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Molecules to Cells - Genetics and Virology > Lecture 27. Chromatin and epigenetic effects > Flashcards

Lecture 27. Chromatin and epigenetic effects Flashcards

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1
Q

When are prokaryotic RNAs translated into proteins ?

A

Co-transcriptionally - as soon as they are made

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2
Q

Why are prokaryotic RNAs translated as soon as they are made ?

A

Due to the absence of the nuclear envelope

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3
Q

When are eukaryotic RNAs translated ?

A

They are first modified and then transported from the nucleus to cytoplasm

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4
Q

Why is eukaryotic RNA transported into the cytoplasm for translation?

A

Eukaryotic DNA is compartmentalized within the nucleus

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5
Q

What needs to happen to eukaryotic RNA to be transported into the cytoplasm ?

A

Addition of sequences to the 5’ end of the RNA (5’cap) as well as the 3’ end (the polyA tail)

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6
Q

What is the function of adding sequences to the 5’end and the 3’end of eukaryotic RNA ?

A
  1. Regulates stability of mRNA molecules

2. Exert a level of control over gene expression that prokaryotes don’t have

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7
Q

What do eukaryotic RNA undergo that prokaryotic RNA do not ?

A

Splicing

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8
Q

Where does splicing occur ?

A

In the nucleus

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9
Q

What is the purpose of splicing ?

A

Remove introns

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10
Q

What is an advantage of splicing to eukaryotes ?

A

Adds another layer of control and complexity over eukaryotic gene expression

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11
Q

What is the function of eukaryotic mRNA modification ?

A
  1. Stabilizes mRNA

2. Facilitate mRNA export from the nucleus

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12
Q

What does mRNA from higher eukaryotes undergo ?

A

Splicing by small nuclear RNAs

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13
Q

What function does splicing by small nuclear RNAs in mRNA in higher eukaryotes have ?

A
  1. Removes introns

2. Generate splice variants of genes

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14
Q

What do eukaryotic RNA polymerase require ?

A

Transcription factors

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15
Q

What is eukaryotic RNA polymerase’s transcription factors access to DNA regulated by ?

A
  1. Histones

2. DNA binding proteins

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16
Q

Why is gene expression in eukaryotes constitutively off at most promoters ?

A
  1. The requirement for specific and general transcription factors
  2. The physical inaccessibility of gene promoters
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17
Q

What do specific and general transcription factors regulate ?

A

The binding of the RNA polymerase complex to the promoter

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18
Q

What makes gene promoters physically inaccessible ?

A

Histones

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19
Q

What do histones form ?

A

Particles called nucleosomes

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20
Q

What do nucleosomes bind tightly to ?

A

DNA

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21
Q

What is the structure of a nucleosome ?

A

Has 200 base pairs of DNA wound around it and other DNA binding proteins

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22
Q

How do DNA binding promoters regulate the binding of RNA polymerase to the promoter region ?

A

Compacts DNA into a closed state that blocks access of the RNA polymerase complex to the promoter

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23
Q

What do eukaryotic RNA polymerases require that prokaryotic polymerases do not to initiate transcription ?

A

Transcription factors to be bound to the promoter region

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24
Q

What is RNA polymerase 1 responsible for ?

A

Generating rRNA precursor molecules

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25
Q

What is RNA polymerase 2 responsible for ?

A

Generating mRNA and RNA

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26
Q

What is RNA polymerase 3 responsible for generating ?

A

Small RNAs such as tRNA and 5S rRNA

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27
Q

What do RNA polymerase 2 promoters regulate ?

A

mRNA synthesis

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28
Q

Where are RNA polymerase 2 promoters located ?

A

-30 to the transcription start site at a TATA box

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29
Q

What is the actual sequence of of the TATA box in RNA polymerase 2 promoters ?

A

TATAAAA

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30
Q

Do all polymerase 2 promoters have TATA boxes ?

A

No

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31
Q

Where is the CCAAT box found ?

A

-75 region

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32
Q

What is the upstream elements of polymerase 2 promoters ?

A

GGCCCAATCT element or CCAAT box

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33
Q

What is the general rules about promotes recognized by RNA pol II ?

A

Typically contain a TATA box and at least one other upstream element

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34
Q

What is the purpose of transcription factors for eukaryotic polymerases ?

A

need transcription factors to assist in eukaryotic RNA polymerases are recognizing the promoter regions of genes on their own

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35
Q

What are the two types of transcription factors ?

A
  1. General

2. Gene specific

36
Q

What are the 7 general transcription factors that collaborate with RNA Pol II ?

A
  1. TFIIA
  2. TFIIB
  3. TFIID
  4. TFIIE
  5. TFIIF
  6. TFIIH
  7. TFIIJ
37
Q

What does TFIID contain ?

A

Many subunits including the TATA box binding protein

38
Q

Where does the TATA box binding protein (TBP) bind to ?

A

The TATA box bringing TFIID

39
Q

What does the DNA binding domain of the TBP consist of ?

A

A large B-sheet that forms a saddle shaped structure that sits astride the DNA in the region of the TATA box

40
Q

What does the binding of TBP to the TATA induce ?

A

A dramatic distortion

41
Q

What does TBP binding cause structurally ?

A

A large kink in the DNA helix causing the DNA duplex to unwind over an 8 base pair span

42
Q

What does TBP binding allow access of ?

A

Allows access of the RNA polymerase to the template

43
Q

What does TFIID serve as ?

A

A platform for organisation of other transcription factors which then bind in the following order; D, A, B, F+ Pol II, E, H and J

44
Q

What order to transcription factors bind ?

A

D, A, B, F + Pol II, E, H, J

45
Q

What happens upon assembly of the RNA Pol II preinitiation complex ?

A

The C-terminal domain of the largest subunit of RNA polymerase II becomes heavily phosphorylated

46
Q

What is most likely the largest subunit of RNA polymerase II that becomes heavily phosphorylated ?

A

TFIIH

47
Q

What is TFIIH ?

A

A kinase

48
Q

What does the phosphorylation of the largest subunit of RNA polymerase II do ?

A

A trigger that uncouples the polymerase from transcription factors allowing the polymerase to move along the DNA template

49
Q

What are general transcription sufficient to enable ?

A

A basal level of transcription

50
Q

What are some gene-specific transcription factors ?

A
  1. Myc
  2. Max
  3. Fos
  4. Jun
  5. NfkB
  6. NFAT
51
Q

What are the 4 classes that contain motifs that allow interaction between the transcription factors and the major grooves of DNA ?

A
  1. Zinc finger motif
  2. Helix-loop-helix motif
  3. Leucine zipper motif
  4. High mobility group box motif
52
Q

What is the purpose of the four motifs ?

A

Allow recognition of specific DNA sequences by the transcription factors

53
Q

What do most motifs contain ?

A

A segment (often alpha helix) that is inserted into the major groove of DNA

54
Q

What do motifs that contain a segment recognise and form ?

A
  1. Recognise the side chains of the bases lining the groove

2. Forms non-covalent interactions with the side chains

55
Q

What makes the otherwise weak strength of the contact between the transcription factor and the DNA very high ?

A
  1. The number of contacts

2. The overall strength and specificity of the transcription factor DNA interaction

56
Q

Where are enhancer sequences often found ?

A

Thousands of base pairs away from a promoter region that the enhancer controls

57
Q

What is chromatin looping facilitated by ?

A

Specific transcription factors and mediators (associated proteins)

58
Q

What is the function of chromatin looping ?

A

Brings the promoter region in close proximity to the TATA box and the associated RNA pol II complex

59
Q

What an histones be modified by ?

A
  1. Acetylation
  2. Methylation
  3. Phosphorylation
60
Q

What do modifications that neutralize the positive charged on histones do ?

A

Reduce their affinity for DNA

61
Q

What is a histone code ?

A

The number of possible patterns of histone modifications

62
Q

What is another name for the modification of the histone c-terminal tail

A

Acetylation

63
Q

What is the enzyme involved in acetylation ?

A

Histone acetyltransferases

64
Q

What is the enzyme responsible for the reverse modification of acetylation ?

A

Histone deacetyltransferases

65
Q

What does acetylation lead to ?

A

A more open chromatin state due to neutralization of the negative charges on histones thereby loosening the histones contact with DNA

66
Q

What do histones associated with more active genes tend to be rich in ?

A

Acetyl modifications

67
Q

What can some histone modifications also recruit ?

A

Proteins for example polycomb proteins

68
Q

What is epigenetic control ?

A

Inherited modifications that are not present in a DNA sequence

69
Q

What is gene expression regulated by ?

A

DNA binding proteins called transcriptional regulators as well as the accessibility of the stretch of DNA harbouring the gene (chromatin state)

70
Q

What are nucleosomes ?

A

Histone octamers

71
Q

What causes nucleosomes to be moved off promoters to facilitate the initiation of transcription ?

A

Switch/Sniff complex or SWI/SNF complex

72
Q

What do all eukaryotic cells contain and what its function ?

A

A large multi subunit complex that can disrupt histone-DNA interactions in an ATP dependent manner and allow binding of transcription factors to gene regulatory regions

73
Q

How was the SWI/SNF complex discovered ?

A

Screen genes involved in growth on sucrose and screens the genes involved in the ability to switch mating type. One of the genes was found in common

74
Q

What is the function of SWI/SNF complex ?

A

Bulldoze histones off promoters and facilitate access of the RNA Pol complex to the promoter

75
Q

How many proteins is the yeast SWI/SNF complex comprised of ?

A

11

76
Q

What does the yeast SWI/SNF complex act as ?

A

An ATP driven nucleosome plough to facilitate transcription

77
Q

How do certain transcription factors function ?

A

By attracting the SWI/SNF complex to the promoter to facilitate transcription

78
Q

Where are 1% of nucleotides methylated at ?

A

Cytosine residues

79
Q

What does the methylated nucleotides produce ?

A

5-methylcytosine

80
Q

What does the 5-methylcytosine modification act as ?

A

A molecular tag that allows certain regions of DNA to be regulated differently than others

81
Q

Where are almost all methylated cytosines found ?

A

CG dinucleotides within symmetrical sequences

82
Q

Where do symmetrical sequences occur (methylated) ?

A

Tend to be clustered in G rich regions called CpG islands close to gene regulatory regions

83
Q

Where are unmethylated CpG islands found ?

A

Near active gene promoters

84
Q

What is methylation likely involved in ?

A

Silencing gene expression

85
Q

What is methylation in vertebrates ?

A

Dynamic

86
Q

What does DNA methylation correlate with ?

A

Gene expression patterns

87
Q

How does methylation inhibit transcription ?

A
  1. By interfering with the recognition of DNA binding sites by transcription factors
  2. By attracting transcriptional repressors to certain sites

Molecules to Cells - Genetics and Virology (16 decks)

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