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POM Exam 1 > L3 Gene Expression: Regulation > Flashcards

L3 Gene Expression: Regulation Flashcards

1
Q

key regulators of biological function in health and disease

A
  • changing RNA and protein levels
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2
Q

gene expression is regulated when?

A
  • at multiple steps
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3
Q

changes in gene expression underlie carcinogenesis

A
  • mutations in regulatory genes, including genes involved in chromosome modification result in cellular dysfunction and can lead to cancer
  • mutations in regulatory genes and chromatin modifiers can affect expression of many genes
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4
Q

epigenetics

A
  • broadly - changes in chromatin state
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5
Q

at what levels can you affect gene regulation?

A
  • transcriptional control
  • RNA processing control
  • RNA transport and localization control
  • mRNA degradation control
  • translational control
  • protein activity control
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6
Q

transcriptional activation via enhancers requires what

A
  • opening of chromatin to allow transcription factor access at promotor
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7
Q

enhancer binds TF activators through

A
  • through the mediator complex

- interacts with general TFs and RNA pol II to position RNA pol II at the promoter and allows transcription to occur

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8
Q

chromatin as transcriptional control

A
  • major aspect of transcriptional control is opening and closing of chromatin
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9
Q

enhancers

A
  • interact with general TFs to control transcription
  • promote polymerase mediated transcription - recruit Pol II to the promoter
  • enhancer is the sequence of DNA within the gene
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10
Q

enhancers can control

A
  • spatial
  • temporal
  • inducible (hormonal, cell signaling)
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11
Q

transcription factors classified according to

A
  • presence or absence of DNA binding motif
  • activity
  • chromatin modification
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12
Q

presence or absence of DNA binding motif

A
  • DNA binding factors
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13
Q

co-regulators

A

(interact with DNA binding TF’s but don’t bind DNA)

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14
Q

DNA binding motifs

A
  • zinc finger
  • homeobox
  • basic helix loop helix
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15
Q

activity

A
  • transcriptional activator

- transcriptional repressor

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16
Q

chromatin modification

A
  • acetylene or deacetylase activity

- open or closed chromatin

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17
Q

modularity of transcription factors

A
  • have multiple functional domains
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18
Q

DNA binding domain of TFs

A
  • often recognize sequence-specific patterns of hydrogen bond donors and acceptors in the major groove of DNA
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19
Q

specificity of DNA binding

A
  • dimerization or protein interaction domains
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20
Q

histone modification domains

A
  • acetylene and deacetylase activities
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21
Q

ligand binding

A
  • nuclear hormone receptors (steroids, toxins)
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22
Q

cis control elements

A
  • eukaryotic transcription factors bind short consensus sequences
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23
Q

how to TFs bind to a DNA

A
  • as a homodimer or heterodimer

- must be present in high concentrations

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24
Q

PXR:RXR nuclear receptor in absence of ligand

A
  • PXR:RXR binds a corepressor of proteins
  • transcription is off
  • HDAC3 removes acetyl groups from histones - closes chromatin
  • active repression as it sits on the enhancer and is actively repressing transcription
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25
Q

PXR:RXR nuclear receptor in presence of ligand

A
  • PXR:RXR undergoes conformational change and binds a coactivator complex (HMT, HAT, NRA)
  • turns transcription on
  • HAT adds acetyl groups to histones - opens chromatin and allows polymerases to be recruited
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26
Q

glucocorticoid receptor

A
  • example of enhancer driven transcription

- TF with a DNA binding domain, an activation domain, ligand-binding domain, and nuclear localization sequence

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27
Q

GR in absence of steroid

A
  • GR present in the cytoplasm bound a heat shock protein
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28
Q

GR in presence of steroid (its ligand)

A
  • ligand binds to GR and displaces the heat shock protein
  • conformational change that causes the HSP to fall off
  • nuclear localization signal has been unmasked
  • GR forms a homodimer and translocates to the nucleus
  • GR binds to DNA at GRE enhancer and activation domain TAD recruits coactivators
  • GR coactivator complex binds general TFs and activates transcription
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29
Q

mediator

A
  • large multiprotein complex that “mediates” the effects of enhancer binding to the promoter
  • different subunits interact with activators, GTFs, and Pol II
  • stabilizes the binding of Pol II and GTFs at the promoter
  • DNA often loops to bring activators and mediator together
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30
Q

chromatin

A
  • DNA packaged into nucleosomes
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31
Q

core particle

A
  • octamer particle with two histones H3 H4 H2A and H2B proteins
  • DNA wrapped around core
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32
Q

histone tails

A
  • have tails that are accessible for modification and transcriptional function
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33
Q

Histone H1

A
  • linker histone residing on DNA between nucleosomes
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34
Q

histone modifications

A
  • acetylation
    • HAT can relax or open chromatin
    • HDAC results in closed chromatin
  • methylation
  • phosphorylation
  • ubiquination
  • can really affect whether chromatin is condensed or not
35
Q

HAT

A
  • adds acetyl groups
36
Q

HDAC

A
  • removes acetyl groups
37
Q

HMT

A
  • adds methyl groups
38
Q

KDM

A
  • removes methyl groups
39
Q

chromatin remodeling

A
  • open and close chromatin to allow to deny access of transcription factors
40
Q

chromatin remodeling carried out by

A
  • histone modifications

- ATP-dependent complexes that move or restructure nucleosomes

41
Q

nucleosome unwrapping

A
  • can unwrap DNA from nucleosome to allow DNA binding protein access
42
Q

nucleosome mobilization

A
  • can move nucleosome around to allow for binding for transcription
43
Q

nucleosome ejection

A
  • Can get rid of nucleosome
44
Q

histone dimer exchange

A
  • can exchange one of the histones for another hone with different modification
45
Q

DNA methylation and transcriptional control

A
  • promoter (Cpg) is unmethylated and gene can be transcribed

- promoter (Cpg) is methylated and gene is silenced

46
Q

what methylates the CpG promoters?

A
  • DNA methyltransferase
47
Q

methylation importance in imprinting and cancer

A
  • tumor suppressor gene CpGs can be methylated and silence
48
Q

common insulator binding protein

A
  • CTCF
49
Q

insulators and enhancers

A
  • can block an enhancer from activating an adjacent gene
50
Q

insulators and repressors

A
  • can block the spread or activation of repressive chromatin from silencing the gene activity
51
Q

chromosomal domains

A
  • insulator-binding protein joins two insulators to form a loop and isolates sites of active or inactive transcription
52
Q

barrier sequence

A
  • prevents spread of heterochromatin to adjacent genes
53
Q

alternative splicing

A
  • exon skipping
  • intron retention
  • alternative 5’ splice site
  • alternative 3’ splice site
  • mutually exclusive exons
54
Q

exon skipping

A
  • splice 1 and 2 together, but skip over exon 3
55
Q

intron retention

A
  • keep one of the introns
56
Q

alternative 5’/3’ splice site

A
  • start splice in different sites to form larger or smaller exon
57
Q

mRNA editing

A
  • some mRNAs change bases after transcription due to an editing mechanism
  • occurs in cytoplasm
  • only on specific mRNAs at defined sites; not widespread
58
Q

transferrin

A
  • blood protein that transports iron
59
Q

transferrin receptor

A
  • membrane protein that binds transferrin allowing iron to enter the cell
  • control at level of mRNA stability
60
Q

iron is low - transferrin

A
  • mRNA transferrin levels are high

- iron regulatory proteins bind transferrin receptor mRNA and stabilize it to protect it from degradation

61
Q

iron is high - transferrin

A
  • mRNA levels are low
  • iron regulatory proteins bind iron but do not bind iron regulatory elements.
  • transferrin receptor mRNA is degraded
62
Q

ferritin

A
  • iron binding protein that stores iron for future use
  • control at level of translation
  • iron response element at 5’ end can block translation
63
Q

cellular iron levels high - ferritin

A
  • need to store iron
  • ferritin levels are high
  • iron binds to iron regulatory protein and prevents binding to iron response element
  • translation of mRNA initiated
64
Q

cellular iron levels low - ferritin

A
  • no need to store iron

- iron response element bind to iron regulatory protein and blocks translation

65
Q

microRNA control of translation

A
  • miRNAs are not translated
  • form a hairpin which is trimmed in the nucleus
  • miRNA binds to RNAs with different effects depending on the extent of the sequence homology
66
Q

Dicer

A
  • further trims pre-miRNA followed by degradation of one strand by Argonaute and RISC
67
Q

strong match with miRNA

A
  • degrades mRNA
68
Q

weak match with miRNA

A
  • inhibits mRNA translation
69
Q

P bodies

A
  • processing bodies
  • cytoplasmic sites of translationally repressed RNAs and RNA degradation proteins
  • possible role in regulating RNA levels and translation
70
Q

RNPs and storage droplets

A
  • can form storage droplet by phase separation
71
Q

regulation of translation by guanine exchange factors

A
  • one response to stress condition is a reduction in protein synthesis
  • stress results in phosphorylation of translation initiation factors - reducing protein synthesis
72
Q

regulation by GEF process

A
  • eIF2-GTP is regenerated by guanine exchange factors called eIF2B during translation
  • phosphorylation of eIF2B-GDP by protein kinases renders eIF2 inactive but still binds and sequesters eIF2B so it cannot reinitiate protein synthesis
73
Q

ubiquination result

A
  • targets for degradation
74
Q

SUMOylation result

A
  • targets for degradation
75
Q

phosphorylation result

A
  • activity
76
Q

acetylation result

A
  • activity
77
Q

methylation result

A
  • activity
78
Q

what happens to misfolded proteins?

A
  • they are targeted for degradation by specific proteases

- phosphorylation allows degradation

79
Q

how does degradation occur?

A
  • occurs by the ubiquitin/proteasome system
80
Q

ubiquitin/proteasome system?

A
  • ubiquitin added to protein
  • forms proteasome
  • get two things
    • peptide fragments
      • later degraded further into amino acids
    • released ubiquitin
81
Q

E1

A
  • ubiquitin activating enzyme
  • adenylates ubiquitin and attaches it to a high energy thioester on the enzyme
  • recognized E2 enzymes
82
Q

E2

A
  • ubiquitin conjugating enzyme
  • receives activated ubiquitin from E1
  • binds to specific E3 enzymes
83
Q

E3

A
  • ubiquitin ligase

- recognize specific proteins and transfers ubiquitin onto them

84
Q

protein decay and the inflammatory response

A
  • Inflammatory response is initiated by the NFkB transcription factor in response to inflammatory signals (TNFa, IL1)
  • NFkB is sequestered in an inactive form by binding to IkB
  • IkB is phosphorylated in response to signaling
    • When the phosphates are added, it is now a target for ubiquination
  • Creates an E3 binding site ➞ IkB is ubiquitinated and degraded
  • Releases NFkB ➞ translocates into nucleus resulting in transcription of pro-inflammatory genes
    • Initiation of inflammatory response

POM Exam 1 (16 decks)

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