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MCB2050 > h. Lecture 6 Slide Deck (January 25th) > Flashcards

h. Lecture 6 Slide Deck (January 25th) Flashcards

1
Q

a) What is the fxn of a silencer?
b) is it DNA or a protein?
c) are they position dep or indep? What does this mean?

A

a) they repress genes
b) DNA
c) position-dep = their ability to repress the gene depends how close it is to that gene (will only work is gene is in close proximity)

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2
Q

The following are 2 examples of ____________ from the model organism S. cerevisia (yeast)
1. mating type loci
2. sub-telomeric genes

A

positional repression

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3
Q

Describe the 6 steps to mating type loci repression in yeast using the following terms; HML/HMR, Rap1, Sir2, Sir3, Sir4, histone deacetylase, heterochromatin, hypo-acetylation, co-repressor.

A
  1. the genes HML/HMR are repressed due to being close to a silencer
  2. Rap1 binds to repressed loci of HML/HMR
  3. the co-repressors Sir3 and Sir4 are recruited to the repressed loci
  4. the histone deacetylase Sir2 is recruited to the histones at HML/HMR
  5. HML/HMR binds tighter to the histones producing heterochromatin
  6. This hypo-acetylation causes gene repression
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4
Q

T or F - the genes HML and HMR in yeast are the same

A

F - they represent sexual dimorphism in yeast thus one leads to male yeast while the other to female yeast

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5
Q

ANS the following wrt Sir proteins
a) what does Sir stand for?
b) What is Sir2? who recruits it?
c) What is Sir3? who recruits it?
d) What is Sir4? who recruits it?
e) In the end what is the purpose of the Sir proteins?

A

a) silence information region
b) a histone deacetylase recruited by Sir 3 and 4
c) a co-repressor recruited by Rap1
d) a co-repressor recruited by Rap1
e) to repress gene expression

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6
Q

T or F - Sir 3 and Sir 4 do the same thing

A

T

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7
Q

T or F - Sir 3 and Sir 2 do the same thing

A

F - 3 is a co-repressor that recruits 2 which is a histone deacetylase

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8
Q

Describe the 5 steps involved w/ the repression of sub-telomeric gene in yeast using the following terms; Rap1, Sir2, Sir3, Sir4, telomere, co-repressor, histone deacetylase, heterochromatin

A
  1. Rap1 binds to the telomeres
  2. the co-repressors Sir3 and Sir4 are recruited
  3. the histone deacetylase Sir2 is recruited and deacetylates the histone tails
  4. The DNA in the telomeres bind tightly to the histones forming heterochromatin
  5. DNA is repressed
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9
Q

a) which AA is enriched on the histone tail (location of acetylation)
b) What would happen if you replaced that AA w/ arginine?
c) what would happen if you replaced that AA w/ glutamine?

A

a) lysine
b) R, unlike K, cannot be acetylated thus the positive charge of the tail will remain. Preventing the genes from being active
c) While Q is neutral in charge (representing acetylated K) it cannot be deacetylated thus it will never be positive keeping them from being repressed.

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10
Q

Match the following
a) deacetylation of histone tail
b) acetylation of histone tail
1. active gene
2. repressed gene

A

a) 2
b) 1

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11
Q

Match the following
a) deacetylation
b) acetylation
1. add a positive charge
2. remove the positive charge

A

a) 1
b) 2

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12
Q

a) What is the Sir complex made of - 3
b) What does the complex bind to?

A

a) Sir2, Sir3, Sir4
b) Rap1

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13
Q

promoter-________ repression/activaiton is position-________. What does this mean? (there are two ANS)
a) dep, indep
b) dep, dep
c) indep, dep
d) indep, dep

A

a) activation/repression depends on their promoters but the position wrt the gene doesn’t matter
c) activation/repressor depends on their position wrt the gene (must be in close proximity) but the promoters do not matter

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14
Q

Describe the following. Are they position dep or indep?
a) Ume6
b) Rpd3L complex
c) Sin3
d) Rpd3
e) URS1

A

1.
a) a repressor
b) a co-repressor complex
c) subunit of the Rpd3L complex
d) a histone deacetylase
e) repressor sequence
2. position-independent

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15
Q

Describe the following. Are they position dep or indep?
a) Gcn4
b) SAGA complex
c) Gcn5
d) bromo-domains - 2

A

a) activator
b) co-activator
c) histone acetyl-transferase
d) domains on the acetylated histones that recruit more co-activators
2. position-indep

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16
Q

Describe the 4 steps to repressor-directed histone deacetylation using the following terms; URS1, Ume6, DNA-binding-domain (DBD), repressor domain (RD), Sin3, Rpd3, Rpd3L, co-repressor complex, histone deacetylase/acetylase, histone

A
  1. the Ume6 repressor binds to the URS1 sequence via its DBD
  2. recruitment of the Rpd3L co-repressor complex
  3. The Sin3 subunit of the co-repressor complex associates w/ the RD of Ume6
  4. the histone deacetylase Rpd3 from the co-repressor complex deacetylates the N-terminal tails of the histones
  5. DNA is repressed
17
Q

Describe the 4 steps to activator-directed histone deacetylation using the following terms; UAS, Gcn4, DNA-binding-domain (DBD), activator domain (AD), SAGA complex, co-activator, activator, histone deacetylase/acetylase, histone

A
  1. the activator Gcn4 binds to the UAS sequence via the DBD
  2. the co-activator SAGA complex is recruited and binds to the AD of the activator
  3. the histone acetylase acetylates the N-terminal tails of the histones
  4. DNA is activated
18
Q

Describe the 4 steps to chromatin-remodeling using the following term; transcriptional activators, histone acetyl-transferase, chromatin-remodeling complex, ATP, nucleosome, DNA, promoters, histone, co-activator, nucleosome-DNA interaction

A
  1. transcriptional activators recruit the co-activators histone acetyl-transferases and chromatin-remodeling complexes
  2. the histone acetyl-transferase acetylates the histones loosening the nucleosome-DNA interaction
  3. the chromatin-remodeling complexes use ATP to push the nucleosomes down the DNA
  4. promoters are now available for gene transcription = gene activation
19
Q

Describe the following wrt chromatin remodeling
a) histone acetyl-transferase
b) chromatin-remodeling complex

A

a) co-activator that acetylates histones
b) co-activator that moves nucleosomes away from promoters

20
Q

this image is demonstrating
a) heterochromatin
b) decondensed chromatin
c) euchromatin
d) condensed chromatin
e) a and d
f) b and c

A

e

21
Q

this image is demonstrating
a) heterochromatin
b) decondensed chromatin
c) euchromatin
d) condensed chromatin
e) a and d
f) b and c

A

f

22
Q

the mediator is a complex that recognizes all of the following except
a) GTFs
b) activators
c) co-activators
d) repressors
e) they recognize all of these

A

d - the mediator is an example of a co-activator thus it will not interact w/ repressors

23
Q

T or F - the mediator can only interact w/ one transcriptional activator at a time

A

F - they can interact w/ many transcriptional activators

24
Q

T or F - A mediator is an example of an activator

A

F - its a co-activator b/c it doesn’t contain a DBD but instead interacts w/ other activators/co-activators

25
Q

a) label the following image.
b) What is this image of

A

a)
- blue = middle
- pink = head
- yellow = tail
b) a mediator

26
Q

Describe the 2 reasons for the transmission of ‘memory’ by epigenetic means

A
  1. the differentiate b/w cells that all contain the same genome
  2. to transfer that differentiation from father to daughter cells
27
Q

What differentiates a liver cell from a skin cell?

A

certain genes are expressed while other genes are not

28
Q

Describe epigenetic memory of transcription

A

the act of maintaining the memory of gene expression through the reconstitution of the same chromatin structure

29
Q

What are the 3 controls that maintain epigenetic memory of transcription

A
  1. methylation of DNA
  2. methylation of histones
  3. acetylation of histones
30
Q

Describe epigenetic marks

A

the methylated/acetylated parts of a genome that are copied over from father to daughter DNA to keep its memory

31
Q

When does methylation of DNA occur?

A

immediately after the passage of the replication fork

32
Q

Describe the following types of modifications. how do these affect charged molecules?
a) acetylation
b) methylation
c) phosphorylation

A

a) the act of adding acetyl groups (C=O) - reduce charge
b) the act of adding methyl groups - reduce charge
c) the act of adding a phosphate gr - makes more negative

33
Q

Describe the 4 steps that follow the methylation of CpG islands using the following terms; Me-DNA-biding proteins (MeBPs), acetylate/deacetylate, histones, chromatin, condense/decondense, daughter strand

A
  1. the daughter strand is methylated
  2. the methylated strand recruits MeBPs
  3. the MeBPs deacetylate the histones
  4. chromatin is condensed
34
Q

Describe the 4 steps that follow the unmethylation of CpG islands using the following terms; histone 3-Lysine 4 (H3-K4), transcription initiation machinery, epigenetic mark, methylation, histone,

A
  1. the unmethylated strand recruits H3-K4
  2. H3-K4 methylates histones at a specific position
  3. the transcription initiation machinery recognizes H3-K4 as an epigenetic marker
  4. the epigenetic marker dictates gene expression
35
Q

a) What are the 3 sites of methylated modification on histones
b) Which AA is being methylated?
c) does it activate or repress transcription?

A
  1. H3 - K4 = activation
    - the 4th lysine in the histone tail
  2. H3 (K9, K27) = repression
    - the 9th and 27th lysine in the histone tail
36
Q

a) What happens wrt the reconstitution/build up of H3-K9Me after the passage of the replication fork? - 2
b) what is the purpose of this?

A

a)
1. the old histones w/ the H3-K9Me are recycled and sent behind the replication fork
2. histone-methyl-transferase recognizes the H3-K9Me marks and methylates the new histones accordingly (rebuild the epigenetic mark)
b) to ensure that replicated cell expresses the same genes as their parent cell

37
Q

a) What happens wrt the reconstitution/build up of H3-K27Me after the passage of the replication fork? - 2
b) what is the purpose of this?

A

a)
1. PRC2 a methyltransferase acts as a co-repressor and associates w/ heterochromatin
2. PRC2 is recycled and sent behind the replication fork where it methylates H3-K27
b) to ensure that the replicated cell expresses the same genes as their parent cell

38
Q

Describe the following co-repressors and co-activators
a) PRC2
b) PRC1
c) trithorax complex

A

a) polycomb repression complex 2 = maintains repression by methylating H3-K27
b) polycomb repression complex 1 = recognizes H3-K27-Me and compacts the chromatin
c) activates by methylating H3-K4 during chromosome replication

MCB2050 (18 decks)

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