Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

MCB 2050 > Lecture 7 > Flashcards

Lecture 7 Flashcards

1
Q

What do RAP1 and SIR proteins do?

A

repression of the silent mating type loci and the telomeres of yeast

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What does RAP1 bind within?

A

DNA silencer sequences associated with HML and HMR

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What are silencers?

A

positions in the genome where large heterochromatin blocks are built

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What occurs with genes that are close to silencers?

A

strongly repressed, the repression of the gene depends on their position relative to the silencer and does not depend on their promoters

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What are HML and HMR?

A

mating type loci that are constantly repressed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What are the two proteins that repress HML and HMR?

A

Rap1 - binds next to the repressed loci and recruits Sir proteins
Sir proteins spread away and over nearby genes, recruited by rap1

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What does sir1 do?

A

deacetylase, it deacetylates the histones within HML and HMR, the deacetylated histones bind tighter to DNA and form heterochromatin to prevent the association of txnl activators to the promoters

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Where do Rap1 and SIR proteins bind on the chromosome?

A

the telomeres, Sir proteins spreading the sub-telomeric regions and cover them with condensed hyperacetylated nucleosomes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What occurred in the mutation analysis of lysine -> arginine substitutions in histone tails?

A

arginine retains a positive charge only, cannot be acetylated
the DNA histone interaction is strong, chromatin is compact, gene repression can not be revered by acetylating the histones
these mutants maintain permanent gene repression at telomeres

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What occurred in the mutation analysis of lysine -> glutamine substitutions in histone tails?

A

glutamine has a neutral charge, resembles acetylated lysine, can not be deacetylated to gain a positive charge
chromatin is decondensed, gene can not be repressed
these mutations maintain permanent gene activation at telomeres

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What does acetylation of histone tails do?

A

reduces their positive charge and allows for the opening of chromatin and for txn

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What does the deacetylation of histone tails do?

A

reconstitutes positive charge, strengthens DNA-histone interactions, compact chromatin and suppresses txn

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

How do Rap1 and Sir bind to the telomeres to repress genes in yeast?

A

*RAP1 and SIR2, 3, and 4 proteins – bind to each other
*SIR3 and SIR4 – bind to histone H3 and H4 N-terminal tails that are maintained in a largely nonacetylated state by SIR2 deacetylase
*SIR3 – localized in the repressed telomeric heterochromatin. (RAP1, SIR2, and SIR4 also colocalize with the repressed telomeric heterochromatin.)
* Multiple copies of RAP1 – bind to a simple repeated sequence at each telomere region that lacks nucleosomes
*SIR3 and SIR4 bind to RAP1, and SIR2 binds to SIR4.
*SIR2 deacetylates the tails on the histones neighboring the repeated RAP1-binding site.
* The hypoacetylated histone tails – binding sites for SIR3 and SIR4
*SIR3 and SIR4 bind additional SIR2, which deacetylates neighboring histones.
*Process repetition – spreads region of hypoacetylated histones with associated SIR2, SIR3, and SIR4
* Interactions between complexes of SIR2, SIR3, and SIR4 cause the chromatin to condense and several telomeres to associate.
*Higher-order chromatin structure – sterically blocks other proteins from interacting with the underlying DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What are the names of rap1, telomere, sir3, sir4, sir2?

A

rap1 - repressor
telomere - silencer
sir3/sir4 - co-repressors
sir2 - histone-deacetylase
sir2/3/4 complex binds rap1 then spreads away from the telomere

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What do dots inthe fluorescent microscope image of telomeres in yeast represent?

A

SIR3 on the telomeric cluster

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What is Ume6

A

txn repressor and the effector molecule

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

what is sin3/rpd3

A

complex is a corepressor

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

what is rpd3

A

histone deacetylase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

what is gcn4

A

txn activator

20
Q

what is SAGA

A

complex is a coactivator

21
Q

what is gcn5

A

histone acetyl-transferase (acetylates histomnes)

22
Q

how can acetylate histone recruit more coactivators?

A

bromo-domains

23
Q

how are histones on yeast genomes acetylated and deacetylated?

A

*Repressors can direct histone deacetylation at specific genes.
*(a) Ume6 repressor-directed deacetylation of histone N-terminal tails:
*DNA-binding domain (DBD) – interacts with a specific URS1 upstream control element of the genes it regulates
*Repression domain (RD) – binds Sin3, a subunit of a multiprotein complex that includes Rpd3, a histone deacetylase
*Rpd3:
*deacetylates histone N-terminal tails on nucleosomes in the region of the Ume6-binding site –
*inhibits general transcription factor binding to the TATA box
*represses gene expression
*(b) Gcn4 activator-directed hyperacetylation of histone N-terminal tails:
*DNA-binding domain – interacts with specific UAS upstream activating sequences of yeast genes it regulates
*Activation domain (AD) – interacts with a multiprotein SAGA histone acetylase complex that includes the Gcn5 catalytic subunit
*Gcn5:
*hyperacetylates histone N-terminal tails on nucleosomes in the vicinity of the Gcn4-binding site
*decondenses chromatin to facilitate access by the general transcription factors to the TATA box
*activates gene expression.
*acetylation of specific histone lysines – also generates binding sites for proteins containing bromodomains found in transcription activators
*Repression and activation of many genes in higher eukaryotes occur by similar mechanisms.

24
Q

What do txl activators bind and recruit?

A

histone acetyl-transferases and another class of co-activators called chromatin remodelling complexes, they also stimulate the loading of the pol and the initiation of txn via coactivators

25
Q

What happens to nucleosomes when histones are acetylated

A

nucleosomes-dna interaction becomes loose, chromatin-remodelling complexes then use ATP to push nucleosomes along DNA to open promoters

26
Q

What is an example of a chromatin-remodelling factor?

A

SWI/SNF ATPases

27
Q

What do chromatin-remodelling factors do?

A

move nucleosomes along dna by sliding or transferring them, they shift nucleosomes away from the promoter/enhancer sites and gives txn factors access to DNA, chromatin-remodelling factors use atp to move nucleosomes

28
Q

What is the mediator?

A

huge complex containing a variety of proteins, including enzymes, proteins that recognize activators, proteins that recognize GTF’s and other coactivators, different mediator complexes contains proteins required for specific genes

29
Q

What does the mediator interact with?

A

*directly interacts with transcriptional activators
one mediator complex can interact with multiple transcriptional activators
*directly interacts with GTF’s

30
Q

What is the structure of a mediator

A

Head, middle, tail, and CKM modules

31
Q

What are some regions of the mediator complex?

A

*Promoter region chromatin “open” structure – allows general transcription factor binding with the Mediator multisubunit co-activator complex
*Mediator complex – forms a molecular bridge between activator bound to cognate DNA site and Pol II
*Activation domain – Mediator interactions stimulate assembly of the preinitiation Pol II complex (PIC) on the promoter.

32
Q

How do different dna bound activators interact with a single mediator?

A

*Individual Mediator subunits bind to specific activation domains
*Multiple activators may influence transcription from a single promoter by interacting with a Mediator complex simultaneously or in rapid succession.
*Different Mediator subunits interacting with specific activation domains – may contribute to integration of signals from several activators at a single promoter

33
Q

How do the cells remember which genes to express?

A

the memory of gene expression is achieved mainly through reconstitution of the same chromatin structure after the passage of the replication fork, this is called epigenetic memory of txn

34
Q

What is epigenetic control of txn maintained by?

A

dna methylation and methylation and acetylation of histones

35
Q

What are epigenetic marks

A

dna methylation and methylation and acetylation of histones in order to maintain epigenetic control of txn

36
Q

When are epigenetic marks built during dna rep?

A

during and/or soon after the passage of the replication fork

37
Q

What are histone post-translational modifications (PTMs)?

A

methylation, acetylation and phosphorylation

38
Q

What is dna methylation always associated with?

A

heterochromatin and repressed genes

39
Q

What are the histone modifications associated with?

A

Histone acetylation - associated with active genes and euchromatin
Histone deacetylation - associated with gene repression and heterochromatin
Histone methylation - associated with both gene activation and repression, depending on the specific modifications

40
Q

What are the histone post tnl modifications associated with active and repressed genes?

A

acetylated lysine:
sites of mod - H3, H4, H2A, H2B
effect on txn - all activation

methylated lysine:
sites of mod - H3 (K4), H3 (K9)
effect on txn - H3 (K4) is activation, H3 (K9) is repression

41
Q

What does methylation of CpG islands lead to?

A

condensation of chromatin

42
Q

What does methylated dna recruit?

A

special class of Me-DNA-binding proteins (MeBPs)

43
Q

What do MeBPs recruit?

A

factors that deacetylate histones and condense chromatin

44
Q

When is methylation of DNA rebuilt?

A

immediately after the passage of the replication forks

45
Q

What occurs when the replication fork passes through heterochromatin?

A
  • If DNA was methylated prior to the passage of fork, the newly synthesized DNA is immediately methylated after the passage of the fork
  • if histones are deacetylated prior to the passage of the fork, the newly incorporated histones are deacetylated very soon after the passage of the fork
  • heterochromatin is rebuilt
46
Q

What occurs when the fork passes through euchromatin?

A
  • the newly synthesized DNA is not methylated
  • the newly incorporated histones are acetylated or methylated exactly as they were prior to the passage of the fork
  • euchromatin is rebuilt
47
Q

How is the H3-K9Me reconstituted after the passage of replication fork

A

*H3 lysine 9 methylation is maintained following chromosome replication.
*Mechanism:
*Chromosomal DNA replication
*Parent histones randomly associate with the two daughter chromosomes.
*Unmethylated histones synthesized during S phase assemble into other nucleosomes in both daughter chromosomes.
*Histone H3 lysine 9 methyl transferases (H3K9 HMT) –
*associate with parent nucleosomes bearing histone 3 lysine 9 di- or trimethylation marks
*methylate the newly added unmodified nucleosomes
Maintains histone H3 lysine 9 methylation marks during repeated cell divisions, unless they are specifically removed by a histone demethylase

MCB 2050 (11 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions