription of distant genes
silencers
DNA sequences that block the effects of enhancers, as long as they lie between an enhancer and a promoter
insulators
explain how genes can coordinately be expressed by responding to the same stimulus
these genes share response elements, which can all be activated by the same stimulus and give the same response
short stretches of DNA that usually contain the same consensus sequences at varying distances from the genes being regulated
response elements
what is the purpose of pre-mRNA splicing?
it allows pre-mRNA to be spliced in multiple ways, to yield different proteins
what is mRNA splicing dependent on?
presence of consensus sequences at 5’ splice site, 3’ splice site, and branch point, which determine the locations of introns and exons
what are the purpose of exonic/intronic splicing enhancers and splicing silencers
they help promote or repress the use of particular splice sites during the process of RNA splicing, resulting in alternative splicing outcomes
SF2 protein (SR proteins)
serine- and arginine- rich proteins that are involved in splice-site selection
explain how SF2 proteins interact with multiple 5’ splice sites
usage of two different 5’ splice sites produce mRNA with different lengths, and different proteins
SF2 proteins enhance the use of one of the other splice site
purpose of snRNPs (small nuclear ribonucleoproteins)
snRNPs participate in pre-mRNA splicing by recognizing the critical sequence elements present in the introns, thereby forming active spliceosomes, and splice the pre-mRNA
the amount of available mRNA depends on what two things?
the rate of mRNA synthesis and the rate of mRNA degradation
what are more stable, eukaryotic mRNAs or bacterial mRNAs
eukaryotic mRNAs are more stable, where bacterial mRNAs are degraded quickly
cellular RNA is degraded by what enzymes?
ribonucleases
describe mRNA degradation
shortening of 3’ poly(A) tail allows for 5’ cap to be removed, then ribonucleases degrade the mRNA by removing nucleotides from the 5’ end.
what are the role of Poly(A)-binding proteins (PABPs)
they bind to the poly(A) tail and enhance its stability to the 5’ end and protection
how do P bodies help control gene expression through mRNA degradation?
A lot of RNA degradation takes place in P bodies, where they temporarily store mRNA molecules
P bodies regulate which RNA molecules are degraded and which are saved for later release
describe RNA silencing (RNA interference)
miRNAs or siRNAs combine with proteins to form RISC, which pairs with complementary base sequences in specific mRNA molecules, silencing it
what are the four mechanisms siRNAs and miRNAs regulate gene expression through?
- cleavage of mRNA
- inhibition of translation
- transcriptional silencing
- degradation of mRNA
describe how cleavage of mRNA regulates gene expression
RISCS with siRNA pair with an mRNA molecule and mRNA is cleaved by Slicer enzyme. mRNA is further degraded, preventing its translation into proteins
describe how inhibition of translation regulates gene expression
miRNAs inhibit translation of complementary mRNAs through stalling the ribosome or prematurely terminating transcription
describe how transcriptional silencing regulates gene expression
siRNAs combine with proteins to form RITS, which binds to complementary sequence in mRNA, and represses transcription
RITS attracts enzymes that methylate the histone tails. this alters the chromatin structure, in which DNA binds more tightly and restricts protein access
describe how slicer-independent degradation of mRNA regulates gene expression
miRNAs bind to AU-rich elements and trigger RNA degradation
how can eukaryotic proteins be modified after translation (posttranslational modifications)
-selective cleavage and trimming of amino acids
-acetylation
-adding phosphate groups, carboxyl groups, methyl groups, carbohydates…
