transcription
changing DNA into RNA
RNA polymerase
multiprotein complex that transcribes DNA from the 3' to the 5' end of the DNA
5' to 3'
RNA is generated from ___ _____ ____ end
promoter regions
places on double-stranded DNA that RNA polymerase binds to
pre-mRNA strand
complementary base pairing
RNA polymerase builds the _______ ___________ that is ________________________ to the DNA template by _________ ____________________ (elongation)
releases
dissociates
Once finished, RNA polymerase _______ the RNA and _________________ from the DNA strand
DNA processing
non-coding regions (including introns) are removed from the pre-mRNA and the exons are spliced together by the splieosome
5' cap
poly-a tail
enzymes
A ___ _____ and a _______________ are added to protect the mRNA from _____________ and to allow export into the cytoplasm.
translation
changing of mRNA into proteins
5' to 3'
start codon (AUG methionine)
Ribosome reads mRNA from ___ ___ ___ until it finds the ________ ________ (____ __________).
Eukaryotic translation initiation factors (EIFs)
facilitate initiation of translation (by assembling the ribosome 43's pre-initiation complex and 80s initiation complex) and elongation
3
amino acyl tRNA
___ nucleotide codons are matched to the correct _______ ________ ____
amino acids
__________ __________ are linked by the ribosome to form a chain.
translation elongation factors
facilitate chain elongation so that the amino acid chain can become a protein
release factors
recognize the stop codons to terminate translation
helicase
unwinds the mRNA secondary structure so that the nucleotide sequence can be read by the ribosome
40S
80S
E, P, A
Ribosomes have a small (_____) and a large (_____) subunit, and 3 tRNA binding sites (____________).
hydrolysis of GTP
acts as quality control at each step of translation (initiation, elongations, translocation of ribosomes, and termination)
DNA synthesis
creating DNA from DNA
DNA polymerase
reads the DNA template from 3' to 5' and builds new DNA from 5' to 3'
Helicase
primase
DNA polymerase
____________________ unwinds the DNA strand, _____________ makes short RNA primers, _____ ______________ builds the DNA strand that is complementary to the DNA template
topoisomerase
removes torsional stress in unwound strands during DNA synthesis
leading strand
orazaki fragments
DNA ligase
The ________ ___________ is generated continuously but the lagging strand is made of short ____________ ____________ that are stitched together by _____ ______________.
semi-conservative
Synthesis is _________________ (old parent and new daughter strands are paired together in the new DNA double helix
bidirectional
DNA replication is ____________________________ because two helicases unwind the DNa duplex in both directions from an origin.
genes
units of heredity
alleles
different forms of a gene
genotype
set of alleles carried by an individual
phenotype
observable traits
DNA cloning
method to increase expression of DNA of interest
Sanger Method
used to determine nucleotide seuqences
plasmid
bacterial host
removed
restriction enzymes
fragments
electrophoresis
PCR polymerase
expression
During DNA cloning, DNA is inserted into _____________ and expanded in a _____________ _________. Then it is ______________ from the plasmid using ___________ _______________. ______________________ are separated using _______________________. ___________
southern blot
quantified DNA expression in a sample
Northern Blot
quantifies RNA expression in a sample
Western Blot
quantifies protein expression in a sample
in-situ hybridization
localizes RNA in tissue
DNA microarray
measures changes in expression of mRNA corresponding to multiple genes
transfection
method of introducing gene expression into an animal cell
plasmid uptake
type of transfection that occurs via electroporation or chemical agents or viruses that are modified to carry the gene of interest
green fluorescent protein
localizes gene expression in tissue or label cell for gene expression
transgenic mice
used to knock out or knock in expression of a gene to study it in vivo
RNA interference
used to eliminate expression of a gene to study its function in vivo
protein coding genes
RNA coding genes
Tandemly-repeated genes
Non-protein Coding Functional RNA's
Repetitious DNA
Unclassified Spacer DNA
6 major classes of DNA
protein coding genes
55% of DNA that participate in alternative splicing
alternative splicing
produces different isoforms of a protein by introducing variations in the incorporation of the exons or coding regions of mRNA
tandemly-repeated genes
0.4% of DNA that includes small nuclear RNA and ribosomal RNA
small nuclear RNA
RNA confined to the nucleus that are involved in splicing or other RNA processing actions
ribosomal RNA
RNA required in the ribosome for protein synthesis
non-protein coding functional RNA's
non-coding RNA that is not translated into proteins and is used to regulate gene expression at the transcriptional and post-transcriptional levels
small nucleolon RNA
non-protein coding function RNA that is involved in rRNA processing and base modification
microRNA
non-protein coding functional RNA that regulates messenger RNA translation and stability
repetitious DNA
simple-sequence DNA, which has short repeats, and includes micro- and mini-satellites
micro satellites
DNA regions with short, repeated sequences (1-13 base pairs)
mini-satellites
DNA regions with larger, repeated sequences (14-100 base pairs)
DNA fingerprinting
technique to compare lengths of mini-satellites using southern blotting
interspersed repeats
longer sequences, composed of transposable elements
DNA transposons
small piece of DNA that inserts itself into another place in the genome
retrotransposons
transpose as DNA or RNA that is then reverse transcribed to DNA
long terminal repeat retrotransposons
flanked by LTR region, similar to retroviral genome
mitochondria and chloroplasts
contain their own genome
histones
achieve packing and organizing of chromosomal DNA
chromatin
DNA/Histone complex
euchromatin
least compact form of DNA that appears as beads called nucleosomes on a string
heterochromatin
most compact form of DNA that wraps around and forms a double helix
metaphase
phase in which chromosomes are in the most compact form of two chromatids of identical DNA molecules joined at the centromere with telomere sequences at the ends to prevent shortening
karyotype
the number, size, and shape of chromosomes during metaphase
replication origins
centromere
telomeres
3 functional elements required by eukaryotic chromosomes to replicate and segregate
telomeres
repeated sequence (TTAGGG) at the end of a chromatid that protect the chromosomes from enzymatic degradation
shorten
divisions
primers
Telomeres _________________ with progressive cell ________________ because RNA ____________ are degraded on the lagging strand.
DNA
loss
5'
Standard _______ replication leads to loss of DNA at the _____ end of each strand.
telomerase
prevents shortening by reverse transcribing its RNA template into DNA and active in germ, stem, and cancer cells but turned of in most "adult" cells
transcription (initiation/elongation)
RNA processing
mRNA export from the nucleus
translation into protein
points at which gene regulation can occur during the gene expression process
polymerase I
RNA polymerase that deals with rRNA (ribosomes)
polymerase II
RNA polymerase that deals with mRNA, sRNA (RNA splicing), siRNA(transcription control), miRNA (translation control)
polymerase III
RNA polymerase that deals with tRNA, rRNA, snRNA
RNA polymerase II
transcription
elongate
Transcription of a gene is regulated by the ability of _________________________ to intitiate __________________ or ______________ the RNA strand.
operons
functional groups of proteins located adjacent in chromosone with a single promoter
operator
short region of regulatory DNA that is recognized by the repressor protein
lac operon
operon that endoces 3 proteins to bring lactose into the cell and metabolize it
activators and repressors
control initiation of lac operon by monitoring what nutrients is available in the cell
glucose
lactose
galactose
glucose
When lactose and glucose are both present, cells preferentially metabolize _____________ becuase _________________ requires an enzyme to break it apart into ________________ and ______________.
no lactose but ample glucose
lac repressor binds to the operator region and blocks mRNA transcription
have lactose and glucose
lac repressor releases and transcription occurs at a low rate
have lactose but no glucose
lac repressor releases and there is an increased intracellular concentration of cAMP which binds to CAPs and activates them, filitates binding of RNA polymerase, and has a high rate of transcription
promoter
DNA sequence that specified where RNA polymerase binds and initiates transcription of a gene (true for both eukaryotes and prokaryotes)
transcription factors
proteins that bind to the transcription control regions (which include promoter and regions upstream and downstream from the gene, within intron or beyond the gene regions) to repress or activate transcription
multiple
alternative control elements
Transcription of a single gene may be regulated by the binding of _________________ different transcription factors to __________________ ________________________ ______________________.
transcription control regions
a eukaryotic gene transcription control factor that includes the promoter and the DNA region involved in regulating gene transcription
far
transcription factor binding sites
gene expression
Transcription control regions may have some regulatory sequences that can be located ______ from the promotor as well as ____________ __________ ________________ __________ that enhance or inhibit ________ _____________.
TATA boxes
binding site that is associated with highly transcribed genes and helps to correctly position RNA polymerase II at the transcription binding site
CpG Islands
binding sites that are large quantities of CG sequences that can have several alternative start sites surrounding the gene
promoter
consists of a core (including TATA box) where transcription factors and Polymerase II bind, and promotor proximal element, where transcription factors bind
promoter proximal element
a regulatory sequence of DNA located 2000 base pairs from the start site
general transcription factors (TFIIA, TFIIB, etc)
needed in order for RNA Polymerase II to initiate transcription
promoter
binding protein
DNA
pre-initiation
Factors must assemble at the __________ which includes the TATA box __________ ____________ that distorts the _________ to facilitate formation of the _________________________ complex.
pre-initiation complex
includes TBP, RNA Polymerase II, all other general transcription factors, and a helicase that unwinds the DNA strand
increase
decrease
transcription
General transcription factors can also be regulated to ____________ or ____________ the rate of ___________________.
pairing of DNA into chromatin via histone modification
regulates the availability of genes for transcription
inactive genes
regulated in highly compacted regions of heterochromatin
transcribed genes
located in less compact regions of euchromatin
activators and repressors
interact with RNA Polymerase II to regulate assembly of the initation complex
attract
modify
RNA Polymerase II
Activators ___________, position, and _____________ transcription factors as well as _________________________ at the start of transcription.
mediator of transcription complex
pre-initiation complexes
Activors interact with ______________ _____ ___________ ____________ that binds to RNA Polymerase II and regulates assembly of ________________ ____________________.
chromatin-modifying
accessibility
Transcription may require ________________________ enzymes (chromatin remodeling complexes and histone acetylases) to increase ___________________ of DNA.
RNA polymerases
elongation factors
During transcription elongation, ___________ ______________________ are associated with _____________ _________________.
elongation factors
prevents polymerase from dissociating with DNA before it reaches stop site, and help it transverse through more compacted regions of chromatin during transcription elongation
transcription factors
can inhibit elongation or release elongation inhibitors
repressors
can compete with activators for DNA binding sites, or bind to activation domains of activators to inhibit them
chromatin remodeling complex:
multi-protein structure rewired for assembly of the transcription machinery at the promotor site
the co-activator complex mediator binds
After the chromatin remodeling complex remodels the chromatin to an open structure:
co-activator complex
interacts with multiple activators bound at enhancer or promotor-proximal elements to stimulate assembly of pre-initiation complex of the promotor
hormones
regulate gene expression in multiple cells and multiple genes
lipid-soluble
cell membrane
receptors
Hormones are small, _____________________ molecules that diffuse through the _____ ______________ to bind to _____________________ in the cytosol.
heterodimeric
type of receptors for hormones located in the nucleus that repress transcription without hormones boudn to DNA by histone dacetylation
receptors
histone acetylation
mediator
When a heterodimeric hormone receptors is bound to a hormone, the ________________ promote ___________ _____________ and bind to the __________________.
cytoplasm
where heterodimeric receptors are located
Heterodimeric receptors
hormone binding releases inhibitors
nucleus
chromatin remodeling
histone
mediator
heterodimeric receptor + hormones tanslocates to the ____________ to interact with ______________ ___________, ____________ acetylase complexes, and the ___________
heat shock genes
genes always in a state of paused transcript
heat shock TFs
heat shock activates ________ _________ __
proximal promoter regions
pol II
rapid
heat shock TFs bind to ___________ ___________ __________ of HS genes that then stimulates _____________ __ to continue elongation which induces ________ translation of HS genes
Epigenetics
transcription memory
permanent
semi-permanent
do not
Epigenetics involve ________________ or _____________________ alterations to gene expression that (Do/do not) affect the genome sequence
diet
behavior
stress
toxin exposure
possibly mental trauma
starvation
Epigenetics is caused by
TFs
cell differentiation
Epigenetics initially results from activity of ____ that regulate ________ ______________
post-translational
histones
dna methylation
multiple cell divisions
epigenetics changes are maintained by _________-_________________ modification of _________ ( includes acetylation, methylation, ubiquitinylation, phosohorylation, etc) and _______ _________________ (position 5 of cytosine pyrimidine ring) through _______
germ cell modifications
may be passed to offspring
mRNA processing
Export from nucleus could be blocked
Stability in cytoplasm
Based on location in cytoplasm
Affecting translation
Methods of Post-transcriptional control of gene expression
mRNA processing
Alternative splicing and choice of poly A sites
poly A tail
5' cap
Export from nucleus could be blocked if mRNA is missing ________ ______ or __ _____.
deadenylation
decapping
cytoplasmic exosomes
Stability in cytoplasm could be degraded by _________________ and ________________, followed by degradation by ________________ ____________ (note: longer poly A tails slow rate of degradation)
co-transcriptional
Pre-mRNA processing is often __________________________
7-methyl
5'
dimeric
carboxyl terminal domain
_________ guanylate capping of ___ end and by ____________ enzymes that associate with ___________ ______________ __________ (CTD) of RNA poly II
ribonucleoprotein particles
RNA associates with heterogeneous ____________________________ __________ (hnRNPS) that protect the mRNA from degradation
heterogenous ribonucleoprotein particles
hnRNPs
polyadenylation
hnRNPS also participate in splicing, _______________, and export to the cytoplasm
long genes
introns are spliced out (co-trranscriptional for ______ ______ only)
cleaved
polyadenylation
introns
transcription terminates, poly A site is __________, ____________________ occurs, ________ are spliced out (for short genes only)
mRNP
mature" mRNA + hnRNP proteins
snRNA
small nuclear ribonucleoprotein particles
___________ associated with certain proteins to form snRNPs ( ____ __________ _______________________ _____________)
exonic splicing enhancers
RNA binding proteins
Exon is recognized at regions called ________ _________ ____________ by ___ ________ __________ (SR proteins, which are a type of hnRNP)
pre-mRNA
spliceosome
RNA binding proteins assemble on a __________ to form a ______________=snRNA + pre-mRNA and force the branch point A of the pre-mRNA to bulge out
exons
intron
Proteins join 2 _______ and release the ________ as a "lariat structure
linear strands
nucleases
3' to 5'
In the last step of splicing, introns are converted to ___________ ________ and digested by _____________ in the exosome (from ___ __ ___)
RNA editing
alters the sequence of pre-mRNA so that the sequence of amino acids differs from that in the genome
protozoans
plants
eukaryotes
RNA editing is common in ____________ and _______ , but rare in _____________
nuclear envelope
nuclear pores
To transport to the cytosol, the mRNA must cross the __________ _________ through __________ ______
Nucleoporin proteins
forms nuclear pores
F6
molecular cloud
___ nucleoporins extend into the pore and form a ______________ ________ that blocks movement through the pore
mRNP complex
nuclear exporters
____ __________ (mature mRNA + hnRNPs) associates with ________ _______ (NXF1/NXT1) (hydrophobic regions bind transiently to F6 domains)
nuclear exporters
dissociates in cytoplasm and return to nucleus
5' cap
cytoplasmic poly a
Translation initiation factor binds to ___ ______ and nuclear poly A binding protein PABPII is replaced with ____________ _____ ___ binding protein PABPI
miRNAs
3'
inhibit
Cytoplasmic gene control: ________ (~22 nucleotides) hybridize to the mRNA (at ___ region) to ___________ translation
siRNAs
degraded
Cytoplasmic gene control: ________ signal for the mRNA to be ___________
siRNA
hybridizes perfectly with mRNA which leads to cleaving and degradation
proteins
Cytoplasmic gene control: ___________ can bind to 3' or 5' end of mRNA (binding to mRNA inhibits assembly of translation initiation complex)
mRNA degradation
Decapping pathway
Deadenylation-dependent pathway
Endonucleolytic pathway (cleavage)
transcription
changing DNA into RNA
RNA polymerase
multiprotein complex that transcribes DNA from the 3' to the 5' end of the DNA
5' to 3'
RNA is generated from ___ _____ ____ end
promoter regions
places on double-stranded DNA that RNA polymerase binds to
pre-mRNA strand
complementary base pairing
RNA polymerase builds the _______ ___________ that is ________________________ to the DNA template by _________ ____________________ (elongation)
releases
dissociates
Once finished, RNA polymerase _______ the RNA and _________________ from the DNA strand
DNA processing
non-coding regions (including introns) are removed from the pre-mRNA and the exons are spliced together by the splieosome
5' cap
poly-a tail
enzymes
A ___ _____ and a _______________ are added to protect the mRNA from _____________ and to allow export into the cytoplasm.
translation
changing of mRNA into proteins
5' to 3'
start codon (AUG methionine)
Ribosome reads mRNA from ___ ___ ___ until it finds the ________ ________ (____ __________).
Eukaryotic translation initiation factors (EIFs)
facilitate initiation of translation (by assembling the ribosome 43's pre-initiation complex and 80s initiation complex) and elongation
3
amino acyl tRNA
___ nucleotide codons are matched to the correct _______ ________ ____
amino acids
__________ __________ are linked by the ribosome to form a chain.
translation elongation factors
facilitate chain elongation so that the amino acid chain can become a protein
release factors
recognize the stop codons to terminate translation
helicase
unwinds the mRNA secondary structure so that the nucleotide sequence can be read by the ribosome
40S
80S
E, P, A
Ribosomes have a small (_____) and a large (_____) subunit, and 3 tRNA binding sites (____________).
hydrolysis of GTP
acts as quality control at each step of translation (initiation, elongations, translocation of ribosomes, and termination)
DNA synthesis
creating DNA from DNA
DNA polymerase
reads the DNA template from 3' to 5' and builds new DNA from 5' to 3'
Helicase
primase
DNA polymerase
____________________ unwinds the DNA strand, _____________ makes short RNA primers, _____ ______________ builds the DNA strand that is complementary to the DNA template
topoisomerase
removes torsional stress in unwound strands during DNA synthesis
leading strand
orazaki fragments
DNA ligase
The ________ ___________ is generated continuously but the lagging strand is made of short ____________ ____________ that are stitched together by _____ ______________.
semi-conservative
Synthesis is _________________ (old parent and new daughter strands are paired together in the new DNA double helix
bidirectional
DNA replication is ____________________________ because two helicases unwind the DNa duplex in both directions from an origin.
genes
units of heredity
alleles
different forms of a gene
genotype
set of alleles carried by an individual
phenotype
observable traits
DNA cloning
method to increase expression of DNA of interest
Sanger Method
used to determine nucleotide seuqences
plasmid
bacterial host
removed
restriction enzymes
fragments
electrophoresis
PCR polymerase
expression
During DNA cloning, DNA is inserted into _____________ and expanded in a _____________ _________. Then it is ______________ from the plasmid using ___________ _______________. ______________________ are separated using _______________________. ___________
southern blot
quantified DNA expression in a sample
Northern Blot
quantifies RNA expression in a sample
Western Blot
quantifies protein expression in a sample
in-situ hybridization
localizes RNA in tissue
DNA microarray
measures changes in expression of mRNA corresponding to multiple genes
transfection
method of introducing gene expression into an animal cell
plasmid uptake
type of transfection that occurs via electroporation or chemical agents or viruses that are modified to carry the gene of interest
green fluorescent protein
localizes gene expression in tissue or label cell for gene expression
transgenic mice
used to knock out or knock in expression of a gene to study it in vivo
RNA interference
used to eliminate expression of a gene to study its function in vivo
protein coding genes
RNA coding genes
Tandemly-repeated genes
Non-protein Coding Functional RNA's
Repetitious DNA
Unclassified Spacer DNA
6 major classes of DNA
protein coding genes
55% of DNA that participate in alternative splicing
alternative splicing
produces different isoforms of a protein by introducing variations in the incorporation of the exons or coding regions of mRNA
tandemly-repeated genes
0.4% of DNA that includes small nuclear RNA and ribosomal RNA
small nuclear RNA
RNA confined to the nucleus that are involved in splicing or other RNA processing actions
ribosomal RNA
RNA required in the ribosome for protein synthesis
non-protein coding functional RNA's
non-coding RNA that is not translated into proteins and is used to regulate gene expression at the transcriptional and post-transcriptional levels
small nucleolon RNA
non-protein coding function RNA that is involved in rRNA processing and base modification
microRNA
non-protein coding functional RNA that regulates messenger RNA translation and stability
repetitious DNA
simple-sequence DNA, which has short repeats, and includes micro- and mini-satellites
micro satellites
DNA regions with short, repeated sequences (1-13 base pairs)
mini-satellites
DNA regions with larger, repeated sequences (14-100 base pairs)
DNA fingerprinting
technique to compare lengths of mini-satellites using southern blotting
interspersed repeats
longer sequences, composed of transposable elements
DNA transposons
small piece of DNA that inserts itself into another place in the genome
retrotransposons
transpose as DNA or RNA that is then reverse transcribed to DNA
long terminal repeat retrotransposons
flanked by LTR region, similar to retroviral genome
mitochondria and chloroplasts
contain their own genome
histones
achieve packing and organizing of chromosomal DNA
chromatin
DNA/Histone complex
euchromatin
least compact form of DNA that appears as beads called nucleosomes on a string
heterochromatin
most compact form of DNA that wraps around and forms a double helix
metaphase
phase in which chromosomes are in the most compact form of two chromatids of identical DNA molecules joined at the centromere with telomere sequences at the ends to prevent shortening
karyotype
the number, size, and shape of chromosomes during metaphase
replication origins
centromere
telomeres
3 functional elements required by eukaryotic chromosomes to replicate and segregate
telomeres
repeated sequence (TTAGGG) at the end of a chromatid that protect the chromosomes from enzymatic degradation
shorten
divisions
primers
Telomeres _________________ with progressive cell ________________ because RNA ____________ are degraded on the lagging strand.
DNA
loss
5'
Standard _______ replication leads to loss of DNA at the _____ end of each strand.
telomerase
prevents shortening by reverse transcribing its RNA template into DNA and active in germ, stem, and cancer cells but turned of in most "adult" cells
transcription (initiation/elongation)
RNA processing
mRNA export from the nucleus
translation into protein
points at which gene regulation can occur during the gene expression process
polymerase I
RNA polymerase that deals with rRNA (ribosomes)
polymerase II
RNA polymerase that deals with mRNA, sRNA (RNA splicing), siRNA(transcription control), miRNA (translation control)
polymerase III
RNA polymerase that deals with tRNA, rRNA, snRNA
RNA polymerase II
transcription
elongate
Transcription of a gene is regulated by the ability of _________________________ to intitiate __________________ or ______________ the RNA strand.
operons
functional groups of proteins located adjacent in chromosone with a single promoter
operator
short region of regulatory DNA that is recognized by the repressor protein
lac operon
operon that endoces 3 proteins to bring lactose into the cell and metabolize it
activators and repressors
control initiation of lac operon by monitoring what nutrients is available in the cell
glucose
lactose
galactose
glucose
When lactose and glucose are both present, cells preferentially metabolize _____________ becuase _________________ requires an enzyme to break it apart into ________________ and ______________.
no lactose but ample glucose
lac repressor binds to the operator region and blocks mRNA transcription
have lactose and glucose
lac repressor releases and transcription occurs at a low rate
have lactose but no glucose
lac repressor releases and there is an increased intracellular concentration of cAMP which binds to CAPs and activates them, filitates binding of RNA polymerase, and has a high rate of transcription
promoter
DNA sequence that specified where RNA polymerase binds and initiates transcription of a gene (true for both eukaryotes and prokaryotes)
transcription factors
proteins that bind to the transcription control regions (which include promoter and regions upstream and downstream from the gene, within intron or beyond the gene regions) to repress or activate transcription
multiple
alternative control elements
Transcription of a single gene may be regulated by the binding of _________________ different transcription factors to __________________ ________________________ ______________________.
transcription control regions
a eukaryotic gene transcription control factor that includes the promoter and the DNA region involved in regulating gene transcription
far
transcription factor binding sites
gene expression
Transcription control regions may have some regulatory sequences that can be located ______ from the promotor as well as ____________ __________ ________________ __________ that enhance or inhibit ________ _____________.
TATA boxes
binding site that is associated with highly transcribed genes and helps to correctly position RNA polymerase II at the transcription binding site
CpG Islands
binding sites that are large quantities of CG sequences that can have several alternative start sites surrounding the gene
promoter
consists of a core (including TATA box) where transcription factors and Polymerase II bind, and promotor proximal element, where transcription factors bind
promoter proximal element
a regulatory sequence of DNA located 2000 base pairs from the start site
general transcription factors (TFIIA, TFIIB, etc)
needed in order for RNA Polymerase II to initiate transcription
promoter
binding protein
DNA
pre-initiation
Factors must assemble at the __________ which includes the TATA box __________ ____________ that distorts the _________ to facilitate formation of the _________________________ complex.
pre-initiation complex
includes TBP, RNA Polymerase II, all other general transcription factors, and a helicase that unwinds the DNA strand
increase
decrease
transcription
General transcription factors can also be regulated to ____________ or ____________ the rate of ___________________.
pairing of DNA into chromatin via histone modification
regulates the availability of genes for transcription
inactive genes
regulated in highly compacted regions of heterochromatin
transcribed genes
located in less compact regions of euchromatin
activators and repressors
interact with RNA Polymerase II to regulate assembly of the initation complex
attract
modify
RNA Polymerase II
Activators ___________, position, and _____________ transcription factors as well as _________________________ at the start of transcription.
mediator of transcription complex
pre-initiation complexes
Activors interact with ______________ _____ ___________ ____________ that binds to RNA Polymerase II and regulates assembly of ________________ ____________________.
chromatin-modifying
accessibility
Transcription may require ________________________ enzymes (chromatin remodeling complexes and histone acetylases) to increase ___________________ of DNA.
RNA polymerases
elongation factors
During transcription elongation, ___________ ______________________ are associated with _____________ _________________.
elongation factors
prevents polymerase from dissociating with DNA before it reaches stop site, and help it transverse through more compacted regions of chromatin during transcription elongation
transcription factors
can inhibit elongation or release elongation inhibitors
repressors
can compete with activators for DNA binding sites, or bind to activation domains of activators to inhibit them
chromatin remodeling complex:
multi-protein structure rewired for assembly of the transcription machinery at the promotor site
the co-activator complex mediator binds
After the chromatin remodeling complex remodels the chromatin to an open structure:
co-activator complex
interacts with multiple activators bound at enhancer or promotor-proximal elements to stimulate assembly of pre-initiation complex of the promotor
hormones
regulate gene expression in multiple cells and multiple genes
lipid-soluble
cell membrane
receptors
Hormones are small, _____________________ molecules that diffuse through the _____ ______________ to bind to _____________________ in the cytosol.
heterodimeric
type of receptors for hormones located in the nucleus that repress transcription without hormones boudn to DNA by histone dacetylation
receptors
histone acetylation
mediator
When a heterodimeric hormone receptors is bound to a hormone, the ________________ promote ___________ _____________ and bind to the __________________.
cytoplasm
where heterodimeric receptors are located
Heterodimeric receptors
hormone binding releases inhibitors
nucleus
chromatin remodeling
histone
mediator
heterodimeric receptor + hormones tanslocates to the ____________ to interact with ______________ ___________, ____________ acetylase complexes, and the ___________
heat shock genes
genes always in a state of paused transcript
heat shock TFs
heat shock activates ________ _________ __
proximal promoter regions
pol II
rapid
heat shock TFs bind to ___________ ___________ __________ of HS genes that then stimulates _____________ __ to continue elongation which induces ________ translation of HS genes
Epigenetics
transcription memory
permanent
semi-permanent
do not
Epigenetics involve ________________ or _____________________ alterations to gene expression that (Do/do not) affect the genome sequence
diet
behavior
stress
toxin exposure
possibly mental trauma
starvation
Epigenetics is caused by
TFs
cell differentiation
Epigenetics initially results from activity of ____ that regulate ________ ______________
post-translational
histones
dna methylation
multiple cell divisions
epigenetics changes are maintained by _________-_________________ modification of _________ ( includes acetylation, methylation, ubiquitinylation, phosohorylation, etc) and _______ _________________ (position 5 of cytosine pyrimidine ring) through _______
germ cell modifications
may be passed to offspring
mRNA processing
Export from nucleus could be blocked
Stability in cytoplasm
Based on location in cytoplasm
Affecting translation
Methods of Post-transcriptional control of gene expression
mRNA processing
Alternative splicing and choice of poly A sites
poly A tail
5' cap
Export from nucleus could be blocked if mRNA is missing ________ ______ or __ _____.
deadenylation
decapping
cytoplasmic exosomes
Stability in cytoplasm could be degraded by _________________ and ________________, followed by degradation by ________________ ____________ (note: longer poly A tails slow rate of degradation)
co-transcriptional
Pre-mRNA processing is often __________________________
7-methyl
5'
dimeric
carboxyl terminal domain
_________ guanylate capping of ___ end and by ____________ enzymes that associate with ___________ ______________ __________ (CTD) of RNA poly II
ribonucleoprotein particles
RNA associates with heterogeneous ____________________________ __________ (hnRNPS) that protect the mRNA from degradation
heterogenous ribonucleoprotein particles
hnRNPs
polyadenylation
hnRNPS also participate in splicing, _______________, and export to the cytoplasm
long genes
introns are spliced out (co-trranscriptional for ______ ______ only)
cleaved
polyadenylation
introns
transcription terminates, poly A site is __________, ____________________ occurs, ________ are spliced out (for short genes only)
mRNP
mature" mRNA + hnRNP proteins
snRNA
small nuclear ribonucleoprotein particles
___________ associated with certain proteins to form snRNPs ( ____ __________ _______________________ _____________)
exonic splicing enhancers
RNA binding proteins
Exon is recognized at regions called ________ _________ ____________ by ___ ________ __________ (SR proteins, which are a type of hnRNP)
pre-mRNA
spliceosome
RNA binding proteins assemble on a __________ to form a ______________=snRNA + pre-mRNA and force the branch point A of the pre-mRNA to bulge out
exons
intron
Proteins join 2 _______ and release the ________ as a "lariat structure
linear strands
nucleases
3' to 5'
In the last step of splicing, introns are converted to ___________ ________ and digested by _____________ in the exosome (from ___ __ ___)
RNA editing
alters the sequence of pre-mRNA so that the sequence of amino acids differs from that in the genome
protozoans
plants
eukaryotes
RNA editing is common in ____________ and _______ , but rare in _____________
nuclear envelope
nuclear pores
To transport to the cytosol, the mRNA must cross the __________ _________ through __________ ______
Nucleoporin proteins
forms nuclear pores
F6
molecular cloud
___ nucleoporins extend into the pore and form a ______________ ________ that blocks movement through the pore
mRNP complex
nuclear exporters
____ __________ (mature mRNA + hnRNPs) associates with ________ _______ (NXF1/NXT1) (hydrophobic regions bind transiently to F6 domains)
nuclear exporters
dissociates in cytoplasm and return to nucleus
5' cap
cytoplasmic poly a
Translation initiation factor binds to ___ ______ and nuclear poly A binding protein PABPII is replaced with ____________ _____ ___ binding protein PABPI
miRNAs
3'
inhibit
Cytoplasmic gene control: ________ (~22 nucleotides) hybridize to the mRNA (at ___ region) to ___________ translation
siRNAs
degraded
Cytoplasmic gene control: ________ signal for the mRNA to be ___________
siRNA
hybridizes perfectly with mRNA which leads to cleaving and degradation
proteins
Cytoplasmic gene control: ___________ can bind to 3' or 5' end of mRNA (binding to mRNA inhibits assembly of translation initiation complex)
mRNA degradation
Decapping pathway
Deadenylation-dependent pathway
Endonucleolytic pathway (cleavage)