PCB4522- EXAM 4 STUDY GUIDE

25 July 2022
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question
How do you pack a large amount of DNA in small volumes?
answer
The negative charges on the phosphodiester backbone are neutralized by the binding of basic proteins.
question
What is the density of the packaging of DNA for the following? bacteria eukaryotic nucleus phage T4
answer
bacteria - 10 mg/ml eukaryotic nucleus - 100 mg/ml phage T4- 500 mg/ml
question
Define packaging ratio.
answer
The ratio between the length of DNA and the actual length it has after it has been packaged (greatly condensed)
question
What is the packing ratio number?
answer
7000
question
What is the ratio of interphase chromatin?
answer
1,000 to 2,000 During mitosis it increases to 5,000 to 10,000
question
What is the nuclear DNA length of a human nucleus?
answer
1.8 meter
question
What is a major difference between filamentous and icosahedron packaging type?
answer
Filamentous packaging type has no size limitation and the protein shell is assembled around the nucleic acid. While the icasahedron the DNA is stuffed inside an empty shell, and it requires terminase/
question
What is the function of terminase?
answer
-cuts and packages DNA into capsid - Forms the Integration host factor (IHF) (USES ATP)
question
What role does the IHF play?
answer
IHF is incorporated into the head to allow the condensed packaging
question
The bacterial nucleoid is _______% DNA by mass while the eukaryotic chromosomes is _______% by mass.
answer
80;50
question
What unfolds DNA?
answer
Agents that act on RNA or protein
question
What is the average density of supercoiling?
answer
1 supercoil / 100 bp
question
How are bacterial genomes organized?
answer
into supercoiled loops
question
List four DNA binding proteins in E.coli that participate in the packaging of bacteria
answer
HU (dimer that condenses DNA into bead-like structure, similar to eukaryotes) IHF(integration host factor) H1 (interacts with bent DNA) Protein P (resembles protamine which is found in sperm; very basic)
question
Where is DNA located in bacteria?
answer
nucleoid
question
Are there any histones in bacteria?
answer
No, but histones are present in eukaryotes and in archae.
question
Loops are also known as
answer
domains
question
Why is there supercoiling?
answer
Supercoiling helps condense the chromosome
question
How are 10 nm fiber released?
answer
by lysing cells on top of a sucrose gradient
question
How do you relax the tension of a supercoil?
answer
Requires 1 nick per 85 kb to relax the tension
question
The loop(domain) structure is about __________kb and goes attached to a central proteinaceous core ____________.
answer
30-90; scaffold
question
T/F In Eukaryotes, 50% is DNA and 50%is protein based. If the scaffold is about 8% of the protein then the rest (42%) is histone.
answer
True
question
What is a similarity in packaging between bacteria and eukaryotes?
answer
Their supercoiling is both 1 neg, turn per 100 bp.
question
The base of the DNA loops attach to the nuclear matrix that is comprised of lamen proteins is called __________ and also known as _______________ ____________ _____________.
answer
MAR; matrix associated region
question
Does MARS have a consensus sequence?
answer
No, it has a 70% A-T rich region instead
question
MARs have sites for _____ binding and recognition sites for ____________; therefore, it functions in opening the chromatin and DNA tension.
answer
cis-acting; topoisomerase II
question
What controls the degree of supercoiling in eukaryotes?
answer
topoisomerase II
question
What functions in opening the chromatin and DNA tension?
answer
MARs
question
What is the difference between interphase chromatin and mitotic chromosomes?
answer
The mitotic chromosome has 30 nm fibers and zig zig two start helix while interphase chromatin has both euchromatin and heterochromatin.
question
The interphase chromatin has both Euchromatin and Heterochromatin, which of the two is more condensed?
answer
Heterochromatin
question
Which of the two is accessible for transcription? (Euchromatin or Heterochromatin)
answer
Euchromatin
question
T/F Euchromatin is composed of only 30 nm.
answer
FALSE Euchromatin is composed of both 10 nm fiber and 30 nm fiber. Heterochromatin is composed of only 30 nm fiber.
question
There are two forms that make up the heterochromatin, which of the two serve as a structural element of the chromosome and is composed of regions that are not expressed since they remain condensed.
answer
Constitutive
question
Which form of heterochromatin has entire chromosomes that are inactive in one cell lineage?
answer
Facultative
question
The lampbrush chromosome is known to be about ~___ times less packed since the loop out regions are heavily transcribed and is formed during _____ _______ in amphibians such as a newt.
answer
30; extended meiosis
question
The lampbrush chromosome correspond to places that are
answer
actively transcribed
question
What is the direction of transcription when a lampbrush chromosome is present?
answer
From right around the top to left.
question
The polytene chromosome is observed in larval salivary gland interphase nuclei of a drosophila, with a packaging ratio of ~__. Transcriptionally active bands are called _____ and an extreme case of this is called ________ _______. The chromosome builds up _____ _____ running longitudinally by doubling the chromosome up to__times.
answer
20; puffed bands; balbiani rings; parallel fibers; 9
question
Where would you go looking for lampbrush chromosomes? around the dumpster for a large supermarket. under a rock in a stream in the dirty laundry hamper near a deep sea thermal vent
answer
under a rock in a stream (present in some amphibians such as newt and frog.
question
T/F Each chromosome contains a single duplex strand of DNA and is replicated a semi-conservative mechanism.
answer
True.
question
Each chromatid consists of a fiber with a diameter of _____nm and higher.
answer
30 nm
question
T/F Interphase chromatin is a mixture of the 10 nm and 30 nm fibers.
answer
True. 10 nm + 30 nm fibers = euchromatin 30 nm fiber= heterochromatin
question
The sites at the two regions where microtubules are attached to either the centromere (at the kinetochore) and/or the centrioles are called _______ ______ _______ or _ _ _ _.
answer
microtubule organizing center or MTOCs
question
What is found in the cytoplasm of metazoan cells, but not in plants and fungi?
answer
Centrioles
question
T/F MTOCs are present in all eukaryotes.
answer
False, present in most but not present in all. I.E sponges do not have MTOCs
question
Centromeres are essential for segregation, but what holds the two chromatids together?
answer
Cohesins (glue proteins)
question
25. There are three types of centromeres, name them.
answer
Metacentric Acrocentric Telocentric
question
During telophase a fragment breaks off and stays behind, this fragment is called _____ because it does not get attached to a mitotic spindle since it does not have its own centromere.
answer
acentric fragment
question
There is a fibrous structure found at the centromere that is attached to the microtubule during mitosis. What is this structure called?
answer
Kinetochore
question
Which structure provides the MTOC for the chromosome?
answer
Kinetochore
question
Yeast has an unusual kinetochore called the ____complex
answer
Dam 1
question
Centromeres can take a variety of forms: recite them. Insects, mammals and plants have what type of centromere? Nematodes have what type of centromere? Budding yeast have what type of centromere?
answer
Budding Yeast-- Point centromere Insects, mammals, and plants- Regional centromere Nematodes- Holocentric chromosome
question
There are alternating patterns of H3 ______and ______tetramers within the centromere. The location of the _____ ________ seems to be epigenetically controlled and are involved in recruiting proteins that form the _________.
answer
There are alternating patterns of H3 ___OCTAMERS___and _CENH3_____tetramers within the centromere. The location of the __CENH3 ___ _TETRAMERS_______ seems to be epigenetically controlled and are involved in recruiting proteins that form the ___KINETOCHORE______.
question
CEN DNA sequence composition in yeast consist about ~120 bp and is divided in 3 parts: CDE-I, CDE-II, and CDE-III. Which of the three is the longest and is AT rich? Which of the three is highly conserved, and why?
answer
CDE II- Longest and A-T rich (important length) CDE III- highly conserved ( only 11 bp) (important sequence)
question
The minimal sequence that can confer mitotic stability on a plasmid (yeast) is known as:
answer
CEN fragment
question
What is an example of the point centromere?
answer
CEN
question
Which of the following has the most critical function thus a single mutation in it is disruptive? CDE I CDE II CDE III
answer
CDE III
question
What is the MTOC made up of?
answer
Centrioles(centrosomes) and centromeres(kinetochores)
question
Mutations in _________ severely disrupt segregation and prevent CBF3 binding. CDE I CDE II CDE III
answer
CDE III
question
CBF1 (centromere binding factor 1) binds which of the CDE? What about CBF3?
answer
CBF1 binds to CDE I CBF3 binds to CDE III
question
Which of the following is associated with intrinsic bending? CDE I CDE II CDE III
answer
CDE II
question
What is the human homolog to yeast Cse4p?
answer
CENP-A
question
Which protein found at the CEN resembles a histone?
answer
Cse4P
question
Cse4p in yeast is the homolog for which type of histone?
answer
H3
question
In Yeast, Cse4p resembles a nucleosome: how many turns does DNA wrap around the Cse4p?
answer
1
question
Which histone is required to form 10nm fiber coil into a 30nm fiber, and is not part of a nucleosome?
answer
H1
question
What protects chromosome ends from fusing due to the activity of repair systems and the ends must be disguised so they do not look like ds-breaks?
answer
Telomeres
question
Chromosomes ends are disguised so they don't look like double strand break causing repair mechanisms to fuse both ends and from DNase activity. The telomere has a consistent repeat what is it? Hint:C>1( / )1-4
answer
C>1(A/T)1-4
question
What are the two ways to generate a GT rich strand overhang?
answer
- C-A strand is degraded to produce G-T overhang - G-T strand is extended
question
What is the telomerase in humans?
answer
hTERT
question
Many human cell lines can be immortalized by the introduction of the _________. While other tissue types require _______ plus the ______________ antigen to be immortalized.
answer
hTERT; hTERT + SV40 T
question
Normal tissue types can be transformed to oncogenic lines by introduction of what three genes?
answer
hTERT SV40 T antigen ras-V12
question
What protein keeps the G-T protruding 3' end from going to far((prevents excessive of the 5' end)?
answer
Stn 1
question
What protein binds to the telomere repeats and what two proteins does it recruit?
answer
Cdc13; Stn1,Telomerase
question
What extends the protruding 3' end?
answer
Telomerase
question
What forms as a result of strand invasion?
answer
D-loop
question
When the the tail of the telomere is paired with the homologous strand it forms?
answer
T- Loop
question
Which telomere protein makes complex with other proteins & stabilizes chromosome ends?
answer
TRF2
question
What protects the ends of chromosomes from recombination repair which would try to fuse the ends?
answer
T- loop
question
Which protein is critical to forming the T-Loop?
answer
TRF2
question
The Shelterin complex binds to the end of the telomere and is involved in
answer
-T-loop formation -heterochromatin formation
question
Which protein binds to ssDNA of the G-T strand?
answer
POT1
question
Which protein triggers heterochromatin?
answer
RAP1
question
What are three major roles of the telomere?
answer
-Protect the ends from fusing -Provide mechanism for the ends to be extended -Faciliatate meiotic chromosome recognition
question
What protein identifies the G-hairpins and causes the telomerase to move forward?
answer
hnRNP A1 (disrupts ssDNA secondary structure)
question
What is a reverse transcriptase that carries its own RNA template?
answer
Telomerase
question
How does telomerase position itself?
answer
By base pairing between the RNA template and the protruding single stranded primer
question
The telomerase extends which strand?
answer
3" OH end of the G-T strand (primer)
question
How long is the template that the telomerase carries? Its equivalent to?
answer
15-22 bases; 2 repeats of the CA rich repeating concensus
question
The length of the protruding G-T 3" end remains constant. In humans the GT strand is 150 nt, how is this controlled?
answer
A balance is maintained between the extension of the GT strand and degradation of the CA strand
question
How many generations could plants (arabidopsis) survive if telomerase is absent?
answer
10 generations
question
What happens if you mutate telomerase?
answer
You affect growth and number of cell division
question
Telomeres shorten about _____ bp per generation in plants.
answer
500bp
question
How does telomeres form heterochromatin?
answer
1- Rap1 binds to DNA 2- Sir3/4 bind to H3/H4 3-Sir2 deacetylates histones 4- Sir3/Sir4 polymerize along chromatin 5- Sir3/Sir4 attach to matrix
question
What protein mimics lamen that is found in nuclear matrix?
answer
Sir3
question
Which protein binds CnA/T repeats at telomeres to initiate heterochromatin formation?
answer
RAP1
question
Which protein(s) binds to Step1 protein, histone 3 and 4 tails?
answer
Sir3/ Sir4
question
Which protein deacetylates the histone tails?
answer
Sir2
question
Which protein may be responsible for telomere clustering to the nuclear periphery?
answer
Sir3
question
How many nucleotides per nucleosome?
answer
200 bp
question
How much of chromatin is histones?
answer
50%
question
What are two of the most highly conserved proteins in evolution, even in archaea till this day?
answer
H3 and H4
question
How many turns is DNA wound around the outside of the core particle?
answer
1.67 turns
question
Which fiber is known as the beads on a string?
answer
10 nm fiber
question
What is the packaging ratio of 10 nm fiber histones?
answer
6
question
What are examples of the 10 nm fiber histones?
answer
H3,H4,H2A, and H2B
question
How are 30 nm fibers made?
answer
they form from a coil of the 10 nm fiber
question
Which fiber requires the nucleosomal histones with the addition of histone H1?
answer
30 nm fiber
question
What is the packaging ratio of 30 nm fiber?
answer
40
question
What is the final packaging ratio for 50nm and above in euchromatin? What about mitotic chromosome & heterochromatin?
answer
1000; 10,000
question
How many base pair does a mononucleosome have when low levels of DNase is present? What about in very high levels of DNase activity? The highest level of DNase activity is known as ___ ___?
answer
Low levels of DNase= 200bp High levels of DNase= 146 bp core particles (limit digestion)
question
How many bp of DNA does a nucleosome contain and what how many histones are present?
answer
200 bp of DNA 2 copies of H2A, H2B, H3, H4
question
What is average distance between nucleosomes?
answer
200 bp
question
What is the length of the core DNA that is found on the core particles produced by PROLONGED digestion with micrococcal nuclease?
answer
146 bp (resistant core/limited digestion)
question
What would the average size of the fragments of chromatin be if you added just enough nuclease to hit once per nucleosome? 146 bp 165 bp 200 bp
answer
200 bp
question
How many bp does it take to make two turns around th octomer?
answer
165 bp
question
H1 does not participate in forming the histone octamer, so where does it mostly bind to?
answer
to linker DNA between nucleosomes
question
Which species lacks H1 histone and the 30 nm fiber? Why?
answer
Archae Archea have a tetramer and since they don't have tails they don't get regulated to be uncondensed because they are already uncondensed. meaning the H1 Is not present to help form the 30nm fiber
question
Nucleosomal DNA is divided into the ____DNA and_____DNA
answer
core; linker
question
Which histones interact with each other and hold the tetramer together?
answer
H3 interacts with H3 to hold the tetramer together.
question
Which histone sits behind H3?
answer
H4
question
Which histones form the core?
answer
H3/H4
question
Which histones form the cap?
answer
H2A/H2B
question
What does a histone fold have?
answer
Helix loop helix loop helix
question
How many nucleosomes per turn does the 30nm fiber have?
answer
6
question
Would a zig zag two-start helix be present in Archaea?
answer
No, because it does not have a 30 nm fiber
question
The six nucleosomes in the 30 nm fiber are organized into a
answer
solenoid
question
Which histone is required for formation of the STABLE 30nm fiber?
answer
H1
question
The ________-terminal tails are flexible and extend from the core and are sites of modification normally known as the ______________ _____________________.
answer
N-terminal; histone code.
question
Why do Archaea have no histone tails?
answer
Because since they only have the 10 nm fiber they dont form the higher orders that form the tails.
question
What are three most common types modifications?
answer
Acetylation( HATSs and HDACs), methylation (Methylases), phosphorylation (Kinases)
question
Which kind of acetylation is associated with gene activation? HAT or HDAC
answer
HAT
question
Which kind of acetylation is associated with gene repression? HAT or HDAC
answer
HDAC
question
What does HAT stand for?
answer
histone acetyltransferase
question
What does HDAC stand for?
answer
histone deacetylase
question
What are the names of modifications that deal with methylation?
answer
Methylases
question
What are the names of modifications that deal with phosphorylation?
answer
kinases
question
What neutralizes the positive charge on lysine?
answer
Acetylation
question
What introduces negative charges on serine?
answer
Phosphorylation
question
T/F The positive charge on lysine is neutralized upon acetylation, while methylated lysine and arginine retain their positive charges.
answer
True
question
The pattern of histone modification associatied with gene activation state is known as ?
answer
Histone Code
question
What kinds of modifications are associated with transcription activation?
answer
Acetylation Methylation Phosphorylation
question
What kinds of modifications are associated with nucleosome assembly?
answer
Acetylation
question
What is the main reason that when you acetylate lysine it will cause the chromatin to decondense?
answer
When you acetylate lysine you neutralize the positive charge, remember the DNA is negatively charged. If lysine isn't neutralized then the DNA will tightly bind itself to it, so it wont decondense.
question
How many methyl groups are required to successfully neutralize the positive charge?
answer
3
question
What does HDAC do?
answer
Removed the acetyl groups. This results in repression cause the acetyl is what neutralize the charge of lysine so that the DNA doesnt bind so tightly and the chromatin isnt so condensed.
question
Are histone octamers conserved or preassembled during replication?
answer
preassembled
question
What are the accessory proteins that are required to assist the assembly of nucleosomes? (two that act as chaperones)
answer
Nucleoplasmin and N1
question
Which proteins are associated with replication dependent assembly?
answer
CAF1 and Asf1
question
What is the name of the protein required for DNA-dependent nucleosome assembly that is recruited by the clamp (PCNA)?
answer
CAF1
question
Once DNA has been replication, nuclesomes assemble. Where does CAF1 bind to and what is added to that complex?
answer
CAF1 binds to new H3/H4 tetramer, then H2A/H2B is added
question
T/F Nucleosome assembly in vivo: Step 1- DNA wraps around H3/H4 tetramer Step 2- One H2A/H2B dimers are bound to form the octamer.
answer
True
question
In replication dependent nuclesome assembly, which auxillary factor assists CAF1 in nucleosome reassembly on the leading strand(de novo assembly), and participates in transferring old nucleosome on lagging strand (parental histone transfer)
answer
Asf1 acts as a chaperone, grabs H3/H4 and transfers them to lagging strand duplex.
question
What are two pathways of nucleosome assembly?
answer
DNA replication dependent and replication independent
question
Some extremely heavily transcribed genes appear to be so active in transcription they have no nucleosomes structure at all. What kinds of genes are they?
answer
Ribosomal RNA genes
question
Which genome can be extracted from cells with nucleosme attached and transcription in progress?
answer
SV40 genome
question
What proteins are associated with replication independent nucleosome assembly?
answer
FACT HIRA
question
What protein displaces histone octamers during transcription by releasing H2A/H2B dimers and remains attached to the H2A/H2B dimers after transcription to facilitate next round of transcription?
answer
FACT
question
In replication independent nucleosome assembly: what is the name of the histone that slowly replaces H3 in non differentiating cells, after transcription and after repair?
answer
H 3.3
question
What is the name of the protein that is used in independent nucleosome assembly and is not recruited by a clamp nor is it bound to it?
answer
HIRA
question
What does yeast use instead of H3?
answer
Cse4p
question
What do mammals use instead of H3?
answer
CENP-A
question
An enhancer activates a promoter in its vicinity, but can be blocked from doing so by an ________________________________ located between them.
answer
INSULATOR
question
What do insulators do?
answer
it blocks the enhancer from activating the promoter
question
In Drosophila heat shock locus the ________ and ________ serve as insulators that do not directly regulate gene activity but function as barriers.
answer
scs and scs'
question
T/F RNA pol II and insulator proteins do not co-occupy the same regions.
answer
True
question
What protein binds to the scs/scs' insulators found in Drosophila heat shock locus?
answer
BEAF (Booundary associated factors
question
When are histone variants used?
answer
After repair
question
Eukaryotic transcription occurs on chromatin, not naked DNA as in bacteria. What are two requirements for transcription to occur?
answer
-Chromatin must be decondensed -Nucleosomes at the promoter must be removed in order for RNA polymerase to bind
question
Eukaryotic RNA polymerase cannot read DNA, so how does it initiate transcription?
answer
Requires a large number of proteins to pre-bind the promoter. Then RNA pol recognizes this complex as the promoter
question
What are basal transcription factors?
answer
proteins that bind to the core promoter near the start point for transcription and are required to recruit RNA polymerase
question
What is a core promoter?
answer
Region of RNA that binds to basal factors
question
DNA of the promoter that corresponds to the first nucleotide transcribed. RNA pol contacts it directly, but does not select it.
answer
Start point of transcription
question
What does the full promoter contain?
answer
Core promoter (basal factors) and Upstream elements (trans-activators).
question
What are the three major RNA polymerases that eukaryotes have? What are their function?
answer
RNA pol 1 (makes rRNAs 18S/28S) in nucleolus RNA pol II -makes heterogeneous nuclear RNA and small RNAs RNA pol III- makes tRNA, in cytoplasm.
question
Rank the RNA polymerases in order of most active to least active.
answer
RNA pol 1--> RNA pol II--> RNA pol III
question
Which RNA polymerase mRNA is the least abundant RNA in the cytoplasm and are internal?
answer
RNA pol III
question
T/F All eukaryotic RNA polymerases have ?12 subunits and are aggregates of >500 kD.
answer
True
question
What is the difference between the subunits in Eukaryotes and Archae?
answer
Same subunits except that in Archaea the B' subunit is in two parts.
question
Which RNA polymerase accounts for most cellular RNA synthesis and resides in the nucleolus?
answer
RNA pol 1
question
Which RNA polymerase accounts for most of the remaining activity in the cell and it sensitive to a- amanitin?
answer
RNA pol II
question
Core Promoters for pol I and II are _______ of the start point. Some pol III promoters are ________ to the transcribed region.
answer
upstream; internal
question
Do eukaryotic RNA polymerases have a sigma like in bacteria?
answer
No
question
The largest subunit in RNA polymerase __ has a CTD (carboxy-terminal domain) consisting of multiple repeats of a heptamer. What subunit is that?
answer
II, B'
question
What serves as a trigger to transition from initiation to elongation in eukaryotic transcription?
answer
phosphorylation of CTD
question
What two proteins bind to RNA pol I?
answer
SL1 and UBF
question
Which core-binding factor consisting of TBP and 3 other proteins is involved in positioning the RNA polymerase and directs a low level of constitutive transcription?
answer
SL1
question
Which upstream binding factor consisting of a single peptide ensures high-frequency initiation?
answer
UBF
question
What transcription factor is involved in initiation by all three RNA polymerases?
answer
TBP
question
The factor ____________ wraps DNA around a protein structure to bring the core and UPE into proximity.
answer
UBF1
question
RNA polymerase binds to the ___________ complex at the core promoter.
answer
UBF1-SL1
question
Which of the following is responsible for determining the start point of transcription? UBF Sigma 70 RNA pol I SL1
answer
SL1
question
What is the commitment factor for Pol III promoters?
answer
TFIIIB
question
What enables TFIIIB to bind at the startpoint of type 1 promoters by binding to the concensus sequences?
answer
TFIIIA & TFIIIB
question
TFIIIB has _________ as one subunit and enables RNA polymerase to bind. Positions the polymerase.
answer
TBP
question
What determines where polymerase should start?
answer
TFIIIB
question
What is the major difference between type 1 and type 2 promoters?
answer
Type 2 does not use TFIIIA (only uses TFIIIC and TFIIIB) and does not have boxC Has 2 TFIIIC
question
TFIIIA and TFIIIC are ______________________________.Their only role is to direct TFIIIB to the right location. These can be removed once TFIIIB has bound and transcription can still proceed correctly.
answer
Assembly factors
question
What is the only true initiation factor?
answer
TFIIIB
question
Which of the three assembly factors have a Zinc Finger? and Which has a similar size to the RNA pol?
answer
TFIIIA- zinc finger TFIIIC- same size as RNA polymerase
question
What two other subunits does TFIIIB have other than TBP and what are their functions?
answer
Brf- looks like RNA pol II B''- assist in melting the promoter
question
Which TFIIIB subunit is similar to sigma?
answer
B''
question
Type 1 pol III promoter is found only in __________________.
answer
5S RNA genes
question
Where does the (HAT) co-activator bind? Directly on DNA or on trans-activators?
answer
On the trans-activators.
question
Where does RNA pol II bind?
answer
At the core promoter in the basal factors area
question
Where does the repressor HDAC bind?
answer
In the silencer, in between the enhancer and the promoter
question
What are the steps of gene activation?
answer
Step 1- Trans-activators bind Step 2- Trans-activators open chromatin Step 3- Trans-activators recruit basal factors Step 4- Basal factors recruit RNA pol II
question
What is the function of the trans-activators/enhancers?
answer
- Bind to DNA -Open chromatin -Recruit basal factors
question
What basal factors does RNA polymerase II require to initiate transcription?
answer
TFIIxyz
question
What do RNA pol II startpoint promoters look like? Do they have a special sequence?
answer
Py2CAPy5 (short conserved sequence) InR (initiator) at the startpoint
question
The TATA box is a common component of RNA polymerase _____ promoters. It consists of an ____ rich octamer locates ______ bp upstream of the startpoint?
answer
II, A-T, 25-30 bp
question
The _____ is a common component of RNA polymerase II promoters that do not contain a TATA box?
answer
DPE
question
What does the minimal promoter for RNA polymerase II include?
answer
InR [always] and TATA box or DPE [either or]
question
List the commitment factor for pol I, II and III
answer
Pol 1- SL1 Pol II- TFIID Pol III- TFIIB
question
What is involved in initiation of RNA synthesis of all pol II promoters and forms the preinitiation complex?
answer
Basal factors
question
Transactivators, transfactors are known to be ________________ ________________, which bind upstream elements are are specific to different promoters.
answer
Non-inducible upstream factors
question
A type of upstream factor that controls highly regulated (inducible) transcription; binds to a response element, is known as?
answer
Inducible factors
question
T/F Cis-elements may be located upstream, downstream, or in introns. Most commonly found upstream.
answer
True
question
Elements may be _____________ in distribution, or organized in clusters called ___________.
answer
scattered; enhancers
question
The two types of transcription are Basal and Activated. Which has low level activity and which has High level of activity? Which one only requires a minimal promoter? Which one requires Upstream factors/cis-elements?
answer
Basal- low level of activity, only requires minimal promoter Activated- High level of activity, requires upstream cis-element.
question
The minimal promoter is from the -__ to +__.
answer
-45 +20
question
Key step in activated transcription performed by ________________ __________________.
answer
activator proteins
question
What does TFIID consist of?
answer
TBP and 11 TAFs (TBP associated factors)
question
Where does TBP bind to the TATA box, in the minor groove or major groove?
answer
Minor groove
question
What forms a saddle around the DNA and bends it by 80 degrees?
answer
TBP
question
Some of the TAFs resemble histones and may form a structure resembling a histone octamer. What does TAF stand for? How many TAFs are within the TFIID?
answer
TBP associated factors; 11
question
What basal factor binds to the C terminal stirrup? What about N terminal stirrup?
answer
TFIIB- binds to C terminal stirrup TFIIA- binds to the N terminal stirrup
question
What elements determine the polarity of transcription?
answer
Polarity
question
TBP forms a saddle around the DNA and bends it by how many degrees? It does this by introducing kinks in the DNA that are the result from insertions of how 2 _________.
answer
80 degree, phenylalanines The 2 phenylalanines are inserted and help form this 80 degree bend.
question
What are the structures of the TFIIB?( hint: 4 structures)
answer
B-Reader helix/B-loop, zinc ribbon (n term),linker
question
What protrudes into RNA exit pore of RNA pol II and interacts with 5' end of transcript?
answer
N-terminal
question
What melts the promoter 20 bp upstream from TATAA?
answer
B-linker
question
What contacts the -8 of the initiator element?
answer
B-reader helix
question
What has structural similarities and performs many of the functions of sigma in eukaryotes?
answer
TFIIB
question
What contacts position -1?
answer
B reader loop
question
The ________ and _________ contact the 5-end of the nascent transcript RNA and block its entry into the RNA exit channel similarly to sigma domain 3.2.
answer
B reader loop and B-reader helix
question
The TFIIB N-term protrudes into RNA pol ____ ____.
answer
active site
question
What is required for the recruitment of the add poly(A) complex involved in termination?
answer
Phosphorylation of TFIIB
question
What are basal factors that bind to RNA polymerase?
answer
TFIIE TFIIH TFIIF
question
Which basal factor plays a role in transcriptin and nucleotide excision repair?
answer
TFIIH
question
Why are TFIIE and TFIIH required during initiation?
answer
They help melt DNA to allow the polymerase movement
question
What is required for elongation to begin?
answer
Phosphorylation of the CTD. Further phosphorylation of the CTD is required at some promoters to end abortive initiation. (P-TEFb kinase)
question
What plays a major role in phosphorylation CTD?
answer
TFIIH
question
List the 6 Involvements of the CTD of the largest subunit of RNA pol II in RNA processing.
answer
- 7 mG capping of 5' end - SCAFs recruit splicing factors - Polyadenylation and cleavage of the 3'end. -Enlongator complex that has HAT -Phosphorylation of CTD for initiation to elongation -Ubiquitination
question
Which of the following is NOT a function of the CTD? Recruits the polyadenylation enzymes Transition from initiation to elongation Recruits enzymes to add Gm7 Melts the promoter
answer
Melts the promoter
question
Mutations in the ______ component of the TFIIH cause three types of human diseases.
answer
XPD
question
What roles does TFIIH play?
answer
-Provides a kinase at initiation -Provides a repair complex at elongation
question
T/F Gene Expression Is not associated with De-methylation of the DNA at the 5? end of the gene (promoter) and is not necessary for transcription.
answer
False, it is necessary for transcription
question
Methylation of the C in a CpG doublet leads to? why?
answer
repression; because proteins MeCP1, MeCP2 and Sin3 binds to methylated CpG sequences and these proteins repress transcription in vitro.
question
What does MeCP2 do?
answer
Binds to Sin3 repressor complex which has HDAC activity, this removes chromatin to condense resulting in repression
question
How many CpG islands are in the human genome?
answer
29,000, or 45,000 if you include the alu repeats
question
The density of a CpG is about ~_/100bp. The density of a CpG island is about ~_ _/100bp.
answer
1/100 bp ; 10/100 bp
question
Drosophila and Nematodes methylation differences are?
answer
Drosophila- very little methylation, but the gene for the methylase is present in the genome Nematodes- No methylation of DNA
question
Methylation of CpG islands seems to regulate which type of genes? Environmentally inducible Those activated by strong enhancers Constitutive genes
answer
Constitutive genes
question
Which of the following protein bind to methylated CpG islands? MeCP1 and MeCP2 SCAFs P-TEFb Mfd
answer
MeCP1 and MeCP2
question
TFIID is about ~800 kD, is this larger than RNA Pol II?
answer
Yes, TFIID is 500 kD
question
Does TBP of TFIID bind to the TATAA promoters?
answer
Yes.
question
Which TAF is the largest?
answer
TAF1
question
Which TAF is the smallest?
answer
TAF 14/15
question
Whic commitment factor does not bind to TATA even though it has a TATA domain?
answer
TFIID
question
Which component of TFIID blocks TBP from binding TATA?
answer
TAF1
question
What induces genes in eukaryotes?
answer
-Pathogen attack -Heat -Oxidative stress -Developmental issues -Differentiation
question
Does Archaea have TAFs?
answer
No, just TBP
question
List the four functions of TFIID
answer
-Recognition of core promoter -Target for recruitment by transactivator proteins -Binds other basal factors -Enzymatic activities
question
Which TAFs cooperate together to recognize initiator region?
answer
TAF1 and TAF2
question
Which TAFs cooperate together to recognize the DPE (downstream promoter element)?
answer
TAF6 and TAF9
question
Which TAFs serve as targets for recruitment transactivator proteins (acidic activators)?
answer
TAF6 and TAF9
question
Which TAFs contact TFIIF?
answer
1,5,6
question
Which TAF contacts TFIIA?
answer
4
question
TAF1 has 3 enzymatic activities what are they?
answer
Ubitquitination kinase HAT
question
What uses the N-terminal to fold around and form a mimic of the TATA sequence?
answer
TAND 1 and TAND 2
question
TAF7 is blocking the HAT activity that will de-condenses the chromatin what events cause Taf7 to lose affinity for TAF1 and bind to TBP?
answer
Autophosphorylation when RNA poL II touches TAF1
question
Which TAF have histone fold like structures?
answer
- TAF 4b - TAF 6 - TAF 9 - TAF 12
question
Which TAF resembles H3/H4?
answer
TAF 9- H3 TAF 6- H4
question
Which TAF resembles H2A/H2B?
answer
TAF4B- H2A TAF12 - H2B
question
TFIID Promoters that lack TATA are ___________.
answer
Constitutive
question
TBP can function with SAGA and PCAf.
answer
True
question
SAGA is the complex in _____________, while PCAF is the complex in ________________.
answer
yeast; humans
question
Those that have TATAA do not require ______
answer
TFIID
question
Whats the name of the transactivator that recruits SAGA but is unable to recruit TF2D?
answer
GCN4
question
What subunit has the HAT in the following? TFIID SAGA PCAF
answer
TFIID- TAF1 SAGA- GCN5 PCAF-PCAF
question
What complexes have the HAT activity?
answer
TAF1 GCN5 P300/CBP PCAF
question
Which of the TFIIF shows similarity to bacterial sigma factor domains 2 and 3.2?
answer
RAP30
question
What is required for RNA pol II to join the PIC?
answer
CTD must be unphosphorylated. (Phosphorylation of CTD is linked to the transition between initiation and elongation)
question
T/F The CTD does not bind the mediator.
answer
False
question
TFIIF assists promoter targeting when it binds onto who?
answer
TFIIB N-terminal zinc ribbon
question
Who puts the Phosphate groups onto the CTD?
answer
TFIIH Cdk7 subunit
question
Who stimulates a phosphatase to remove them? when do we see this stimulation?(hint: is it at the PIC or not at the PIC)
answer
TFIIH, only when TFIIB is not in the vicinity in other words not at the PIC
question
TFIIF is bound to the polymerase, who is recruited after, TFIIE or TFIIH?
answer
TFIIE
question
Who modulates and assists TFIIH kinase, ATPase, helicase and promoter melting activities?
answer
TFIIE
question
Which protein is involved in initiation and elongation and decreases pausing and protects elongation complex from arrest?
answer
TFIIF
question
What has to occur in order for the polymerase to leave the pre-initiation complex?
answer
The tail has to become phosphorylated
question
List the function of TFIIE.
answer
- binds RNA pol II and recruits TFIIH -modulates TFIIH, ATPase, and kinase activities -Assists TFIIH in promoter melting.
question
T/F TFIIE-alpha is also found in Archaea.
answer
True
question
Which complex is involved in promoter melting through helicase activity, promoter clearance by CTA kinase activity and functions in nucleotide excision repair?
answer
TFIIH
question
What things do Archaea have that eukaryotes have?
answer
TBP TFIIB TFIIE
question
TFIIH has a promoter melting and a Nucleotide excision repair. Both are helicases activity. What are their directions (hint: 5'to 3' or 3' to 5')
answer
NER is 5-3 the promoter melting, helicase is 3-5
question
What happens when TFIIH phosphorylates the CTD?
answer
It becomes the trigger for the complex to undergo initiation to elongation making the RNA pol clear the promoter
question
What phosphorylates the CTD? Explain the process.
answer
CAK; The mediator phophorylates cycH which causes cyH to activate Cdk7 leading to the phosphorylation of the CTD.
question
What is the CAK homolog in yeast?
answer
TFIIK
question
CTD Kinase also known as _ _ _ _ is regulated by ______ _ which in turn its regulated by _____ module of the mediator while _____ serves as the structural subunit of CAK.
answer
CDK7, cyclin H, CDK8, mat1
question
How does the process work when TFIIH is involved in nucleotide excision repair?
answer
When TFIIH is involved in excision repair, the kinase (CAK) is removed and specialty subunits that function in nucleotide excision repair take its place.
question
CDK8 phosphorylates _____ and shuts off _________.
answer
Cyclin H; Cdk7
question
Only one structure of the TFIIH is involved in both transcription and NER. What is the structure?
answer
the core
question
Who facilitates the reaction of forming 1st phosphodiester?
answer
TFIIH and TFIIE
question
Which complexes melt the transcription start site using one of its helicases (3' to 5')?
answer
TFIIE and TFIIH
question
What serves as the trigger that transitions from initiation to elongation?
answer
Phosphorylation of the CTD by TFIIH
question
The multistep assembly: Activator binds first and recruits _ who recruits A or B either order_ joins to pol2 forming Pol2/_ complex and joins PIC then_ joins the complex and recruits _.
answer
TFIID, TFIIF, TFIIE, TFIIH
question
Transcription cycle: ______ phosphorylates the CTD and the mediator loses affinity for the CTD , the CTD dislodges from TBP and from Mediator. RNA pol II initiates and clears the promoter then later the CTD is dephosphorylated by a phosphatase activity stimulated by______ (in the absence of _____). Termination: RNA pol II/TFIIF complex leaves the template, forms complex with the________ and reinitiates with the CTD in the underphosphorylated state.
answer
TFIIH, TFIIF( in the absence of TFIIB), Mediator
question
Which factors remain at the promoter and which leave?
answer
Remain at the promoter: TFIIA, TFIID, TFIIE, TFIIH Leave: TFIIF, TFIIB
question
Mediator only attaches to the _______________________ CTD.
answer
under phosphorylated
question
When does the mediator lose affinity for the CTD?
answer
After the CTD is hyperphosphorylated
question
A large complex of proteins known as the _________________ is also part of the preinitiation complex.
answer
Mediator
question
T/F The Mediator is called an integrator of positive and negative signals, which determines the amplitude of transcription.
answer
True
question
Mediator is in an extended conformation, with ______, _____, and ____domains clearly distinguishable.
answer
head, mid body and tail
question
What helps the mediator bind to the CTD?
answer
SRBs
question
The mediator (in yeast) is divided in two subunit groups: SRB ( suppressor of RNA pol B (II)), and ____, which its functions is still unknown.
answer
MEDs
question
What is the target of Cdk8?
answer
Cyclin H of TFIIH which in turn regulates cyclin 7
question
What happens if you delete or mutate the SRB4 subunit from the head?
answer
You lose 93% of all transcriptional activity.
question
Mediator subunits can be biochemically purified as modulues like:
answer
SRB4 (Head) Med9/10 (Middle) Gal 11 (Tail, Sin4)
question
What is found in the middle of the mediator?
answer
Med9/10
question
What is the function of Gal 11 (tail)?
answer
Makes contacts with transactivators and repressor proteins.
question
What happens if you mutate or delete Sin4 from the tail?
answer
The rest of the tail falls off, defective activated transcription
question
What are the Cdk8/CycC SRB names? (Hint: Srb__/Srb__ respectively)
answer
Cdk8= Srb10 CycC= Srb11
question
What role does Srb10(Cdk8) and Srb11 (CycC) play?
answer
They inhibit TFIIH by phosphorylating the cycH subunit of H.
question
What are two ways to purify the mediator?
answer
-Affinity column with immobilized CTD -Use VP16 acidic activator column
question
Which of the following is dissociable? (Cdk8)Srb10 (CycC)Srb11
answer
Cdk8
question
What are two ways that the mediator inhibits transcription?
answer
- Inhibits TFIIH and transcription by Srb10/Cdk8 phosphorylating cyclin H subunit of TFIIH - Prevents pol II from joining the preinitiation complex by Srb10/Cdk8 phosphorylating the CTD of pol II before initiation.
question
What do proteins disrupt nucleosome structure resulting in 30 fold increase in binding of transactivator proteins. (require ATP)?
answer
SWI/SNF
question
What triggers the opening of the clamp?
answer
Mediator contact with Rbp4/7 subunits
question
What determines the startpoint for transcription?
answer
basal apparatus
question
What determines the frequency of transcription?
answer
activators
question
What connects activators to basal factors?
answer
Coactivators
question
The role of the _______________ domain is to bring the transcription-activation domain into the vicinity of the promoter.
answer
DNA-binding domain
question
Nuclear receptors are the same as ______________ ______________ and they also have a zinc containing binding domain.
answer
steroid receptor
question
What is a unique feature of the zinc finger?
answer
It could ONLY recognize 3 bases at a time with a little bit affinity for four but does not have any big DNA binding domains involved in reading the sequence.
question
How could you build a transcription factor if its going to be specific to any gene, if could only read 3 bases?
answer
Polydactyl zinc fingers
question
Three zinc fingers fit into the ___________ groove.
answer
major
question
T/F Polydactyl zinc finger proteins can deliver any protein to a specific genomic address.
answer
True
question
Steroid receptors have two zinc modules, one bind _________, the other involved in ________________. Each module contains __ zinc ion and __ cysteines.
answer
binds; dimerization, 1,4
question
What must steroid receptors do to activate transport to the nucleus?
answer
Bind ligand (hormone)
question
What are two things that determine which steroid receptor binds to which particular promoter?
answer
- Actual sequence -spacing between sites where monomers bind.
question
What is an amphipathic helix?
answer
Helix with hydrophobic and hydrophilic amino acids on a side.
question
T/F Acidic activators are a major class and may be the only one in yeast.
answer
True
question
How does glucocorticoid receptor activate transcription?
answer
1- Glucocorticoid diffuses through the membrane and binds to the GR. 2- This disrupts the interaction between Hsp90 and the GR which allows the hormone/receptor complex to translocate to the nucleus. 3-In the nucleus it dimerizes and binds to the promoter to target genes activating transcription.
question
How happens if the interaction between GR and Hsp90 is not disrupted?
answer
Hsp90 would bind to GR keeping glucocorticoid from going to the nucleus.
question
What happens when glucocorticoid binds to the receptor?
answer
It changes the conformation so that it loses its grip or affinity for Hsp90
question
One property determines their activity for the whole group called __________ _____________________, when they should be active, they end up going to the nucleus otherwise they are sequestered in the cytoplasm.
answer
nuclear localization
question
Estrogen receptor recruits a coactivator called __________
answer
P160
question
What must happen for the coactivator P160 to be active?
answer
It must bind to a binding pocket that is protected by helix 12.
question
How could P160 bind to the binding pocket if it is protected by helix 12?
answer
Helix 12 rotates when ligand binds. This allows P160 to bind later.
question
What happens when you bind estrogen to the binding pocket?
answer
It changes the conformation of heloix 12 so that it rolls forward exposing the binding site for the coactivator P160
question
What blocks helix 12 so you cant get activation by estrogen?
answer
Taxmoxifen
question
How does taxmoxifen block further access of P160?
answer
Taxmoxifen mimics the structure of estrogen except when it binds to the coactivator P160, it causes the helix to roll the other war in a way that blocks further access of P160
question
_________ _____________ do not directly recruit members of the preinitiation complex. Instead, they make contact with _____________, which in turn, recruit basal factors.
answer
Steroid activators, coactivators
question
T/F P160 recruits HAT complexes since it has no HAT activity.
answer
False, it has HAT activity
question
How do steroids activate transcription.
answer
Step 1- recruit HAT activity (coactivators) Step 2- recruit Mediator
question
What leaves once the mediator arrives during steroid transcription?
answer
CPB/p300 PCAF
question
Which hormones form homodimers and recognize the sequence TGTTCT?
answer
Glucocorticoid mineralocorticoid androgen progesterone
question
Which hormones form heterodimers and recognize half elements TGACCT?`
answer
Thyroid (T3R) Vitamin D (VDR) Retinoic acid (RAR) 9 cis retinoic acid (RXR)
question
Which of the following half sites are palindromes? homodimer heterodimer
answer
homodimer
question
Homodimer steroid activators bind the ____ sequence with a difference in spacing.
answer
same
question
Heterodimer steroid activators ________ determines specific recognition.
answer
spacing
question
Which have head to head receptors and which have head to tail receptors?
answer
Head to head- homodimers Head to tail - heterodimers
question
The _________ receptor and the ________ receptor bind the SMRT corepressor at the promoter in the absence of ligand. Binding of the ligand reduces the affinity for the corepressor and allows binding to coactivators.
answer
Thyroid; retinoic acid
question
Why happens when the thyroid hormone is not around?
answer
It recruits a corepressor names SMRT, this represses transcription if there is no thyroid hormone around.
question
What happens when the thyroid hormone arrives?
answer
It changes the configuration of the receptor so that it loses affinity for the SMRT corepressor complex.
question
Which hormones act both as activators and repressors?
answer
Thyroid receptor and retinoic acid receptor
question
Hormone activated transcription in plants: What triggers the activation of the glucosinolate pathway in plants?
answer
Insect feeding
question
How is insect feeding activate transcription?
answer
Insect feeding causes the synthesis of JA-LLE which binds to JAZZ, causing the proteasome degradation of JAZZ. Once JAZZ is degraded the NINJA and Topless corepressor with HDAC leave the complex and then MYC2 the transactivator recruits Med25 which reciuits PIC and recruits RNA pol II which then initiates transcription.
question
How does the Topless corerepressor repress? What does it use?
answer
Uses Ubiquitylation as a trigger