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BMSC 320 > Lectures 23 & 24 > Flashcards

Lectures 23 & 24 Flashcards

1
Q

Do DNA binding domains recruit or block RNA pol

A

either

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2
Q

What are the 5 steps of eukaryotic transcription cycle

A

Recruitment/ Assembly
Initiation
Elongation
Termination
Recycling

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3
Q

What are general transcription factors? What are the 6

A

Universal proteins required to get RNA pol II working

TFIID
TFIIA
TFIIB
TFIIF
TFIIE
TFIIH

ABDEFH

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4
Q

Describe the formation of the preinitiation complex

A

TFIID containing TBP binds the TATA box

TBP causes DNA to partially unwind

TFIIA binds TFIID and stabilizes the association with DNA

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5
Q

What does TFIIA do

A

TFIIA binds TFIID and stabilizes the association with DNA
Makes TFIID binds better to DNA

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6
Q

What does TFIIB do

A

Binds the promoter at the TFIIBRE (recognition element)

By binding TFIIB the potential symmetry of TFIID binding is given directionality
Once TFIIB is bound, RNA pol II can be recruited to the promoter

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7
Q

What does TFIIF do

A

Stabilizes the binding of pol II to TFIIB

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8
Q

What are the stabillizing TFs

A

TFII-A stabilizes the binding of TFII-B
TFII-F stabilizes the binding of pol-II to TFII-B

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9
Q

Once the polymerase is bound, it need to form the _______ ________ to start RNA initiation

A

Transcription bubble

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10
Q

what is the role of the mediator

A

various sequences and proteins act to turn genes “on” and these signals are all integrated by the mediator complex to bring RNA pol II to the gene when it is needed

The Mediator integrates multiple signals

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11
Q

What is an enhancer? why can they act over long distances? Where are they located?

A

A sequence which binds a specific transcription factor & recruits/stabilizes mediator to increase the likelihood of transcription

Can act over huge distances due to the organization in the nucleus creating large loops

Can be upstream or downstream but has to be somewhere in the genome

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12
Q

What are insulators? Example?

A

Keeps loops distinct

Prevents enhancers from activating genes in other loops

CTCF is an example which is very important in vertebrates

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13
Q

Describe the process from pre-initiation to initiation

A

TFIIE and TFIIH finish up the pre-initiation complex
TFIIE assists forming the open-complex as it stabilizes ssDNA and also increases the activity of TFIIH

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14
Q

what is TFII H

A

Helicase
using ATP it unwinds DNA creating the open-complex
Also has kinase activity to phosphorylate the tail of RNA pol I

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15
Q

what is abortive initiation

A

production of very short RNA molecules that get stuck
The proteins bound to promoter sequences are also preventing RNA pol II from moving away from those same sequences

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16
Q

what does RNA pol II struggle with? How can it get past it?

A

Like it’s prokaryotic counterpart, it struggles with abortive initiation

Phosphorylation of the RNA pol II CTD by TFII-H will allow it to disengage from proteins bound at the promoter and undergo what is called “promoter escape

17
Q

What is the pol II CTD

A

Unlike RNA pol I and III, RNA pol II has a C-terminal domain, which is a tail of these heptad repeats which can be phosphorylated

18
Q

What are the states of phosphorylation during the transcription cycle

A

Loading onto promoter: CTD is dephosphorylated

Initiation: Phosphorylated at Ser5 by TFIIH

Elongation: Ser5 and Ser2 is phosphorylated

Termination: dephosphorylation of Ser5, Ser 2 is still phosphorylated

19
Q

how does incorporating the wrong nucleotide affect the polymerase

A

it can pause/stall the polymerase

20
Q

Why are there misincorporations

A

Nucleotides and ribonucleotides can spontaneously created different forms (tautomers) that exist transiently

If the tautomer is integrated while it is in the incorrect form then the RNA polymerase will stall and can’t proceed until the nucleotide is removed

21
Q

What does TFIIS do

A

TFIIS fixes the stalled RNA pol II

TFII-S stimulates the backtracking and RNA proofreading activity of pol II to hydrolyze misincorporated rNTPs

22
Q

Overview of the transcription cycle for RNA pol II

A

TFIID binds TATA box (in TATA-less promoters it binds the initiator sequence and downstream promoter element)

TFIIA stabilizes TFIID

TFIIB binds the BRE and orients the loading of RNA pol II

TFII-F associated with RNA pol II associates with TFII-B for proper RNA pol II placement

Mediator integrates signals from activators/repressors

TFII-E stabilizes ssDNA (transition from closed to open complex)

TFIIH acts as the helicase and phosphorylates Ser5 of RNA pol II CTD to allow promoter escaped

TFIIS enhances removal of misincorporated nucleotides to prevent RNA pol II stalling

P-TEFb adds Ser-2-P to differentiate initiation from elongation

during elongation the polymerase associates with and carries along RNA modifying/processing proteins

23
Q

What is epigenetic gene control

A

a layer of heritable gene expression that lies above the DNA sequence

24
Q

How is epigenetic control expressed through chromatin/histones

A

Histones can block access to DNA sequences

Heterochromatin is tightly bound and inaccessible

Euchromatin is loosely bound and accessible

25
Q

Describe histone tails

A

tails extending from the core that can be modified to all the overall binding affinity

Can be modified by enzymes

26
Q

Describe the histone code

A

the effect of various modifications of the four histones on the chromatin state of gene expression

four types of modification

Their effect extends far beyond simply loosening the association between histones and DNA, and can also recruit activators or inhibitors to the promoter

27
Q

four types histone modification

A

Acetylation, methylation, phosphorylation, and ubiquitination

28
Q

Describe Lysine acetylation

A

Uses HATs and HDACs
HAT = histone acetyl transferases
HDAC = histone deacetylases

Acetylation removes the positive charge from lysing, reducing the affinity of histones to the DNA backbone

29
Q

describe the effects of histone acetylation and deacetylation

A

activation of transcription and transition to euchromatin often involve specific histone acetylations

Repression and transition to heterochromatin often involve deacetylations

Many different HATs and HDACs exist in the nucleus

30
Q

which TF has HAT activity

A

TFIID

31
Q

Which residues can be methylation

A

Lysine and arginine

Methylation is additive lysine can be trimethylated
Arginine can be dimethylated

32
Q

T/F Acetylation and methylation are not mutually exclusive

A

false, can’t be methylated an acetylated. methylation is a way to prevent acetylation

33
Q

T/F Modification don’t affect other modifications

A

False

34
Q

What is the typical effect of methylation

A

usually silencing but there is some activation

35
Q

how can the histone code be visualized

A

ChIP and a series of antibodies that are specific for individual acetylation and methylation

The code can be visualized when overlaid on important gene sequences

BMSC 320 (18 decks)

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