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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
Galactose is present in the cell what happens?
Enzyme-encoding genes are expressed (Gal 1,2,7,10) to import and breakdown galactose
25
Gal 7,10,1,2 and the mRNA transcription are
transcribed seperately. Each gene makes diff mRNA
26
Trancription in the yeast GAL system (3) | Key regul+binds+express
- Key regulator is Gal 4 (activator) - Gal 4 binds to UAS (Upstream activation sequence) to activate transcription - Gal 4 is always expressed
27
How is Gal4 prevented from activating gene expression in the abscene of galactose? (4)
- 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
Chromatin (2) | What it is+ compared to linear DNA?
- A complex of DNA and proteins that make up eukaryotic chromosomes - 10 times from compact then linear DNA
29
Nucleosome
The basic unit of eukaryotic chromosome structre: Composed of histone proteins and DNA
30
Histone octomers contain----- and are
- 2 of each H2A, H2B, H3 and H4 - Are + charged
31
Histones have a ---- and ----
folded core and flexible tails
32
What does a histone tail do?
Interact with adjacent nucleosomes and other proteins
33
Constitutive heterochromatin (3) | What it is+ genes+ ex
- DNA that always stay compact no matter what cell cycle - No genes transcribed - Ex: centromere and telomere
34
Faculative Heterochromatin (2) | WHat it is+ with the professional names
- DNA that can be compact or open up - Can change between constitutive and euchromatin
35
Euchromatin (2)
- Open form of chromatin - Transcriptionally active
36
Heterochromatin
Condensed DNA, which comes in multiple varieties. These varieties lie on a continuum between the two extremes of constitutive heterochromatin and facultative heterochromatin.
37
Level of compaction determines which DNA is acessible to
transcription machinery
38
Chromatin remodeling
Physically repositioning / removing/ replacing histone octomers along the DNA
39
Chromatin Modification includes (2)
histone modification DNA modification
40
Histone modifcations: Acetylation
- 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
Histones are primarily modified in the
tails
42
Two effects of Acetylation:
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
Proteins with bromodomain (coregulators/ co activator) binds to aceylated lysine and
- 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
histone code hypothesis (2) | what it propose+ over....
Proposes that different combinations of histone modifications specify different transcription outcomes Over 2 million possible combinations of modifications
45
HAT
Adds acetyl group to histones
46
Acetyl group can
create binding site for protein
47
Mature mRNA has (7)
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
DNA modification: Methylation (2) | What is methylated?
- usually C followed by G that gets methylated (CPG) - cytosine methylated (5th carbon)
49
DNMT
DNA methyltransferase, recognizes CpG sites and add methyl groups
50
CpG and methylation (4) | percentage of methylation+unmethylated/methylated in genes+ islands
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
CpG islands are found in most
gene promotors
52
unmethylated CpG islands are associated with (2)
1. Open chromatin 2. Active transcription
53
How does methylation affect gene expression (2)
1. Methylation of CpGs prevent transcription factors binding 2. methylaion creates binding sites for histone deacetylase (HDAC) *acetylation causes open chromatin
54
methylated CpGs are generally
alone, not in islands
55
DNA methylation an histone modifications contribute to
epigentic inheritance | changing pattern of inheritance but not DNA itself
56
How does DNA methylation patterns get kept?
57
Igf2
Igf2 derived from the mother is silences (not expressed) igf2 derived from the father is actice (expressed)
58
imprinted genes
get methylated on promotor so they cant be expressed (established in gamete)
59
TFIID
can acts both a transcription factor and as a coactivator
60
Maternally imprinted=
mother genes passed on not expressed

BIOL311 (15 decks)

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