Cell Bio: Chapter 9 - Transcriptional Control of Gene Expression
what is important to know about eukaryotic transcription?
- all the RNA in a cell is made by transcription - the RNA chain is called the transcript - 3 types of RNA
what happens in chain elongation during transcription?
- dissociation of the sigma subunit, which allows the core RNA polymerase enzyme to proceed along the DNA template
what happens in eukaryotic transcriptional control?
- inactivated genes are assembled into condensed chromatin - binding by TFs and histone acetylates enable binding by RNA polymerase 2
what is the process with the sigma factor? [picture]
- loose association w/ DNA & core enzyme/not connected - sigma factor binds/helps enzyme - association of complete enzyme w/ DNA at proper site and opening of double helix - sigma factor removed as RNA chain is elongated
what basically happens in eukaryotic transcription control?
- when turning on a particular gene, must unfold the gene, decondense the chromatin - when you post translationally modify DNA or a protein, you invariably change the charge which changes the conformation
what are the 3 types of promoters in eukaryotes? [promoters meaning telling polymerase where to template strand of a double-stranded DNA molecule]
1) TATA box 2) initiator sequence 3) CpG Islands
what makes up/what to know about prokaryotic DNA promoter?
1) consensus sequence 2) Pribnow box 3) +1 4) Rho
what are the functions of euchromatin and heterochromatin?
1) gene expression 2) gene repression 3) DNA transciption
what are the 3 types of RNA?
1) rRNA 2) mRNA 3) tRNA
what are the three protein-binding regions of the transctiotiona-control region?
1) the CAP-site 2) lac promotor 3) lac operator
how many types of polymerase are there?
3
what are the 3 major components of the nucleolus?
FC = fibrillar centers DFC = dense fibrillar components GC = granular component
where is heterochromatin found?
ONLY in eukaryotes
P2 what does snRNAs do?
RNA splicing
what is the order of binding?
TFIID, TFIIA, TFIIB, - TFIIF, TFIIE, TFIIH [DAB--Fried Every Hamburger]
who, what, when, where and why of transcription:
[RNA polymerase 2 transcribes mRNAs] who: transcrtiption-control regions [regulate expression of euk protein-cding genes] what: enhancer control type of cell in which gene is transcribed when: enhancer determines how frequently transcribed where: promotors determine where transcription begins why:
1) what is a TATA box?
a DNA sequence that indicates where a genetic seen can be read and decoded -- type of promotor sequence that specified to other molecules where transcription begins
2) what are initiator sequences?
a core promoter; alternative promoter element to the TATA box [that is similar in function to the Pribnow box [for prokaryotes]
1) what is the consensus sequence?
a sequence of DNA having similar structure and function in different organisms
what is heterochromatin?
a tightly packed form of DNA that comes in different varieties - tighter DNA packaging - contains more DNA [- chromosomal material of different density from normal (usually greater), in which the activity of the genes is modified or suppressed]
what is the 3-D structural different of bacterial and eukaryotic RNA polymerases?
bacterial RNAP-II has 5 subunits and yeast RNAP-II has 12 subunits --eukaryotic = more subunits
what is a sigma factor?
bacterial transcription initiation factor that enables specific binding of RNA polymerase to gene promotors
[9.1] what does binding of a repressor to an operator do?
binding of a repressor to an operator inhibits transcriptional initiation or elongation
[9.1]what is the 1st step in the initiation of the transcription in E.coli?
binding of a sigma-factor completed with an RNA polymerase to a promoter
what does the TATA box bind?
binds RNA polymerase 2
what does the TATA binding protein (TBP) bind?
binds TATA box and unwinds DNA
what is an operator?
binds a repressor protein
what does the CAP-site do?
binds catabolite activator protein
what does the lac operator do?
binds the lac repressor
what does the lac promotor do?
binds the sigma 70-RNA polymerase complex
P2 what does siRNAs do?
chromatin-mediated repression, translation control
what is an enhancer?
control the type of cell in which the gene is transcribed; and how frequently it is transcribed
E.coli can repress or activate the initiation of lac operon transcription under different conditions. what controls this transcription of the lac operon?
controlled by lac repressor protein and catabolite activator protein [CAP]
what are the genes within an operon are what?
coordinately regulated --> they are all activated or repressed at the same time to the same extent
what happens when transcription of a gene is repressed?
corresponding mRNA and encoded protein(s) are synthesized at low rates
where does translation occur?
cytoplasm
what happens if DNA doesn't bind to the right parts of the inner nuclear membrane [INM]?
diseases like the aging early disease
what do these two factors do?
each binds to a specific DNA sequence in the lac transcription-control region
when does chromatin with generally active transcription replicate?
early [green dots on the inner portion of the nucleus]
what does sigma factor do?
enables core polymerase to interact with specific DNA sites [promotor]
what are operons?
encodes enzymes involved in a particular metabolic pathway or proteins that interact to form one multi-subunit protein complex
P2 what does mRNA do?
encodes protein
what does tRNA do?
forms adapters that select amino acids and places them on a ribosome for incorporation into a protein - involved in translation
what does rRNA do?
forms core of ribosomes
[9.1] what regulates gene expression in prokaryotes and eukaryotes?
gene expression in both prokaryotes and eukaryotes is regulated primarily by mechanism that control gene transcription
[9.1] genes transcribed by sigma54-RNA polymerase is regulated by activators that bind to enhancers that are located where? what forms when the activator and sigma54-RNA polymerase interact?
genes transcribed by sigma54-RNA polymerase is regulated by activators that bind to enhancers that are located about 100 base pairs upstream from the start site. - when the activator and sigma54-RNA polymerase interact, the DNA between their binding sites forms a loop
of heterochromatin and euchromatin, which is active? which is open?
heterochromatin = inactive/ condensed euchromatin = active/ open
what are the two types of chromatin?
heterochromatin and euchromatin
what does the pribnow box do?
identifies the exact start of transcription - has the function similar to the TATA box that occurs in promoters in eukaryotes and archaea
[9.2] what should you know concerning distance in eukaryotic genomes?
in eukaryotic genomes, DNA transcription-control elements may be located many kilo bases away from the promotor they regulate - different control elements can control transcription of the same gene in different cell types
where does transcription occur in eukaryotes?
in the nucleus
[9.1] in two-component regulatory systems, one protein acts as what? what does the sensor do?
in two-component regulatory systems, one protein acts as a sensor. a sensor monitors the level of nutrients or other components n the environment.
what does mRNA do?
information for protein synthesis
what is the take home message?
interphase positioning of the chromosome domain relative to each other and to nuclear landmarks is not random and has important roles in genome function --> DNA in the nucleus is not random
what is the basic function of chromatin?
it is responsible for: - packaging DNA into smaller volumes so that they can fit inside the cell - for strengthening the DNA for mitosis and meiosis - for preventing damage to the DNA - controls gene expression and replication of DNA
what is special about polymerase II?
it transcribes all protein-coding genes/functions in production of mRNAs - produces 4-5 snRNAs that take part in RNA splicing and miRNAs involved in translation control
what happens in a +lactose and +glucose environment?
lac repressor binds lactose and dissociates from the operator, allowing sigma70-RNA polymerase to initiate transcription at a low rate
when does chromatin with generally repressive transcription replicate?
late [purple dots on the outer surface -- interacting with the nuclear lamina]
what is euchromatin?
lightly packed material; rich in gene concentration; less intense than heterochromatin
what causes transcriptional silencing during mitosis?
loss of activity and/or modifications of transcription factors [rather than inaccessibility of DNA] [accessible meaning proteins can get there]
what happens in a +lactose and --glucose environment?
maximal transcription of lac operon -cAMP increase s in response to the low glucose conc. and forms a CAP-cAMP complex that binds to the CAP site, where it interacts with the RNA polymerase to increase the rate of transcription initiation
where does regulation of genes expression occur?
may occur at several of the various steps in gene expression: - transcription - initiation - elongation, - RNA processing - RNA export from the nucleus - mRNA degradation control - mRNA translation into protein - protein degradation
do most genes have or lack a TATA box?
most genes lack a TATA box
can the TATA box bind both TFs and histones?
no, TATA box is a binding site for general transcription factors or histones -- binding of histones blocks binding of TFs and vise versa
where is polymerase I? what does it do?
nucleolus [defined region of nucleus] makes rRNA
what is polymerase II? what does it do?
nucleus makes mRNA
what is polymerase III? what does it do?
nucleus makes tRNA
what are the 3 types of polymerase?
polymerase I polymerase II polymerase III
what direction does it move?
polymerase moves 3' to 5' RNA grows 5' to 3'
how does this work if translation is in the cytoplasm and transcription is in the nucleus?
processed mRNAs must be transported from the nucleus to the cytoplasm before translation can occur - protein-lined pores in the nuclear membrane allow the bidirectional transport of macromoleules between nucleus and cytoplasm
P3 what does tRNA do?
protein synthesis
4) what is Rho?
protein that has a role in termination
what are repressor and activator proteins used for?
recognize and bind to specific DNA sequences to control transcription of a nearby gene
what are enhancers?
regulatory DNA sequences that, when bound by specific TFs, enhance the transcription of an associated gene
what are riboswitches?
regulatory segments of mRNA that binds metabolites to change production of the proteins encoded by the mRNA/regulated transcription elongation
P1 what do pre-rRNA do?
ribosome components, protein synthesis
what is the nucleolus?
site of assembly of ribosome subunits
what is a promoter?
site on DNA to which RNA polymerase binds [binding aided by TFs]
what is a promoter?
site where sigma factors bind
[9.1] what modulates the DNA-binding activity of most bacterial repressors? what does this allow?
the DNA-binding activity of most bacterial repressors is modulated by small-moleculate ligands - this allows bacterial cells to regulate transcription of specific genes in response to changes in the concentration of various nutrients in the environment and metabolites in the cytoplasm
what is the basic function/way of looking at sigma factors?
the core enzyme doesn't bind randomly to the promotor site of interest--> it needs help from the sigma factor
what is the energetic advantage of having a TATA box?
the energy to melt the DNA is not great the energy to melt the TATA is quite small; unfolding it/melting requires less energy; giving it an energetic advantage through melting easier
3) what is +1?
the exact start of transcription
what is important to know?
the genes are spatially and temporally distinct
[9.1] what regulates lac operon and other bacterial genes? how is frequency of transcription initiation increased?
the lac operon and some other bacterial genes are also regulated by activator proteins that bind next to a promotor and increase the frequency of transcription initiation by interacting directly with RNA polymerase bound to that promotor
what happens when transcription of a gene is activated?
the mRNA and encoded protein(s) are produced at higher rates
[9.1] what is the major sigma factor in E.coli? what does it do?
the major sigma factor in E.coli is sigma 70 [several other less abundant factors are also found] - each recognize different consensus promoter sequences or interacting with different activators
[9.1]what determines the strength of a promoter?
the nucleotide sequence of a promotor determines its strength/how frequently different RNA polymerase molecules can bind and initiate transcription per minute
[9.2] what is the primary purpose of gene control in multicellular organisms?
the primary purpose of gene control in multicellular organisms is the execution of precise developmental programs so that the proper genes are expressed in the proper cells at the proper times during embryologic development and cellular differentiation
2) what is a Pribnow box?
the sequence TATAAT of six nucleotides that is an ESSENTIAL PART OF PROMOTER site on DNA for transcription to occur in bacteria - part of the Pribnow box is the TATA box
what is interesting about bacterial rRNA?
there is only RNA -- no protein-- in and around the reaction sites of ribosomes [which is weird bc ribosomes catalyze protein]
what is locationally different between translation and transcription?
they happen in two different places so they are separated by a membrane that surrounds the nucleus
what is true of all polymerases?
they have subunits and accessory proteins that either enhance or slow down transcription
[9.1] what also regulates transcription in bacteria? what is this control exerted by?
transcription in bacteria can also be regulated by control of transcriptional elongation in the promotor-proximal region. - the control can be exerted by ribosome binding to the adjacent mRNA, as in the case of the E. coli trp operon or by riboswitches, RNA sequences that bind small molecules to determine whether a stem-loop followed by a string of uracils forms, causing the bacterial RNA polymerase to pause and terminate transcription
[9.1] what regulates transcription initiation by all E.coli RNA polymerases [except those containing sigma54]?
transcription initiation by all E.coli RNA polymerases [except those containing sigma54] can be regulated by repressors and activators that bind near the transcription start site
[9.2] what is transcriptional control?
transcriptional control is the primary means of regulating gene expression in eukaryotes, as it is in bacteria
P2 what do miRNAs do?
translation control
what happens in a --lactose environment?
very little lac mRNA is produced bc the lac repressor binds to the operator, inhibiting transcription initiation by sigma 70-RNA polymerase
by controlling transcription, what can a cell regulate?
which proteins it produces and how rapidly they are synthesized
can transcription of sigma-RNA polymerase bind far?
yes, transcription by sigma-RNA polymerase is controlled by activators that bind far from the promotor
