Lecture 9 - Transcription

Front 1

The transcription bubble is ____ bp long.



About ____ bases of RNA hydrogen bond to the DNA template at one time

Back 1

14, 9

Front 2

Bacteria have___ RNA polymerase, whereas eukaryotic cells have ___.

Back 2

One, three

Front 3

The bacterial RNA polymerase subunits

Back 3

B, B', 2 copies of alpha, and w (omega)

Front 4

Bacterial RNA polymerase is shaped like a

Back 4

crab claw

Front 5

The bacterial RNA POLYMERASE hactive site contains only one tightly bound ______.
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Back 5

Magnesium ion

Front 6

What three things usually have a single poly peptide RNA polymerase?

Back 6

viruses, mitochondria, and chloroplasts

Front 7

The +1 region is the

Back 7

transciption start site

Front 8

TRANSCRIPTION INITIATION:

1. ________________= double stranded DNA
then conformational change in polymerase
called _______________occurs on the DNA

2. ___________________= DNA strands melt open

3. __________________ ESCAPE

Back 8

CLOSED COMPLEX, ISOMERIZATION

OPEN COMPLEX

PROMOTER

Front 9

in bacteria, a __________ factor binds the core enzyme to form the rna polymerase holoenzyme prior to initiation.

Back 9

sigma (usually sigma70)

Front 10

Region ____ of the sigma factor binds to the -10 promoter elelment, while region ___ binds to the -35 promoter element

Back 10

2, 4

Front 11

Features of bacterial promoters:

The majority of them have ___ and ____ elements

Back 11

-10, -35

Front 12

____________ element is present in strong promoters such as rRNA genes. It is bound by the ________ subunit, not sigma.

Back 12

UP, alpha

Front 13

extended -10 region is present in genes used to metabolize _________.

It is bound by the sigma through region ___.
There is no -35 element in an extended -10 promoter.

Back 13

galactose, 3

Front 14

The -10 discriminator element in a promoter is bound by region ___ through sigma.

Back 14

1

Front 15

The C-terminal domain is on the ____ subunit of the RNA polymerase. It extends out from the rest of the polymerase and binds to the ___ element.

Back 15

alpha, UP

Front 16

During isomerization, tightening of pincers and movement of ________ opens downstream DNA channel allowing the melting of DNA and formation of open complex
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Back 16

SIGMA 1.1

Front 17

_______ blocks RNA exit channel. Growing RNA chain pushes _______ out of the way.
This loosens the binding of SIGMA subunit to other subunits of RNA polymerase
causing SIGMA to fall off RNA polymerase after promoter escape.

Back 17

SIGMA 3/4, SIGMA 3/4

Front 18

3 DIFFERENT MODELS OF NON-PRODUCTIVE RNA INITIATION THAT LEADS TO mRNA strands less than 10bp long

Back 18

transient excursions - polymerase moves forward and then back

inchworming - only part of the polymerase goes forward and then back

scrunching - the RNA polymerase pulls DNA into it and then releases

Front 19

Data indicates that the __________ model is correct

Back 19

scrunching

Front 20

2 mechanisms for proofreading during transcription

Back 20

1. pyrophosphorolytic editing
2. hydrolytic editing

Front 21

What is pyrophosphorolytic editing?

Back 21

reversal of normal rxn. addition of a pyrophosphate to remove an incorrect nucleotide

Front 22

What is hydrolytic editing?

Back 22

RNA polymerase backtracks and then hydrolyzes the incorrect nucleotide. this rxn is stimulated by Gre factors.

Front 23

If RNA polymerase becomes stuck, the _____ protein removes it and recruits the _____ nucleotide excision repair proteins (transcription-coupled repair).
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Back 23

TRCF, UvrA-D

Front 24

In bacteria there a 2 different sequences in the transcribed RNA that can signal for termination:

Back 24

Rho dependent and rho independent

Front 25

Rho is a ___________ protein

Back 25

hexameric

Front 26

Rho binds _______ sites that are 40 nt sequences of RNA that are __-rich. They lack a secondary structure and do not contain ribosomes

Back 26

rut, c

Front 27

Rho either

1. ________ the polymerase off DNA
2. _________ RNA out of polymerase
3. induces a ____________ ____________ so polymerase can dissociate from DNA

Back 27

push, pull, conformational change

Front 28

Rho independent (intrinsic) have certain termination sequences. On the DNA there is a ________ symmetry. The RNA transcript of this DNA forms a termination _____________ followed by a stretch of __'s.

Back 28

dyad, hairpin, U

Front 29

The hairpin formed on the RNA knocks the
RNA polymerase off DNA when the DNA:RNA
basepairing in the transcription bubble is
mainly___ , the weakest baseparing couple

Back 29

A:U

Front 30

The eukaryotic rna polymerase II is used to transcribe what kind of genes?

Back 30

protein-coding

Front 31

In the pre-initiation of RNA polymerase II, the ________ of __________ binds the TATA box

Back 31

tata binding protein (TBP), TFIID

Front 32

Other proteins in TFIID are called_______.

Back 32

TAF (TBP - associated factors)

Front 33

After binding the TATA box ___________ and ___________ bind TFIID.

Following, ___________-______________ complex bind.

Back 33

TFIIA AND TFIIB


TFIIF-POLII

Front 34

Next, ____________ and ______________ bind

Back 34

TFIIE AND TFIIH

Front 35

TFIIH has _______________ activity. It is ATP-dependent and unwinds DNA.

Back 35

helicase

Front 36

Phosphorylation of __________ residues on 7 amino acid repeat on the ____ (CTD) of the polymerase is achieve through _____________ kinase activity. This leads to...

Back 36

serine, tail, TFIIH

Front 37

When the TBP of TFIID binds DNA, TBP ________ DNA and allows _____________ to bind DNA.

A______________ of TFB BINDS TO THE ___________ ____________ of DNA

Back 37

BENDS, TFIIB, BETA-SHEET, MINOR GROOVE

Front 38

What two things are needed so that polymerase can transcribe through nucleosomes?

Back 38

The mediator and chromatin remodeling complexes

Front 39

Which mediator protein is required for transcription of almost all protein encoding genes?

Back 39

Med17

Front 40

During elongation, _______ ______________ enzymes are recruited by the phosphorylation of the _______ of Pol II while _____________ _____________ and ______________ are lost.

Back 40

RNA processing, CTD tail, initiation factors, Mediator

Front 41

Elongation factors TFII__ and ________ join.

Back 41

S, hSPT5

Back 42

capping, hSPT5, TFIIS

Front 43

Phosphorylation of serine at position 2 by __________ kinase is seen during elongation and is associated with recruitment of _________ factors.

Back 43

P-TEFb, splicing

Front 44

P-TEFb also phosphorylates _______ which increases _______________.

Back 44

hSPT5, proofreading

Front 45

__________ in eukaryotes and __________ in bacteria increases proofreading of RNA polymerase. Although the proteins are so different, they essentiall act in the same way.

Back 45

TFIIS, GreB

Front 46

A protein complex called _________ helps the RNA polymerase transcribe through nucleosomes. This complex is made of __________ and __________. It removes ________-__________ dimers and then reassembles the nucleosome with the help of ___________ once the polymerase passes.

Back 46

FACT (FAcilitates Chromatin Transcription), Spt16 + SSRP1, H2A-H2B, SPT6

Front 47

The additon of the 5' - 7 - methylguanosine cap to the RNA is added _____________ elongation begins.

It protects the RNA from ______________.

The cap adding machinery dissociates after ______ phosphorylation on the CTD tail of Pol II.

Back 47

before, degradation, Ser 5

Front 48

Describe the rxn of 5' - 7 - methylguanosine cap in three steps.

Back 48

1. First, a gamma phosphate from the 5' end of RNA is removed.

2. The GMP moeity is added using a 5'-5' linkage

3. The nucleotide is then modified by the addition of a 7- methyl group to the guanine cap.

Front 49

IN THE 3'-POLYADENYLATION OF RNA TRANSCRIPTS, two factors are first found on the CTD of Poll II. They then bind the transcribing poly-A signal sequence, leaving the CTD tail. This leads to the cleavage of the RNA following the sequence.

What are the two factors?

Back 49

CPSF = CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR

CstF - cleavage stimulation factor

Front 50

After RNA cleavage following the poly-A signal sequence, which factor dissociates and which stays attached to the cleaved RNA via the signal sequence?

Back 50

CstF dissociates and CPSF remains on the RNA

Front 51

The ____________ polymerase then comes in, binds to the end of the cleaved RNA and transcribes ~200 ___'s at the end of the transcript without a template.

Back 51

poly-A, A

Front 52

Finally, _____ _____________ ____________ come in and bind and stabilize the mRNA transcript from _________________ and allow transport from the _____________.


Additional poly-A binding proteins lead to the dissociation of ______ and ________ from the mRNA transcript.

Back 52

poly-A binding proteins, degradation, nucleus


Poly-A polymerase and CPSF

Front 53

The two models of EUKARYOTIC transcription termination?

Which one is the current favored model?

Back 53

Torpedo and allosteric

torpedo is favored

Front 54

TORPEDO: After the cleaving of RNA via CstF and CPSF, _______ comes in and degrades the uncapped RNA still in Pol II. It then knocks off the ____________ from ______ when it reaches it.

Back 54

Rat1/hXrn2

Pol II, DNA

Front 55

ALLOSTERIC: A _______________ ______________ occurs in the polymerase after it passes the poly-A transcription site. This causes the polymerase to lose __________________ and fall of DNA.

Back 55

conformational change, processivity