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BIOL311 > Topic 11: Eukaryotic Gene regulation > Flashcards

Topic 11: Eukaryotic Gene regulation Flashcards

1
Q

What makes transcription in eukaryotes more complex than prokaryotes? (6)

A
  1. Eukaryotes have more genes that are further apart
  2. Eukaryotes have 3 RNA polymerases
  3. Transcription takes place in the nucleus
  4. Dna in eukaryotes is packaged into chromatin
  5. More regulatory DNA sequence elements (cis-acting)
  6. More protein factors (trans-acting)
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2
Q

RNA pol 1

A

rRNA

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3
Q

RNA pol 2

A

mRNA

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4
Q

RNA pol 3

A

tRNA

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5
Q

transcription and translation in prokaryotes

A

happen in the same time

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6
Q

General transcription factors

A

Bind to DNA sequences in the core promotor (-50 to +50 bp of +1 start site)

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7
Q

Promotor elements (3)

A

core promoter, proximal promoter, and distal promoter.
The core promoter is the site for binding of proteins required for transcribing all genes, such as TATA-binding protein and RNA polymerase, but the promoter-proximal elements are unique to sets of genes that are regulated together.

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8
Q

Preinitiation complex (PIC) (2)

What it is+ c-terminal

A
  • Complex of RNA pol 2 and general transcription factors
  • C-terminal domain of RNA pol 2 is phosphorlated to facilate processing of the 5’ end of the mRNA (capping m7G)
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9
Q

Capping (2)

What it is + assits in

A
  • addition of a meythlated guanine nucleotide (m7G) cap on the 5’ end of the mRNA protects it from decay by exonucleoses
  • Assist in splicing and translation
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10
Q

Polyadenylation (3)

What it is, How it is added, what it does

A
  • conserved sequences in the 3’ UTR signal for cleavage of RNA from RNA pol 2 and additional of the poly A tail
  • Addition of 50-250 adenosine (A) on the 3’ end of the mRNA after transcription ends
  • Protects from decay and aids in translation
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11
Q

How pre-mRNA is spliced (2)

A
  • 5’ GU and 3’ AG are recognized by the spliceosome
  • a single pre-mRNA with exon+introns are spliced in diff ways to produce mature mRNAs that encode diff proteins
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12
Q

5’ untranslated region is (3)

A

landing site for ribosome, regulatory functions , kozak sequence

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13
Q

Co-regulators

A

do not directly bind to DNA, can bridge the interaction between transcription factors and RNA pol 2

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14
Q

Transcription factors and co-regulators can be

A

repressors or activators

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15
Q

TFIIA is a

A

Coactivator

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16
Q

Enhancer

A

DNA sequence far away from gene upstream/ downstream but still influence wether RNA pol transcribes

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17
Q

Core promotor (2)

bp?

A

Region surrounding the transcription start site. Where the general transcription factors bind
- within 100bp

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18
Q

proximal promotor

A

Not where generall transcription factors bind but other transcription factor can bind here

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18
Q

Transcription factors can. have multiple domains, explain it all

A

Have either a activatio domain or repression domain for transcription.

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19
Q

Yeast can use —- as an energy source in the anscence of glucose

A

galactose

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20
Q

Gal 2,1,7,10 are

A

enzymes involved in the import and metabolism of galactose (gal)

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21
Q

Tell me about the galactose enzyme location

A

Gal 7, Gal 10, Gal 1 are enzyme on the same chromosome (2)
Gal 2 is on chromosome 12

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22
Q

Regulatory proteins: (4)

What they are+ what they do

A

Gal 4, Gal 3, Gal 80
Regulate transcription of the enzyme-encoding genes

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23
Q

What we expect with no galactose for the enzyme encoding genes

A

No expression of Gal 2,1,7 and 10. Enzyme-encoding genes are not expressed

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24
Q

Galactose is present in the cell what happens?

A

Enzyme-encoding genes are expressed (Gal 1,2,7,10) to import and breakdown galactose

25
Q

Gal 7,10,1,2 and the mRNA transcription are

A

transcribed seperately. Each gene makes diff mRNA

26
Q

Trancription in the yeast GAL system (3)

Key regul+binds+express

A
  • Key regulator is Gal 4 (activator)
  • Gal 4 binds to UAS (Upstream activation sequence) to activate transcription
  • Gal 4 is always expressed
27
Q

How is Gal4 prevented from activating gene expression in the abscene of galactose? (4)

A
  • Gal 3 and Gal 80 are always expressed
  • Gal 80 is repressor of Gal 4 and initially, it is always binded tgt to precent transcription
  • In the presence of galactose, Gal 3 undergo conformation change in the presescence of galactose (they bind)
  • The changed conformation of Gal 3 displaces Gal 80 from Gall 4
28
Q

Chromatin (2)

What it is+ compared to linear DNA?

A
  • A complex of DNA and proteins that make up eukaryotic chromosomes
  • 10 times from compact then linear DNA
29
Q

Nucleosome

A

The basic unit of eukaryotic chromosome structre: Composed of histone proteins and DNA

30
Q

Histone octomers contain—– and are

A
  • 2 of each H2A, H2B, H3 and H4
  • Are + charged
31
Q

Histones have a —- and —-

A

folded core and flexible tails

32
Q

What does a histone tail do?

A

Interact with adjacent nucleosomes and other proteins

33
Q

Constitutive heterochromatin (3)

What it is+ genes+ ex

A
  • DNA that always stay compact no matter what cell cycle
  • No genes transcribed
  • Ex: centromere and telomere
34
Q

Faculative Heterochromatin (2)

WHat it is+ with the professional names

A
  • DNA that can be compact or open up
  • Can change between constitutive and euchromatin
35
Q

Euchromatin (2)

A
  • Open form of chromatin
  • Transcriptionally active
36
Q

Heterochromatin

A

Condensed DNA, which comes in multiple varieties. These varieties lie on a continuum between the two extremes of constitutive heterochromatin and facultative heterochromatin.

37
Q

Level of compaction determines which DNA is acessible to

A

transcription machinery

38
Q

Chromatin remodeling

A

Physically repositioning / removing/ replacing histone octomers along the DNA

39
Q

Chromatin Modification includes (2)

A

histone modification
DNA modification

40
Q

Histone modifcations: Acetylation

A
  • The tail of histones are all amino acids.
  • We add an acetyl grouo to a lysine amino acid
  • When acetylated, lysine is no longer +. Since DNA is -, the interaction loosens and no more DNA compaction
41
Q

Histones are primarily modified in the

A

tails

42
Q

Two effects of Acetylation:

A
  1. Reduce chromatin compaction (Losseningi interaction between histones+DNA) for transcription factors
  2. Creates binding site for protein domain called bromodomain found in many transcriptional activators
43
Q

Proteins with bromodomain (coregulators/ co activator) binds to aceylated lysine and

A
  • play an important role in anchoring the complexes of which they are a part to acetylated chromatin
  • acetylating histones, remodeling chromatin, and recruiting other factors necessary for transcription.
44
Q

histone code hypothesis (2)

what it propose+ over….

A

Proposes that different combinations of histone modifications specify different transcription outcomes
Over 2 million possible combinations of modifications

45
Q

HAT

A

Adds acetyl group to histones

46
Q

Acetyl group can

A

create binding site for protein

47
Q

Mature mRNA has (7)

A
  1. exons
  2. 3’ Poly A tail
  3. Kozak sequence
  4. 5’ m7G cap
  5. Start/stop codon
  6. 5’ UTR
  7. 3’ UTR
48
Q

DNA modification: Methylation (2)

What is methylated?

A
  • usually C followed by G that gets methylated (CPG)
  • cytosine methylated (5th carbon)
49
Q

DNMT

A

DNA methyltransferase, recognizes CpG sites and add methyl groups

50
Q

CpG and methylation (4)

percentage of methylation+unmethylated/methylated in genes+ islands

A
  1. About 85% of CpGs are methylated
  2. unmethylated CpGs are clustered in CpG islands
  3. unmethylated CpG islands are generally in expressed genes
  4. methylated CpG islands are generally in unexpressed genes
51
Q

CpG islands are found in most

A

gene promotors

52
Q

unmethylated CpG islands are associated with (2)

A
  1. Open chromatin
  2. Active transcription
53
Q

How does methylation affect gene expression (2)

A
  1. Methylation of CpGs prevent transcription factors binding
  2. methylaion creates binding sites for histone deacetylase (HDAC) *acetylation causes open chromatin
54
Q

methylated CpGs are generally

A

alone, not in islands

55
Q

DNA methylation an histone modifications contribute to

A

epigentic inheritance

changing pattern of inheritance but not DNA itself

56
Q

How does DNA methylation patterns get kept?

A
57
Q

Igf2

A

Igf2 derived from the mother is silences (not expressed)
igf2 derived from the father is actice (expressed)

58
Q

imprinted genes

A

get methylated on promotor so they cant be expressed (established in gamete)

59
Q

TFIID

A

can acts both a transcription factor and as a coactivator

60
Q

Maternally imprinted=

A

mother genes passed on not expressed

BIOL311 (15 decks)

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